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"entry": "000003-senzai-2017", "entry_title": "Granule cells and mossy cells of the dentate gyrus (Senzai and Buzsaki 2017)", "description": "Tests the findings of Senzai and Buzsaki (2017) on dandiset 000003, which holds silicon probe recordings of the dentate gyrus and CA3 in 16 mice, in 101 files from 94 recording days, with labelled granule cells, mossy cells, CA3 pyramidal cells and interneurons, sleep states, dentate spikes, light pulses, and positions on a circular T-maze and in open fields. It covers firing by brain state, theta and gamma phase locking, recruitment by dentate spikes, optogenetic tagging, monosynaptic transmission, place fields and remapping, and, on the 17 files that give each unit's shank, depth and the classification of granule and mossy cells.", "notebooks": [ { "path": "reproduce_senzai_2017.ipynb", "title": "Reproducing Senzai and Buzsaki (2017) from dandiset 000003", "executed": "notebooks/000003-senzai-2017/reproduce_senzai_2017.html" } ], "outcomes": [ { "claim": "unit-counts", "statement": "The second-stage classification divided dentate excitatory neurons into 586 putative granule cells (GC) and 500 putative mossy cells (MC).", "source": "Results, Identification of granule cells and mossy cells; Figure 1F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "The files hold 609 GC (paper 586, within tolerance) and 568 MC (paper 500, outside the tolerance of 450 to 550), from all 16 mice, counting each of the 101 files once.", "deviations": [ "Counts come from the dandiset's labels; the paper's classification was not re-run on all files." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "first-stage-labels", "statement": "Narrow-waveform interneurons have a trough-to-peak latency below 0.425 ms, and among wide-waveform units the excitatory cells have a burst index above the threshold separating them from wide-waveform interneurons.", "source": "Figure 1A; STAR Methods, Unit classification", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Under both burst thresholds (1.2 in the Methods, 1.8 in the Figure 1A legend), 98.2% of GC and MC are wide-waveform and bursty and 91.7% or 93.3% of wide-waveform interneurons are wide and not bursty, but 82.5% of narrow-waveform interneurons have a latency below 0.425 ms (40% to 100% by mouse), short of the 90% criterion. The labels pool dentate and CA3 interneurons; 92.7% are below 0.525 ms, the paper's CA3 threshold, and in the 17 files that give the shank 94.4% of the 71 narrow-waveform interneurons on shanks with GC or MC and no CA3 unit are below 0.425 ms (variants). The stored waveforms have their trough at 0.80 ms, so latencies above about 0.75 ms cannot be measured. On the wide-band signal of the 17 files, 64.7% (unfiltered) or 88.5% (300 Hz high-pass) of narrow-waveform interneurons are below 0.425 ms.", "deviations": [ "Latency measured on the mean of the first 200 stored waveforms (1.6 ms long, filtering not stated in the files); the paper used unfiltered waveforms.", "The Methods and the Figure 1A legend give different burst thresholds (1.2 and 1.8); both were tested." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "interneuron-rates", "statement": "Narrow-waveform interneurons fire faster than wide-waveform interneurons (medians 7.97 and 2.11 Hz; Kruskal-Wallis P < 0.00001).", "source": "Results, Identification of granule cells and mossy cells", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Narrow-waveform interneurons fire faster than wide-waveform ones (Kruskal-Wallis P = 5.3e-17 over the recording span, 1.4e-15 in awake periods), but the medians are outside tolerance under both readings (5.96 and 2.57 Hz over the recording; 8.75 and 3.08 Hz awake). In the 17 files that give the shank, interneurons on shanks with GC or MC and no CA3 unit have medians of 8.56 and 2.29 Hz over the recording, both within tolerance (P = 3.7e-08); this variant does not decide the outcome.", "deviations": [ "The interneuron labels include CA3 interneurons, which the paper counts apart, and the files do not say which region an interneuron is in.", "The paper does not define the rate; two readings were tested." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gc-narrower-waveform", "statement": "The waveform of granule cells is narrower than that of mossy cells.", "source": "Results, end of Identification of granule cells and mossy cells; Figure 1E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "GC median trough-to-peak latency 0.710 ms against MC 0.740 ms (Mann-Whitney P = 2.3e-14). The stored waveforms have their trough at 0.80 ms of 1.6 ms, and 43% of GC and 67% of MC have their peak at the end, so the result partly reflects how often each type is cut off; among units with the peak inside the window GC are not narrower (0.660 against 0.645 ms, P = 0.057). On the wide-band signal of the 17 files (window to 2.4 ms), the unfiltered waveform the Methods use gives GC 0.755 against MC 0.840 ms (P = 0.017); after a 300 Hz high-pass they do not differ (0.710 against 0.720 ms, P = 0.4).", "deviations": [ "Measured as trough-to-peak latency on the stored waveforms, where the paper describes the waveform shape through a PCA of its second derivative." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "optotag-drd2", "statement": "In DRD2-Cre::Ai35 mice, 29 of 107 putative mossy cells were suppressed by green light, against none of 202 putative granule cells, 8 of 68 wide-waveform and none of 69 narrow-waveform interneurons.", "source": "Results, Optogenetic validation; Figure 1H; STAR Methods, Optogenetic tagging", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "In 26 DRD2-Cre::Ai35 sessions with 20 ms pulses (4 mice), 68 of 106 MC (0.642) are suppressed by at least 20% with the baseline before the pulse and 71 (0.670) with the baseline later in the cycle, against 6 (0.030) and 13 (0.066) of 198 GC. Wide-waveform interneurons 20 of 88, narrow-waveform 14 of 132. The MC fraction is far above the paper's 29 of 107 and GC are not zero; MC exceed four times the GC fraction under both readings. At a 50% threshold the MC fraction is 0.066. Adding a one-sided Poisson test (P < 0.05) to the 20% rule keeps all 68 MC and 5 GC. The 37 units of the Figure 1H legend equal the 29 MC and 8 wide-waveform interneurons of the text.", "deviations": [ "The Methods do not define the baseline of the light-pulse histogram; two readings were tested.", "The fifth DRD2 mouse (YutaMouse45) has no 20 ms pulses and is not included." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "mc-more-active", "statement": "Mossy cells are more active than granule cells during both waking and NREM sleep (Kruskal-Wallis P < 0.0001 for each).", "source": "Results, Physiological properties; Figure 2A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "MC median 0.736 Hz against GC 0.077 Hz in awake periods (Kruskal-Wallis P = 1.8e-114), 0.727 against 0.083 Hz with quiet wake, and 0.913 against 0.391 Hz in NREM (P = 2e-29). With home-cage awake time as wake (a variant), 0.692 against 0.077 Hz (P = 8.1e-102).", "deviations": [ "Wake is read as the `awake` periods, or `awake` with `quiet`; the states table does not describe its labels." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gc-nrem-highest", "statement": "Granule cells fire most during NREM sleep and at similar rates during wake and REM.", "source": "Results, Physiological properties; Figure 2A", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "GC fire most in NREM (median 0.391 Hz against 0.077 Hz awake and 0.198 Hz REM; adjusted P 1.3e-86 and 8.7e-31), but REM rates exceed wake rates (adjusted P = 1.4e-25 with awake periods, 6.3e-23 with quiet wake), so wake and REM are not similar by the paper's test. With home-cage awake time as wake (a variant), wake and REM still differ (adjusted P = 3.3e-24).", "deviations": [ "The post hoc test is taken as Bonferroni-corrected Mann-Whitney tests; the paper names Kruskal-Wallis only." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ca3-wake-highest", "statement": "CA3 pyramidal neurons are most active during wake and least active during REM.", "source": "Results, Physiological properties; Figure 2A", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "CA3 pyramidal cells fire least in REM (0.287 Hz; adjusted P = 1.1e-15 against NREM and 5.4e-09 against wake), but the NREM median (0.459 Hz) is above the wake median (0.441 Hz awake, 0.433 Hz with quiet wake) and the two do not differ (adjusted P = 0.77 and 0.59). The REM part of the claim holds. With home-cage awake time as wake (a variant), the wake median is 0.412 Hz and NREM against wake gives adjusted P = 0.14; CA3 units fire at similar rates awake in the home cage and during behaviour (0.424 and 0.415 Hz).", "deviations": [ "The paper's CA3 units come from a separate classification (Figure S2); here the dandiset's `pyramidal cell` label is used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "nrem-wake-ratio", "statement": "Granule cells increase their firing in NREM sleep compared with waking, while mossy cells fire at equivalent rates in the two states.", "source": "Figure 1D; Discussion, first paragraph", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Median NREM to wake ratio 4.63 for GC and 1.11 for MC (Mann-Whitney P = 3.9e-141; 4.28 and 1.11 with quiet wake), and the GC ratio is above the MC ratio in every mouse with both. The part saying MC fire at equivalent rates does not fully hold, as MC NREM rates are slightly above wake rates (Wilcoxon P = 1.4e-06). With home-cage awake time, 4.56 and 1.10.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "theta-modulation", "statement": "Granule cells are more strongly phase-modulated by theta oscillations than mossy cells and fire at later theta phases (Kruskal-Wallis P < 0.0001 for both).", "source": "Results, Physiological properties; Figure 2C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Modulated units 483 GC and 532 MC. Theta MRL GC 0.422 against MC 0.339 (Kruskal-Wallis P = 1.5e-20); GC fire later (circular means 30.8 and 12.0 degrees from the peak; P = 1e-17 with phases on (-pi, pi], 0.82 on [0, 2 pi)). After subtracting the uniform-phase expectation for the spike count (GC have fewer spikes), GC are still higher, at P = 0.00056. The bias-corrected MRL comparison (P = 0.00056) does not reach the paper's P < 0.0001. In the 17 files where it can be checked the theta-reference channel has a positive DS2 (+459 to +786 uV), so it lies below the DS2 reversal.", "deviations": [ "Phases from the theta-reference channel the conversion flagged, during up to an hour of awake periods per file; the paper's periods and reference channel are not stated.", "Phase comparisons depend on where the cycle is cut; both cuts are shown and the claim holds on one." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gamma-modulation", "statement": "Granule cells are more strongly phase-modulated by gamma oscillations than mossy cells and fire at earlier gamma phases (Kruskal-Wallis P < 0.0001 for both).", "source": "Results, Physiological properties; Figure 2B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Modulated units 345 GC and 475 MC. Gamma MRL GC 0.319 against MC 0.212 (P = 4.8e-43; 0.219 against 0.166, P = 4.1e-18, after subtracting the uniform-phase expectation); GC fire earlier (circular means -20.2 and 1.7 degrees; P = 1.2e-23 on (-pi, pi], 0.18 on [0, 2 pi)).", "deviations": [ "As theta-modulation." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gamma-rate-correlation", "statement": "Slow-firing neurons are more strongly coupled to gamma than fast-firing ones (GC r = -0.176, MC r = -0.184, P < 0.0001 for each).", "source": "Results, Physiological properties", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Over all units with a gamma MRL, GC r = -0.177 (P = 3.6e-05, within tolerance) and MC r = -0.161 (P = 0.00013, just outside the tolerance and above P = 0.0001). Over modulated units, GC -0.397 and MC -0.253, both P below 0.0001 and outside tolerance.", "deviations": [ "The paper does not say which units or which rate the correlation uses; two unit sets were tested with the rate over the recording span." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ds2-recruitment", "statement": "Granule cells are more effectively recruited by type 2 dentate spikes than mossy cells and fire earlier (Kruskal-Wallis P < 0.0001 for both).", "source": "Results, Physiological properties; Figure 2D and 2E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Median DS2 peak ratio GC 6.88 against MC 4.82 (Kruskal-Wallis P = 1.1e-10); median peak time -3.0 against +1.0 ms (P = 2.2e-09). 10 GC and 14 MC dropped for a zero baseline.", "deviations": [ "The DS2 events are those stored in the files; the peak-ratio baseline (50 to 100 ms on both sides) is a choice, as the paper does not give it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "monosyn-gc-to-mc", "statement": "5.5% of granule cells monosynaptically excite mossy cells (32 pairs), whereas no mossy cell significantly excites a granule cell.", "source": "Results, Granule cell-mossy cell spike transmission; Figure 3B and 3C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Among 4713 GC-MC pairs the automatic test finds 65 GC to MC pairs and 8 MC to GC pairs. The fraction is 0.107 (pairs over GC), 0.0805 (GC with a target over GC) or 0.0138 (pairs over tested pairs), none within 0.0495 to 0.0605. GC to MC pairs outnumber MC to GC pairs 65 to 8. Stricter thresholds lower both counts (56 and 6 at the 99.99999th percentile). For 22 GC to MC pairs the largest bin is the first of the window (1.5 to 2 ms); without them 43 pairs remain (0.0706 of GC). Of the 8 MC to GC pairs, 6 are in YutaMouse33, 4 involve one GC (unit 3 of YutaMouse33-150224) that is also synchronous with each of those MC, and 5 are also detected as GC to MC pairs, which fits common input. In the 17 files that give the shank, 17 of 39 GC to MC pairs are on one shank.", "deviations": [ "The paper inspected and refined each detection by hand; the automatic test alone is used here.", "The fraction 5.5% can be read three ways; all are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "burst-facilitation", "statement": "Spike transmission probability from granule cells to mossy cells increases from the first to the second spike of a granule cell burst (P < 0.001).", "source": "Results, Granule cell-mossy cell spike transmission; Figure 3E to 3G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "For the 65 detected pairs, the median transmission probability is 0.0066 for first and 0.0334 for second burst spikes, higher in 58 pairs (Wilcoxon P = 1.2e-09); it holds with bursts at 4 ms (P = 4.4e-08) and 10 ms (P = 5.5e-10). The detected pairs are partly reproduced (see monosyn-gc-to-mc) and number 65 against the paper's 32. It also holds with only burst intervals of 3.5 to 6 ms, where the two response windows do not overlap (58 of 65, P = 7.6e-10), with a baseline hollowed by 60% (P = 1.2e-09), and without the 22 first-bin pairs (41 of 43, P = 3.8e-11). First spikes transmit less than single spikes (0.0066 against 0.0147), which the outputs do not explain.", "deviations": [ "Bursts are spikes at most 6 ms apart, a choice; the paper does not define them.", "Transmission is the excess over the plain Gaussian baseline of the Methods." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "state-transmission", "statement": "GC to MC spike transmission is lower during NREM sleep than during waking (n = 31, P < 0.005).", "source": "Results, State-dependent changes; Figure 4B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "For 65 detected pairs, median transmission 0.0125 from GC spikes in awake periods and 0.0108 in NREM, lower in NREM for 34 pairs; Wilcoxon P = 0.39. The pairs are the automatic detections (see monosyn-gc-to-mc), not the paper's 31. Without the 22 first-bin pairs NREM is lower in 24 of 43 (P = 0.27); in the 17 files that give the shank, in 20 of 39 (P = 0.86).", "deviations": [ "Uses the automatic pair detections in place of the paper's curated pairs." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "zero-lag-synchrony", "statement": "Synchronous co-activation within 1 ms is found in 23% of mossy cells and 9% of CA3 pyramidal cells, but in fewer than 0.2% of granule cell pairs.", "source": "Results, Granule cell-mossy cell spike transmission", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "GC pairs 4 of 3155 (0.0013, within the claim). MC 0.0766 of pairs or 0.433 of cells; CA3 0.0120 of pairs or 0.102 of cells; none within the tolerance of 0.23 and 0.09. Read as cells, MC and CA3 exceed the GC pair fraction more than ten times. In the 17 files that give the shank no synchronous pair is on one shank (0 of 160 MC, 0 of 51 CA3), so leaving out same-shank pairs changes little (cells MC 0.494, CA3 0.267 there); 143 of 160 synchronous MC pairs are on neighbouring shanks. No synchronous pair shares more than 15% of the sparser unit's spikes within 0.5 ms (MC at most 5.8%), so none looks like one neuron sorted twice.", "deviations": [ "Automatic detections without the paper's manual refinement.", "Pairs recorded on one shank cannot be left out in 83 of 101 files, which do not give the shank; in the other 17 files none of the synchronous pairs is on one shank." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "tmaze-central-active", "statement": "On the circular T-maze, the fraction of active neurons (above 1 Hz) is higher in the central arm than in the side arms, for granule cells, mossy cells and CA3 pyramidal cells (Kruskal-Wallis P < 0.00001 for each).", "source": "Results, Spatial and memory properties; Figure 5B", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "The central-arm median fraction of active units is above the side-arm median for GC (0.020 against 0.018, P = 0.043), MC (0.314 against 0.272, P = 2.2e-06) and CA3 (0.214 against 0.189, P = 0.048); only MC reach P < 0.00001. The bin-wise test treats smoothed, neighbouring bins as independent; compared unit by unit (a variant) the central arm is more active for MC (P = 2.8e-05) but not for GC (higher in 17, lower in 31 of 253 units, P = 0.83) or CA3 (P = 0.21).", "deviations": [ "T-maze runs are taken from the start of the central arm to 10 cm before the reward port in trials without light; the paper uses the time from gate opening to arrival at the reward.", "The meaning of the linearised T-maze positions is inferred from the values and the maze dimensions." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "tmaze-multiple-fields", "statement": "Few granule cells have two or more place fields on the T-maze (6.6%), against 57.8% of mossy cells and 36.1% of CA3 pyramidal cells (Kolmogorov-Smirnov P < 0.0001).", "source": "Results, Spatial and memory properties; Figure 5C and 5D", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Of all units, 4.3% of GC (253), 63.7% of MC (303) and 43.1% of CA3 (341) have two or more fields; of units with a field, 24.4%, 78.1% and 66.8%. No reading puts all three in tolerance (MC misses by 0.001 under reading a). GC have the fewest fields (KS P = 3.2e-53 against MC). The units come from 7 mice; the paper reports 213, 225 and 249 units from 9 mice.", "deviations": [ "Fields are counted on a map of the central arm from all runs plus each side arm, smoothed per segment; the paper builds left and right choice maps without saying how fields are combined.", "The 'local maximum' of the field rule is taken iteratively from the highest unassigned bin." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "tmaze-peak-info", "statement": "Granule cells have the lowest within-field peak firing rates (GC against MC, Kolmogorov-Smirnov P < 0.003) and the lowest spatial information of the three types (P < 0.0005).", "source": "Results, Spatial and memory properties; Figure 5E and 5F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Within-field peak GC 2.63 Hz against MC 5.68 Hz (KS P = 4.5e-05); spatial information GC 0.035 bits/s against MC 0.603 (P = 1.6e-49) and CA3 0.293 (P = 1.5e-29).", "deviations": [ "As tmaze-multiple-fields." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "tmaze-splitters", "statement": "The fraction of splitter cells, whose central-arm firing predicts the coming turn, is comparable in granule cells, mossy cells and CA3 pyramidal cells.", "source": "Results, Spatial and memory properties", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Splitters 0 of 17 GC, 4 of 179 MC and 4 of 141 CA3 with a central-arm field; chi-square P = 0.76. Fisher's exact test gives P = 1 for GC against MC and against CA3 and 0.73 for MC against CA3. Under equal fractions 0.40 GC splitters would be expected, so the GC comparison has almost no power.", "deviations": [ "The paper names no test for comparing the fractions; a chi-square test was fixed in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "remap-positive", "statement": "For neurons with stable place fields, the remapping index between open fields A and B is above zero in each group (Wilcoxon signed-rank; GC P < 0.05, MC and CA3 P < 0.00001).", "source": "Results, Spatial and memory properties; Figure 6C and 6D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "Place cells GC 27, MC 116, CA3 145 (paper 30, 111, 144), of which 27, 116 and 143 have a remapping index; median remapping index 0.128 (P = 0.0013), 0.293 (P = 1.5e-13) and 0.207 (P = 8.6e-14). Units per type 246, 182 and 317 in 5 mice (paper 247, 181, 317 in 5 mice).", "deviations": [ "The place-field 'local maximum' is the map's peak; the speed is from positions smoothed over 0.25 s." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "remap-gc-lt-mc", "statement": "Granule cells with stable place fields remap less than mossy cells (Kruskal-Wallis P = 0.034; post hoc GC against MC P = 0.028).", "source": "Results, Spatial and memory properties; Figure 6D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "The GC median index (0.128) is below the MC median (0.293) but neither test is significant (Kruskal-Wallis P = 0.306; GC against MC P = 0.114, 0.342 after Bonferroni). With the variant place-cell rule, GC against MC P = 0.0648.", "deviations": [ "The paper's post hoc test is not named; Bonferroni-corrected Mann-Whitney tests are used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "remap-fractions", "statement": "Only 36.7% of granule cells with place fields (11 of 30) remap, against 61.3% of mossy cells (68 of 111) and 55.6% of CA3 pyramidal cells (80 of 144).", "source": "Results, Spatial and memory properties; Figure 6C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "11 of 27 GC (0.407), 65 of 116 MC (0.560) and 73 of 143 CA3 (0.510) place cells remap. MC and CA3 are within tolerance; GC is 0.003 above it. GC remap least at every threshold shown (0.1 to 0.3).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pv-remap", "statement": "Population-vector remapping is smaller for granule cells than for mossy cells and CA3 pyramidal cells, for populations of 5, 10, 15 and 20 place cells.", "source": "Results, Spatial and memory properties; Figure 6E to 6G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "For 5, 10, 15 and 20 cells, the GC median index (0.162 to 0.210) is below the MC (0.253 to 0.302) and CA3 (0.251 to 0.352) medians, Kruskal-Wallis P from 5.8e-35 to 8.1e-190. 71% to 89% of GC draws fall below the MC median. These P values treat 1000 overlapping draws from the same 27 GC as independent and do not measure the evidence. With all place cells together the index is 0.22 for GC and 0.25 for MC, and permuting the GC and MC labels gives P = 0.32 for that difference.", "deviations": [ "Place cells pooled across sessions and mice for the draws; the paper does not say whether it pooled." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "inheritance-tmaze", "statement": "Mossy cells rarely inherit place fields from single presynaptic granule cells; of 10 place fields of connected granule cells, only 2 overlapped a field of the postsynaptic mossy cell.", "source": "Results, Transmission of place information; Figure 7A and 7B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "5 of 16 GC fields (0.31) of GC with a detected MC partner overlap a partner MC field, within the criterion of at most a third; 15 of 23 GC partners have no T-maze field (paper 11 of 18). The result is close to the criterion's limit and uses the automatic pair detections (see monosyn-gc-to-mc). With the partner replaced by a random other MC of the session (1000 draws), the overlap is 0.38 (5th to 95th percentile 0.19 to 0.62) and 33% of draws are at or below 0.31, so the overlap with the connected MC is at the chance level.", "deviations": [ "\"Rarely\" was fixed as at most a third of GC fields; the paper gives 2 of 10.", "Pairs are automatic detections, not the paper's curated pairs." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "inheritance-openfield", "statement": "In the open fields, the rate maps of connected granule cells and mossy cells are not correlated within the granule cell's place field (median near 0, n = 19, Wilcoxon P = 0.60).", "source": "Results, Transmission of place information; Figure 7J", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "18 comparisons from 6 pairs in 4 sessions; median r = -0.038, Wilcoxon P = 0.67; 5 of 18 above 0.5 (paper 2 of 19). The 18 comparisons come from only 6 pairs, so they are not independent.", "deviations": [ "Pairs are automatic detections; the open-field sessions include the curtain sessions, as the paper's five sessions per pair do." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "mc-deeper", "statement": "Mossy cells are located deeper than granule cells relative to the reversal of the type 2 dentate spike (DS2) (Mann-Whitney P < 0.001).", "source": "Figure 1G; Results, Identification of granule cells and mossy cells", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "In the 17 files with the wide-band signal and shanks (4 mice; 139 GC, 226 MC with at least 20 spikes in the wide-band window), the DS2 amplitude at the unit's site, read from the wide-band signal, has a median of +580 uV for MC and +232 uV for GC (Mann-Whitney P = 2e-40); 100% of MC (to two decimals) and 80% of GC sit where DS2 is positive, and MC are deeper in each of the 4 mice. With the site the electrodes table gives (a variant), +271 against -38 uV (P = 5.7e-09), with YutaMouse33 reversed; the two sites share the LFP column for 9% of units and the DS2 sign for 63%.", "deviations": [ "Depth is read from the DS2 amplitude at the site, as the files give no site coordinates; the paper measures distance from the DS2 reversal.", "17 of 101 files only. The site is the wide-band column where the unit's spike is largest (300 Hz high-pass, about 150 s of signal per file), as the electrodes table's channel map disagrees with the wide-band signal; the criterion's shank channel taken through the table is shown as a variant.", "DS2 amplitude from about 220 s of LFP per file (the two LFP chunks with the most DS2 peaks)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gc-mc-classification", "statement": "K-means clustering on the DS2 amplitude at the unit's site, the NREM to wake rate ratio and two principal components of the waveform's second derivative separates excitatory dentate units into granule cells and mossy cells.", "source": "Results; Figure 1D to 1F; STAR Methods, Unit classification", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_senzai_2017.ipynb", "notes": "On 364 GC and MC of the 17 files (32 dropped for fewer than 20 spikes in the wide-band window, no DS2 site or a zero awake rate), k-means on the DS2 amplitude at the wide-band site, the Methods' NREM to wake ratio and two components of the second derivative of the unfiltered wide-band waveform agrees with the labels for 95.3% of units (93% to 97% by mouse). Without the DS2 amplitude 89.0%, without the first waveform component 88.5%, without the ratio 94.2%. With the log ratio 95.6%, with home-cage awake time 94.8%, with the stored waveforms and the table's site 92.8%.", "deviations": [ "Run on 17 of 101 files (364 of 1177 GC and MC); the paper ran it on all excitatory units.", "The site and the waveform are read from the wide-band signal (about 150 s per file), as the electrodes table's channel map disagrees with it; the stored waveforms with the table's site are a variant.", "Wake is the `awake` periods, as fixed in the criterion; the Methods name awake time in the home cage, shown as a variant.", "The four features are standardised and clustered directly; the paper took a second PCA before k-means, which does not change k-means on all components.", "The second-derivative window starts at the trough; the Methods say 0 to 0.8 ms without naming the origin." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gc-mc-distance", "statement": "Granule cells reside 59 +- 35 um above the mossy cells they drive.", "source": "Results, Granule cell-mossy cell spike transmission; Figure 3D", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the positions of the recording sites in um. The electrodes tables give x, y and z as NaN in every file, the order of sites along a shank is not stated, and 83 of 101 files do not say which shank a unit was on. The paper's own monosynaptic pairs were not converted either. The Methods give 8 sites per shank on the 8-shank probes and 10 on the 6-shank probes, staggered with 20 um vertical separation, but the table's site numbers do not follow depth (the DS2 profile along them crosses zero more than once on 43 of 64 shanks with a crossing), and a unit's largest wide-band column lies on the shank the table gives for only 45% of units. In the 17 files that give the shank, the order of each shank's stored waveform channels can be recovered from the units' spikes in the wide-band signal, and along it the DS2 profile crosses zero once on 43 of the 51 shanks that cross, so it is consistent with depth. This attempt wrote no criterion for the claim and ran no test on that order; a new attempt could test it on these 17 files (39 detected GC to MC pairs).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gc-backpropagation", "statement": "Granule cell spikes show a delay from the soma to the proximal dendrites, absent in mossy cells.", "source": "Results; Figure S3D to S3F", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs each unit's waveform along the shank with the sites' vertical positions; the files give no site coordinates (x, y, z are NaN) and the stored waveforms span 1.6 ms at the channels of the shank without their positions. In 83 files the shank itself is not given. The wide-band signal gives each unit's spike on every column, and in those 17 files the order of each shank's stored channels, recovered from the units' spikes, is consistent with depth (see gc-mc-distance). This attempt wrote no criterion for the claim and ran no test of a delay along that order; a new attempt could.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "format_error", "statement": "In 24 files the end index of the first unit in the units table is short by a multiple of 65,536 spikes (k = 1 to 7). The missing spikes open the second unit's spike train, which then restarts at the beginning of the recording, so the second unit's times are not sorted. The first moved spike follows the first unit's last stored spike by 2 ms to 0.5 s. This looks like an integer overflow at conversion; the waveforms follow the same boundaries." }, { "kind": "metadata_error", "statement": "The genotypes in the files (6 SST-Cre, 5 Drd2-Cre::Ai35, 4 POMC-Cre::Arch, 1 POMC-Cre::Ai35) do not match the paper's 16 mice (7 SST-Cre, 5 DRD2-Cre::Ai35, 3 POMC-Cre::Ai35 and 1 wild type)." }, { "kind": "metadata_insufficient", "statement": "83 of 101 files do not say which shank each unit was recorded on (`shank_id` is a cluster number, and there is no `electrode_group`), and no file gives site coordinates (x, y, z are NaN). The paper's depth measures can be computed for 17 files only, and distances between cells not at all." }, { "kind": "metadata_insufficient", "statement": "The T-maze position series (`twhl_linearized`, `twhl_norm`) are not described. The values show column 0 of `twhl_linearized` runs along the central arm (0 to 2) and column 1 is an angle along the circular side arms, negative for the left arm, which fits the maze in the Methods but is not stated." }, { "kind": "metadata_insufficient", "statement": "The states table holds `awake`, `quiet`, `nrem`, `rem` and `transit` without a description; the paper names wake, NREM and REM, and whether `quiet` counts as wake is not stated." }, { "kind": "metadata_insufficient", "statement": "The interneuron labels (narrow-waveform, wide-waveform) do not say whether the unit is in the dentate gyrus or CA3, which the paper separates; only the excitatory label was split by region (granule cell or CA3 pyramidal cell)." }, { "kind": "data_missing", "statement": "The monosynaptic connections the authors detected and curated (`MonoSynConvClick.mat`) were not converted (the conversion code comments them out), so the pair-based results (Figures 3, 4 and 7) cannot be checked on the authors' pairs." }, { "kind": "other", "statement": "The dandiset holds 568 mossy cells and 609 granule cells against the paper's 500 and 586, and 237 units labelled `missing` (units of the spike sorting with no row in the authors' unit summary)." }, { "kind": "format_error", "statement": "The light-pulse series PulseStim_5V_20ms_LD12 of YutaMouse57-161006 holds 89,086 times of which 24,286 are duplicates, and its times decrease once." }, { "kind": "other", "statement": "The units table has two layouts. 18 files (mice 33, 41, 42 and 54) carry an `electrode_group` column naming each unit's shank, one of them without waveforms (YutaMouse33-150218, which the conversion script lists as excluded); the other 83 files do not." }, { "kind": "metadata_insufficient", "statement": "Seven dates hold two files of one mouse (the second named with `b`). They share no spike trains, so they are different recordings, but the metadata do not say whether they come from a second probe or a second session." }, { "kind": "paper_inconsistency", "statement": "The Methods give a burst index threshold of 1.2 for excitatory cells, and the Figure 1A legend gives 1.8." }, { "kind": "metadata_error", "statement": "In the 17 files with the wide-band signal and each unit's shank, the electrodes table's assignment of columns to shanks and sites disagrees with the data. The column where a unit's spike is largest in the wide-band signal lies on the shank the units table gives for 45% of units (11% to 79% by file) and is the table's own site for 9%, and the DS2 amplitude along the table's site numbers crosses zero more than once on 43 of 64 shanks where it crosses at all. The wide-band and LFP columns match each other. The units' shanks (`electrode_group`) and stored waveform channels fit the wide-band signal under one fixed map of columns, the same in all 4 mice (a map from three mice gives the column of a unit's largest spike for 78% to 89% of units in the fourth, against 5% to 13% for the table), so the error is in the table, whose blocks of 8 rows do not match the probe's columns." }, { "kind": "metadata_insufficient", "statement": "The stored spike waveforms are about 5 times larger than the same spikes in the wide-band signal (median peak-to-peak 421 against 81 uV, 300 Hz high-pass), and their filtering and scaling are not described. They match the wide-band spike best after a 300 Hz high-pass (median correlation 0.987, against 0.981 unfiltered and 0.867 at 800 Hz), with a gain of 5.08, close to 5.13, the inverse of the wide-band conversion of 0.195 uV per count, which is consistent with waveforms stored in ADC counts and read as microvolts. Each holds 1.6 ms with the trough at 0.8 ms, which cuts off the peak of 43% of GC, 67% of MC and 78% of CA3 waveforms." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier queried the archive metadata and tested helper functions on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; all 31 agree with the record.", "agreed": 31, "of": 31, "disagreements": [] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the first revision, the helper module, the claims file and the attempt record, with the paper. The verifier agreed with all 31 outcomes. It also flagged that cell 0 ('The raw wide-band signal is in 17 files and is not used') and cell 5 ('(not used)') are stale, as cells 21, 24, 29, 35, 107 and 110 use the wide-band signal; both were corrected.", "agreed": 31, "of": 31, "disagreements": [] } ] }, { "id": "000004-chandravadia-2020-01", "dandiset": "000004", "dandiset_version": "0.220126.1852", "paper": "10.1038/s41597-020-0415-9", "paper_title": "A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task", "date": "2026-10-15", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "000004-chandravadia-2020", "entry_title": "Human single neurons during a recognition memory task (Chandravadia et al. 2020)", "description": "Tests the data descriptor of Chandravadia et al. (2020) on dandiset 000004, which holds 87 sessions of 59 epilepsy patients with single units from the amygdala and hippocampus during a new/old recognition task. It checks the files against the paper's description of the data records and subjects, and repeats the behavioural results (AUC, ROC asymmetry, accuracy by confidence) and the proportions of visually and memory selective cells of Figure 5.", "notebooks": [ { "path": "reproduce_chandravadia_2020.ipynb", "title": "Reproducing Chandravadia et al. (2020) from dandiset 000004", "executed": "notebooks/000004-chandravadia-2020/reproduce_chandravadia_2020.html" } ], "outcomes": [ { "claim": "counts-neurons-subjects", "statement": "The dataset holds 1863 single neurons recorded from the medial temporal lobes of 59 subjects.", "source": "Abstract; Technical Validation, proportion of selective cells", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "1864 unit rows over 87 files (paper 1863, one more) and 59 subjects. With the 55 units of sessions 44 and 55 counted once, as their spike trains repeat those of sessions 43 and 54, 1809. Both readings are within tolerance. CS sessions hold 1787 units and TWH sessions 77. The paper gives no count per session or site, so the extra unit cannot be identified; no unit is empty (the fewest spikes is 22).", "deviations": [ "The exact count differs from the paper's by one unit; the tolerance is the protocol's 10%." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "counts-sessions", "statement": "The patients performed 87 sessions, listed by subject and session id in Online-only Table 1 (the Methods give 89).", "source": "Methods, Subjects; Online-only Table 1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "The 87 (subject, session) pairs of the files equal those of Online-only Table 1, none missing and none extra. The Methods' 89 sessions disagree with the table and the files. Every task variant of the table corresponds to one stimulus set in the files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "table1-demographics", "statement": "Online-only Table 1 gives the age and sex of every subject; there are 25 female and 34 male subjects.", "source": "Online-only Table 1", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Age and sex match for 56 of 59 subjects. C24 is 57 in the files and 47 in the table, H33 is 30 and 29, and H48 is female aged 32 in the files and male aged 54 in the table. The files have 26 female and 33 male subjects (table 25 and 34), within tolerance. Each subject has one age and one sex across its files. The diagnosis text differs for 19 of 59 subjects. For 8 the files give a broader category; for 6 (H10, H16, H17, H19, C58, T89) they give Lateral Frontal, which adds Lateral to the table's Frontal except for H17 (Left Inferior Frontal in the table). Five differ in substance, C61 (Left Lateral Frontal in the files, Left Mesial Temporal in the table), C34 (Bilateral Independent Temporal against Bilateral Mesial Temporal), C56 and H51, where the files leave out part of the table's diagnosis (orbitofrontal, temporal), and T90, where they add Bilateral. All 87 files have the age and sex of their section in the code's session list, defineNOsessions_release.ini, as printed in the notebook.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "task-structure", "statement": "Each session has 100 encoding trials showing 100 novel images and 100 recognition trials, of which 50 show new and 50 old images, and the images come from 5 visual categories.", "source": "Methods, Task; Data Records, stimuli group; Technical Validation, proportion of selective cells", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "All 87 sessions have 100 recognition trials with 50 per label, 5 categories (ids and names) and one stored image per trial timestamped at its onset. 79 sessions have 100 encoding trials with 100 distinct images; sessions 18, 20, 21, 23, 26, 27 and 44 have 50 and session 123 has 97. In these eight sessions 2% to 48% of the images shown as old have no encoding trial in the file. The images are stored as one ImageSeries per file, not as stimuli_learn_x and stimuli_recog_x.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "new-old-label-coding", "statement": "In the trials table, new_old_labels_recog is 0 for old stimuli (seen during encoding) and 1 for new stimuli.", "source": "Data Records, interval group", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "The labels are coded the other way. In 79 of 87 sessions every label-1 image and no label-0 image was shown during encoding; in no session do label-0 images match the encoding block. Label 1 draws \"old\" responses (4 to 6) more often than label 0 in 86 of 87 sessions (medians 0.70 and 0.24, sign test p = 1.1e-24). In the 8 sessions with short encoding blocks, 52% to 98% of the label-1 images are among the stored encoding trials and no label-0 image is. The paper's code reads 1 as old, and every analysis here does the same; with the stated coding the mean AUC is 0.247.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ttl-codes", "statement": "The events stream holds the TTL markers 55, 1, 2, 3, 20 or 21, 31 to 36, 6 and 66 with the meanings of Table 1, and the events and experiment_ids streams have one entry each, in the same order.", "source": "Data Records, acquisition group; Table 1", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Events and experiment_ids have the same length and timestamps in all 87 files, and 17019 of 17047 trials show the codes 1, 2, 3, a response and 6 in order. 78 files meet every condition. Codes not in Table 1 occur in sessions 43 (98, 99), 58 (23), 93 (99), 123 (0), 127 (0), 128 (4), 2001 (22, 23), 2002 (23) and 2003 (23). Seven files (sessions 92, 93, 96, 97, 99, 100, 101) have no start code 55 and session 2001 has a third end code 66; these do not enter the criterion. In every trial that shows the sequence the response is of its phase's kind (20 or 21 in learning, 31 to 36 in recognition), 17019 of 17019. In 6 files 1 to 18 trials have a response event that differs from the trials table's response_value; the analysis uses response_value.", "deviations": [ "The criterion did not give a number for most files in a partial result; 78 of 87 was taken as most." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "experiment-ids", "statement": "The learning block is labelled with one of 80, 83 or 88 and the recognition block with one of 81, 84 or 89.", "source": "Data Records, acquisition group; Table 2", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "83 of 87 files use the ids of Table 2. Session 55 uses 80 and 82, session 77 uses 81 and 82, and sessions 100 and 105 use 82 and 83 (learning and recognition, identified by their responses). The files' data_collection field states the same ids.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "session-dates", "statement": "To protect patient information, session_start_time keeps only the year and month of the experiment, with the day set to the first of the month for all sessions.", "source": "Data Records, structure of the NWB file", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "86 of 87 files start on the first of a month; session 48 starts on 2010-03-13. Session 68 is dated 2000-01-01, outside the 2006 to 2019 span of the others.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "units-table", "statement": "The units table holds spike_times, waveform_mean_encoding, waveform_mean_recognition (sampled at 100 kHz), origClusterID, SNR, IsolDist and electrodes, with one electrode per neuron.", "source": "Data Records, units group", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "All 87 files hold every column (IsolDist is named IsolationDist) and link each unit to one electrode. The stated waveform sampling rate is 98400 Hz, within tolerance of 100 kHz, with 256 samples. SNR is finite for 1778 of 1864 units (11 infinite, 75 NaN); the isolation distance is NaN for 493 units and above 1e4 for 4 (up to 8.08e+32). Spike times are not in increasing order for 13 units in sessions 21, 58, 68, 70, 73, 77 and 128, and units 35 and 37 of session 58 hold every spike time twice.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "electrodes-table", "statement": "The electrodes table gives each electrode's brain area, MNI coordinates, impedance, the filter applied before spike sorting (300 to 3000 Hz) and the original hardware channel.", "source": "Data Records, general group; Methods, data acquisition", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Location, filtering (300-3000Hz for all) and origChannel are filled for all 887 electrodes. The impedance column is stored as NaN (float64) for all 887. Coordinates are missing for 99 electrodes in sessions 7, 20, 21, 23, 24, 50, 52 and 2004; where given, the sign of x matches the hemisphere of the location for all 788.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "isi-criterion", "statement": "Clusters were accepted as units only when fewer than 3% of their interspike intervals were shorter than 3 ms.", "source": "Methods, data acquisition", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "1858 of 1864 units (99.7%) have fewer than 3% of interspike intervals below 3 ms (median 0.19%). Six units are at or above 3%, four at or above 5% and two above 20% (maximum 50.1%); the two above 20% are the session 58 units whose spike times repeat. With the spike times as stored, 1860 units pass. All 77 TWH units pass.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-mtl-locations", "statement": "All neurons were recorded from the medial temporal lobe, in the amygdala and the hippocampus.", "source": "Abstract; Figure 5a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "All 1864 units are on electrodes in the right amygdala (594), left amygdala (498), right hippocampus (407) or left hippocampus (365).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-auc-all", "statement": "Subjects distinguished new from old images; the behavioural AUC averaged over all sessions is 0.74 \u00b1 0.10.", "source": "Technical Validation, behaviour; Figure 5b and 5c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Mean AUC 0.753, SD 0.094 over 87 sessions (range 0.445 to 0.919; 6 sessions below 0.6, one at or below 0.5). Against chance (0.5), t = 25.1, p = 2.2e-41. With sessions 44 and 55 dropped, 0.754 and 0.095. Recomputed with the label coding the paper states (0 = old), the mean AUC is 0.247 (0.081 to 0.555).", "deviations": [ "The tolerance of the mean is the stated spread (0.10), as the protocol prescribes; the spread itself was held to 10%." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-auc-sites", "statement": "Performance was similar at the two study sites, with an average AUC of 0.74 \u00b1 0.09 for CS sessions and 0.69 \u00b1 0.13 for TWH sessions.", "source": "Technical Validation, behaviour; Figure 5c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "CS 0.760 \u00b1 0.085 over 78 sessions and TWH 0.688 \u00b1 0.138 over 9, all within tolerance. Welch's t-test between sites p = 0.161 (difference 0.072).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-roc-asymmetric", "statement": "The ROC curve is asymmetric (p < 0.05), as expected for declarative memory.", "source": "Technical Validation, behaviour; Figure 5b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Six sessions (59, 60, 93, 99, 119, 2008) have all five interior z(FA) or z(H) points equal, so their fitted slope is not an estimate (negative in four, 0 in one); they are left out. Over the other 81 sessions the z-ROC slope has mean 0.792, median 0.795, SD 0.289, and is below 1 in 64. One-sample t-test against 1, t = -6.49, p = 6.6e-09; Wilcoxon W = 487, p = 3.3e-08. With all 87 sessions, mean 0.726, below 1 in 70, t-test p = 1.631e-09, Wilcoxon p = 1.586e-09. The pooled ROC has slope 0.816. Per-session AUC and slopes are printed.", "deviations": [ "The paper names no measure or test for asymmetry; the z-ROC slope of the paper's code and a t-test against 1 were fixed in the criterion.", "Sessions whose interior z-ROC points do not allow a fit are left out of the mean and the tests, after the second verification round; all 87 sessions are a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5d-confidence-accuracy", "statement": "Accuracy is significantly higher in high than in low confidence trials (P < 0.001, paired t test) across all sessions.", "source": "Technical Validation, behaviour; Figure 5d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Fixed split, high 80.1% against low 60.9% over 84 sessions, high above low in 73, paired t-test p = 3.2e-16. Dynamic split, 78.3% against 60.4%, paired p = 1.2e-13. Sessions 93, 99 and 2008 have no responses in one group and are left out. The unpaired test of the code gives p = 3.4e-17 and 1.3e-15.", "deviations": [ "Three sessions without responses in one confidence group are left out; the paper says all sessions." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "vs-cells-proportion", "statement": "343 of the 1863 cells (18.4%) are visually selective, by a one-way ANOVA (P < 0.05) of the firing rate in recognition trials, in a 1 s window starting 200 ms after stimulus onset, across the 5 visual categories.", "source": "Technical Validation, proportion of selective cells; Figure 5f", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Methods' window (200 to 1200 ms), 332 of 1864 units (17.8%), within tolerance. The code's window (200 to 1700 ms) gives 343 of 1864 (18.4%), the paper's count. Counting duplicated spike trains once, 326 of 1809 (18.0%). Shuffled categories give 4.7% (10 shuffles per unit). At p < 0.01, 8.6%; at p < 0.1, 25.6%. Among sessions with at least 20 units, 0.0% to 35.7%.", "deviations": [ "The main result uses the Methods' 1 s window; the paper's code uses 1.5 s, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ms-cells-proportion", "statement": "146 of the 1863 cells (7.8%) are memory selective, by a two-tailed bootstrap comparison of mean firing rates (1,000 runs, P < 0.05) between the 50 novel and 50 familiar recognition trials in a 1 s window starting 200 ms after stimulus onset.", "source": "Technical Validation, proportion of selective cells; Figure 5f", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "The Methods' test (all 50 new and 50 old trials, 200 to 1200 ms) selects 110 of 1864 units (5.9%), against the paper's 146 (7.8%). With labels shuffled (10 per unit, 18640 tests) 5.39% are selected (95% CI 5.07% to 5.73%); 110 is not distinguishable from this null (one-sided binomial p = 0.18) and only just above 5% (p = 0.044). A second bootstrap seed gives 118 (6.3%), also outside tolerance; 22 units are selected under one seed only. Correct trials only in the Methods' window give 143 and 140 under the two seeds, and the code's choices (correct trials only, 200 to 1700 ms) 147 and 149, all within tolerance (147 against 5%, p = 7.1e-08). With labels shuffled among the correct trials in the code's window the null is 5.58% (95% CI 5.26% to 5.92%), and 147 exceeds it (104.1 expected, one-sided binomial p = 2.5e-05). All trials in the code's window give 108 and 109. The paper's number therefore follows its code's restriction to correct trials, which the Methods do not mention, and the outcome comes from that disagreement, not from the data. It is judged on the Methods' procedure, as the protocol requires. Per-unit p-values of the 288 units selected under some reading or seed are printed.", "deviations": [ "The paper's code restricts the test to correct trials and uses a 1.5 s window; the Methods describe all 50 and 50 trials and a 1 s window. The Methods give the main result.", "The bootstrap uses the code's algorithm with a fixed seed." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dual-cells-proportion", "statement": "26 cells (1.4%) are both visually and memory selective.", "source": "Technical Validation, proportion of selective cells; Figure 5f", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Under the Methods' tests 12 of 1864 units (0.6%) are both VS and MS, against 19.6 expected if the two were independent and the paper's 26 (1.4%); 14 with the second bootstrap seed. The code's choices give 26 (1.4%) under both seeds. Counting duplicated spike trains once, 11 of 1809. As for ms-cells-proportion, the outcome comes from the Methods disagreeing with the code.", "deviations": [ "Depends on ms-cells-proportion, whose main test follows the Methods and not the code." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-site-proportions", "statement": "The percentages of VS, MS and dual cells are comparable between CS sessions (18.4%, 7.7% and 1.4%) and the new TWH sessions (19.4%, 10.4% and 1.3%).", "source": "Technical Validation, proportion of selective cells; Figure 5f (the values as written into plotFigure5.ipynb at commit 1d95162)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Fisher's exact test finds no difference between sites (VS p = 0.360, MS p = 0.215, dual p = 1.000). Under the Methods' tests CS has 17.6%, 5.8% and 0.7% and TWH 22.1%, 9.1% and 0.0%; only CS VS is within tolerance. The code's choices give CS 18.4%, 7.8% and 1.4% (328, 139 and 25 of 1787) and TWH 19.5%, 10.4% and 1.3% (15, 8 and 1 of 77), matching Figure 5f to within 0.1 point, so the partial outcome comes from the Methods disagreeing with the code. With 77 TWH units the 95% intervals of the TWH percentages are 13.4% to 33.0% (VS), 3.7% to 17.8% (MS) and 0.0% to 4.7% (dual), so the Fisher tests have little power.", "deviations": [ "The paper names no test for \"comparable\"; Fisher's exact test was fixed in the criterion.", "The expected values come from plotFigure5.ipynb, which writes them into the plot as constants." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "twh-sessions", "statement": "The dataset includes 9 sessions from a new institution, Toronto Western Hospital.", "source": "Technical Validation, proportion of selective cells; Online-only Table 1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Sessions 2001, 2002, 2003, 2004, 2005, 2007, 2008, 2009 and 2011, from 8 subjects, with 77 units; all name Toronto Western Hospital as institution.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-example-vs-neuron", "statement": "Neuron 132-177-4-RA (session 132, channel 177, cell 4, right amygdala) is visually selective, responding most to images of animals.", "source": "Figure 4", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "Session 132 has one unit on channel 177, at electrode row 4 in the right amygdala, which matches the label 132-177-4-RA. It is the file's unit at 0-based index 4 of 8, so the label's cell number equals both its electrode row and its 0-based unit index. ANOVA across categories p = 1.2e-22 (Methods' window) and 7.9e-19 (code's window); mean rate 6.75 Hz for animals against 0.25 to 0.85 Hz for the other four categories.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "previous-release-link", "statement": "The sessions of the earlier release (Faraut et al. 2018) are found in this dandiset under the same subject, session id and task variant.", "source": "Faraut et al. 2018, Scientific Data 5, 180010 (doi:10.1038/sdata.2018.10), Table 1", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "64 of the 65 sessions of Table 1 of Faraut et al. 2018 (98.5%) are in the dandiset by session id, all under the same subject and task variant. Session 98 of subject H48 is not; its section in the code's session list is commented out. Age and sex agree for 39 of the 42 matched subjects; C24, H33 and H48 differ, the same three that differ from Online-only Table 1, whose values the 2018 table shares.", "deviations": [ "The claim was added after the first verification round, to link the earlier release's session list to the dandiset for previous-release-additions." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "previous-release-additions", "statement": "Relative to the earlier release of this task's data (Faraut et al. 2018), this release adds 23 sessions, 17 subjects and 288 neurons.", "source": "Background and Summary; Technical Validation", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chandravadia_2020.ipynb", "notes": "The dandiset has 23 sessions not in the earlier list (14 CS, 9 TWH) from 17 subjects with no earlier session, the paper's numbers. The new sessions hold 325 units, outside the tolerance of 288; the sessions also in the earlier release hold 1539 units, where Faraut et al. 2018 gives 1576 neurons for 65 sessions. 1576 + 288 = 1864, the dandiset's unit count, so the paper's 288 matches a difference of totals and not a count of the new sessions. The differences of the stated totals are 22 sessions, 17 subjects and 287 neurons. The link holds for 64 of 65 earlier sessions; the missing session 98 does not change which sessions or subjects are new, and may account for part of the difference in the earlier sessions' unit count.", "deviations": [ "The earlier release's session list is Table 1 of Faraut et al. 2018, not its Dryad archive, which refuses automated download (HTTP 403 on the file stream, and its API asks for a bearer token).", "In the first version of this attempt the claim was blocked for want of the list; it was tested after the first verification round." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig3-example-vs-neuron", "statement": "Neuron 144-140-3-RH (session 144, channel 140, cell 3, right hippocampus) is visually selective for phones.", "source": "Figure 3", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The neuron's session id, 144, is not among the dandiset's 87 sessions, nor in Online-only Table 1 or in the session list of the paper's code. The paper's demo script (python/export/demo/export.py, printed, not run) sets NOID 144 under the comment session 'TWH103_111918', and the code's session list gives subject T103 one section, session 2009. In session 2009 two units are on channel 140 in the right hippocampus (unit indices 1 and 2, both at electrode row 1, clusters 352 and 414); unit 2 is visually selective (ANOVA p = 1.3e-09) and fires most to phones. The Figure 4 neuron's cell number 4 is its electrode row and its 0-based unit index (its 1-based index is 5); under that convention the candidate is cell 2 or 1, not 3. With neither the cell number nor a recorded mapping of 144 to 2009, the neuron cannot be identified. The candidates and the cell-number test are printed in the notebook.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The new_old_labels_recog column is described in every file, and in the paper, as 0 for old and 1 for new stimuli. The data have 1 for old; label-1 images are those shown during encoding and draw most \"old\" responses. The paper's code reads it correctly, but a user following the description gets an AUC of 0.25." }, { "kind": "other", "statement": "Sessions 43 and 44 (subject H23) and sessions 54 and 55 (subject H42) hold identical spike trains for every unit, 23 and 32 units. In each pair the units are the same neurons, so 55 of the 1864 units are repeats and the paper's neuron count includes them twice. Session 55 also repeats session 54's learning block trial for trial and differs only in its recognition block." }, { "kind": "data_missing", "statement": "Seven sessions (18, 20, 21, 23, 26, 27, 44) have 50 encoding trials and session 123 has 97, where the paper describes 100. Only 52% to 98% of the images later shown as old are in the stored encoding blocks of these sessions." }, { "kind": "metadata_insufficient", "statement": "Electrode impedance is empty for all 887 electrodes, though the paper lists it in the electrodes table. MNI coordinates are missing for 99 electrodes in 8 sessions." }, { "kind": "metadata_insufficient", "statement": "The isolation distance is NaN for 493 of 1864 units and implausibly large for 4 (up to 8.08e+32), and SNR is NaN for 75 units and infinite for 11." }, { "kind": "format_error", "statement": "The spike times of 13 units in 7 sessions (21, 58, 68, 70, 73, 77, 128) are not in increasing order, and units 35 and 37 of session 58 hold every spike time twice, which doubles their firing rates and puts half their interspike intervals at zero." }, { "kind": "metadata_error", "statement": "Age or sex differ from the paper's Online-only Table 1 for three subjects (C24 57 against 47, H33 30 against 29, H48 female 32 against male 54). The files follow the code's session list; Table 1 of Faraut et al. 2018 gives the same values as Online-only Table 1." }, { "kind": "metadata_error", "statement": "Session 48 keeps the day of the experiment (2010-03-13) in session_start_time, where the paper says every day was set to the first of the month to protect patient information. Session 68 is dated 2000-01-01." }, { "kind": "metadata_error", "statement": "Experiment ids outside Table 2 are used in four files (sessions 55, 77, 100, 105), and event codes outside Table 1 (0, 4, 22, 23, 98, 99) occur in nine files. In six files 1 to 18 trials have a response event that differs from the trials table's response_value." }, { "kind": "paper_inconsistency", "statement": "The Methods state 89 sessions; Online-only Table 1 and the dandiset have 87. The paper gives 1863 neurons; the dandiset has 1864 unit rows." }, { "kind": "code_mismatch", "statement": "The Methods select memory selective cells by comparing all 50 novel and 50 familiar trials in a 1 s window. The paper's code uses correct trials only and a 200 to 1700 ms window for both selections. The paper's counts (343 VS, 146 MS, 26 dual) and Figure 5f follow the code; the Methods' procedure gives 332, 110 and 12." }, { "kind": "code_mismatch", "statement": "plotFigure5.ipynb, the notebook the code provides to reproduce Figure 5, writes the per-site percentages of Figure 5f into the plot as constants and does not compute them." }, { "kind": "identifier_missing", "statement": "The example neuron of Figure 3 is labelled as from session 144, which is not in the dandiset or in the paper's session list. The paper's code names NOID 144 as a recording of subject T103, whose one session in the dandiset is 2009, but nothing maps 144 to 2009." }, { "kind": "data_missing", "statement": "Session 98 of subject H48, listed in the earlier release (Faraut et al. 2018, Table 1), is not in the dandiset or in Online-only Table 1; its section in the code's session list is commented out." }, { "kind": "other", "statement": "The 23 sessions that are new relative to the earlier release hold 325 units, where the paper says 288 neurons were added; 288 is the dandiset's 1864 units minus the earlier release's 1576." }, { "kind": "other", "statement": "The institution is written \"Hunigton Memorial Hospital\" in 28 files and \"Hunington Memorial Hospital\" in 6, and the device as \"Neuralynx-cheetah\" and \"Neuralynx-Cheetah\"." } ], "verifications": [ { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text. The verifier checked the helper's copy of Online-only Table 1 against the paper, tested the helper functions on synthetic data (bootstrap_p, anova_p, zroc_slope, auc, window_rates) and compared bootstrap_p with bootstrapMeanEqualTest.m at commit 1d95162. Report in transcripts/000004/verifier-1-report.md.", "agreed": 24, "of": 24, "disagreements": [] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the revised run, with the conclusions and the summary, the helper module, the claims file and this record. The verifier downloaded the paper and Faraut et al. 2018, checked the helper's copy of Faraut 2018 Table 1 against the PDF (42 subjects, 65 session ids, no differences), and ran zroc_slope on a synthetic session answering only 1 and 6. Report in transcripts/000004/verifier-2-report.md. Its round-1 problem 4 (the shared clock shown for only 38 of 87 sessions) is tied to no claim; it records it as acknowledged and unchanged, and cell 10 states it.", "agreed": 25, "of": 25, "disagreements": [] } ] }, { "id": "000006-economo-2018-01", "dandiset": "000006", "dandiset_version": "0.220126.1855", "paper": "10.1038/s41586-018-0642-9", "paper_title": "Distinct descending motor cortex pathways and their roles in movement", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "000006-economo-2018", "entry_title": "Two types of pyramidal tract neuron in mouse motor cortex (Economo et al. 2018)", "description": "Tests the findings in the abstract of Economo et al. (2018) that dandiset 000006 can test. The dandiset holds silicon probe recordings from the anterior lateral motor cortex of 12 mice in a delayed response task, with tagged PTupper and PTlower units. The notebook measures the selectivity for lick direction of the tagged units in the sample, delay and response epochs, and compares the two types. The transcriptomic and anatomical findings are not testable on it.", "notebooks": [ { "path": "reproduce_economo_2018.ipynb", "title": "Reproducing Economo et al. (2018) from dandiset 000006", "executed": "notebooks/000006-economo-2018/reproduce_economo_2018.html" } ], "outcomes": [ { "claim": "pt-types-transcriptomic", "statement": "Single-cell transcriptional profiling and axonal reconstructions identify two types of pyramidal tract (PT) neuron in motor cortex.", "source": "Abstract", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds electrophysiology only. The single-cell RNA-seq was described in an earlier paper, the bulk RNA-seq is at GEO (GSE119182), and Seq.zip and Axons.zip of the Figshare record hold sequencing and axon data; none is in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-types-shared-targets", "statement": "Both types of PT neuron project to several targets in the basal ganglia and brainstem.", "source": "Abstract", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No anatomy or axonal reconstructions are in the dandiset; Anatomy.zip and Axons.zip of the Figshare record hold them.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-upper-thalamus-projection", "statement": "One type of PT neuron projects to thalamic regions that connect back to motor cortex.", "source": "Abstract", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No anatomy is in the dandiset. The files label tagged units PTupper without naming a projection target; the link to thalamus-projecting neurons comes from the paper's code.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-lower-medulla-projection", "statement": "The second type of PT neuron projects to motor centres in the medulla.", "source": "Abstract", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No anatomy is in the dandiset. The files label tagged units PTlower without naming a projection target; the link to medulla-projecting neurons comes from the paper's code.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-preparatory-activity", "statement": "Descending PT neurons in layer 5 of motor cortex carry preparatory activity, which predicts the upcoming movement before it is initiated.", "source": "Abstract (stated as background to the study)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_economo_2018.ipynb", "notes": "72 of 100 included tagged units are selective for lick direction in the delay epoch (rank-sum p < 0.01); the label-shuffle null has a 99th percentile of 0.040 (p = 0.001). PTupper 29 of 44, PTlower 43 of 56; every animal 25% to 85%. 76 units at p < 0.05 and 67 at p < 0.001. The selective units lie at nominal depths of 430 to 1600 um; the files give no layer per unit, so the statement's \"layer 5\" is not checked. With one session per animal 26 of 36 units are selective (p = 0.001), and among the paper's 130 units from its processed data 89 are (p = 0.001).", "deviations": [ "Claims written from the abstract only; the criterion and the shuffle test of chance are this attempt's.", "Epoch rates are spike counts on the file's clock; the paper's code averaged a causally smoothed PSTH of spikes already assigned to trials. Leaving out the spikes that overlap the next trial, as far as the stored order shows them, gives 73 of 100.", "Units recorded on different days in one animal are counted separately, as in the code; they may be the same neurons (44 of 100 lie within 20 um of a unit of the same animal on another day, and the files hold no waveforms). A variant keeps one session per animal.", "The dandiset holds 44 of the paper's 61 PTupper and 56 of its 69 PTlower units; the code's inclusion rule gives the paper's counts on its processed data and the same decision for every unit the dandiset holds." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-upper-early-preparatory", "statement": "The thalamus-projecting PT type produces early preparatory activity.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_economo_2018.ipynb", "notes": "27 of 44 included PTupper units (0.614) are selective in the sample epoch (-2.5 to -2.1 s), against a null 99th percentile of 0.045 (p = 0.001); in the baseline epoch 2 of 44 (p = 0.079). All 8 PTupper animals have sample-selective units (25% to 100%). 0.795 at p < 0.05, 0.432 at p < 0.001; 26 of 44 without flagged spikes. One session per animal gives 8 of 20 (null 99th percentile 0.100, p = 0.001); the paper's 61 PTupper units give 40 of 61 (p = 0.001).", "deviations": [ "Claims written from the abstract only; \"early\" is read as the code's sample epoch, the first 400 ms after the pole comes in." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-upper-persistent", "statement": "The early preparatory activity of the thalamus-projecting PT type persists until the movement is initiated.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_economo_2018.ipynb", "notes": "(a) 27 of 44 PTupper units are selective in the late delay (null 99th percentile 0.046, p = 0.001). (b) The cosine similarity of sample and late delay d' is 0.495, against a shuffle null median of 0.182 and 95th percentile of 0.433 (p = 0.016). The code's Pearson correlation gives r = 0.496 (p = 0.0006). 17 of the 27 sample-selective units keep the sign of their d' in the late delay. Both parts hold without flagged spikes, without the trials marked not good, with one session per animal ((a) 12 of 20, p = 0.001; (b) cosine 0.670, p = 0.006) and on the paper's 61 PTupper units ((a) 38 of 61, p = 0.001; (b) cosine 0.514, p = 0.002).", "deviations": [ "The code compares coding directions with bootstraps and plots the correlation; the shuffle test of the similarity is this attempt's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-lower-late-and-motor", "statement": "The medulla-projecting PT type mainly produces late preparatory activity and motor commands.", "source": "Abstract", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_economo_2018.ipynb", "notes": "Among 56 PTlower units, 0.714 are selective in the late delay and 0.482 in the sample epoch (one-sided McNemar p = 0.0096), and 0.643 in the response epoch (p = 0.088 against the sample epoch), so part (a) holds and part (b) does not. The rise rests mostly on anm369962 (0.30 in the sample epoch, 0.90 in the late delay); the other three animals stay between 0.44 and 0.77 in all three epochs. At p < 0.001 both parts hold (p = 0.0033 and 0.018), at p < 0.05 neither (0.054 and 0.14). The response epoch rate differs from baseline in 53 of 56 PTlower units and 37 of 44 PTupper units (one-sided Fisher p = 0.080). The variants give the same split. With one session per animal (16 units) part (a) holds (p = 0.016) and part (b) does not (p = 0.23). On the paper's 69 PTlower units from its processed data, (a) holds (0.507 against 0.652, p = 0.049) and (b) does not (0.551, p = 0.37); there both parts hold at p < 0.001 and neither at p < 0.05.", "deviations": [ "Claims written from the abstract only; \"mainly late\" is read as more units selective late than in the sample epoch, and \"motor commands\" as selectivity in the first 400 ms after the go cue (a change from baseline is shown as a variant).", "The outcome depends on the test threshold, which the code sets at p < 0.01 for counting selective units." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pt-types-differ-in-timing", "statement": "The two PT types differ in when they carry information about the movement; the thalamus-projecting type carries early preparatory activity, the medulla-projecting type mainly late preparatory activity and motor commands.", "source": "Abstract", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_economo_2018.ipynb", "notes": "(a) Sample epoch selectivity is 0.614 for PTupper and 0.482 for PTlower (one-sided Fisher p = 0.134). (b) Response epoch selectivity is 0.643 for PTlower and 0.841 for PTupper, the reverse of the claim (p = 0.99; p = 0.022 for the reverse). Over animals neither holds (Mann-Whitney p = 0.30 and 0.93). The code's coding-direction variant points the abstract's way but is not significant. The sample to late delay similarity is 0.473 +/- 0.214 for PTupper and 0.216 +/- 0.204 for PTlower, with PTupper higher in only 83 of 100 bootstraps. Without the bootstrap, PTupper's similarity is above its shuffle null (p = 0.007) and PTlower's is not (0.177, p = 0.43). On the paper's 130 units from its processed data, (a) is 0.656 against 0.507 (p = 0.062) and (b) is reversed (0.551 against 0.770, p = 0.007 for the reverse); with one session per animal, (a) p = 0.28 and (b) is reversed (0.438 against 0.800). The paper's measure of early information (Extended Data Fig. 9, single-unit decoding accuracy in the sample epoch, at least 70%) goes the abstract's way, with 7 of 44 PTupper against 1 of 56 PTlower units here (Fisher p = 0.012) and 12 of 61 against 1 of 69 on the paper's units (p = 0.0005), where the legend gives 15 of 61 against 3 of 69; the means match the legend (0.638 and 0.586 against 0.644 and 0.589), and the smaller counts are not explained. Part (a) is thus supported under the paper's measure but not under the criterion's. Part (b), selectivity for lick direction in the response epoch, is reversed in every variant. Under the variant reading of \"motor commands\" as a response epoch rate that differs from baseline, PTlower is ahead, 53 of 56 against 37 of 44, without reaching significance (one-sided Fisher p = 0.080). The reversal thus shows that PTlower units are less often direction-selective in the response epoch, not that they lack movement-related activity.", "deviations": [ "Claims written from the abstract only; the comparison of fractions between types is this attempt's reading of the contrast in the abstract, and the paper may compare the types differently.", "Each animal holds one type (8 PTupper and 4 PTlower animals), so type and animal are confounded; the PTlower recordings include sessions in both hemispheres.", "The dandiset lacks 17 of the paper's 61 PTupper and 13 of its 69 PTlower units; the variant on the paper's units gives the same outcome." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "11 sessions of the paper's processed data (Figshare doi:10.25378/janelia.7007846) that hold tagged units are not in the dandiset. They hold 17 of the 61 PTupper and 13 of the 69 PTlower units the paper analysed, so the dandiset holds 44 and 56. Every tagged unit the dandiset does hold is in the processed data with the same label and the same inclusion decision under the paper's code. The dandiset's description says some files were found to be broken and were left out, without naming them." }, { "kind": "data_missing", "statement": "The dandiset holds the electrophysiology only. The transcriptomic and anatomical data behind four of the abstract's findings (the two PT types and their projection targets) are not in it; they are at GEO (GSE119182) and on Figshare (doi:10.25378/janelia.7007846)." }, { "kind": "format_error", "statement": "Spike times are not sorted in 1120 of 1149 units. They were written trial by trial as trial start + go cue time + the spike time from the go cue. Each trial's spikes cover 6.4 s from about 0.97 s before the pole comes in, and trial starts are a median 6.4 s apart (5.4 to 7.9 s from the 1st to the 99th percentile), so consecutive trials overlap on the file's clock and some spikes of one trial lie in the next trial's early epochs (11.7% of the spikes counted in the baseline epoch, under 2% in later epochs, are detectably out of order). Trial membership of a spike cannot be recovered in full from the files." }, { "kind": "format_error", "statement": "The trial table's stop_time is NaN in every file, and pole_in_time, pole_out_time and cue_start_time are relative to the trial start without saying so. On the file's clock the go cue of a trial often falls after the next trial's start_time." }, { "kind": "metadata_insufficient", "statement": "The tagged unit labels PTupper and PTlower are not described in the files or the dandiset metadata, and the projection targets (thalamus and medulla) that the paper uses to name the types are stated only in the paper's code." }, { "kind": "metadata_insufficient", "statement": "Unit quality mixes two vocabularies (single, and Excellent, Good, Fair, Poor) and has undescribed empty values ([], 0, blank). Sex is U and genotype empty for every mouse, the electrode positions are all zero, and every electrode group gives layer 5 whatever the depth." }, { "kind": "other", "statement": "In the paper's processed data, in every one of the 53 sessions the dandiset holds, the spike windows of the first ten trials start later relative to the pole than those of the other trials (by about 2.7 s in the session examined in detail); the paper's code leaves out the first ten trials of each unit, which hides this. The files carry the same shift, as their spike times equal the processed ones in every unit." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. The header still listed the outcomes.", "agreed": 9, "of": 9, "disagreements": [] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run with its conclusions and summary, the helper module, the claims file, the README and this attempt record, and the public Nature page of the paper with its Extended Data legends and Data availability statement.", "agreed": 9, "of": 9, "disagreements": [] } ] }, { "id": "000035-scala-2021-01", "dandiset": "000035", "dandiset_version": "0.211014.0808", "paper": "10.1038/s41586-020-2907-3", "paper_title": "Phenotypic variation of transcriptomic cell types in mouse motor cortex", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-5" }, "tier": "runs", "entry": "000035-scala-2021", "entry_title": "Patch-seq neurons of mouse motor cortex at physiological temperature (Scala, Kobak et al. 2021)", "description": "Tests the findings of Scala, Kobak et al. (2021) that can be tested on dandiset 000035, which holds the paper's follow-up recordings at 34 degrees C (185 neurons, mostly layer 5 Sst and excitatory cells). It extracts the paper's 17 electrophysiological features from the traces, checks the cohort and the stimulus against the Methods, tests whether IT and ET neurons overlap electrophysiologically, and compares Sst t-types between temperatures using the paper's published room-temperature features. The findings on the main room-temperature data set are in dandiset 000008 and are not tested here.", "notebooks": [ { "path": "reproduce_scala_2021.ipynb", "title": "Reproducing Scala, Kobak et al. (2021) from dandiset 000035", "executed": null } ], "outcomes": [ { "claim": "fig1-ttype-coverage", "statement": "After quality control, 1,227 Patch-seq neurons from mouse primary motor cortex were assigned to transcriptomic types, covering 77 of the 90 neuronal t-types of the reference taxonomy.", "source": "Results, \"Patch-seq of mouse primary motor cortex\"; Figure 1a", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The finding rests on the 1,329 cells of the main data set and their sequencing. The dandiset holds only the 185 cells of the follow-up at 34 degrees, with their t-type labels but no gene counts. The main data set's recordings are in dandiset 000008, its sequencing data at NeMO (dat-kq04hua) and GEO (GSE163764), and its processed tables in the paper's repository.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-rrr-prediction", "statement": "A sparse reduced-rank regression of 17 electrophysiological features on gene expression, using 25 genes and a rank-5 latent space, reached a cross-validated R2 of 0.38, with cross-validated correlations of 0.90, 0.74 and 0.67 between the first three pairs of projections.", "source": "Results, \"Distinct phenotypes of major families\"; Figure 2", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs gene expression and features of the main data set. The dandiset holds no gene counts and none of the main data set's cells; they are in dandiset 000008 and at NeMO and GEO.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed5-rrr-ion-channels", "statement": "A reduced-rank regression restricted to ion channel genes did not perform much worse than the full model, with a cross-validated R2 of 0.33 and correlations of 0.86, 0.71 and 0.56.", "source": "Results, \"Distinct phenotypes of major families\"; Extended Data Figure 5e-f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As fig2-rrr-prediction.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-families-separate", "statement": "In a k-nearest-neighbour classification of cells into seven transcriptomic families from electrophysiological features, the confusion matrix was mostly diagonal, with only the ET and IT subclasses strongly overlapping.", "source": "Figure 3a, d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the main data set's cells, which are in dandiset 000008. The same classifier was run on the 34 degree cells for ed6-it-et-overlap, where Lamp5, Vip and CT cells are absent.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-morphology-combined", "statement": "Families were less separable by morphology than by electrophysiology among inhibitory neurons, and most separable when electrophysiological and morphological features were combined.", "source": "Figure 3b-d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs morphological reconstructions, which are not in the dandiset (none were recovered in the 34 degree experiments). They are in the Brain Image Library, with features in the paper's repository.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-distance-correlation", "statement": "Across 200 pairs of t-types from the same family, the transcriptomic distance and the electrophysiological distance between t-types were correlated with r = 0.60.", "source": "Figure 4c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the main data set's cells (dandiset 000008) and the reference 10x expression data.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-it-depth", "statement": "Among IT t-types, transcriptomic distances were strongly correlated with differences in average soma depth, r = 0.70.", "source": "Figure 4d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the main data set's IT cells (their soma depths are in the paper's repository and dandiset 000008) and the reference 10x expression data.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-ttypes-between-families", "statement": "Most t-types were classified into their own family from electrophysiology, but some, such as Sst Pvalb Calb2, Lamp5 Egln3_1 and Vip Mybpc1, were often classified into another family.", "source": "Figure 5a", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the main data set's cells, in dandiset 000008. The t-types named in the claim are not among the 34 degree cells except Sst Pvalb Calb2.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-ttype-variability", "statement": "Many t-types had a normalized total variance of electrophysiological features well above that of k-means clusters, while some, such as Pvalb Vipr2_2, appeared homogeneous.", "source": "Figure 5b", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the main data set's cells, in dandiset 000008.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6-cohort", "statement": "At physiological temperature, 185 neurons were sequenced from 8 adult mice (7 Sst-Cre/Ai9 and 1 Pvalb-Cre/Ai9); 177 got a t-type (110 Sst, 43 IT, 12 ET, 10 Pvalb, 2 NP); 175 were in layer 5; electrophysiological features were extracted for 184.", "source": "Methods, \"Experiments at physiological temperature\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scala_2021.ipynb", "notes": "Every count matches the Methods. All 17 features are defined for 185 cells against 184 in the paper, within the 10% tolerance. Families are read from the t-type names in the files; the 12 ET cells are named L5 PT_1 to L5 PT_4 there.", "deviations": [ "The number of cells with features comes from the re-implemented extraction here; the paper's table has no row for 20200406_sample_4." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6-stimulus-protocol", "statement": "Cells at physiological temperature were stimulated with the same paradigm as the main data set, 600 ms current pulses from -200 pA upwards in 20 pA steps up to 1,380 pA, sometimes stopped earlier.", "source": "Methods, \"Patch-seq recording procedures\" and \"Experiments at physiological temperature\"", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_scala_2021.ipynb", "notes": "In all 185 cells every step lasts 600 ms and consecutive steps differ by 20 pA; all 14,054 sweeps with a nonzero step start at 0.1 s and end at 0.7 s, and 139 cells end at 1,380 pA. 174 of 185 (94.1%) conform to the whole ladder. Nine cells of mouse_UEQOU end at 1,400 to 1,580 pA, and two cells of other mice start at -180 pA and -100 pA and end above 1,380 pA. The intervals of 1.3 or 1.4 s between pulses cannot be checked because every series has an undefined starting time.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6-it-et-overlap", "statement": "Follow-up experiments at 34 degrees C confirmed the electrophysiological overlap between IT and ET neurons seen at room temperature.", "source": "Results, \"Distinct phenotypes of major families\"; Extended Data Figure 6a-g", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scala_2021.ipynb", "notes": "With the paper's kNN classifier (k = 10, leave-one-out, 17-feature representation, all 185 cells), 58.3% of ET cells (7 of 12) are classified as IT and no IT cell as ET; Sst cells are classified as Sst 100% of the time and Pvalb cells 60%. ET cells go to IT in both mice with ET cells (1 of 3 and 6 of 9). The overlap is one-sided and partly reflects that IT cells are 78% of IT and ET cells. With IT subsampled to 12 cells and an odd k (no ties), 10.5% (k = 9) and 12.4% (k = 11) of ET cells go to IT and 33.4% and 36.5% of IT cells to ET; a class-balanced logistic regression separates layer 5 IT from ET with a balanced accuracy of 0.83 against a shuffled-label null of 0.50 (p = 0.005). The result on layer 5 cells alone, and without 20200406_sample_4 (the paper's 184 cells), is the same as on all cells (58.3% and 0%). All ET cells come from two mice. Within mouse_UEQOU alone (10 IT, 9 ET), the kNN classifies 33.3% of ET cells as IT and 20.0% of IT cells as ET, and the logistic regression reaches 0.78 (p = 0.025). The criterion does not require a test within mouse.", "deviations": [ "The paper shows the 34 degree comparison as feature distributions and two-feature scatter plots (Extended Data Fig. 6a-g); it reports no classifier at 34 degrees. The test applies the room-temperature classifier of Fig. 3d to the 34 degree cells, with four families present instead of seven.", "Features are computed by the re-implementation here; link-features shows they agree with the paper's.", "The main test uses all 185 cells, including 20200406_sample_4 (layer 5 IT), which the paper leaves out; the 184-cell result is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6-it-et-ap-threshold", "statement": "At 34 degrees C, the AP threshold showed a prominent difference between layer 5 IT and ET neurons.", "source": "Extended Data Figure 6e and its legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scala_2021.ipynb", "notes": "Layer 5 IT median -27.0 mV (43 cells) against ET -33.1 mV (12 cells), Mann-Whitney p = 0.00035, area under the curve 0.84; second of 17 features after input resistance (p = 0.0001). Without 20200406_sample_4, p = 0.00026 (42 IT cells). Same sign in both mice with both subclasses, but within mouse_UEQOU alone the gap is smaller and not significant (-29.3 against -31.8 mV, area under the curve 0.73, p = 0.094, 10 IT and 9 ET cells). All ET cells come from two mice, so a difference between mice may contribute; the criterion does not require a test within mouse. The ranking of the first two features is the one the paper's code prints for 34 degrees.", "deviations": [ "The ranking covers the 17 features used here, not all 29 the paper's code ranks.", "The main test uses all 185 cells, including 20200406_sample_4, which the paper leaves out; the 184-cell result is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "link-cells", "statement": "The dandiset's recordings are the cells of the paper's published table of the 34 degree cohort, with the same t-type, layer and soma depth.", "source": "Data availability; mini-atlas data/m1_patchseq_phys_temp_meta_data.csv", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_scala_2021.ipynb", "notes": "All 185 files match a row of the paper's table by cell id and no row lacks a file. Family, layer, soma depth and mouse agree for every cell; the files' inferred layer equals the layer the paper's code computes from soma depth and cortical thickness. The t-type name agrees for 93.5% of cells, below the criterion's 95%, only because the 12 ET cells are named L5 PT_1 to L5 PT_4 in the files and L5 ET_1 to L5 ET_4 in the table, one to one; with that renaming the agreement is 100%. The partial outcome reflects the names, not a mismatch of cells. The verifier of round 1 would call this reproduced; the outcome is kept because the criterion, written before the analysis, compares t-type names.", "deviations": [ "The criterion did not anticipate renamed t-types and was applied as written, to the names." ], "disagreed": true, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "link-features", "statement": "The electrophysiological features computed here from the dandiset's traces agree with the paper's published features for the same cells.", "source": "Methods, \"Extraction of electrophysiological features\"; mini-atlas data/m1_patchseq_phys_temp_ephys_features.csv", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scala_2021.ipynb", "notes": "184 of the 185 cells are in the paper's feature table. The Spearman correlation between the features computed here and the published ones is at least 0.9 for 16 of 17 features and 0.877 for the lowest, the AP coefficient of variation. The median absolute difference is zero to three decimals for all features but the AHP (0.011 mV). By mouse, 0.895 (mouse_UEQOU) to 0.995 of values are within 10% of the paper's. The maximum number of APs differs between the Methods' and the code's definitions for 3 cells.", "deviations": [ "The extraction is a re-implementation of the paper's methods and code (scala34.py), not the paper's code, which is under the Allen Institute's license.", "The maximum number of APs follows the Methods (sweeps with spikes in the 100 ms before or the 200 ms after the step are excluded before taking the maximum); the code's version is shown." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "ed6-sst-temperature", "statement": "For layer 5 Sst t-types, AP amplitude and AP width changed the most between room temperature and 34 degrees C, but the relative differences between t-types stayed roughly the same; AHP, input resistance, rebound and sag ratio changed little, and the relative differences between t-types stayed the same.", "source": "Extended Data Figure 6h and its legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scala_2021.ipynb", "notes": "147 layer 5 Sst cells at 25 degrees (published features) and 101 at 34 degrees (computed here); seven t-types have at least 5 cells in both. Shifts in units of the 25 degree SD are AP width -1.78, AP amplitude -1.66, input resistance -0.61, rebound -0.33, AHP -0.25 and sag ratio -0.02, so AP width and amplitude change most. Spearman correlations of t-type medians between temperatures are 0.75 (AP amplitude), 0.88 (AP width), 0.93 (AHP, input resistance, rebound) and 0.96 (sag ratio), median 0.93. The same holds with the paper's published 34 degree features and with t-type means. In each of the 7 mice with such cells, the 34 degree medians of AP amplitude and width lie below the room-temperature medians.", "deviations": [ "The room-temperature side uses the paper's published features of dandiset 000008's cells, not features recomputed from that dandiset.", "The legend says the relative differences \"stayed roughly the same\"; the criterion turns this into Spearman correlations of t-type medians and a shift measured in standard deviations." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "ed6-sst-transcriptomic-distance", "statement": "At physiological temperature, as at room temperature, morpho-electric properties of layer 5 Sst neurons varied continuously across the transcriptomic landscape, and the electrophysiological distance between Sst t-types correlated with their transcriptomic distance.", "source": "Results, \"Continuous phenotypic variation\"; Extended Data Figure 6i", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "The transcriptomic distance between Sst t-types needs the average expression of each t-type in the single-cell 10x v2 reference data (Yao et al. 2021). The paper's code reads it from reduced-allen-data.zip on Zenodo (doi:10.5281/zenodo.5118962), member 10X_cells_v2_AIBS.pickle. The notebook reads the archive's directory (87.9 MB compressed, 517.0 MB uncompressed) and times a 1 MB range request. In the delivered run the rate was 62 kB/s, about 24 minutes for the member. The rate varies between runs; in the earlier runs of this attempt (not in the delivered notebook) it was 27, 114, 44, 149 and 58 kB/s, about 55, 13, 33, 10 and 25 minutes. A run that fetched the member would have exceeded the 30 minute limit in two of these six runs and fitted in the others, so the claim was not tested. The reference is public, and the verifier of round 2 holds that the claim is testable; the block reflects this attempt's choice not to make the run depend on Zenodo's rate. Proposed change for another round, fetch the member in the run, write a criterion for the claim (it has none), and test it. The original reference data at NeMO are much larger. The electrophysiological half is computed from the dandiset as in the paper's code (cell 19 of physiological-temperature.ipynb), for 9 layer 5 Sst t-types with at least 5 cells (Sst Chodl left out), as the paper's code prints, with distances between their mean standardized features of 1.54 to 5.24. It tests nothing without the transcriptomic half. A proxy transcriptomic distance from the paper's own 34 degree Patch-seq counts was not computed, as it differs from the paper's method. The paper reports the correlation and its p-value only inside the figure.", "deviations": [], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "Every voltage series states the unit volts and every stimulus series amperes, with a conversion of 1, but the values are in millivolts (-150 to 67) and picoamperes (-200 to 1,580)." }, { "kind": "metadata_insufficient", "statement": "Every series has an undefined (NaN) starting time, so the timing of sweeps relative to each other is not recorded. Within a sweep the response and the stimulus share a clock (onset at 0.1 s, offset at 0.7 s)." }, { "kind": "metadata_insufficient", "statement": "The t-type of the 12 ET cells is stored under the older names L5 PT_1 to L5 PT_4, which differ from the paper's and its tables' L5 ET_1 to L5 ET_4; no mapping is given. All other t-type names match the paper's table." }, { "kind": "metadata_error", "statement": "The dandiset's description repeats the main data set's \"over 1300 neurons\"; the dandiset holds 185 neurons of the follow-up at 34 degrees." }, { "kind": "metadata_error", "statement": "In the published version the contributor list has a placeholder \"Last, First\" with Zizhen Yao's ORCID, the brain region is typed as a disorder, and the assets summary gives no approach or measurement technique. The unpublished draft corrects these." }, { "kind": "other", "statement": "Eleven cells were stimulated beyond the 1,380 pA the Methods give (up to 1,580 pA), and two of them started at -180 pA and -100 pA, not -200 pA. Nine of the eleven are from one mouse (mouse_UEQOU)." }, { "kind": "code_mismatch", "statement": "The paper's code takes the maximum number of APs before excluding sweeps with spikes outside the step, and looks for those spikes over the whole trace before and after the step; the Methods exclude such sweeps first and look 100 ms before and 200 ms after. The two definitions differ for 3 of the 185 cells." }, { "kind": "paper_inconsistency", "statement": "The Methods build the electrophysiological representation from 17 principal components of 17 features and later call it \"the 16-dimensional electrophysiological representation\"; the paper's code uses all 17." }, { "kind": "paper_inconsistency", "statement": "The legend of Extended Data Fig. 6j describes it as \"the same analysis as in (c)\", but in the paper's code panel j is the 34 degree version of panel i (the Sst overlay and the transcriptomic-distance correlation), not of panel c." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier listed the version's assets through the DANDI API and ran synthetic checks of the helper functions (input resistance, time constant, sag, rebound, spike counts, rheobase, family_of, layer_from_depth, knn_family_confusion).", "agreed": 16, "of": 17, "disagreements": [ { "claim": "link-cells", "outcome": "reproduced", "reason": "185 of 185 cells match, and layer, soma depth and mouse agree 100%. Literal t-type agreement is 93.5% because the files say L5 PT_k where the table says L5 ET_k. The mapping is one-to-one, and after renaming agreement is 100%. The claims file itself treats PT as ET." } ] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the first revision, with its conclusions and summary, the helper module, the claims file, the README and this attempt record, with the paper.", "agreed": 16, "of": 17, "disagreements": [ { "claim": "link-cells", "outcome": "reproduced", "reason": "As in round 1. The only mismatch is the one-to-one PT/ET renaming. After renaming, agreement is 1.000 (cell 26), and the claims file itself treats PT as ET. The record states the disagreement correctly." } ] } ] }, { "id": "000041-watson-2016-01", "dandiset": "000041", "dandiset_version": "0.250624.0419", "paper": "10.1016/j.neuron.2016.03.036", "paper_title": "Network Homeostasis and State Dynamics of Neocortical Sleep", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000041-watson-2016", "entry_title": "Firing rates across sleep states in rat frontal cortex (Watson et al. 2016)", "description": "Tests the findings of Watson, Levenstein, Greene, Gelinas and Buzsaki (2016) on dandiset 000041, which holds silicon probe recordings of units, LFP and sleep states from the frontal cortex of 10 rats in their home cage. It compares firing rates and bursting across WAKE, nonREM and REM, how rates of fast and slow firing cells change over sleep and within nonREM packets, how they relate to LFP band power, and the rate changes across state triplets. UP and DOWN state and spindle analyses are blocked, as their methods are in the unavailable supplement.", "notebooks": [ { "path": "reproduce_watson_2016.ipynb", "title": "Reproducing Watson et al. (2016) from dandiset 000041", "executed": "notebooks/000041-watson-2016/reproduce_watson_2016.html" } ], "outcomes": [ { "claim": "dataset-composition", "statement": "The recordings come from 11 rats and 27 sessions of 294 plus or minus 137 min, yielding 995 putative pyramidal cells and 126 putative interneurons.", "source": "Results, identification of brain states and assessment of firing patterns; Experimental Procedures", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Two of five values are within tolerance, 10 rats and a mean session duration of 286.8 min (SD 150.2). The files hold 22 sessions, 826 excitatory and 96 inhibitory units (and 23 of unknown type); the 21 usable sessions hold 812 pE and 89 pI cells. Per session the pE count is close to the paper's (mean 38.7, range 10 to 105, against 36.9 and 10 to 104).", "deviations": [ "Counted on the files as deposited, with session duration from the state table." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-median-rates", "statement": "Median firing rates of pE cells are 0.76 Hz in WAKE, 0.69 Hz in nonREM and 0.88 Hz in REM; of pI cells 5.59, 4.69 and 4.25 Hz.", "source": "Results, assessment of firing patterns; Figure 2A", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Under reading (a) the three pE medians are within tolerance (0.755, 0.662 and 0.825 Hz) and the three pI medians are below it (3.92, 2.73 and 3.06 Hz, against 5.59, 4.69 and 4.25). Reading (b) gives the same counts (pE WAKE 0.748). The pI sample is 89 cells in 9 subjects, with per-subject medians from 0.07 to 13.4 Hz across subjects and states.", "deviations": [ "812 pE and 89 pI cells from 21 sessions, against 995 and 126 from 27.", "WAKE excludes microarousals derived from the Awake label, not the paper's scored MAs." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-skewed-wide-distribution", "statement": "The distribution of pE firing rates is strongly positively skewed and spans three orders of magnitude, from 0.05 to 5 Hz.", "source": "Results, assessment of firing patterns; Figure 2A", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "WAKE rates have skewness 4.57 and a 97.5th percentile of 7.17 Hz (within a factor of 2 of 5 Hz), but the 2.5th percentile is 0.0124 Hz, about four times below 0.05 Hz. 13 of 812 cells have a WAKE rate of zero. The log10 rates are skewed to the left (-0.74).", "deviations": [ "The paper's range is read from a log axis; the factor-of-2 tolerance was fixed in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-fraction-above-2hz", "statement": "The fraction of pE cells firing above 2 Hz is 19.2% in WAKE, 19.2% in REM and 8.8% in nonREM (chi-square, p < 1e-10).", "source": "Results, assessment of firing patterns; Figure 2A", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "REM (18.7%) and nonREM (9.1%) are within tolerance, WAKE (17.0%) is not. nonREM is lower than WAKE (chi-square 21.5, p = 3.5e-06) and REM (30.5, p = 3.4e-08), but neither test reaches p < 1e-10, which the criterion requires. The direction of the effect is as in the paper, with fewer cells than the paper had. Without the seven sessions whose LFP could not be checked against the spikes, WAKE is 20.2% (within tolerance) and both tests still miss p < 1e-10.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-wake-nrem-slope", "statement": "Per-cell nonREM and WAKE rates are highly correlated (R = 0.82), and the slope of their relation is below 1 (95% confidence interval 0.66 to 0.71), so state transitions act differently across the rate spectrum.", "source": "Results, assessment of firing patterns; Figure 2B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "On log10 rates (799 cells, 13 with a zero rate left out), R = 0.862 and the slope of nonREM on WAKE is 0.757 (95% CI 0.727 to 0.788). In Hz the slope is 0.583 (0.560 to 0.607), outside the widened interval. The reverse regression on log10 rates gives 0.982 (0.942 to 1.022), so the slope below 1 may in part be regression to the mean. Per subject the slope ranges from 0.41 to 0.91. A split-half control (alternate WAKE epochs of each cell) gives a slope of 0.936 between halves and a reliability of 0.961 for the log10 WAKE rate; corrected for this noise the slope is 0.788 (0.756 to 0.821), still below 1. The rest of the gap to 1 comes from the WAKE-nonREM correlation being below 1, which is also regression to the mean. The ratio of the SDs of log10 rates, nonREM over WAKE, is 0.878 (Pitman-Morgan p = 9.8e-13, 95% interval resampling sessions 0.777 to 0.971), so the spread of rates is narrower in nonREM.", "deviations": [ "The paper does not say whether the slope is on log or linear rates; both readings are shown and the log reading matches." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-burst-index-by-state", "statement": "The burst index (fraction of spikes with inter-spike intervals under 15 ms) is highest in nonREM (median 11.8%), lowest in WAKE (4.0%), with REM (5.5%) slightly above WAKE (Kruskal-Wallis, p < 0.05).", "source": "Results, assessment of firing patterns", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "The order nonREM > REM > WAKE holds under both readings, with Kruskal-Wallis p = 5.7e-36 (a) and 7.3e-38 (b), and REM above WAKE (paired Wilcoxon p = 1e-32). Reading (a), the fraction of intervals under 15 ms, gives medians of 6.35, 2.64 and 3.65%, none within tolerance; reading (b), the fraction of spikes in such an interval, gives 11.67% in nonREM (within tolerance), 4.95% in WAKE and 6.71% in REM (above). The measured values are those of reading (a), the first listed. The paired Friedman test over the 753 cells with all three values gives p = 3.9e-151.", "deviations": [ "The definition \"fraction of spikes with ISIs under 15 ms\" can be read two ways; both are shown and neither matches all three medians." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-acg-peaks", "statement": "The average spike autocorrelogram of pE cells peaks near 8 ms in nonREM, with a smaller peak near 125 ms (theta) in REM and WAKE.", "source": "Results, assessment of firing patterns; Figure 2C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "The nonREM autocorrelogram peaks at 8.5 ms. The smoothed REM and WAKE autocorrelograms are highest at the 60 ms edge of the 60 to 250 ms window, so the criterion finds no theta peak. In a variant that divides the 21 ms smoothing by a 101 ms one, WAKE has a maximum at 118.5 ms (ratio 1.016) and REM at 142.5 ms (1.017). Per subject the REM maximum falls within 112.5 to 137.5 ms in two subjects (Bogey 135.5, Dino 125.5). Without the seven sessions whose LFP could not be checked, the nonREM peak is at 6.5 ms, outside 7 to 9 ms, so the nonREM part rests on the sample as well as on the method. A fix to the binning (lags rounded to 1 ns, so that float error does not move a lag on a bin edge) moved the nonREM peak from 7.5 to 8.5 ms.", "deviations": [ "The peak location criteria (windows, 21 ms smoothing) were fixed here; the paper shows the peaks in a figure only." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-acg-decay", "statement": "The autocorrelogram of pE cells decays faster in nonREM than in WAKE and REM (decay fit exponent medians -1.35, -0.83 and -0.80; Kruskal-Wallis p < 0.05).", "source": "Results, assessment of firing patterns; Figure 2C", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The main text gives decay fit exponents but not what is fitted (function, lag range); the Supplemental Experimental Procedures, which would say, could not be retrieved (PubMed Central and the publisher answer with a browser check). The autocorrelograms themselves are computed for fig2c-acg-peaks.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-rate-group-correlations", "statement": "In nonREM, pairs of fast-firing pE cells are positively correlated, while pairs of one slow and one fast cell are negatively correlated.", "source": "Results, assessment of firing patterns; Figure 2F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Over 20764 same-session pE pairs (169 without a defined correlation), the (6,6) mean correlation of 100 ms counts in nonREM is 0.0424, the largest of the 21 group combinations, and correlations rise with the rates of both cells. The (1,6) mean is 0.0089, above zero (t = 10.85, p = 8.7e-26); 22.8% of all pairs are negative, but no group combination has a negative mean. Reading (b) gives the same pattern ((6,6) 0.0401, (1,6) 0.0087).", "deviations": [ "The correlation measure is Pearson correlation of raw counts in 100 ms bins; the paper's measure and test are in the unavailable supplement and may differ (for example a correction for the shared UP/DOWN modulation)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ma-statistics", "statement": "Microarousals have a median duration of 15.9 plus or minus 3.3 s, occur 0.32 plus or minus 0.12 times per minute and occupy 9.1 plus or minus 3.5% of SLEEP (790 in total).", "source": "Results, identification of brain states", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Under reading (a), median MA duration 19.0 s (within the spread), 0.096 MAs per minute of SLEEP and 3.22% of SLEEP time; reading (b) gives 19.0 s, 0.127 per min and 4.23%. The paper reports 0.32 and 9.1%. 391 MAs in 21 sessions (262 inside SLEEP periods), against 790 in 27. Looser rules raise the counts but none reaches both values: Non-REM on at least one side and under 60 s gives 0.177 per min and 7.63% of SLEEP; every Awake epoch inside SLEEP gives 0.245 per min and 13.66%. Of the short Awake epochs left as WAKE, 186 lie between REM and Non-REM and 120 between two REM epochs.", "deviations": [ "The dandiset has no microarousal label. MAs are derived from Awake epochs under 40 s between two Non-REM epochs, without the paper's EMG and theta criteria; 345 short Awake epochs elsewhere are left as WAKE.", "The state table has 1 s resolution and may not be the scoring the paper used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ma-fraction-over-nrem-episodes", "statement": "The fraction of time occupied by MAs decreases over the course of nonREM episodes (R = -0.85, p < 1e-10).", "source": "Results, identification of brain states", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Over 243 episodes with an MA, pooled episode bins give R = -0.087 (p = 1.7e-05); the bin means give R = -0.451 (p = 0.19). Neither reaches -0.85 or p < 1e-10. The mean fraction rises from 0.067 to 0.157 over the first six bins and falls to 0.010 in the last. With a looser MA rule (Awake under 60 s with Non-REM on at least one side, 757 MAs) the bin means give R = -0.602 (p = 0.066) and pooled bins R = -0.111 (p = 2.8e-08), the same judgment.", "deviations": [ "MAs derived from the Awake label (see ma-statistics); the binning was fixed here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "packet-duration", "statement": "The duration of nonREM packets spans two orders of magnitude, with a median of 111 s.", "source": "Results, identification of brain states", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Over all 1069 Non-REM epochs the median is 108 s (5th to 95th percentile 12 to 484 s, range 6 to 1199 s). Inside SLEEP periods (685 epochs) the median is 128 s, outside tolerance. Per subject medians range from 76 to 219 s.", "deviations": [ "A packet is one Non-REM epoch of the dandiset's state table." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "wake-sleep-cycles", "statement": "The dataset holds 54 WAKE-SLEEP episodes (at least 7 min of WAKE followed by at least 20 min of SLEEP), an average of 2.0 per session, and sessions without one were discarded.", "source": "Results, identification of brain states and firing pattern changes across sleep", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "30 cycles in 21 sessions, 1.43 per session, and 3 sessions (BWRat18-020513, BWRat19-032413, BWRat20-101013) have none. Accepting SLEEP ended by the end of the recording gives 34 cycles (1.62 per session) and one session without a cycle. In the three sessions without a cycle, the long sleep segments fail because the Awake before them lasts 3.6 or 5.0 min, under 7 min, or because the recording ends them (BWRat18-020513 and BWRat20-101013).", "deviations": [ "SLEEP and cycles are rebuilt from the Results' definitions on the dandiset's state table; the paper's Table 1 was not available, and its state scoring and MAs may differ." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-population-decline", "statement": "The mean firing rate of pE cells declines over the course of SLEEP, restricted to nonREM (R = -0.11, p < 1e-3).", "source": "Results, firing pattern and LFP changes across sleep; Figure 3B", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Per packet R = -0.267 (p = 4.3e-06, 287 packets in 30 cycles); in 10 bins R = -0.285 (p = 7.6e-07). The decline is steeper than the reported R = -0.11. R is negative in 8 of 9 subjects with a cycle.", "deviations": [ "The paper does not give its binning or normalization; two readings were fixed in the criterion.", "30 cycles from 21 sessions, against 54 from 27." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-first-last-packet", "statement": "The mean pE rate is lower in the last than in the first nonREM packet of SLEEP (1.04 plus or minus 1.20 against 0.88 plus or minus 0.91 Hz; Wilcoxon p < 0.02).", "source": "Results, firing pattern and LFP changes across sleep", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Over 1070 cell and cycle pairs, 1.0915 plus or minus 1.483 Hz in the first packet and 0.9679 plus or minus 1.241 Hz in the last (the upper bound of tolerance is 0.968), Wilcoxon p = 3.9e-06. The decrease is significant within 3 of 9 subjects. With one value per cycle the last packet is lower in 22 of 30 cycles (Wilcoxon p = 0.015). Without the seven sessions whose LFP could not be checked, the last mean is 1.006 Hz, outside tolerance.", "deviations": [ "30 cycles from 21 sessions, against 54 from 27." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-first-last-slope", "statement": "Comparing the same neurons in the first and last nonREM packets of SLEEP, the regression slope departs from 1 (95% confidence interval 0.827 to 0.880), as fast cells slow down and slow cells speed up.", "source": "Results, firing pattern and LFP changes across sleep; Figure 3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "On log10 rates (1021 pairs, 49 with a zero rate left out) the slope of last on first is 0.801 (95% CI 0.768 to 0.834); in Hz 0.723. The reverse regression gives 0.864 (0.829 to 0.900), and the second half of the first packet regressed on its first half gives 0.855 (0.829 to 0.881), above the first-to-last slope. Corrected for the noise of the first-packet rate (reliability 0.946 from its halves), the slope is 0.846 (0.812 to 0.881), still below 1. The ratio of the SDs of log10 rates, last over first packet, is 0.963, a narrowing of about 4% that is significant over pairs (Pitman-Morgan p = 0.028) but not when cycles are resampled (95% interval 0.892 to 1.029). Most of the slope below 1 comes from the first-to-last correlation being below 1 (R = 0.832), so the claim's reading that fast cells slow down and slow cells speed up is weakly supported. The criterion, fixed before the analysis, judges the slope alone.", "deviations": [ "The paper does not say whether the regression is on log or linear rates; both are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-wake-before-after", "statement": "pE rates are lower in the 5 min of WAKE after SLEEP than in the 5 min before (p < 1e-6, Wilcoxon), with a decrease in the top three sextiles and an increase in the lowest.", "source": "Results, firing pattern changes across sleep and sleep sub-states induce lasting changes; Figure 3E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Reading (a), 1070 cell and cycle pairs, mean 1.341 Hz before and 1.180 Hz after, Wilcoxon p = 4.1e-09. Sextiles 4, 5 and 6 decrease (one-tailed p = 0.03, 0.00063, 2.4e-05); sextile 1 does not increase (mean change -0.002 Hz, p = 0.3), and sextiles 2 and 3 decrease. Reading (b), 727 cells, gives the same pattern (population p = 1.4e-09, sextile 1 p = 0.36). In 23 of 30 cycles the WAKE after SLEEP is shorter than 300 s. With the pre-sleep window cut to the length of the post-sleep one, the result is the same (population p = 1.7e-09, sextile 1 p = 0.18, sextile 6 p = 1.8e-05). With one value per cycle the population decrease holds (20 of 30 cycles, p = 0.016) and sextile 6 decreases (p = 0.048), but sextiles 4 and 5 do not (p = 0.87 and 0.12); the sextile part rests on pooling cells within cycles. With only the 7 cycles that have a full 300 s of WAKE after SLEEP, the population p is 0.055 and sextile 6 p is 0.27 (sextile 5 p = 0.0034), so the result depends on the cycles with a shorter post-sleep window.", "deviations": [ "Where the WAKE after SLEEP is shorter than 5 min, all of it is used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-sextiles-over-sleep", "statement": "Over SLEEP, restricted to nonREM, the fastest sextile decreases its rate while the slowest shows a marginal increase.", "source": "Results, firing pattern changes across sleep; Figure 3B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Per packet, sextile 6 R = -0.447 (p = 3.1e-11) and sextile 1 R = +0.163 (p = 0.0074); sextile 5 R = -0.341 and sextile 2 R = +0.143. In bins, sextile 6 R = -0.430 (p = 2e-11) and sextile 1 R = +0.094 (p = 0.11). Sextile 6 has a negative R in all 7 subjects where it can be computed.", "deviations": [ "Binning and normalization fixed here (see fig3b-population-decline)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-cv-over-sleep", "statement": "The coefficient of variation of pE firing rates decreases over the course of SLEEP (R = -0.05, p < 0.01).", "source": "Results, firing pattern changes across sleep", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "R = -0.026 (p = 0.66) per packet and R = -0.014 (p = 0.81) in bins.", "deviations": [ "The CV is taken across a session's pE cells at each point; the paper does not define it further." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4iv-sextiles-within-nrem", "statement": "Within both nonREM episodes and nonREM packets, the fastest sextiles decrease their rates while the slowest increase.", "source": "Results, firing rate and LFP changes within nonREM; Figure 4A and 4B, panel iv", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Within 622 episodes, sextile 6 R = -0.083 (p = 3.7e-08) and sextile 1 R = +0.060 (p = 6.3e-06); within 952 packets, R = -0.055 (p = 4.4e-06) and +0.061 (p = 2e-08). The signs hold with 5 or 20 bins and with a 60 s minimum. The effects are small, and per subject within packets sextile 6 increases in Rizzo (R = +0.121) and does not decrease in BWRat19 and BWRat20. With one R per session, sextile 1 increases in episodes (p = 0.049) and packets (p = 0.011) and sextile 6 decreases in episodes (p = 0.013) but not in packets (median R -0.025, 6 of 16 sessions positive, p = 0.19).", "deviations": [ "10 bins, a 20 s minimum and normalization within each interval were fixed here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4v-cv-within-nrem", "statement": "The coefficient of variation of binned population rates decreases within nonREM episodes (R = -0.13) and packets (R = -0.12), both p < 1e-10.", "source": "Results, firing rate and LFP changes within nonREM; Figure 4A and 4B, panel v", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Episodes R = -0.005 (p = 0.71), packets R = 0.011 (p = 0.28); no variant exceeds an absolute R of 0.011.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4vi-burst-within-nrem", "statement": "The 15 ms burst index of pE cells increases within nonREM episodes (R = 0.09) and packets (R = 0.08), both p < 1e-10.", "source": "Results, firing rate and LFP changes within nonREM; Figure 4A and 4B, panel vi", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Episodes R = 0.029 (p = 0.022), packets R = 0.024 (p = 0.021); variants give R = 0.020 to 0.047 with p from 0.069 to 0.0008. The burst index rises in the reported direction, but far from p < 1e-10.", "deviations": [ "The burst index per bin is pooled over the session's pE cells (fraction of intervals under 15 ms)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4i-band-power-within-nrem", "statement": "Delta and sigma power increase over nonREM episodes and packets, while gamma power decreases over episodes but not over packets.", "source": "Results, firing rate and LFP changes within nonREM; Figure 4A and 4B, panel i", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Sigma rises within episodes (R = 0.135) and packets (R = 0.104), both p < 1e-20. Delta rises within episodes (R = 0.069, p = 1.1e-07) but not within packets (R = -0.005, p = 0.61; with a 60 s minimum R = 0.022, p = 0.063). Gamma rises within episodes (R = 0.062) and packets (R = 0.182), where the paper reports a fall over episodes. Without the seven sessions whose LFP could not be checked against the spikes the judgment is the same; delta over packets is +0.014 (p = 0.27) and gamma over episodes +0.005 (p = 0.77).", "deviations": [ "One LFP channel per session, the one the conversion flags as spindle reference, in raw units; the paper's channel choice is not stated in the main text.", "The LFP of Dino-061914 is left out (scrambled samples)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-delta-packet-length", "statement": "Mean delta power within whole packets, normalized by nonREM delta power, is positively correlated with packet length (R = 0.31, p < 0.05).", "source": "Results, firing rate and LFP changes within nonREM", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Over 915 packets of at least 20 s, R = 0.334 (p = 2.8e-25), near the upper edge of 0.279 to 0.341; Spearman rho = 0.555. Positive in 9 of 10 subjects (Templeton -0.101). Without the seven sessions whose LFP could not be checked against the spikes the judgment is the same (R = 0.297).", "deviations": [ "One LFP channel per session; Dino-061914 left out." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4cd-packet-rate-lfp", "statement": "Per packet, the rate of the fastest sextile is negatively correlated with delta power (R = -0.28) and positively with gamma power (R = 0.44), and the rate of the slowest sextile is positively correlated with sigma power in the last 20 s of the packet (R = 0.25), all p < 1e-10.", "source": "Results, firing rate and LFP changes within nonREM; Figure 4C and 4D", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "All three signs as stated. Sextile 6 against delta R = -0.416 (p = 1.3e-28) and against gamma R = 0.570 (p = 4.2e-57), both stronger than reported; sextile 1 against sigma in the last 20 s R = 0.104 (p = 0.0029), weaker than 0.25 and above p < 1e-10. None within tolerance. Without the seven sessions whose LFP could not be checked against the spikes the judgment is the same (R = -0.428, 0.533 and 0.132).", "deviations": [ "One LFP channel per session; Dino-061914 left out; z-scoring per session fixed here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-nrem-between-ma", "statement": "An intervening nonREM packet reduces the rates of the top two sextiles from one MA to the next (both p < 0.01).", "source": "Results, sleep sub-states induce lasting changes; Figure 5B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "148 triplets, 6073 cell and triplet pairs. Sextile 6 mean change -0.104 Hz (p = 0.077), sextile 5 -0.011 Hz (p = 0.24). With per-cell means, sextile 6 -0.120 Hz (p = 0.029) and sextile 5 p = 0.79. With one value per triplet or per session neither sextile 5 nor 6 changes at p < 0.1. With a looser MA rule (Awake under 60 s with Non-REM on at least one side), 343 triplets, sextile 5 p = 0.14 and sextile 6 changes by +0.029 Hz (p = 0.92), the same judgment.", "deviations": [ "MAs derived from the Awake label (see ma-statistics)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-wake-between-packets", "statement": "An intervening WAKE episode increases the rate of the fastest sextile from one nonREM packet to the next (24 triplets).", "source": "Results, sleep sub-states induce lasting changes; Figure 5B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "265 triplets (the paper had 24). Sextile 6 mean change -0.051 Hz (p = 0.092); sextiles 1 and 3 increase slightly (p = 0.0063 and 0.015). The intervening WAKE lasts 40 to 3945 s (median 102). No minimum WAKE duration from 40 to 900 s gives a sextile 6 increase at p < 0.05; at 900 s, 23 triplets remain, near the paper's 24, with a mean change of -0.185 Hz (p = 0.5).", "deviations": [ "Every Awake epoch of at least 40 s between two Non-REM epochs counts as WAKE here; the paper's 24 triplets suggest a narrower selection that the main text does not describe." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-ma-between-packets", "statement": "An intervening MA increases the rates of slow-firing pE cells from one packet to the next and does not affect fast-firing cells.", "source": "Results, sleep sub-states induce lasting changes; Figure 5B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "391 triplets. Sextile 1 mean change +0.0034 Hz (p = 0.082); sextiles 5 and 6 decrease (p = 0.0023 and 6.8e-05), and sextile 2 increases (p = 0.00019). With one value per triplet sextile 1 increases (p = 0.037), but per session it does not (p = 0.17); the decrease of sextiles 5 and 6 holds per session (p = 0.0094 and 0.00015). With a looser MA rule (Awake under 60 s with Non-REM on at least one side), 463 triplets, sextile 1 increases (+0.0048 Hz, p = 0.016; per triplet p = 0.029, per session p = 0.11) and sextiles 5 and 6 decrease (p = 0.0041 and 5.3e-06), which would meet the partial condition. The outcome follows the MA rule fixed in the claims file before the analysis, and rests on it.", "deviations": [ "MAs derived from the Awake label (see ma-statistics)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-rem-between-packets", "statement": "An intervening REM episode decreases the rates of all sextiles from one packet to the next.", "source": "Results, sleep sub-states induce lasting changes; Figure 5B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Only 17 triplets, as 49 of 534 REM epochs are followed directly by Non-REM. Sextiles 4 and 5 decrease (p = 0.022 and 0.011); the other four do not change significantly, and sextiles 1 and 2 have positive mean changes. With one value per triplet only sextile 4 decreases at p < 0.05.", "deviations": [ "The paper does not give its number of REM triplets; the dandiset's state table yields few." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-rem-duration", "statement": "Longer REM episodes produce a proportionally larger decrease of rates from one packet to the next (R = -0.22, p < 1e-2).", "source": "Results, sleep sub-states induce lasting changes; Figure 5C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Per triplet R = -0.047 (p = 0.86, 17 triplets); per cell and triplet R = -0.061 (p = 0.21, 436 pairs). REM durations 8 to 157 s. Without BWRat21-121813, whose state labels could not be checked against the spikes, 13 triplets give R = -0.452 (p = 0.12).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-sigma-ma", "statement": "Sigma power in the last 20 s of a packet between two MAs correlates with a larger increase of the slowest sextile from one MA to the next (R = 0.181, p < 0.01).", "source": "Results, sleep sub-states induce lasting changes; Figure 5C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Over 125 MA, packet, MA triplets with sextile 1 cells and LFP, R = 0.033 (p = 0.71). Without the seven sessions whose LFP could not be checked against the spikes the judgment is the same (R = -0.001). With a looser MA rule (Awake under 60 s with Non-REM on at least one side), 293 triplets give R = 0.110 (p = 0.06), the same judgment.", "deviations": [ "MAs derived from the Awake label; one LFP channel per session; Dino-061914 left out." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-delta-change", "statement": "The increase of the slowest sextile's rate from one packet to the next is positively correlated with the change of delta power between the packets, regardless of the intervening state.", "source": "Results, sleep sub-states induce lasting changes; Figure 5C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Over 613 consecutive packet pairs, R = 0.183 (p = 5.3e-06) for sextile 1, and R = -0.368 for sextile 6. Per subject the sextile 1 correlation is positive in 4 of 8 subjects, so the pooled result rests on some animals. With one R per session (14 sessions with at least 5 packet pairs) the median R is +0.025, positive in 7, Wilcoxon p = 0.43, so the correlation does not hold per session; the criterion uses the pooled pairs. Without the seven sessions whose LFP could not be checked against the spikes the judgment is the same (R = 0.114, p = 0.011).", "deviations": [ "One LFP channel per session; Dino-061914 left out." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5-within-wake-rem", "statement": "Within WAKE the two fastest sextiles increase and the two slowest decrease their rates; within REM all sextiles except the fourth increase.", "source": "Results, firing rate and LFP changes within nonREM, last paragraph (Figure S5A and S5B)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_watson_2016.ipynb", "notes": "Within 495 WAKE epochs sextiles 5 and 6 decrease (R = -0.122 and -0.120, p < 1e-12), opposite to the claim, and sextile 2 increases (R = +0.067). Within 388 REM epochs no sextile changes at p < 0.05.", "deviations": [ "The paper's analysis for this claim is in Figure S5, which was not available; entry into WAKE may have been analysed differently (for example aligned to WAKE onset)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-wake-movement", "statement": "WAKE periods with more movement have a larger effect on the rate increase of the fastest sextile from one packet to the next (R = 0.43, p < 0.05).", "source": "Results, sleep sub-states induce lasting changes; Figure 5C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds no movement, accelerometer, video or EMG data (acquisition is empty; the files hold units, LFP, spike waveforms and the state table), and no other public source of the movement measurements was found.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "updown-durations", "statement": "DOWN states have a median duration of 0.19 s and UP states 0.47 s.", "source": "Results, assessment of firing patterns (Figure S4A)", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "UP and DOWN states were detected with spike and LFP criteria whose thresholds are given only in the Supplemental Experimental Procedures, which could not be retrieved. The spikes and LFP needed are in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-slow-oscillation-spindles-over-sleep", "statement": "Over SLEEP, the incidence of spindles (R = -0.093), UP states (R = -0.10) and DOWN states (R = -0.08) decreases and DOWN state duration increases, while spindle duration, frequency and amplitude do not change.", "source": "Results, firing pattern and LFP changes across sleep; Figure 3C", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs UP/DOWN state and spindle detection, described only in the unavailable supplement (see updown-durations); the main text says only that spindles were detected after filtering and integration.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4ii-iii-updown-spindles-within-packets", "statement": "Within packets the incidence of UP and DOWN states increases, UP states shorten and DOWN states lengthen, and spindle incidence and duration increase.", "source": "Results, firing rate and LFP changes within nonREM; Figure 4A and 4B, panels ii and iii", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs UP/DOWN state and spindle detection (see fig3c-slow-oscillation-spindles-over-sleep).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2de-up-state-sequences", "statement": "pE cells fire in stable sequences early in UP states, and the latency of a cell's first spike is negatively correlated with its firing rate.", "source": "Results, assessment of firing patterns; Figure 2D and 2E", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs UP state onsets (see updown-durations).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-4e-within-up-rates", "statement": "Within UP states, the fastest sextile and pI cells decrease and the slowest sextile increases from early to late SLEEP, and within packets the fastest sextile drops while pI cells increase.", "source": "Results; Figure 3F and Figure 4E", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs UP state detection (see updown-durations).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds 22 sessions from 10 rats, where the paper and the dandiset's own description report 27 sessions from 11 rats; the files hold 945 units (826 excitatory, 96 inhibitory, 23 unknown) against the 995 putative pyramidal cells and 126 interneurons analysed. Which sessions and units were left out, and why, is not stated." }, { "kind": "format_error", "statement": "In sub-Dino_ses-Dino-072114 the spike times are whole seconds divided by 20000 (8451 distinct values from 0 to 0.4252 s, in a recording of 7959 s). The conversion read this session's spikes from a CellExplorer file with a hard-coded 20 kHz rate. The session's spikes cannot be used." }, { "kind": "format_error", "statement": "In sub-Dino_ses-Dino-061914 the LFP has 125 columns for 128 electrodes, lasts 331.7 min against 291.9 min of states and spikes, and its samples are scrambled (lag-1 autocorrelation 0.28 on the reference channel, against 0.99 or more in every other session), consistent with a 128-channel file read as 125 channels." }, { "kind": "data_missing", "statement": "The state table holds only Awake, Non-REM and REM. The paper scores microarousals as a state of their own and builds WAKE-SLEEP episodes, nonREM packets and episodes, UP/DOWN states and spindles, none of which is in the dandiset. MAs derived from short Awake epochs are fewer than the paper reports (391 in 21 sessions, against 790 in 27)." }, { "kind": "selection_undocumented", "statement": "The dandiset does not say how the state table was scored. The conversion code takes it from each session's SleepState.states.mat; it yields 30 WAKE-SLEEP cycles in 21 sessions (3 sessions with none, though the paper kept only sessions with a full cycle), and only 49 of 534 REM epochs are followed directly by Non-REM, so it may not be the scoring the paper used." }, { "kind": "metadata_error", "statement": "The dandiset description gives 11 animals, 27 sessions and 1360 units, the paper's numbers, while the files hold 10 animals, 22 sessions and 945 units (the archive's summary counts 10 subjects). The description gives an age of 4-7 months, the files 3-7 months." }, { "kind": "format_error", "statement": "The LFP is stored as int16 with unit volts and conversion NaN, so it cannot be converted to volts." }, { "kind": "metadata_insufficient", "statement": "Every electrode's location is \"unknown\" and every unit's region is \"CTX\" or \"unknown\", although the paper records from medial prefrontal, orbitofrontal, anterior cingulate and secondary motor cortex; only the electrode groups carry a region." }, { "kind": "metadata_insufficient", "statement": "23 units of sub-BWRat21_ses-BWRat21-121613 have cell type and region \"unknown\", with no description of what the label means." }, { "kind": "data_missing", "statement": "No movement, accelerometer or EMG data are in the dandiset, though the paper uses EMG to score states and movement to define WAKE and to relate WAKE to rate changes." }, { "kind": "other", "statement": "The state labels are consistent with the spikes in 20 of 21 sessions (not established for BWRat21-121813), but in 14 sessions the best agreement is with the table shifted 5 to 60 s earlier, so state boundaries may lag the activity. The LFP agrees with the spikes to within 50 ms in 14 of 21 sessions. Of the other seven, three (BWRat21-121113, Bogey-012615, Dino-072414) have a clear cross-correlation extreme 56 to 64 ms from zero lag; in three (BWRat17-121912, BWRat21-121613, BWRat21-121813) the extreme is less than three times the value at plus or minus 1 s, so agreement is not established; and the LFP of Dino-061914 is scrambled." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file, with the main text of the paper (the supplement could not be retrieved). The verifier checked the blocked claims in the archive, checked the LFP starting time and rate in all 22 files, and tested the helper functions on synthetic inputs. Report in transcripts/000041/verifier-1-report.md.", "agreed": 39, "of": 39, "disagreements": [] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run, the helper module, the claims file and the attempt record, with the main text of the paper re-downloaded from PubMed Central (paper/PMC4873379.xml and .txt); the supplement could not be retrieved. Report in transcripts/000041/verifier-2-report.md. Two points not tied to one claim were also answered: the README's run time, which the notebook does not print, was removed, and the round-1 reasons were completed with the B items the verifier noted as missing (B1, B4 and B5).", "agreed": 39, "of": 39, "disagreements": [] } ] }, { "id": "000044-grosmark-2016-01", "dandiset": "000044", "dandiset_version": "0.261005.2101", "paper": "10.1126/science.aad1935", "paper_title": "Diversity in neural firing dynamics supports both rigid and learned hippocampal sequences", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000044-grosmark-2016", "entry_title": "Rigid and plastic hippocampal sequences (Grosmark and Buzsaki 2016)", "description": "Tests the findings of Grosmark and Buzsaki (2016) on dandiset 000044, which holds eight sessions of CA1 units, LFP, sleep states and track positions from four rats, each with sleep before and after exploring a novel track. It decodes candidate ripple events with a Bayesian decoder, compares sequence scores across PRE, MAZE and POST, estimates each place cell's contribution to sequences, and relates firing rate and ripple gain to coactivation and replay.", "notebooks": [ { "path": "reproduce_grosmark_2016.ipynb", "title": "Reproducing Grosmark and Buzsaki (2016) from dandiset 000044", "executed": "notebooks/000044-grosmark-2016/reproduce_grosmark_2016.html" } ], "outcomes": [ { "claim": "sessions-and-tracks", "statement": "Recordings were made in four rats, in eight novel exploration sessions, each a PRE sleep, a MAZE epoch on one of two linear tracks or a circular track, and a POST sleep.", "source": "Results, paragraph 2; Figure S1 (as cited in the text)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "4 subjects and 8 sessions, each with PRE, MAZE and POST epochs in that order (8 of 8), on a 1.6 m linear track (4 sessions), a 2 m linear track (1) and a circular track (3). PRE lasts 2.98 to 5.37 h, MAZE 34.5 to 92.7 min and POST 2.22 to 4.51 h. The rooms the paper names are not in the files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "place-cell-count", "statement": "The Bayesian decoder was built from 491 place cells over the eight sessions.", "source": "Results, paragraph 2", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "417 of the 562 pyramidal units have a smoothed rate-map peak of 1 Hz or more on running, below 491 by more than the tolerance of 49. At 0.5 Hz the count is 480 (within tolerance), at 2 Hz 352, so the count depends strongly on the threshold; the criterion fixes 1 Hz and the other thresholds are variants that do not decide the outcome. By subject, Achilles 181, Buddy 30, Cicero 127, Gatsby 79.", "deviations": [ "The place-cell definition is a common choice (peak of 1 Hz or more on running above 5 cm/s, 2 cm bins, 4 cm smoothing); the paper's definition is in the supplementary Methods, which were not available." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-post-gt-pre", "statement": "Sequence scores (rZ) of candidate events are higher in POST sleep than in PRE sleep (replay).", "source": "Figure 1C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Pooled over sessions, as the criterion fixes the test, POST does not exceed PRE (mean rZ 0.763 against 0.770, Tukey on ranks after Kruskal-Wallis p = 0.412). Within sessions it does; POST is higher in 8 of 8 sessions (sign test p = 0.0039; one-sided rank-sum p < 0.05 in 6), and with each session's PRE mean subtracted POST is higher by 0.106 (p = 2.3e-14). The pooled test is dominated by the three circular-track sessions, which score lower in every epoch (PRE 0.161 and POST 0.260 against 1.112 and 1.207 on the linear tracks, where the event takes the better of two templates) and supply 11161 of 23801 POST events but 5912 of 16448 PRE events. The same test run on each kind of track finds POST above PRE on the five linear-track sessions (Tukey on ranks p = 5.1e-07) and on the three circular-track sessions (p = 1.1e-05). By subject, POST minus PRE is +0.089 (Achilles), +0.185 (Buddy), +0.021 (Cicero) and -0.173 (Gatsby) when pooled within subject.", "deviations": [ "Candidate events are population bursts of all units holding a ripple (150 to 250 Hz envelope above 3 SD on one LFP channel per session), outside REM in PRE and POST and below 5 cm/s in MAZE; the paper's detection is in the unavailable Methods.", "The rZ null is 200 column-cycle shuffles of the posterior; the paper's shuffle is not stated in the main text.", "On the linear tracks each event takes the better of the two direction templates, which raises their scores over those of the single-template circular track.", "The Tukey comparison is scipy's Tukey HSD on the pooled ranks, not MATLAB's Tukey-Kramer after kruskalwallis.", "Immobility for MAZE candidate events is taken from the 2D head speed, while running for the rate maps is taken from the speed of the linearized position, both at 5 cm/s." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-maze-gt-pre", "statement": "Sequence content is higher in MAZE immobility events than in PRE sleep events.", "source": "Figure 1C; Figure 2C legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "MAZE events score higher than PRE events (mean rZ 1.270 against 0.770, n = 2460 and 16448; Tukey on ranks p printed as 0), and MAZE is higher in all 8 sessions (one-sided rank-sum p from below 0.0001 to 0.0405). It holds on the linear-track sessions (p printed as 0) and on the circular-track sessions (p = 0.0007) separately. MAZE has 76 to 953 scored events per session.", "deviations": [ "Events and scores as for fig1c-post-gt-pre." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-strong-contributors", "statement": "216 neurons showed significant PCC scores in PRE or POST and were considered to contribute strongly to sequences.", "source": "Results, paragraph 3; Figure 2B", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "The test fixed in the criterion (one-sided signed-rank test of a cell's contributions over its events, p < 0.05) finds 303 strongly contributing cells (72.7% of 417 place cells), against 216. With every rate map shifted it calls 56.1% of cells significant (0.843 on the 1.6 m tracks, 0.905 on the 2 m track, 0.140 on the circular track), so about 234 would be expected by chance. The paper calls these PCC scores significant, which implies a 5% false-positive rate; this test is far from it, so it is not the paper's procedure. The excess is on the linear tracks, where the contribution is taken on the template the event was selected for. A best-template variant of the contribution has a false-positive rate of 0.206 (0.132 in PRE, 0.118 in POST) and finds 188 cells, outside the tolerance; at alpha 0.001 its false-positive rate is 0.031 and it finds 95. The false-positive rates are measured on every fourth PRE and POST event, so on all events they would likely be higher. The best-template numbers are not identical across machines (the verifier's executed copy printed 190 cells and 0.129 in PRE); no conclusion rests on the difference. The PCC definition and its test are in the unavailable Methods.", "deviations": [ "The PCC and its significance test are choices made here, as the Methods were not available.", "The 20 shifts of a cell's map are drawn afresh for every event." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-pre-post-overlap", "statement": "Most neurons strongly contributing to PRE sequences (73%) also contributed to POST sequences.", "source": "Results, paragraph 3; Figure 2C as cited", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Blocked as it depends on fig2b-strong-contributors. Of 248 PRE strongly contributing cells, 235 (94.8%) also contribute in POST, against a chance level of 69.5%. With the best-template variant 72 of 102 (70.6%), within 73 +/- 7.3, against a chance level of 37.9%.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-shuffle-high-dpcc", "statement": "The PRE to POST increase in sequence score is eliminated when the place fields of the 10 to 20% of cells with the highest dPCC are shuffled, and remains after shuffling the bottom 75%.", "source": "Results, paragraph 3; Figure 2D", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "On the pooled test of the criterion replay is absent after shuffling the top 10% (POST minus PRE -0.100, p = 1.0) and the top 20% (-0.127, p = 1.0), but also after shuffling the bottom 75% (+0.022, p = 0.21), so one of the two conditions holds. The pooled test finds no replay before shuffling either (-0.008, p = 0.916), so on all sessions it cannot show a removal. On the five linear-track sessions replay is present before shuffling (+0.101, p < 0.0001), absent after shuffling the top 10% (+0.015, p = 0.23) or 20% (-0.039, p = 0.995) and present after the bottom 75% (+0.098, p < 0.0001); shuffling a random 10% or 20% leaves it (+0.099, +0.088). dPCC is measured on the events that are decoded again. Ranking cells on the even-numbered events and measuring replay on the odd-numbered ones, on the linear tracks replay falls from +0.116 to +0.046 (p = 0.024) after the top 10% and +0.042 (p = 0.038) after the top 20%, so out of sample it is reduced but not removed.", "deviations": [ "Variant decodes use 50 column-cycle shuffles per event in place of 200.", "dPCC is the difference of the criterion's PCC, whose significance test is not the paper's (fig2b-strong-contributors); the ranking does not use that test." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-remove-plastic", "statement": "The PRE to POST increase in sequence content is attributable to a small number of plastic cells; removing them, unlike removing rigid cells, removes the increase.", "source": "Figure 2E", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Blocked as it depends on fig2b-strong-contributors. On the pooled test, removing plastic cells gives POST minus PRE -0.168 (p = 1.0) and removing rigid cells +0.038 (p = 0.019); removing as many random strongly contributing cells gives -0.023 (p = 0.99). On the linear-track sessions -0.060, +0.136 and +0.094. With classes from the even-numbered events and replay on the odd-numbered ones, the linear tracks give -0.009 (p = 0.54) and +0.090 (p = 0.0027). With the best-template classes, pooled, -0.125 and +0.020 (p = 0.24).", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2-track-distribution", "statement": "Rigid and plastic neurons were similarly distributed along the track.", "source": "Results, paragraph 3; fig. S2 as cited", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Blocked as it depends on fig2b-strong-contributors. Rate-map peaks of rigid and plastic cells do not differ by the KS test (medians 0.419 and 0.486 of the track, D = 0.145, p = 0.072); with the split over all place cells p = 0.079, with the best-template classes p = 0.12.", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-plastic-specificity", "statement": "Plastic neurons had higher place-specific indices and fewer place fields than rigid cells.", "source": "Results, paragraph 4; Figure 3A", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Blocked as it depends on fig2b-strong-contributors. Plastic cells carry more spatial information (median 0.904 against 0.594 bits per spike, p = 1.9e-05; best-template classes p = 0.0035), but the number of fields does not differ (means 1.484 and 1.685, p = 0.073).", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-plastic-improve", "statement": "Plastic but not rigid neurons increased their spatial specificity (in-field versus out-of-field firing ratio) steadily during the MAZE session.", "source": "Results, paragraph 4; Figure 3B", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Blocked as it depends on fig2b-strong-contributors. Both groups raise their in-field ratio over the session (change of log10 ratio, plastic median 0.155, p = 0.0079; rigid 0.129, p = 0.030; between groups p = 0.41). With the best-template classes plastic p = 0.020 and rigid p = 0.28.", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4a-rigid-faster", "statement": "Session-wide firing rates of rigid neurons were higher than those of plastic neurons.", "source": "Results, paragraph 5; Figure 4A", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Blocked as it depends on fig2b-strong-contributors. Rigid cells fire somewhat faster (median 0.700 against 0.591 Hz) without significance (p = 0.062; split over all place cells p = 0.053; best-template classes p = 0.74).", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4a-plastic-ripple-burst-coactivation", "statement": "Ripple-related spiking, bursting and pairwise coactivation were higher in plastic than in rigid neurons.", "source": "Results, paragraph 5; Figure 4A", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Blocked as it depends on fig2b-strong-contributors. Ripple gain (4.489 against 3.939, p = 0.015) and bursting (0.180 against 0.147, p = 0.028) are higher in plastic cells; coactivation is not (0.028 against 0.027, p = 0.90). With the best-template classes none reaches p < 0.05 (gain p = 0.15, bursting p = 0.11).", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-pre-fast-coactivation", "statement": "In PRE sleep, coactivation was dominated by fast-firing neurons.", "source": "Results, paragraph 5; Figure 4C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "PRE coactivation rises with firing rate, from 0.0208 in the slowest window to 0.0486 in the fastest; Spearman correlation 0.861 on the averaged curve, positive in 6 of 8 sessions. The POST minus PRE change of the fastest window does not differ from 0 over sessions (sign-rank p = 0.383), which fits the statement that these correlations remain into POST.", "deviations": [ "Coactivation over whole epochs, all states; the paper's restriction, if any, is not stated in the main text." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-slow-coactivation-increase", "statement": "Slow-firing neurons showed the strongest increases in coactivation from PRE to POST sleep.", "source": "Results, paragraph 5; Figure 4C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "The POST minus PRE change does not fall with firing rate; Spearman correlation -0.068 on the averaged curve (p = 0.55), negative in 5 of 8 sessions. The averaged change is 0.0019 in the slowest window and -0.0007 in the fastest, with a maximum of 0.0090.", "deviations": [ "Coactivation over whole epochs, all states." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-slow-replay", "statement": "Slow-firing cells showed the greatest replay, the partial correlation between RUN and POST coactivation accounting for PRE.", "source": "Figure 4C legend", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "The partial correlation of MAZE running and POST coactivation given PRE is 0.186 in the slowest window and 0.115 in the fastest, but the Spearman correlation over windows is 0.095 and negative in only 4 of 8 sessions. By subject it is -0.588 (Achilles), -0.646 (Buddy), -0.070 (Cicero) and 0.671 (Gatsby).", "deviations": [ "MAZE coactivation is taken over running bins (above 5 cm/s on the track)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "rate-split-medians", "statement": "Place cells divided into equal groups by sleep firing rate have medians of 0.39 Hz (low-rate) and 1.12 Hz (high-rate).", "source": "Results, paragraph 6", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Split by non-REM sleep rate, the low-rate median is 0.435 Hz under both readings, just outside 0.39 +/- 0.039, and the high-rate median 1.091 Hz (a, within sessions) or 1.092 (b, pooled), within 1.12 +/- 0.112. With the rate over all of PRE and POST (a variant) both are within tolerance (0.395 and 1.041 under reading a). The split is of 417 place cells, not 491.", "deviations": [ "The paper does not say whether the split is within sessions or pooled; both readings are shown and give the same medians.", "Off-line sleep rate is taken as the non-REM rate in PRE and POST; the rate over all of PRE and POST is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs16-low-rate-info-gain", "statement": "Low-rate neurons carried more spatial information per spike on the maze, and increased their within-ripple firing-rate gain from PRE to POST more than high-rate cells.", "source": "Results, paragraph 6; fig. S16 as cited", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "Under reading (a), which the criterion selects as neither reading of rate-split-medians matched, low-rate cells carry more spatial information (median 0.975 against 0.622 bits per spike, p = 4.1e-08), but their ripple-gain change from PRE to POST is not larger (0.251 against 0.155, p = 0.948). Reading (b) gives the same.", "deviations": [ "Ripple gain is the rate within candidate events over the epoch rate; the paper's definition is in fig. S16, which was not available." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-slow-sequences", "statement": "Slow-firing, but not fast-firing, neurons increased their contribution to sequences from PRE to POST sleep, in a decoding restricted to each group.", "source": "Results, paragraph 6; Figure 4D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "On the pooled test neither half shows replay (low-rate POST minus PRE -0.024, p = 0.964; high-rate -0.049, p = 0.9999), as for all cells (-0.008, p = 0.916). In the within-session variant both halves show replay, larger for low-rate cells (+0.116 against +0.058, p of at most 0.0001 for each), which would be the criterion's partial pattern. On the linear-track sessions alone the pooled test also finds both, larger for low-rate cells (+0.077, p = 0.0046, against +0.044, p = 0.018).", "deviations": [ "Variant decodes use 50 column-cycle shuffles per event in place of 200." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-gain-sequences", "statement": "PRE to POST increases in sequence content were limited to cells with high ripple-specific recruitment (gain).", "source": "Results, paragraph 6; Figure 4E", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_grosmark_2016.ipynb", "notes": "On the pooled test neither half shows replay (high-gain -0.001, p = 0.71; low-gain -0.111, p = 1.0). In the within-session variant high-gain cells show replay (+0.111, p < 0.0001) and low-gain cells do not (+0.016, p = 0.14), the paper's pattern. On the linear-track sessions alone the pooled test finds replay in neither half (+0.023, p = 0.25; +0.010, p = 0.21) and the within-session variant finds it in both (+0.045, p = 0.029; +0.050, p = 0.0028).", "deviations": [ "Gain is the rate within PRE and POST candidate events over the PRE and POST rate, split at the session median.", "Variant decodes use 50 column-cycle shuffles per event in place of 200." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "In versions 0.210812.1516 and 0.250624.0426 every position series stores its sampling period (0.0256 s) as its rate, so the positions span about 880 to 2360 hours in place of the MAZE epoch. Version 0.261005.2101 stores 39.06 Hz, which matches the epoch lengths." }, { "kind": "metadata_error", "statement": "In Gatsby_08022013 the POST epoch ends at 30413.6 s, while the LFP, the spikes and the sleep states run to about 32000 s." }, { "kind": "data_missing", "statement": "The dandiset description lists neck EMG and head-mounted accelerometer signals, and the files hold neither; they also hold no wide-band data (acquisition is empty), only the LFP at 1250 Hz." }, { "kind": "data_missing", "statement": "The paper's derived data are not deposited. There are no candidate or ripple events, no place-cell list, no sequence scores and no PCC values or rigid and plastic labels, so the paper's selections cannot be checked against the dandiset and every one must be rebuilt." }, { "kind": "methods_unavailable", "statement": "Neither the paper nor the dandiset links analysis code, and the supplementary Materials and Methods, which define the candidate events, place cells, the PCC and its test, are not openly available (PMC and Science serve them only behind a browser check)." }, { "kind": "metadata_insufficient", "statement": "Every electrode's location is \"unknown\" and no depth or layer is given, so the channel for ripple detection has to be chosen from the signals. Units carry only the hemisphere (lCA1 or rCA1). Subject age is \"/\"." }, { "kind": "metadata_insufficient", "statement": "On the circular track the animals ran toward decreasing linearized position (47 to 63% of samples against 7 to 16% the other way). The series description says the position increases clockwise but not which way the animals ran." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file, with the main text of the paper (the supplement could not be retrieved). The verifier checked the blocked claims against the archive's file list and metadata and tested the helper functions on synthetic inputs. Report in transcripts/000044/verifier-1-report.md.", "agreed": 13, "of": 20, "disagreements": [ { "claim": "fig2d-shuffle-high-dpcc", "outcome": "partially_reproduced", "reason": "This claim ranks all place cells by dPCC and does not use the strong-contributor selection, so the block reason does not apply (problem 4). By the criterion replay is absent after shuffling the top 10% or 20% but also after shuffling the bottom 75% (p = 0.35); the unmanipulated baseline has no pooled replay either (p = 0.92), so \"eliminated\" cannot be judged (uninformative). The within-session variant shows the paper's pattern. dPCC is computed from the same PRE and POST events that are decoded again, so the result is circular and there is no control that shuffles a random X% of cells (problem 3)." }, { "claim": "fig2e-remove-plastic", "outcome": "reproduced", "reason": "Replay is absent without plastic cells (p = 1.0) and present without rigid cells (p = 0.020). The result is circular (problem 3), and with the shift-test classes removing rigid cells leaves no replay (p = 0.11)." }, { "claim": "figs2-track-distribution", "outcome": "not_reproduced", "reason": "KS p = 0.034 (cell 37). This is fragile, p = 0.051 under reading (b) and 0.12 under the shift-test variant." }, { "claim": "fig3a-plastic-specificity", "outcome": "partially_reproduced", "reason": "Spatial information is higher in plastic cells (p = 3e-4). The number of fields does not differ (p = 0.52) (cell 39)." }, { "claim": "fig3b-plastic-improve", "outcome": "partially_reproduced", "reason": "Both groups increase: plastic p = 0.015, rigid p = 0.032 (cell 41)." }, { "claim": "fig4a-rigid-faster", "outcome": "not_reproduced", "reason": "Rigid cells have the higher median, but p = 0.059 (cell 43)." }, { "claim": "fig4a-plastic-ripple-burst-coactivation", "outcome": "partially_reproduced", "reason": "Gain is higher in plastic cells (p = 0.037). Bursting (p = 0.20) and coactivation (p = 0.79) are not (cell 45)." } ] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the revised run, with the helper module, the claims file and the attempt record. The verifier did not need the paper text for this round. Report in transcripts/000044/verifier-2-report.md.", "agreed": 20, "of": 20, "disagreements": [] } ] }, { "id": "000056-peyrache-2015-01", "dandiset": "000056", "dandiset_version": "0.250624.0430", "paper": "10.1038/nn.3968", "paper_title": "Internally organized mechanisms of the head direction sense", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000056-peyrache-2015", "entry_title": "Head-direction cells across waking and sleep (Peyrache et al. 2015)", "description": "Tests the findings of Peyrache, Lacroix, Petersen and Buzsaki (2015) on dandiset 000056, which holds spike times, LED positions and sleep states from 40 sessions of 7 mice recorded in the anterior thalamus and post-subiculum. It classifies head-direction cells, compares their rates and pairwise correlations across waking, REM and slow-wave sleep, estimates the speed of the internal head-direction signal from cross-correlograms, and tests noise correlations and decoding. The units carry no brain region, so the comparisons between the two structures cannot be made.", "notebooks": [ { "path": "reproduce_peyrache_2015.ipynb", "title": "Reproducing Peyrache et al. (2015) from dandiset 000056", "executed": "notebooks/000056-peyrache-2015/reproduce_peyrache_2015.html" } ], "outcomes": [ { "claim": "hd-cell-fraction", "statement": "Of the recorded cells, 242 of 720 in the anterior thalamus and 111 of 357 in the PoS were classified as HD cells, 353 of 1077 in all.", "source": "Methods, Head direction cells; Results, first paragraph", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "By the Methods' criteria 378 units are HD cells in the 38 sessions with position, within 353 plus or minus 35.3. They are 0.218 of the 1731 units with spikes in the open-field epoch (reading a) and 0.205 of all 1848 unit rows of those sessions (reading b), both outside 0.328 plus or minus 0.033. The files hold 1959 unit rows in 40 sessions against the paper's 1077 recorded cells in 42 sessions. By mouse the fraction is 0.108 to 0.386; in the mice that appear to be thalamus only it is 0.133 (133 of 1000) against the paper's thalamic 0.336, and in the mice that appear dual-site 0.335 (245 of 731). With a concentration threshold of 0.8 or 1.2 the count is 424 or 357. None of the 34 units with unsorted spike times in these sessions is an HD cell. The count passes only with Mouse12-120808 as deposited, where position and spikes do not share a clock and no unit passes the criteria. With position realigned by the best shift of each quarter of the epoch, that session has 13 HD cells (12 with one constant shift of -2.6 s), and the count is 391 (390), above the upper bound of 388.3, so the match of the count is fragile. The unit rows cannot be brought down to the paper's 1077 cells from the files (1826 rows fire at 0.05 Hz or more and 1526 at 0.5 Hz or more; unit ids are 0 to N-1 and carry no shank or cluster number). The agreement of the count may therefore also be coincidental. The split into 242 thalamic and 111 PoS HD cells cannot be tested.", "deviations": [ "Regions pooled, as the units carry no region.", "The von Mises fit (maximum likelihood fit to the tuning curve as a distribution of angles) and the Rayleigh test (resultant length of the tuning curve with the number of waking spikes) are choices made here; the Methods do not specify them.", "The open-field epoch is found from position, as the files do not mark it.", "Mouse17-130201 and Mouse32-140820 have no processed position and are left out.", "Mouse12-120808 is counted as deposited, with position and spikes on different clocks; the realigned session is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-rates-preserved", "statement": "The firing rates of HD neurons are strongly correlated between waking and SWS and between waking and REM sleep.", "source": "Figure 2a (ADn n = 215, PoS n = 62 cells)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "Over 378 HD cells in 37 sessions with sleep states, Pearson r of waking against SWS rates is 0.838 (p = 3.7e-101) and against REM rates 0.891 (p = 4.5e-131); with log rates 0.806 and 0.883. By mouse r is 0.718 to 0.889 for SWS and 0.866 to 0.942 for REM. The cell count (378 against the paper's 277) does not decide the outcome; the paper does not say which HD cells were in its figure.", "deviations": [ "ADn and PoS cells pooled; the paper plots them separately." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-pair-correlations-preserved", "statement": "The pairwise correlations between HD neurons, within and across structures, are similar across brain states.", "source": "Results, second paragraph; Figure 2b (ADn pairs n = 970, PoS pairs n = 92)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "Reading (a), 1573 pairs in 33 sessions, waking against SWS pair correlations r = 0.938 and against REM r = 0.963. Reading (b), 2246 pairs, r = 0.925 and 0.952. Every mouse gives r of at least 0.913. 888 of 2461 pairs fail reading (a) for low rates.", "deviations": [ "Pairs within and across structures are pooled, and pairs on the same shank cannot be removed.", "Bin sizes are those of Figure 3a; Figure 2b does not state them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-packet-60-degrees", "statement": "The zero-lag correlation between HD cell pairs falls with the offset of their preferred directions, positive below 60 degrees, negative above it and near zero at about 60 degrees, and this holds in waking, REM and SWS.", "source": "Results, third paragraph; Figure 3a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "The mean zero-lag correlation, in 10 degree bins of the offset of preferred directions, crosses zero at 54.2 degrees in waking, 56.9 in REM and 55.9 in SWS (measured gives the waking value, the lowest), all within 54 to 66. The Pearson correlation of pair correlation with offset is -0.751, -0.741 and -0.671 (p below 1e-200). With 15 degree bins the crossings are 55.4, 57.9 and 57.7 degrees; under reading (b) 54.1, 57.1 and 56.5, the waking value just outside the tolerance. The waking crossing of reading (a) is 0.2 degrees inside the tolerance, so the pass is close to the boundary.", "deviations": [ "ADn-ADn, ADn-PoS and PoS-PoS pairs are pooled." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-sws-tenfold-faster", "statement": "The angular velocity of the internal HD signal, estimated from the temporal profile of pairwise cross-correlograms, is about tenfold faster during SWS than during waking.", "source": "Results, second paragraph; Figure 2e,f; Abstract (\"accelerated tenfold\")", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "Over 1509 pairs (64 of 1573 dropped for a fit at the edge of the speed range), the median ratio of SWS to waking angular velocity is 8.33 (quartiles 5.91 to 11.31), below 9 to 11; SWS is faster in 1420 pairs (sign test p = 4.1e-309). Median speeds are 36.9 deg/s in waking, 33.5 in REM and 324.4 in SWS. By mouse the ratio is 7.89 to 13.52. The Bayesian decoder variant gives a median of 11.53 over 28 sessions. Under reading (b) the median is 8.02 over 2129 pairs; with pairs whose fits reach R2 of 0.25 or 0.5 in every state, 8.46 (1063 pairs) and 8.56 (748 pairs). Median R2 is 0.84 in waking, 0.55 in REM and 0.78 in SWS. The waking estimates are 0.60 times the measured mean angular speed of the head (median over sessions) and correlate with it at r = 0.20 across 33 sessions. On Poisson surrogates driven by the measured head direction and the waking tuning curves, the estimator returns 0.37 of the true mean speed (median 37.0 deg/s, as on the data, against a true 99.9), and for the same trajectory played ten times faster it gives a median ratio of 4.99 (quartiles 2.76 to 7.02), not 10. Scaled by that compression the data's 8.33 becomes 16.69, so the data are consistent with a speed-up below, at or above tenfold. The estimator shows that SWS is faster but does not determine the fold; how far its bias in SWS matches that of the surrogates is not known.", "deviations": [ "The paper does not say how the expected and observed cross-correlograms are put on one scale; a free scale and offset are fitted here.", "The lag range (4 s) and speed grid are chosen here.", "The expectation over the chi-squared speed distribution is computed exactly from its characteristic function.", "Pairs within and across structures are pooled; the paper shows ADn-ADn and PoS-PoS pairs." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-rem-similar-to-wake", "statement": "The angular velocity of the internal HD signal is similar during REM sleep and waking.", "source": "Results, second paragraph; Figure 2e,f", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "The median REM to waking ratio is 0.87 over 1509 pairs (quartiles 0.60 to 1.26), inside 0.67 to 1.5, and 0.85 over 2129 pairs under reading (b); by mouse 0.69 to 1.07; the decoder variant gives 1.05. By a Wilcoxon test of the log ratio the median REM speed is below the waking one (p = 6.3e-18, median log10 ratio -0.060, about 13%), a test the paper does not make, but REM is faster in 581 of 1509 pairs.", "deviations": [ "The paper names no test for \"similar\"; the range 0.67 to 1.5 is chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-noise-correlations", "statement": "During waking, the observed correlations of HD cell pairs exceed those expected from independent rate-coded neurons for pairs with overlapping fields (0 plus or minus 15 degrees), and fall below them for pairs at about 60 degrees.", "source": "Results, fourth paragraph; Figure 4a,b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "With the Methods' formula (mean cross-products over bins where the head direction is known at both times), the noise correlation of pairs at 0 plus or minus 15 degrees is positive in 110 of 118 pairs (median 7.84 Hz2, 0.81 of the chance product, Wilcoxon p = 5.3e-19) and of pairs at 60 plus or minus 15 degrees positive in only 35 of 256 (median -4.08 Hz2, p = 4.2e-32). Under reading (b) the medians are 4.22 and -1.63 Hz2 (p = 2e-24 and 6.8e-42). On independent Poisson surrogates with tuning curves estimated from their own spikes, the measure is biased in the same direction, median +0.64 Hz2 at 0 degrees and -0.37 Hz2 at 60, about a tenth of the observed values; the data exceed their surrogates in 110 of 118 pairs at 0 degrees (p = 5e-19) and fall below them in 223 of 256 at 60 degrees (p = 1.6e-31). It holds in the mice that appear thalamus only. Under the first criterion, with both cross-correlations on a Pearson scale, the 0 degree pairs are negative (median -0.78), which reflects the scale and not the data.", "deviations": [ "The criterion was revised after a first run, before this outcome was recorded, from a Pearson scaling that contradicted the Methods' stated formula to that formula; the first version is shown as a variant.", "Regions pooled." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "decoding-tracks-hd", "statement": "The HD signal decoded with a Bayesian decoder from the HD cells faithfully tracks the head direction of the waking mouse.", "source": "Methods, Bayesian reconstruction of head-direction; Figure 1c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_peyrache_2015.ipynb", "notes": "In 28 sessions with at least 6 HD cells, two-fold cross-validated decoding has a pooled median absolute error of 11.7 degrees (chance 90); session medians 8.1 to 27.2, all at or below 30. With HD cells selected on the training half alone, the same 28 sessions give a pooled median of 11.7 degrees (session medians 8.1 to 24.7).", "deviations": [ "HD cells of both structures are decoded together; the paper decodes one structure at a time.", "The threshold of 30 degrees for \"faithfully\" and the 6 degree angle bins are chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "adn-pos-peak-rate", "statement": "ADn HD cells have peak rates almost three times those of PoS HD cells (p < 1e-10, Mann-Whitney, 242 ADn and 111 PoS HD cells).", "source": "Results, first paragraph; Supplementary Figure 2b", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The units table holds only spike times, with no electrode, shank or region, and every electrode's location is \"unknown\", so units cannot be assigned to the ADn or the PoS.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "adn-pos-hd-information", "statement": "ADn HD cells convey 30% more head-direction information than PoS HD cells (1.44 against 1.11 bits per spike, p < 1e-6).", "source": "Results, first paragraph; Supplementary Figure 2c", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No region per unit (see adn-pos-peak-rate).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ensemble-sizes", "statement": "Ensembles of 8.4 plus or minus 5.1 (s.d.) HD units per session were recorded in the ADn and 5 plus or minus 2.8 in the PoS.", "source": "Results, first paragraph", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No region per unit. Pooled, the sessions hold 0 to 26 HD cells (median 10). In the mice that appear thalamus only there are 7.4 plus or minus 6.2 (s.d.) HD cells per session over 18 sessions (7.8 plus or minus 6.1 without Mouse12-120808), against the ADn's 8.4 plus or minus 5.1; in the mice that appear dual-site 12.2 plus or minus 5.9 over 20 sessions, both structures together. The assignment of mice is consistent with the files but not shown by them, so these numbers do not decide the claim.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-adn-stronger-than-pos", "statement": "Pairwise correlations of HD cells closer than 60 degrees are stronger in the ADn than in the PoS in every brain state (p < 1e-5, 345 ADn-ADn and 55 PoS-PoS pairs).", "source": "Results, third paragraph; Supplementary Figure 5", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No region per unit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-packet-coherence", "statement": "The activity packets in the ADn and the PoS are coherent with the packet expected from the Bayesian decoded HD in waking, REM and SWS.", "source": "Results, third paragraph; Figure 3b", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The coherence is shown per structure, and units have no region. The measure is also described only by reference to earlier work (the bootstrap of population vectors is not fully specified), which would block it as methods_underspecified as well. A version pooled over regions could be run, but the Methods do not say how the actual and expected packets are compared or how the probability is formed from the 5,000 random waking population vectors, so it is not run here.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-noise-adn-vs-pos", "statement": "Noise correlations of HD cell pairs are stronger in the ADn than in the PoS (p < 1e-9, Kruskal-Wallis).", "source": "Results, fourth paragraph; Figure 4c", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No region per unit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-ole-covariance", "statement": "In the ADn the covariance-based optimal linear estimator of HD is about 50% better than the signal-based one, and this gain is larger than in the PoS (p < 0.05, 20 ADn and 8 PoS ensembles).", "source": "Results, fourth paragraph; Figure 4d,e", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The claim compares ADn and PoS ensembles, and units have no region.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-adn-decoded-tuning", "statement": "The HD signal decoded from ADn assemblies during sleep gives tuning curves of PoS cells more similar to their waking tuning than the signal decoded from PoS assemblies does for ADn cells, in all brain states.", "source": "Results, fifth paragraph; Figure 5a,b", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Decoding from one structure to compute tuning in the other needs the region of each unit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5e-adn-predicts-pos", "statement": "ADn assemblies predict PoS spike trains in all brain states better than PoS assemblies predict ADn spike trains, with optimal readout windows of 123 ms (waking), 133 ms (REM) and 79 ms (SWS).", "source": "Results, fifth paragraph; Figure 5c to e", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Predicting one structure from the other needs the region of each unit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6b-adn-synchrony", "statement": "Fast synchrony between ADn HD cell pairs decreases with the difference of their preferred directions in all brain states (p < 1e-10, Kruskal-Wallis, 970 pairs).", "source": "Results, sixth paragraph; Figure 6", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The claim is about ADn pairs on different shanks; units have neither region nor shank. The mice that appear thalamus only could stand in for the ADn, but that assignment is not shown by the files, and without shanks the pairs on the same shank, whose fast synchrony at 1 to 5 ms is distorted by spike sorting, cannot be removed.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-adn-pos-connections", "statement": "Putative monosynaptic connections were found in 4.45% of 6960 ADn to PoS pairs and 0.35% of PoS to ADn pairs; among pyramidal PoS cells, 0.41% against 0.18% (p = 0.014).", "source": "Results, sixth paragraph; Figure 7a,b", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the region of each unit, and for the pyramidal subset waveforms, which the dandiset does not hold for units (raw broadband data are in only 3 of the 40 files).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7d-same-preferred-direction", "statement": "PoS HD cells postsynaptic to ADn HD cells share the preferred direction of their presynaptic cell (12 pairs), and such PoS pyramidal cells convey more HD information than those without an identified presynaptic cell (p = 0.011).", "source": "Results, sixth paragraph; Figure 7d,e", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Depends on the ADn to PoS connections, which need the region of each unit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7c-adn-triggered-pos-lfp", "statement": "ADn HD cell spikes are associated with high-frequency oscillations of the PoS LFP.", "source": "Results, sixth paragraph; Figure 7c", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the region of the units and of the LFP channels; electrode locations are \"unknown\".", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The units tables hold only spike times. No unit has an electrode, shank, brain region, waveform or quality measure, and every electrode's location is \"unknown\". Units cannot be assigned to the antero-dorsal thalamus or the post-subiculum, which blocks 13 of the paper's 21 claims. The electrode groups and ripple annotations are consistent with Mouse24, Mouse25 and Mouse28 being the three dual-site mice, but the files do not say so." }, { "kind": "selection_undocumented", "statement": "The files hold 1959 unit rows (103 with no spikes) in 40 sessions, against the paper's 1077 recorded cells in 42 sessions. Mouse12-120809 alone has 292 units, 167 of them firing below 0.5 Hz. Unit ids run from 0 to N-1 and carry no shank or cluster number, the units table has no quality measure, and 1526 rows fire at 0.5 Hz or more, so the paper's 1077 cells cannot be recovered. Nothing marks which units or sessions the paper analysed (its Methods discard some sessions)." }, { "kind": "metadata_insufficient", "statement": "The open-field exploration (the paper's waking epoch) is not marked. The \"Awake\" state also covers waking in the home cage, and some sessions hold a second exploration or a larger second environment. The epoch had to be found from position." }, { "kind": "format_error", "statement": "In 36 of 40 files one unit's spike times are not sorted. Each such unit holds exactly two sorted runs, and in all 36 the first run ends at an index of the form k x 65536 - 1. The second run starts within 36 s of the start of the recording and the first between 24 and 13704 s, and the two end within 15 s of each other. In 26 units no time of the second run appears in the first; in 10, 821 to 22281 times do. This suggests an error in the conversion." }, { "kind": "other", "statement": "In Mouse12-120808 the position and the spikes do not share a clock. Head-direction tuning is best with position shifted by -1.5 s at the start of the exploration and -3.4 s at its end, and no unit passes the HD criteria as deposited; with position realigned by the best shift of each quarter, 13 units do. In all other sessions the best shift is -0.2 to 0 s." }, { "kind": "metadata_error", "statement": "The raw LED positions in `acquisition` are stated in meters with a conversion of NaN but hold camera pixels (values in the hundreds)." }, { "kind": "data_missing", "statement": "Mouse32-140820 has no sleep-state table and no processed position, and Mouse17-130201 has no processed position; both have raw LED series only. In three Mouse20 sessions the position series ends 11 to 109 minutes before the recording." }, { "kind": "metadata_insufficient", "statement": "The annotation series `dow`, `hdD` and `rip` (labels such as \"DOWN ON 5\", \"HD UP ON\", \"Ripple peak 1\") have no description." }, { "kind": "metadata_error", "statement": "The dandiset's related resource for the paper gives its name and identifier as \"nternally organized mechanisms of the head direction sense\" (first letter missing, and the title in place of a DOI); the URL is correct." }, { "kind": "methods_unavailable", "statement": "Neither the paper nor the dandiset links analysis code, so the von Mises fit, the Rayleigh test, the scaling in the cross-correlogram estimate of angular velocity and the coherence measure had to be chosen or could not be repeated." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier checked the archive metadata for the blocked claims and tested helper functions and two measures on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; all 21 agree with the record.", "agreed": 21, "of": 21, "disagreements": [] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file, the attempt record and the README, with the paper. The verifier agreed with all 21 outcomes. Besides the points below, it found that cell 18 gave the shift of the largest contrast as 10 s in 10 sessions where cell 17 shows -10 s in 9 and +10 s in one, and that the README's run time (nine minutes, five streaming) did not match cells 53 and 1; both are corrected, the README from a new run (10.1 min, 322 s loading). It also noted that the record's finding on the unsorted units had no printed output; the new data check prints it, and the finding now gives what it shows (two runs in all 36 units, all broken at k x 65536 - 1, with repeated times in 10).", "agreed": 21, "of": 21, "disagreements": [] } ] }, { "id": "000059-petersen-2020-01", "dandiset": "000059", "dandiset_version": "0.250624.0444", "paper": "10.1016/j.neuron.2020.05.023", "paper_title": "Cooling of Medial Septum Reveals Theta Phase Lag Coordination of Hippocampal Cell Assemblies", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000059-petersen-2020", "entry_title": "Cooling of the medial septum, hippocampal theta and place cell timing (Petersen & Buzsaki 2020)", "description": "Tests the findings of Petersen and Buzsaki (2020) on dandiset 000059, which holds 50 sessions of five rats running a spatial alternation task on a figure-8 maze while the medial septum was cooled, with MS temperature, trials, position, LFP, wide-band data and sorted units. It tests the slowing of theta with temperature, the increase of choice errors, the oscillation frequency of place cells against LFP theta, place field features, and the time and phase lags of place cell pairs. The hippocampal temperature recordings of the control experiment are not in the dandiset.", "notebooks": [ { "path": "reproduce_petersen_2020.ipynb", "title": "Reproducing Petersen & Buzsaki (2020) from dandiset 000059", "executed": "notebooks/000059-petersen-2020/reproduce_petersen_2020.html" } ], "outcomes": [ { "claim": "session-structure", "statement": "A session holds about 40 control trials, 20 to 60 cooling trials and 20 to 80 recovery trials, 80 to 200 trials in all with a mean of 150.", "source": "Results, first section; STAR Methods, Electrophysiological Recordings", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 45 BEH sessions the mean is 143.8 trials (80 to 204); medians of 39 pre-cooling, 47 cooling and 44 post-cooling trials. 12 sessions have two cooling blocks, which the paper does not mention; in each the second block follows post-cooling trials, and the onset-aligned series stops before it. 'Cooling off' trials (median 14 per session) are counted in no state.", "deviations": [ "45 of the paper's 53 sessions." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "cooling-time-course", "statement": "MS cooling peaked about 60 s after its onset and lasted about 10 to 12 minutes.", "source": "STAR Methods, Electrophysiological Recordings", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 37 sessions with a recorded temperature the minimum comes a median 121 s after the onset (IQR 89 to 138 s; 119 to 122 s for onset thresholds of 0.5 to 2 C), against 60 s. The duration holds under reading (b), 12.16 minutes until the temperature is within 1 C of baseline; under reading (a) the temperature is below 32 C for 8.77 minutes. The median minimum is 21.2 C. The drop is fast and the temperature then stays near its minimum, so the time to the minimum overstates the time to the peak effect. 90% of each session's drop is reached a median 53 s after onset (IQR 44 to 63 s), and the onset-aligned mean trace is within 0.5 C of its minimum from 70 to 152 s. Without the five sessions whose baseline has artefacts above 38 C or whose onset is detected early, the values are 121.5 s and 12.22 minutes.", "deviations": [ "The onset is taken from the temperature trace (1 C below the pre-cooling median), as the files have no time of dry-ice placement; the Methods do not define the onset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2g-theta-freq-temperature", "statement": "Theta frequency decreased linearly with MS temperature (R = 0.81, P = 5.4e-48).", "source": "Results, first section; Figure 2G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "With the code's aligned series, R = 0.789 (P = 2.8e-43, 198 positions) over 37 TEMP sessions under reading (a), and R = 0.758 (P = 3e-38) with the MS10 temperature curves under reading (b); both are within tolerance. Over single trials pooled R = 0.672, slope 0.065 Hz per C. Per rat R is 0.685 to 0.954.", "deviations": [ "37 sessions with a recorded temperature, where the paper used 53; the MS10 temperature in the dandiset is not a recording.", "The theta electrode is the one flagged theta_reference in the files; the code's channel numbers could not be mapped to the files' electrodes." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2h-theta-power-temperature", "statement": "Theta power also decreased with MS temperature, less tightly than frequency (R = 0.54, P = 1.2e-16).", "source": "Results, first section; Figure 2H", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Theta power does not follow temperature, R = -0.056 (P = 0.44) over TEMP sessions and R = 0.123 (P = 0.085) with the MS10 curves; over single trials pooled R = 0.107. Power is the spectrogram magnitude of the band-passed LFP as in calcInstantaneousTheta.m, minus each session's mean, at frames above 30 cm/s, and the 10 cm/s variant gives R = 0.135. Per rat the power R ranges from -0.346 to 0.376.", "deviations": [ "The theta electrode is the one flagged theta_reference in the files, which may differ from the paper's; power depends on the electrode more than frequency does. The LFP column read is that row in every session (checked through the LFP electrodes region).", "Power is taken from the spectrogram of the 4 to 10 Hz band-passed LFP, as in the paper's code (calcInstantaneousTheta.m); the band-pass weights frequencies within the band unequally." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2j-frequency-consistent-across-animals", "statement": "The relationship of theta frequency with MS temperature was more consistent across animals than that of theta power.", "source": "Results, first section; Figure 2J", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "In each of the four rats with a recorded temperature the frequency R is positive (0.685 to 0.954, every P below 1e-22), a range of 0.269, against a range of 0.722 for power (-0.346 to 0.376). The outcome rests on power varying across rats, since power shows no consistent effect (fig2h-theta-power-temperature).", "deviations": [ "Four rats; MS10 has no recorded temperature." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2i-theta-pre-cooling-post", "statement": "Theta frequency and power were lower during MS cooling than before and after it.", "source": "Figure 2I; Results, first section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Frequency is lower during cooling than before (44 of 45 sessions, P = 1.4e-12) and after (45 of 45, P = 5.7e-14). Power is lower than before at P = 0.048 (26 of 45) but not lower than after (19 of 45, P = 0.94); during cooling it is 0.972 of the session mean of the three states.", "deviations": [ "State means over trials, from the dandiset's labels, with 'Cooling off' trials left out." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "disc-theta-frequency-12-percent", "statement": "During MS cooling LFP theta frequency decreased by 12%.", "source": "Discussion, Theta phase organization of hippocampal cell assemblies", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "The decrease is 8.88% (a), 9.18% (b) and 9.23% (c), none within 12 +- 1.2%. The slowest cooling trial of a session is a mean 16.93% below pre. Per rat 4.76% (MS12) to 10.74% (MS21). The paper's within-field values (8.4 and 7.7 Hz) are reproduced in fig4b-fp-flfp-decrease.", "deviations": [ "The paper does not say how the 12% is computed; three readings were tested." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-errors-increase", "statement": "MS cooling increased choice errors about 3-fold, within each rat (P < 0.05 for all animals) and across all animals (P = 1e-6).", "source": "Results, MS cooling increases behavioral errors; Figure 6D and 6E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Errors are 6.67% before and 15.23% during cooling (40 of 45 sessions higher, P = 3e-07), ratios 2.28 (a), 2.31 (b) and 2.53 (c), all below 2.7. Per rat, P = 0.0078 (MS10), 0.039 (MS12), 0.027 (MS21) and 0.064 (MS22, 10 of 12 higher); MS13 has 5 sessions, all higher (P = 0.0625, the smallest possible). Counting 'Cooling off' trials as cooling gives a ratio of 1.98; TEMP sessions alone 1.96.", "deviations": [ "States from the dandiset's trial labels; the code counts errors by time windows from the cooling onsets and offsets, which are not in the files.", "45 of 53 sessions; MS13 has 5 sessions here, too few for an exact signed-rank test to reach 0.05." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6e-errors-recover", "statement": "The error rate after cooling did not differ from the error rate before it.", "source": "Figure 6E (marked ns)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Post 6.49% against pre 6.67% (median difference -0.13 points, P = 0.837, 45 sessions); cooling against post P = 8e-08.", "deviations": [ "The figure's 'ns' was read as pre against post." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-worst-trials-4-to-8", "statement": "The worst memory performance occurred between trials 4 and 8 after the onset of cooling, when MS temperature reached its minimum.", "source": "Results, MS cooling increases behavioral errors; Figure 6C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "The mean smoothed error series over 45 sessions peaks at trial 7 after onset (0.193, against 0.066 over the 40 trials before), the trial of the minimum mean temperature and theta frequency. The peak is narrow and the result fragile. A second rise reaches 0.186 at trial 20, and within single rats the mean peaks later, at trials 14 to 26. All 45 sessions contribute at every trial from 1 to 40.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6f-errors-temperature", "statement": "The incidence of errors correlated negatively with MS temperature (R = -0.35, P < 0.01).", "source": "Results, MS cooling increases behavioral errors; Figure 6F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Negative and stronger than reported, R = -0.838 (a, P = 5.9e-41), -0.789 (b) and -0.868 (c), none within -0.35 +- 0.035. Over single trials pooled R = -0.127 (P = 5.5e-20); per rat -0.298 to -0.860. The paper's value may come from a different unit of analysis, which its text does not give.", "deviations": [ "37 sessions with a recorded temperature." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6g-errors-theta-frequency", "statement": "The incidence of errors correlated negatively with theta frequency (R = -0.35, P < 0.01).", "source": "Results, MS cooling increases behavioral errors; Figure 6G", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "R = -0.868 (a, P = 3.9e-47) and -0.733 (b), stronger than -0.35; per rat -0.341 to -0.829.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6h-errors-theta-power", "statement": "The incidence of errors correlated less with theta power; only 2 of 5 animals had a significant correlation (R beyond -0.3, P < 0.01).", "source": "Results, MS cooling increases behavioral errors; Figure 6H and 6J", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "One rat counts (MS10, R = -0.425, P = 1.1e-09). MS21 is significant with R = -0.202 (P = 0.0063), and MS22 with the opposite sign (R = 0.325, P = 1.2e-05).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6i-errors-not-speed", "statement": "The incidence of errors did not correlate with the running speed of the rat (R about 0.1, P > 0.05 for all animals).", "source": "Results, MS cooling increases behavioral errors; Figure 6I and 6J", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Three of five rats have P < 0.05, MS13 (R = -0.493, P = 8e-11), MS21 (R = 0.216, P = 0.0034) and MS22 (R = 0.247, P = 0.001); MS10 and MS12 do not (P = 0.32 and 0.49). Over all sessions together R = 0.093 (P = 0.19). The correlations are over about 150 to 190 aligned positions, so small R values reach significance.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-speed-decreases-within-session", "statement": "Running speed decreased relatively monotonically within a session.", "source": "Results, Effects of MS cooling on single neuron properties; Figure 4E and 6C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Speed falls with trial number in 44 of 45 sessions (median rho -0.452, P = 4e-13), in every rat; the aligned mean falls from 86.0 to 73.7 cm/s.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-speed-control-cooling", "statement": "Mean running speed was 87.3 +- 8.0 cm/s in control trials and 86.2 +- 9.9 cm/s during MS cooling.", "source": "Results, MS temperature effects on theta time/phase compression", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 15 sessions, reading (a) gives control 78.9 and cooling 74.9 cm/s, both outside; reading (b) gives control 79.6, within 87.3 +- 8.0, and cooling 76.0, 0.3 cm/s below 86.2 +- 9.9. The criterion needs both values within tolerance under one reading, and neither reading gives both. Speed is lower during cooling than in control (P = 0.035 to 0.041).", "deviations": [ "15 of the code's 18 Figure 5 sessions; the paper does not define its speed measure." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppl2-place-cell-rates-decrease", "statement": "Within-field and peak firing rates of place cells decreased moderately during MS cooling (11% and 12%; P < 1e-9 and P < 1e-11).", "source": "Results, Effects of MS cooling on single neuron properties (Supplementary Figure 2)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 636 fields both rates fall (P = 0.0024 and 0.0013), by 3.7% and 5.3% as medians (a), 7.7% and 6.7% as ratios of means (b); reading (c) is dominated by fields with near-zero pre rates (-111% and -70%). Fields with at least 50 spikes in each state give 10.8% and 9.9%. The decrease differs between rats (MS12 rises by 10.1%, MS13 falls by 27.8%).", "deviations": [ "Place fields by the automatic criteria of the Methods for Figure 5; the paper defined the fields of this analysis by hand.", "Putative pyramidal cells typed here from waveforms and rates; the files have no cell types." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "disc-interneuron-rates-decrease", "statement": "Firing rates of interneurons decreased during MS cooling by about 14%.", "source": "Discussion; Results, Effects of MS cooling on single neuron properties", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "127 putative interneurons, lower in 75 (P = 0.0017), by 6.5% (a) or 9.1% (b); thresholds of 0.35 and 0.5 ms, and narrow units alone, give 9.4% to 9.9%.", "deviations": [ "Putative interneurons typed here (trough-to-peak at most 0.425 ms, or above 10 Hz)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppl2d-interneuron-oscillation-slows", "statement": "The theta oscillation frequency of putative fast-spiking interneurons decreased during MS cooling, commensurate with the LFP theta.", "source": "Results, Effects of MS cooling on single neuron properties (Supplementary Figure 2D)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "9.55 to 8.66 Hz (lower in 105 of 114, P = 8.7e-16), a 9.4% decrease against 8.8% for the LFP theta of the same sessions; narrow units alone P = 3.1e-11.", "deviations": [ "Putative interneurons typed here; the paper's fast-spiking interneurons come from CellExplorer." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppl1g-waveforms-unchanged", "statement": "The waveforms of hippocampal action potentials were not affected by MS cooling.", "source": "Results, first section (Supplementary Figure 1G)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 646 units, trough-to-peak differs (P = 4.9e-10, median change 0 as most units do not move by a whole 0.05 ms sample) and amplitude rises by a median 0.8% (P = 0.00057). The windows start 7.1 to 31.8 minutes apart (5.1 to 29.8 minutes from the end of the pre window), so drift cannot be separated from cooling; for interneurons alone neither differs (P = 0.066 and 0.2). Fewer spikes are averaged in the cooling window (median 200 against 247.5), but in the 208 units whose two means both use the 300-spike cap the changes remain (amplitude 0.7%, P = 0.032; trough-to-peak P = 2.2e-05), so the spike count does not explain them. The effect is small, and the outcome follows the paper's test as written; it does not show that cooling changes the waveforms.", "deviations": [ "Waveforms from 120 s windows of the wide-band data at 20 kHz, high-passed at 300 Hz, on the channel of largest amplitude; the paper's measure is in its supplement, which could not be read." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-fp-flfp-decrease", "statement": "MS cooling decreased both the oscillation frequency of place cells (fp) and the LFP theta frequency in their fields (fLFP) by about the same degree, and both recovered (fLFP 8.4, 7.7, 8.5 Hz; fp 10.6, 9.5, 10.4 Hz before, during and after; n = 365).", "source": "Results, Effects of MS cooling on single neuron properties; Figure 4B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 361 fields (paper 365) all six means are within the paper's spreads; fp falls in 311 (P = 3.5e-44) and fLFP in 352 (P = 1.2e-60), by 9.2% and 9.0%, and both recover. Each rat shows the same pattern and every session the decrease; in MS22-180720-110055 fp does not recover (9.92 Hz after, 10.15 Hz during cooling). Fields with at least 100 or 200 spikes per state give the same means.", "deviations": [ "Fields by the automatic criteria of the Methods, from 11 sessions in 4 rats." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-fp-flfp-correlation", "statement": "fp and fLFP were correlated across place fields before, during and after cooling (R = 0.61, 0.59 and 0.36; P < 1e-6 each).", "source": "Figure 4C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "All positive (P = 1.5e-05, 6.7e-19 and 0.0029) and weaker than 0.61, 0.59 and 0.36; within rats R ranges from -0.05 to 0.64.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4ac-fp-flfp-difference-preserved", "statement": "During MS cooling fp and fLFP decreased in parallel, so the difference fp - fLFP remained constant.", "source": "Results, Effects of MS cooling on single neuron properties; Discussion", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "fp - fLFP falls from 2.009 to 1.806 Hz (median change -0.128 Hz, P = 0.000132, 361 fields) and stays at 1.790 Hz after cooling; the ratio fp/fLFP is preserved (1.237 and 1.232, P = 0.84). By rat the mean change is -1.03 Hz (MS12), 0.01 (MS13), -0.19 (MS21) and 0.10 (MS22).", "deviations": [ "The paper names no test; its default paired test was used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4a-frequency-temperature-slopes", "statement": "fLFP and fp measured within place fields decreased linearly with MS temperature (fLFP R = 0.66, slope 0.071 Hz per C; fp R = 0.38, slope 0.09 Hz per C).", "source": "Results, Effects of MS cooling on single neuron properties; Figure 4A", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 52474 windows from 563 fields, fLFP R = 0.678 and slope 0.0716 Hz per C, fp slope 0.0859, within tolerance; fp R = 0.338, just below 0.342. The windows overlap (stepped by one trial), so the P values over windows overstate the evidence; the paper's code does the same.", "deviations": [ "Windows of 20 trials stepped by one trial, as calc_trial_averages.m; the paper's figure does not say which windows it plots." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-field-size-correlated", "statement": "Place field size was highly correlated before and during MS cooling (R = 0.91).", "source": "Results, Effect of MS cooling on place field features; Figure 3C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "R = 0.8197 over 635 fields, at the edge of the tolerance (0.819). With at least 20 or 50 spikes per state R is 0.8348 and 0.8308, with at least 100 it is 0.8136, outside. Sizes do not differ (62.7 and 64.9 cm, P = 0.084).", "deviations": [ "Field size from rate maps of each state (bins above 10% of the peak); the paper does not define it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-size-fp-negative", "statement": "Place field size and fp were negatively correlated before, during and after cooling (R = -0.49, -0.40, -0.40; P < 1e-9).", "source": "Figure 3D", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "All negative with P below 3e-09, weaker than -0.49 and -0.40.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-model-field-size", "statement": "Measured place field size correlated with the size predicted by SPF = v / (fp - fLFP) before (R = 0.55) and during (R = 0.54) cooling, and weakly after (R = 0.11).", "source": "Results, Effect of MS cooling on place field features; Figure 3E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Pre and cooling positive (P = 4.7e-06 and 4.9e-11) and weaker than 0.55 and 0.54; post 0.325 against 0.11. Predicted sizes (median 47 to 48 cm) are smaller than measured (65 cm).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-information-unchanged", "statement": "The information content of place cell spikes was not altered by MS cooling (P > 0.26).", "source": "Figure 3F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 374 place cells information is lower during cooling than before (median change -0.029 against a median of 1.253 bits/spike, P = 0.014) and lower after than before (P = 0.0064); cooling and post do not differ (P = 0.31). The changes are small. Bits per spike rise when fewer spikes are used, and the pre state has the fewest trials, but with each state's spikes subsampled to the same count (360 cells) pre against cooling gives P = 0.0073 and pre against post P = 0.0092, so the decrease does not come from the spike counts.", "deviations": [ "The paper names its comparisons but not its test; its default paired test was used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3hi-population-vector-unchanged", "statement": "The spatial scale of the population vector correlation of pyramidal cells was not affected by MS cooling.", "source": "Results, Effect of MS cooling on place field features; Figure 3H and 3I", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Median change 0.25 cm, P = 0.966 over 11 sessions (paper 21); scales 18.3 to 36.9 cm.", "deviations": [ "The decorrelation scale is computed within maze segments at 5 cm bins; 11 sessions." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-precession-slope-decrease", "statement": "The phase precession slope decreased slightly but significantly during MS cooling (P < 0.007 and P < 0.0003).", "source": "Results, Effects of MS cooling on single neuron properties; Figure 4D", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Under reading (a), the slope magnitude during cooling does not differ from pre (median change 0, P = 0.83) and is smaller than post (P = 0.022); under (b) neither comparison differs (P = 0.32 and 0.15). 87.5% of fields have a negative slope before cooling.", "deviations": [ "The direction of 'decreased' is not stated; two readings were tested.", "Slopes by a grid search of circular-linear regression up to two cycles per field." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4gh-fp-speed", "statement": "fp depended on running speed more strongly than fLFP, and fp during cooling was lower at all velocities.", "source": "Results, Effects of MS cooling on single neuron properties; Figure 4G and 4H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "fp slope 0.0136 Hz per cm/s (P = 3.2e-12), fLFP 0.0061; difference 0.0074 (bootstrap interval 0.0040 to 0.0112). In the three speed bins from 60 to 120 cm/s with at least 10 fields fp is lower during cooling (P below 1e-5 each); below 60 cm/s too few fields had 50 spikes.", "deviations": [ "Speed bins of 20 cm/s; the paper's bins are not stated." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5d-ccg-period", "statement": "The theta-repeated cross-correlograms of place cell pairs had a period of about 85 ms before cooling, which lengthened during MS cooling (P = 0.002), while the period of the phase cross-correlograms was unaffected (P = 0.32).", "source": "Figure 5D, 5E and 5F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Over 9 sessions the period lengthens from 109.2 to 114.0 ms (8 of 9, P = 0.0195) and the phase period does not change (1.740 and 1.760 pi rad, P = 0.59); the control period is not 85 +- 8.5 ms. The criterion's estimator takes the largest neighbouring peak 60 to 200 ms from the main peak, and in 47.7% of pre pairs that peak is more than 1.25 times as far as the nearest one, so it often picks the second neighbour and the 109.2 ms is biased upward. With the nearest neighbouring peak (a variant) the control period is 91.0 ms, within tolerance, and it lengthens to 95.5 ms (7 of 9, P = 0.031); pairs with |Ltr| below 10 cm give 91.0 ms. Under that variant the phase period, also from the nearest peak, does not change (1.285 pi rad in both, P = 0.367), so all three parts of the criterion hold; but that estimator is biased downward, as 211 of 3499 pre pairs give 60 to 70 ms, at the floor of the search window and below any plausible theta period, so its 91.0 ms is not a clean test of 85 ms either. The outcome follows the criterion's estimator. Both control periods are shorter than the LFP theta period (115.7 ms).", "deviations": [ "The period is measured per pair and summarised per session; the paper reads it from the sum over pairs. The criterion was changed to this before the analysis across sessions, after a pilot session showed that the summed correlogram's spectrum follows its envelope; the summed correlogram is shown as a variant (99 to 200 ms).", "9 sessions in 4 rats, against 18 in 5.", "The criterion's period estimator often takes the second neighbouring peak; the nearest-peak estimator is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5cg-compression", "statement": "Distance-time compression of place cell pairs (0.54 cm/ms before cooling) decreased during MS cooling (P = 0.02), while distance-phase compression was unchanged (P = 0.92).", "source": "Figure 5C and 5G; Results", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Pooled pre compression 0.273 cm/ms against 0.54. Per session it is lower during cooling in 8 of 9 sessions without significance (0.298 against 0.191, P = 0.0547); phase compression does not change (P = 0.426). Lag and distance correlate weakly (R = 0.195), so the slope depends on the fit (inverse regression over pooled pre pairs 7.175 cm/ms). The 70 ms window can hold more than one candidate peak; in 10.5% of pre pairs the lag changes when the window is narrowed to half the theta period, which gives 0.156 cm/ms. The compression magnitude cannot be judged from this method. The direction of the change agrees with the paper under the criterion's fit; the inverse slope goes the other way (control 9.085, cooling 10.420 cm/ms, lower in 1 of 9).", "deviations": [ "Lags from each pair's correlogram peak and compression from a regression, where the paper fits a surface to the density of all pairs; pairs without a peak within 70 ms are dropped." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5h-time-lags-increase", "statement": "During MS cooling the theta time lags between place cell pairs increased compared with before and after cooling (P = 8e-5 and P = 0.00032), and did not differ between before and after (P = 0.79).", "source": "Results; Figure 5H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Under reading (a), cooling against pre over 3136 pairs (30.5 against 28.5 ms, P = 1.14e-06) and against post (P = 1.3e-10); pre and post do not differ (P = 0.0967). Reading (b) agrees (P = 0.023, 0.016 and 0.81), and so does the half-period window (P = 3.8e-22 and 2.0e-29).", "deviations": [ "The legend's n = 10 sessions cannot give P = 8e-5 with a signed-rank test over sessions, so the test over pairs was taken as the main reading." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5i-phase-lags-unchanged", "statement": "Theta phase lags between place cell pairs were not affected by MS cooling (P > 0.24 between all conditions).", "source": "Results; Figure 5I", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Phase lags are slightly larger during cooling than before (1.367 against 1.304 rad, mean difference 0.051 rad, P = 0.0015) and after (P = 0.0043); pre and post do not differ (P = 0.51). Per session medians, cooling against pre P = 0.062. The +-pi window spans about 1.15 periods of the phase correlogram (1.74 pi). With the lag picked within +-pi/2 (a variant), 43.3% of pre pairs get another lag or none, and cooling is still above pre (mean difference 0.025 rad, P = 0.0196) but not above post (P = 0.162); pre and post do not differ (P = 0.178). Part of the increase may come from how the lag is picked.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5j-fraction-active-unchanged", "statement": "The fraction of place cells active in a theta cycle was not significantly affected by MS cooling (P = 0.2).", "source": "Results; Figure 5J", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "The fraction active is higher during cooling (0.2405 against 0.226, rank-sum P = 1.5e-22 over 9037 and 10152 cycles). Per session the cooling mean is lower than pre in 5 of 9 sessions (P = 0.734); cooling against post gives P = 0.074 and pre against post P = 0.004. Session means range from 0.159 to 0.315 and sessions contribute different numbers of cycles in each state, so the pooled test reflects the make-up of the pool as much as an effect. Cycles are longer during cooling (131.1 ms against 117.8 and 117.2 ms).", "deviations": [ "The paper does not name its test; the default rank-sum test over cycles was fixed before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5k-spikes-per-cycle-unchanged", "statement": "The number of spikes emitted by all neurons per theta cycle was preserved during MS cooling (P > 0.058 between all conditions).", "source": "Results; Figure 5K", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_petersen_2020.ipynb", "notes": "Pre and cooling do not differ (45.68 and 44.98 spikes, P = 0.0758), but post (51.68) differs from both (P below 1e-50). Per session, cooling differs from neither pre (P = 0.57) nor post (P = 0.129), and post differs from pre (P = 0.02). Session means range from 17.66 to 91.37 spikes, so the pooled tests depend on how many cycles each session contributes.", "deviations": [ "Spikes of all good and good2 units; the paper's 'all neurons' may include other units." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppl1-hippocampal-temperature", "statement": "Hippocampal temperature fell by less than 1.5 C at the time of the largest MS temperature decrease, and later than the MS cooling.", "source": "Results, first section (Supplementary Figure 1H to 1K)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The control experiment that measured temperature in the MS and both hippocampi is not in the dandiset, whose files hold only the MS temperature of the 50 behavioural sessions. The data check lists every series in all 100 files, and the only temperature series is processing/behavior/Temperature. The paper's data statement points to the lab website and CRCNS; no other DANDI deposit of these recordings was found.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The temperature series of the nine MS10 sessions and of the two control sessions of 2018-07-19 (MS21 and MS22) is not a recording. The paper's code lists no temperature channel for these sessions. In the files ten of them run from 17.0 to 37.0 C (exactly in nine; MS10-170313 reaches 16.98 C) and sit at exactly 37.0 C for 16% to 35% of samples, and MS10-170307 is a constant 37.0 C, while no recorded trace repeats its maximum. Nothing in the files says the series is modelled." }, { "kind": "metadata_error", "statement": "The two sessions of 2018-07-19, which the paper's code lists as controls without cooling (cooling_session 0, no onsets), have trials labelled Pre-Cooling, Cooling on, Cooling off and Post-Cooling and a temperature dip; their theta frequency during 'Cooling on' differs from pre by -0.20 and +0.44 Hz, against a median of -0.82 Hz in the cooled sessions." }, { "kind": "data_missing", "statement": "Six of the paper's 53 behavioural sessions are not in the dandiset (MS12-170712, MS12-170715, MS13-171204, MS13-171205, MS13-171206, MS21-180806); four of them were in version 0.210812.1514 as files without behaviour." }, { "kind": "data_missing", "statement": "MS21-180627 has trials without the cooling state and MS21-180712 has no trials, so two more of the paper's sessions cannot be used for the cooling comparisons." }, { "kind": "metadata_insufficient", "statement": "The files hold no cell types, no place field definitions and no electrode locations (every location is 'unknown'), so the putative pyramidal cells and interneurons and the place fields of the paper have to be made again." }, { "kind": "metadata_insufficient", "statement": "The trial state 'Cooling off' (a median 14 trials per session between cooling and recovery) is not described in the files or the paper." }, { "kind": "other", "statement": "In seven sessions (the six MS10 sessions with units and MS12-170723) every unit has quality 'unsorted', so no curated unit can be selected; MS10 has no usable units." }, { "kind": "other", "statement": "In MS21-180621 and MS22-180621 the units carry no spatial information (0.23 and 0.12 bits/spike, the same as with spikes shifted by 60 s), although they are locked to theta, so the clock of spikes and position could not be established there." }, { "kind": "selection_undocumented", "statement": "The dandiset holds three sessions that are not in the paper's behavioural analysis (the two 2018-07-19 controls and MS10-170307, whose temperature is constant) without saying so; they carry the same cooling labels as the analysed sessions." }, { "kind": "other", "statement": "The first published version (0.210812.1514) has no trials table in its files, so the cooling states and choice errors are only in the later versions." }, { "kind": "other", "statement": "The Methods give position tracking at 120 Hz; the MS10 sessions are sampled at 40 Hz (six), 30 Hz (one) and 120 Hz (two)." }, { "kind": "paper_inconsistency", "statement": "The legend of Figure 5H gives P = 8.0e-5 by a sign rank test with N = 10 sessions; an exact signed-rank test over 10 sessions cannot give a P below 0.002, so the test must be over pairs or the N refers to something else." }, { "kind": "paper_inconsistency", "statement": "The Discussion gives a 12% decrease of LFP theta frequency during cooling, while the Results give within-field LFP theta of 8.4 Hz before and 7.7 Hz during cooling, a decrease of about 8%, which this attempt reproduces (9% over trials)." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file, with the PMC author manuscript of the paper. The verifier checked the blocked claim against the archive's file list and metadata and tested the helper functions on synthetic inputs. Report in transcripts/000059/verifier-1-report.md.", "agreed": 37, "of": 38, "disagreements": [ { "claim": "fig5-speed-control-cooling", "outcome": "not_reproduced", "reason": "In cell 58 reading (a) gives 78.9 and 74.9 cm/s, both outside. Reading (b) gives control 79.6 (inside) and cooling 76.0 (just below 76.3)." } ] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the revised run, with the conclusions and the summary, the helper module, the claims file and this record. The verifier did not re-read the paper text this round. Report in transcripts/000059/verifier-2-report.md. It also found that the Summary and the first finding say the MS10 and control temperatures run from exactly 17 to 37 C, which is exact in nine of the ten (MS10-170313 reaches 16.9777 C, cell 11); both now say so. Everything under C of its round-1 report is resolved.", "agreed": 38, "of": 38, "disagreements": [] } ] }, { "id": "000061-girardeau-2017-01", "dandiset": "000061", "dandiset_version": "0.250624.0426", "paper": "10.1038/nn.4637", "paper_title": "Reactivations of emotional memory in the hippocampus\u2013amygdala system during sleep", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000061-girardeau-2017", "entry_title": "Hippocampus and amygdala reactivation during sleep (Girardeau et al. 2017)", "description": "Tests the findings stated in the abstract of Girardeau, Inema and Buzsaki (2017) on dandiset 000061, which holds sorted units of the hippocampus and the amygdala, sleep states, ripple, air-puff and reward events from four rats on an air-puff linear track task. It tests the reactivation of joint hippocampus and BLA patterns in sleep after the run, its peak at ripples, the BLA cells modulated by ripples and their weight in the patterns, and the difference between the air-puff and the safe run direction. The paper's full text was not available, so the methods are common choices fixed before the analysis.", "notebooks": [ { "path": "reproduce_girardeau_2017.ipynb", "title": "Reproducing Girardeau et al. (2017) from dandiset 000061", "executed": "notebooks/000061-girardeau-2017/reproduce_girardeau_2017.html" } ], "outcomes": [ { "claim": "hpc-bla-reactivation-post-sleep", "statement": "Coordinated hippocampus and BLA activity patterns of the training run are reactivated during non-REM sleep after training, more than during non-REM sleep before it.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_girardeau_2017.ipynb", "notes": "15 sessions (9 Rat08, 3 Rat10, 3 Rat11) with 341 hippocampal and 483 BLA units; every session has at least one significant joint pattern, 36 in all. Post-sleep minus pre-sleep Non-REM strength has a median of 0.0119, positive in 28 of 36, Wilcoxon p = 3.6e-05. The median is above zero in each rat (Rat08 0.0170, 18 of 21, p = 0.00013; Rat10 0.0024, 5 of 8, p = 0.74; Rat11 0.0190, 5 of 7, p = 0.11). Non-significant patterns change by a median of 0.0001. The variants (25 and 100 ms bins, the wider BLA labels over 21 sessions, the first pattern of each session) all give positive medians with p of 0.0084 or less. The comparison does not separate reactivation from slow drift of the recording, since post-sleep is next to the run in time.", "deviations": [ "The paper's methods were not available; the joint-pattern method (singular vectors of the run's hippocampus by BLA cross-correlation matrix, shuffle threshold, product of projections), the 50 ms bins and the unit criteria are common choices fixed in the claims file.", "BLA is taken as the units labelled bla or BLA; other undescribed labels that may be parts of the basolateral complex are a variant only.", "Sessions without sleep states or ripples, and Rat09 (no hippocampal units), are left out; which sessions and rats the paper used is not known here.", "Units 0 and 1 of ten files are left out because their spike times are mixed (see findings)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "reactivation-peaks-at-ripples", "statement": "The hippocampus and BLA reactivations peak during hippocampal sharp wave-ripples.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_girardeau_2017.ipynb", "notes": "Reading (a) holds. The mean ripple-triggered strength in post-sleep Non-REM is highest in the bin of the ripple peak, 4.36 times its mean at 0.5 to 1 s; the peak bin exceeds the flanks in 30 of 36 patterns (median 0.103, p = 6e-06), with a positive median in each rat. 22 of 36 patterns have their own maximum within 100 ms of the ripple. The pre-sleep curve also peaks at ripples (0.136 against 0.223 post), and the peak over flanks is larger post than pre (23 of 36, p = 0.022). Reading (b) also holds; the post minus pre change in ripple bins exceeds that outside ripples (median difference 0.0537, 25 of 36, p = 0.0033). Much of the reading (a) peak is already present in pre-sleep, so reading (a) alone does not separate reactivation of the run from co-activation at ripples in general; the post minus pre contrasts do. At session level (15 sessions) the peak over flanks is positive in 13 (p = 0.00031), its post minus pre increase in 10 (p = 0.03), and the reading (b) difference in 10 (p = 0.03).", "deviations": [ "The abstract's \"peaked during SPW-Rs\" can be read in two ways; both readings were fixed in the criterion and both match.", "Ripples are the dandiset's `rip` annotations, not a detection run here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "bla-ripple-up-subgroup", "statement": "A subgroup of BLA cells is positively modulated during hippocampal sharp wave-ripples.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_girardeau_2017.ipynb", "notes": "103 of 822 BLA units in 17 sessions (12.5%) are positively modulated in Non-REM ripple windows, against a chance level of 0.7% (6 units) from the same procedure on windows shifted by 7 s; binomial p = 9.8e-90. Above chance in each rat (Rat08 51 of 496, Rat10 4 of 84, Rat11 48 of 242), also against each rat's own chance level (Rat10 has 0 chance units; p = 0.018 against one unit). 104 units (12.7%) are negatively modulated. At p of 0.05 or less the fraction is 16.3% against 5.6% chance, at 0.002 or less 10.8% against 0.2%. The shifted windows stay mostly in Non-REM (a median of 0.9% of randomly shifted and 1.4% of 7 s shifted ripple peaks fall outside it).", "deviations": [ "The test of modulation (spike count in ripple windows against windows shifted together by 0.5 to 5 s, one-sided p of 0.01 or less) is a common choice; the paper's test is not known here.", "Units are counted once per session; a cell recorded on several days may be counted more than once, as the dandiset does not match units across days." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "reactivation-involves-ripple-up-cells", "statement": "The hippocampus and BLA reactivations involve the subgroup of BLA cells that are positively modulated during sharp wave-ripples.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_girardeau_2017.ipynb", "notes": "In 31 significant patterns with both kinds of BLA unit, the mean squared BLA weight of the ripple-up units exceeds that of the other BLA units (medians 0.0505 and 0.0181; difference positive in 24 of 31, Wilcoxon p = 0.0013). The ripple-up units are a median 20% of a pattern's BLA units and carry 34% of its BLA weight. It holds in Rat08 (17 of 21) and Rat11 (6 of 7) and not in Rat10 (1 of 3). In patterns whose post minus pre reactivation is positive, p = 0.0018. Firing rate accounts for part of the effect; up units fire faster in the run (median 1.66 against 0.41 Hz) and squared weight rises with rate within a pattern (median Spearman 0.46). Against other BLA units of the nearest rate, up units still carry more weight (24 of 31 patterns, p = 0.012). At session level (13 sessions) the difference holds (10 of 13, p = 0.027), the rate-matched difference does not (9 of 13, p = 0.22). The criterion is the pooled per-pattern test, which holds.", "deviations": [ "The abstract does not say how involvement was measured; the pattern weights were chosen here before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "aversive-direction-stronger", "statement": "Reactivation is stronger for the hippocampus and BLA correlation patterns of the run direction that held the air puff than for those of the safe direction.", "source": "Abstract", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_girardeau_2017.ipynb", "notes": "Over 15 sessions, post minus pre reactivation of the air-puff templates exceeds that of the safe templates by a median of 0.0133, in 9 of 15 sessions, Wilcoxon p = 0.11; the criterion needs p < 0.05, and p < 0.1 for a partial outcome. Positive in 6 of 9 Rat08, 2 of 3 Rat10 and 1 of 3 Rat11 sessions. Variants lean the same way with mixed strength; the first pattern of each direction gives p = 0.048 (10 of 15), the pooled per-pattern Mann-Whitney test p = 0.083, equal numbers of template bins (a random subset) p = 0.33, post-sleep strength alone p = 0.45, leaving out the two sessions with fewer than 5 puffs p = 0.15, and templates from the travel part of each lap only (its last part, as long as the session's 10th-percentile lap) p = 0.19. Laps from reward times include the time spent at the end where a lap starts; a median of 33% of the air-puff and 43% of the safe template time is in the travel part, and in the early Rat08 sessions laps last up to 2310 s, so the safe templates of some sessions rest on few bins (5610 against 66804 in Rat08-20130709).", "deviations": [ "Laps, and so run direction, come from the reward times, as the dandiset holds no position; the paper presumably used the position on the track.", "The air-puff direction is the lap direction of the run holding most puffs; in the 15 sessions tested, 295 of their 304 puffs fall in laps of that direction (927 of 957 over the 31 files with units and at least 5 puffs). No minimum number of puffs was set; two sessions with 2 and 3 puffs enter the test.", "Laps include the time spent at the starting end, not only running; templates from the travel part of laps are a variant.", "The measure (mean over significant patterns of post minus pre strength, compared across sessions) was chosen here before the analysis; the paper's is not known here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "rats-learn-puff-location", "statement": "Rats learned the location of an aversive air puff on a linear track.", "source": "Abstract", "outcome": "blocked", "blocked_by": "too_large", "notebook": null, "notes": "Learning the location of the puff is behaviour along the track, which needs the rat's position. The dandiset holds no position tracking. The files hold the raw video frames (360 by 640 pixels, gzip), so position could in principle be tracked, but the 40 run videos have 1920573 frames (1328 GB uncompressed) and streaming 20 frames took 7.2 s in the final run, about 190 hours for the run frames alone (the rate varies between runs); the video timestamps are also not on the session clock. No public copy of the tracking linked to the paper or the dandiset was found. As a description only, laps toward the air-puff end take longer than the other way in the run (median ratio 1.18 over 38 sessions, p = 0.0063) and about as long in the pre-run (0.95) and the post-run (1.00); lap times give no location on the track, and slower laps where puffs are given do not separate learning from the puffs themselves. No criterion was written, so this decides nothing.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The epochs table is stored in milliseconds although its columns say seconds; in all 40 files its last stop time is exactly 1000 times the LFP duration and the last spike time." }, { "kind": "metadata_error", "statement": "Video timestamps are stated in seconds but are in milliseconds and are not on the session clock. The first timestamp matches the start of the video's epoch in 1 of 114 videos, while the spans match the epoch durations in 93 of 114." }, { "kind": "format_error", "statement": "In ten files the spike_times_index is wrong at the first units. Unit 1's spike times fall back once, after 65536 times k spikes, and unit 0 stops part way through the session at the time unit 1 starts, so the first part of unit 1 is the end of unit 0. Units 0 and 1 of these files were left out." }, { "kind": "data_missing", "statement": "Seven files have no units table (Rat08-20130722, five Rat09 files and Rat11-20150403), sixteen have no sleep states and fourteen have no ripple events. The Rat09 files have no hippocampal units and no ripples, so Rat09 cannot enter a hippocampus and BLA analysis." }, { "kind": "data_missing", "statement": "There is no position tracking, only the raw video frames, so behaviour on the track, including the learning of the puff location, cannot be measured without tracking about 1.9 million frames; run direction can only be inferred from reward times." }, { "kind": "metadata_insufficient", "statement": "Unit region labels are undescribed short codes (bla, blv, bmp, ladl, cen, den, ven, pir, plc01, PLCo1, cpu, hpc, HIP, no label), some in two cases for the same region, and Rat09-20140328 has no location column; the electrode table gives every channel as unknown. Which labels make up the paper's BLA cannot be told from the dandiset." }, { "kind": "metadata_insufficient", "statement": "The `trials` table of the Rat08 and Rat09 files is described only as \"experimental trials\"; its intervals of 3 to 5 s fall partly outside the run and are not laps." }, { "kind": "metadata_insufficient", "statement": "The ripple annotations carry a number in each label (for example \"Ripple peak 156\"), presumably the detection channel, with no description; ripples, puffs and rewards are stored as annotation series under stimulus presentation." }, { "kind": "methods_unavailable", "statement": "The paper is not open access and neither it (as far as the abstract shows) nor the dandiset links analysis code, so the reactivation method, unit selection and statistics had to be chosen here." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's abstract (the full text is not open access). The verifier tested helper functions on synthetic inputs and read the archive's asset metadata for the blocked claim. Its report had no attempt record and gave its own outcome for each claim; all six agree with the record on the outcome, and it gave a different reason for the block.", "agreed": 6, "of": 6, "disagreements": [] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file, the attempt record and the README. The verifier agreed with all six outcomes and recomputed the three session-level Wilcoxon tests of cell 35. It found five passages the printed outputs did not support. The video streaming time in the record did not match cell 11; this is corrected from the final run (7.2 s, about 192 hours). The pre-run and post-run were said to have no puffs without a count; cell 51 now prints the puffs by epoch (1195 of 1197 in the run, 2 in the pre-sleep, none in the pre-run or post-run). The 927 of 957 puffs covered only the 31 files of cell 19; cell 20 and the deviation now say so, and cell 48 prints the count for the 15 tested sessions (295 of 304). Cell 40 gave the negatively modulated units as the reason the up units are a subgroup; it now rests that on the fraction being below 1. The README run time was not printed; the notebook now prints its run time (13.9 min in the final run) and the README gives it. All round-1 points were resolved. No outcome changed, and none is proposed to change.", "agreed": 6, "of": 6, "disagreements": [] } ] }, { "id": "000067-fujisawa-2008-01", "dandiset": "000067", "dandiset_version": "0.250624.0419", "paper": "10.1038/nn.2134", "paper_title": "Behavior-dependent short-term assembly dynamics in the medial prefrontal cortex", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "runs", "entry": "000067-fujisawa-2008", "entry_title": "Prefrontal assemblies and monosynaptic dynamics in a working memory task (Fujisawa et al. 2008)", "description": "Tests the findings of Fujisawa, Amarasingham, Harrison and Buzsaki (2008) on dandiset 000067, which holds recordings of three rats from a 64-site prefrontal probe and a CA1 probe during an odor-place matching task. Units are placed on the probes from their waveforms in the wideband signal. It tests the population activity, field sizes and trajectory selectivity of prefrontal neurons, monosynaptic connections found with a jitter test, the cell classes and distances they imply, and the task dependence, short-term plasticity and summation of the connections. The paper's example session and fourth rat are not in the dandiset.", "notebooks": [ { "path": "reproduce_fujisawa_2008.ipynb", "title": "Reproducing Fujisawa et al. (2008) from dandiset 000067", "executed": "notebooks/000067-fujisawa-2008/reproduce_fujisawa_2008.html" } ], "outcomes": [ { "claim": "channel-region-link", "statement": "The dandiset's recording channels can be assigned to the prefrontal probe, the CA1 probe and the nose-poke sensors by the channel map of the CRCNS pfc-2 description of the same recordings (channels 1 to 64 prefrontal, 65 to 96 CA1, 97 right and 98 left nose-poke sensors), and the data agree with that map.", "source": "Methods (8-shank, 64-site probe in mPFC); CRCNS pfc-2 data description, version 0.7", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Records are matched by channel number. In rats EE and FF the CRCNS map holds in every session; the CA1 channels have a theta ratio 1.9 to 2.7 times that of channels 1 to 64, and the more active sensor during the nose poke is the trial's side in 0.97 to 1.00 of trials. In rat GG channels 97 and 98 are not sensors (agreement 0.35 to 0.42); the sensors are on 65 and 66 and the CA1 probe on 70 to 101, and with that correction both checks hold in every session (agreement 1.00). The sensor on 66 is active on trials labelled Right, so in GG the order of the sensors, or the side labels, is reversed relative to EE and FF. Channels 1 to 64 have a lower theta ratio than the CA1 channels in every session (0.16 to 0.27 against 0.37 to 0.54), so the prefrontal probe is placed as the description says in all three rats; every claim that uses PFC units depends on that part, which holds.", "deviations": [ "The map is used with the per-rat correction found in the data, not as published.", "The sensor check of EE.088 uses its LFP only; it has no wideband signal for the theta check." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "rats-and-units", "statement": "633 well-isolated units were recorded from the mPFC of four rats.", "source": "Results, first paragraph", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "The dandiset holds three rats (EE, FF, GG), against four. The eight analysed sessions hold 417 PFC single units under reading (a), 346 under (b) and 491 under (c), all outside 633 plus or minus 63. The 350 units of EE.088 cannot be placed on a probe, and EE.152, EE.165 and EE.188, working memory sessions in the CRCNS table, are not in the dandiset; the paper does not say which sessions its 633 units come from, nor whether units recorded on several days were counted once. Variants; leaving out also the first unit of each shank block gives 416. Placing EE.088's units by the conversion's block order (a block starts at each multi-unit cluster; blocks 1 to 8 taken as prefrontal), a rule that matches the waveform placement in EE.049 and EE.196 (agreement 1.000) but not in FF and GG (0.360 to 0.956), adds 214 PFC single units and gives 631, within tolerance; the count of rats still fails.", "deviations": [ "Units are counted per session; the paper's way of counting is not stated.", "Well-isolated units are selected by a refractory rule chosen here." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "task-performance", "statement": "Rats performed the odor-place matching task at 92% correct (91.9% in the recording sessions).", "source": "Results, second section; Methods, Behavioral task", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The trial table lists correct trials only (the CRCNS description of SessionNP, from which the conversion built the table), so the fraction of correct trials cannot be computed. The position has no y coordinate, so the choice on other trials cannot be recovered from the path. Error trials are not in the dandiset, and the CRCNS data need an account. Every listed run holds one lap found from x1, and the nine sessions hold 100 laps and 147 nose-poke bouts outside the 335 listed trials; if every lap outside a listed run were an error trial, performance would be 77.0%, and if every unlisted nose-poke bout were one, 69.5%. The files do not say which were errors, nor whether every error trial produced a lap or a bout, so these are not bounds in one direction and not a test.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-active-fraction", "statement": "About 10% (layer 2/3) and 20% (layer 5) of the recorded neurons fire at least one spike in any 100 ms window, a fraction that is relatively constant along the maze.", "source": "Results, first section; Figure 2c; Discussion", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Per-rat medians of the session means are 10.2% (EE), 19.7% (FF) and 6.2% (GG); EE fits the layer 2/3 value and FF the layer 5 value, GG fits neither. The ratio of the largest to the smallest position-bin mean is 1.16 to 1.88 in seven sessions and 2.57 in GG.149. Neither part of the criterion holds for every rat; both hold for EE and FF. GG's sessions have 18 or 19 PFC single units each.", "deviations": [ "The layer of each rat is not known; values are matched rat by rat under the layer readings.", "The threshold for \"relatively constant\" (a factor of 2) is chosen here." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2-field-size", "statement": "Neurons are active over similar standardized distances of the maze, 0.27 (62 cm) plus or minus 0.17 (39 cm) (mean and s.d.), from the 50% boundaries of the peak firing rate.", "source": "Results, first section; Figure 2a", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Reading (a), 346 units, mean 0.270 and s.d. 0.196; (b) 0.281 and 0.206; (c) 0.331 and 0.220. The mean is within tolerance under every reading and the s.d. under none (0.17 plus or minus 0.017). No side without spikes entered reading (b); with only sides whose own peak is at least 1 Hz it gives 0.292 and 0.214. With peak thresholds from 0 to 5 Hz the mean of (a) is 0.254 to 0.330 and the s.d. 0.189 to 0.243. Per rat the means are 0.221 (EE), 0.322 (FF) and 0.272 (GG).", "deviations": [ "The mean's tolerance is the paper's stated s.d. of the neurons, as the protocol asks, which accepts a wide range of means; the s.d. carries the test.", "The 1 Hz peak rule is the CRCNS \"Cells\" rule, not the paper's.", "The paper does not say how the 50% boundaries are taken or which trajectory is used; three readings are shown." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2b-trajectory-selective", "statement": "The fraction of neurons with significantly different firing on left and right trials is 16% (layer 2/3) and 18% (layer 5) in the central arm (positions 0 to 0.3), where the trajectories overlap, and 22% (layer 2/3) and 40% (layer 5) in the side arms (0.5 to 1).", "source": "Results, first section; Figure 2b; Methods, permutation tests and global bands", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Central arm, 22.9% (EE), 24.5% (FF) and 26.2% (GG) of units with a peak of at least 1 Hz (24.0% of 346 pooled), against 0.9% with relabelled trials (Fisher p = 7.3e-24; a McNemar test on the same units, 82 against 2 discordant units, p = 1.9e-22); every rat is above the 14.4 to 19.8% range. Side arms, 51.6%, 59.9% and 52.4%, above both layer values. Per session the central-arm fraction is 1.9% to 69.2%. With the s.d. band, 24.3% and 59.8% pooled. The procedure's chance rate (0.9% for each segment) is below the global 5%, as expected for a segment of the track. The selective fractions are higher than the paper's in every rat, so units selective by this test are more common here.", "deviations": [ "The number of permutations (1000) and the 101-point grid are chosen here.", "Layers are matched rat by rat, as the layer of each rat is not known.", "In rat GG the side labels may be swapped (see channel-region-link); this does not change a left-right test." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "traj-diverge", "statement": "Left and right trajectories overlap in the central arm and begin to differ significantly at position 0.3.", "source": "Results, first section; Supplementary Figure 3", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "The claim is about where left and right trajectories separate laterally, which would show along the y coordinate; the second LED series is zero throughout (cell 33), so the dandiset has no y coordinate. x1, the x coordinate of the first head LED, runs along the maze (about 570 px at the start, 190 px near position 0.5, back up towards the reward) on both sides. Under the criterion written in the first revision it differs between sides somewhere in 0.5 to 1 in all 9 sessions, by at most 7 to 57 px, with a median divergence point of 0.49 (8 of 9 sessions have one), which the written criterion would rate as partially reproduced. The divergence point lies within 0.08 of the position where x1 reaches its minimum (0.47 to 0.53) in the seven sessions other than GG.149 (median -0.01 over eight, cell 35), and at position 0.3 the sides differ by a median 2.8 px while x1 falls by a median 244 px from 0 to 0.3. x1 thus begins to differ where the path turns back in x and does not locate a lateral separation, and the criterion's partial rating would follow from any x1 divergence past the turn. Changed to blocked in round 3, with the verifier's agreement. The overlap of the paths in the central arm cannot be judged either; the 5 to 17 px x1 differences there in five sessions do not stand in for a two-dimensional comparison.", "deviations": [ "Only the x coordinate is available; the paper used the two-dimensional position.", "The test (Welch t-test per bin of 0.02, p < 0.01, divergence from the first bin of a run up to 0.6) is chosen here; the paper's is in a supplementary figure that was not available.", "The criterion was written in the first revision, after the verifier's report." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "odor-nosepoke", "statement": "About one quarter of the neurons fire at significantly different rates (P < 0.05 per cell) during nose poking for the two odors.", "source": "Results, first section; Supplementary Figure 6", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "37.8% of 397 units (Mann-Whitney P < 0.05) against 4.0% with relabelled trials (Fisher p = 5.5e-35; McNemar on the same units, 142 against 8, p = 3.9e-33); outside 20 to 30%. A t-test gives 28.5%, which would be within, but the test was fixed beforehand. Per rat 34.9% (EE), 50.3% (FF), 11.1% (GG). Odor and side are the same variable here, as only correct trials are listed, so the difference can come from the odor or from the coming choice; the paper's Supplementary Figure 6 analysis of that point was not available.", "deviations": [ "The paper names no test; a Mann-Whitney test of per-trial rates was chosen.", "The nose-poke period is from the start of the first nose poke to the end of the last (median 4.66 s), as the trial table gives; the paper's window is not stated in the main text." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3-connection-rates", "statement": "Of all ordered pairs of simultaneously recorded neurons, 0.79% had short-latency, narrow peaks or troughs in their cross-correlograms (0.55% excitatory, 0.24% inhibitory), found with a jitter test.", "source": "Results, second section; Figure 3a and 3e; Methods, identifying monosynaptic interactions", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "31754 ordered pairs; connections 1.131%, excitatory 0.898%, inhibitory 0.233%. Only the inhibitory rate is within tolerance. Excitatory connections are 4.01% of same-shank pairs and 0.35% of pairs across shanks; per rat the excitatory rate is 0.84% (EE), 1.05% (FF), 0.94% (GG). The Poisson screen passed 857 unordered pairs to the Monte Carlo test, and none of the 800 unscreened pairs tested anyway was significant. 40 unordered pairs (0.252%) are connected both ways (paper 0.17%). Counting peaks of any width gives 0.938% excitatory. The excess of same-shank peaks may include pairs of clusters split from one neuron, which the paper's curated units may not contain. The inhibitory match is fragile; 34 of the 74 inhibitory connections are troughs in the reverse direction of a pair with a peak, which jittering both trains can produce (on 30 synthetic excitatory pairs with no inhibition, the criterion's rule finds such a trough in 21, and none once they are excluded). Without them the rates are 1.023%, 0.898% and 0.126%, none within tolerance, and 10 pairs (0.063%) are reciprocal.", "deviations": [ "Bins of 1 ms (not stated in the main text) and a Poisson screen before the Monte Carlo test.", "A trough beside a peak in the same direction is not counted as inhibition (chosen here). Troughs that mirror a peak in the other direction are counted, as the criterion was written; the rates without them are shown as a variant.", "The set of well-isolated units is selected here, not by the paper." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3-cell-classes", "statement": "By their connections, 32.5% of units are putative pyramidal cells and 12.5% putative interneurons, a ratio of 2.82 plus or minus 0.51 (s.d.), and 50.7% of the postsynaptic targets of putative excitatory cells themselves inhibit other neurons.", "source": "Results, second section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Of 417 units, 37.9% putative pyramidal and 3.1% putative interneurons, and 21 units have outgoing connections of both kinds. The ratio is 11.92 plus or minus 7.46 over the five sessions with an interneuron (pooled 12.15, mean of rats 12.96), against 2.82 plus or minus 0.51. Of 124 targets of excitatory connections 7.3% are putative interneurons (20.2% have any inhibitory connection), against 50.7%. 54 of the 74 inhibitory connections come from units that also excite others. No value is within tolerance under any reading; the shortfall of interneurons drives the ratio and the targets. Without the troughs that mirror a peak (fig3-connection-rates), 38.6% pyramidal and 2.4% (10 units) interneurons, pooled ratio 16.10, and 4.8% of targets are interneurons, further from the paper.", "deviations": [ "Units with both kinds of connection are counted in neither class (chosen here)." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3f-distance", "statement": "Most connected pairs were recorded on the same shank, and the probability of a connection falls with the distance between the neurons, though connections were found up to 1200 micrometres apart.", "source": "Results, second section; Figure 3f", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Same shank 4.60% against 0.52% across shanks (Fisher p = 1.1e-89), 61.0% of connections on the same shank, and 8 connections at 1000 micrometres or more (largest 1400). The Spearman correlation over 0 to 1400 micrometres is -0.619, p = 0.102, so the second condition fails and the criterion gives not reproduced. The probability falls from 4.60% at 0 to 0.24% at 600 micrometres and is 0.17 to 0.19% from 800 to 1200; the 1400 bin (2 of 310 pairs, 0.645%) breaks the rank order. Over 0 to 1200 micrometres rho = -0.964, p = 0.00045, and over pairs connected pairs are closer than unconnected ones (Mann-Whitney p = 2.3e-87). The fall with distance is present; the outcome comes from the test fixed beforehand on eight points. The distance assumes that the channel groups are in shank order; a unit's second-largest shank is a neighbour of its largest for 47.7% of 407 units, against 25.0% for a random order, which is consistent with it.", "deviations": [ "Distance is the shank separation only; positions within a shank were not estimated." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig4-position-dependence", "statement": "Out of 343 excitatory monosynaptic pairs, 67 showed position dependence of their short-latency coincidences in the maze (P < 0.01), beyond what the firing rates explain.", "source": "Results, third section; Figure 4; Methods, identifying position dependence", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Changed from not_reproduced in the first revision. Reading (a) 10 of 285 excitatory pairs (3.5%); reading (b) 5 (1.8%); rank band 1.4% and 2.1%. The criterion's test compares coincidences with jittered trains, so it finds any excess of coincidences somewhere on the track, not a change of efficacy along it; on synthetic pairs with a constant efficacy driven by real presynaptic trains it flags 30.0% (efficacy 0.05) and 75.0% (efficacy 0.2), against the paper's P < 0.01. By the protocol's rule on stated false-positive rates the procedure is not the paper's, whose thinning step and null are defined in the supplement, which was not available. As a variant, a null of constant efficacy flags 0 of 285 real pairs, none of the constant-efficacy synthetic pairs and 6.7% of synthetic pairs driven only on 0.5 to 0.8 of the track (25.0% of those with at least 50 coincidences), so it has little power at these counts. The median pair has 7 coincidences during runs (range 0 to 442). The rank band cannot reach 0.01 in 183 of 285 pairs.", "deviations": [ "The band is mean plus c times s.d. of the surrogates, not the Methods' rank band, because the rank band cannot reach a one-sided 0.01 with 1000 surrogates on 101 points (it is empty when more than 1% of data sets reach the extreme rank somewhere). This was found after a first run of the rank version gave 1.0% and a synthetic test showed that it could not detect a strong position-limited coupling; the rank result is shown as a variant.", "Event positions are kept at the original presynaptic spike in the surrogates." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig6-facilitation-depression", "statement": "About equal fractions of connected pairs show firing pattern-dependent depression (12.7%) and facilitation (10.7%), comparing the transmission of the first spike of a train with that of later spikes.", "source": "Results, fourth section; Figure 6c", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "Of 284 excitatory pairs with enough spikes, 14 (4.9%) depressing and 44 (15.5%) facilitating. Facilitation is above chance (binomial p = 3.5e-11), depression is not (p = 0.56). Overall later spikes transmit more than first spikes (median 0.0099 against 0.0068, Wilcoxon p = 6.1e-08). With at least 50 or 200 spikes of each kind, 5.0 to 5.3% depressing and 15.4 to 15.9% facilitating. The paper's measure (rate-normalized peak height) was not available, and a measure that normalizes by the postsynaptic rate in each condition could give a different balance.", "deviations": [ "Transmission measured as excess spikes from 1 to 4 ms over the jitter expectation, chosen here in place of the paper's rate-normalized peak height.", "Later spikes are any spike within 40 ms of the previous one (the Figure 6 legend), not only spikes inside trains that began after 200 ms of silence." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig7-supralinear", "statement": "Coincident firing of two or more presynaptic neurons within 5 ms on a common target is more effective than the sum of their separate effects (supralinear), while spikes spread over windows longer than 10 ms add linearly.", "source": "Results, fourth section; Figure 7", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "41 satellites, 40 with at least 20 two-partner events; 15 (38%) supralinear; median excess 0.0145 for one partner and 0.0197 for two; Wilcoxon p = 0.993. Two coincident partners transmit more than one, but less than twice as much. With 20 ms events, 29% supralinear (p = 0.998). The criterion's measure is biased towards sublinear (on synthetic satellites with linear summation it gives -0.0278, s.d. 0.0030). A variant against a linear prediction from each partner's one-spike events, with the response window from the first spike to the last, is unbiased there (0.0016, s.d. 0.0046) and detects supralinear input (0.198); on the data 4 of 40 satellites (10%) are above the linear prediction (median 0.0015 against 0.0239, p = 1), and 12 of 40 (30%) with 20 ms events. That variant's local baseline is biased on the data, as the post rate in the flanks is higher around two-partner events than one-partner events (median 9.44 against 7.26 Hz, 28 of 40 satellites, Wilcoxon p = 0.00022). With the post unit's mean rate as baseline (unbiased on synthetic satellites, -0.0021, s.d. 0.0068), the two-partner response is 0.0135 against a prediction of 0.0337, above it in 9 of 40 (22%), below it by Wilcoxon p = 0.00058; that baseline leaves in more background for two-partner events (median 0.0125 against 0.0074), which favours a supralinear result. No measure finds supralinear summation, and with both baselines the two-partner response is below the one-partner response (0.0135 against 0.0180 with the global one), which these measures do not explain. The paper had 14 satellites converging on interneurons; here any target with two excitatory partners is used, and its definitions of satellite and transmission probability are in the supplementary information, which was not available.", "deviations": [ "Satellites, events and the excess measure are defined here." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3-trajectory-by-class", "statement": "Large fractions of putative pyramidal cells (72.2% in layer 2/3, 84.7% in layer 5) and of interneurons (58.3% and 83%) are trajectory specific.", "source": "Results, second section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fujisawa_2008.ipynb", "notes": "EE, 58.5% of 94 putative pyramidal cells and 60.0% of 5 interneurons are trajectory specific; FF, 66.7% of 57 and 62.5% of 8; GG, 14.3% of 7 and no interneuron. Chance is 0.0 to 2.5%. FF matches the layer 2/3 values within 10%, EE matches neither layer, and GG cannot meet the criterion without interneurons. Large fractions of both classes are trajectory specific in EE and FF, which is the qualitative part of the claim; the interneuron counts are small, as fig3-cell-classes found few interneurons. With the classes without mirrored troughs, EE has 4 interneurons (50.0% specific) and FF 6 (66.7%); GG still has none.", "deviations": [ "Layers are matched rat by rat; trajectory specificity is the test of fig2b-trajectory-selective over the whole track." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "ee188-example-session", "statement": "In the example layer 2/3 session, 117 neurons gave 1172 pairs with 48 excitatory and 30 inhibitory connections, 39 of the 117 cells formed one connected hub, 15 of 36 excitatory connections were active in particular maze segments, and the example pairs (156-136, 197-201, 49-52, 186-201, 197 and 186 onto one interneuron, a satellite on cell 135) show position-dependent, depressing, facilitating and supralinear transmission.", "source": "Figures 2a, 3b to 3d, 4, 5, 6b and 7a", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The CRCNS description names EE.188 (day EE0708) as the session of Figures 2a and 3d, and Figure 5 uses the same session; the dandiset has no file of that day, nor of EE.152 and EE.165. The CRCNS copy needs an account. The example cell numbers cannot be matched to the dandiset's units in any case, as its units carry no original cluster numbers.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds three rats (EE, FF, GG); the paper recorded four. Of the 13 working memory sessions in the CRCNS session table, EE.152, EE.165 and EE.188 are not in the dandiset, and EE.210 has no trial table or position. EE.188 is the paper's example session (Figures 2a, 3b to 3d, 4 and 5)." }, { "kind": "metadata_insufficient", "statement": "The units table holds spike times only. It has no channel, shank, brain region, cell type or quality label, and mixes prefrontal units, CA1 units, multi-unit clusters (cluster 1 of each shank, kept by the conversion) and clusters of the sensor signals. Units can be placed only from their waveforms in the wideband signal, which EE.042 and the ten sessions of 2008-06-27 (EE.080 to EE.089, among them the working memory session EE.088) do not have." }, { "kind": "metadata_insufficient", "statement": "Electrode locations are \"unknown\", coordinates are missing and impedances are -1. The electrode groups \"shank1\" to \"shank13\" are cuts of eight consecutive channels, whatever the probe, so they do not identify the prefrontal shanks, the CA1 shanks or the sensor channels. The layer recorded in each rat is not stated." }, { "kind": "metadata_error", "statement": "In rat GG the channel order differs from the CRCNS description. The nose-poke sensors are on channels 65 and 66 (1-based) and the CA1 probe on 70 to 101, where the description gives 97 and 98 and 65 to 96. The sensor on 66 is active on trials labelled Right, the reverse of the order in rats EE and FF, so either the sensors or the trial side labels of rat GG are swapped." }, { "kind": "metadata_error", "statement": "The trial table's stop_time is the end of the last nose poke, the paper's trial start, and reward_time is the paper's trial end; the column left_or_right carries the description of reward_time (\"Time when subject began consuming reward.\"). Only correct trials are listed, which the files do not say." }, { "kind": "metadata_error", "statement": "The two \"(x,y) coordinates\" series SpatialSeries1 and SpatialSeries2 are the x coordinates of the two head LEDs, in pixels although stated in metres, and the second is zero in every file; untracked frames are -1. The y coordinates are not in the dandiset. The linearized position is stated in metres but runs from 1 (trial start) to 2 (reward), with 0 outside trials." }, { "kind": "format_error", "statement": "In six files (EE.049, EE.088, EE.196, FF.103, FF.130, GG.069) the spike times of unit 1 are not in ascending order. In EE.049 and FF.103, examined in detail, they are two sorted runs one after the other; in the five analysed files the unit is a multi-unit cluster." }, { "kind": "other", "statement": "GG.063, a spontaneous alternation session in the CRCNS table, has a trial table with left and right trials like the working memory sessions; the files do not say which task a session is." }, { "kind": "metadata_insufficient", "statement": "The session description of every file is the paper's abstract, and session start times are dates at midnight; the files do not say which sessions are sleep, test, spontaneous alternation or working memory sessions." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. The verifier could not fetch the full text and read the abstract and the Methods as the claims file quotes them; it checked the blocked claims against the archive's asset list and tested the helper functions on synthetic inputs. Report in transcripts/000067/verifier-1-report.md.", "agreed": 16, "of": 16, "disagreements": [] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run, the helper module, the claims file and the attempt record. The verifier could not fetch the full text (Europe PMC, BioC and PMC refused) and read the abstract only, so it could not check points that rest on the Methods or the supplement. Report in transcripts/000067/verifier-2-report.md. Points not tied to one claim were also answered; in the Summary the rank band sentence now gives 102 of 285 pairs, the sessions are called sessions of the dandiset, and the repeated \"Only correct trials are listed\" was removed.", "agreed": 15, "of": 16, "disagreements": [ { "claim": "traj-diverge", "outcome": "blocked", "reason": "It should stay blocked (data_missing). The x1 divergence point of 0.49 does not measure the paper's 0.3; cell 34 shows x1 falling roughly linearly to its minimum near 0.5 on both sides, so the x1 difference appears where the path turns back in x, not where it separates laterally. The first half of the claim fails by x1 in 5 of 9 sessions, and the criterion's rule rates any x1 result above 0.33 as partial support, whatever the paths do in y." } ] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The proposed change of outcome for traj-diverge only, with the full executed notebook of the final revision (cells 33 to 36), the claims file and the attempt record. No paper text was downloaded this round. Report in transcripts/000067/verifier-3-report.md.", "agreed": 1, "of": 1, "disagreements": [] } ] }, { "id": "000070-churchland-2012-01", "dandiset": "000070", "dandiset_version": "0.260528.0919", "paper": "10.1038/nature11129", "paper_title": "Neural population dynamics during reaching", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000070-churchland-2012", "entry_title": "Rotational dynamics of motor cortex during reaching (Churchland et al. 2012)", "description": "Tests the findings of Churchland, Cunningham, Kaufman, Foster, Nuyujukian, Ryu and Shenoy (2012) that can be tested on dandiset 000070, which holds the paper's two Utah array datasets (monkeys J and N, 108 maze conditions each) and eight further array sessions. It runs jPCA on condition-averaged rates around movement onset and tests the consistency of rotations across conditions, the variance the jPCA planes capture, the fit of rotational dynamics, the shuffle controls, the separate PMd and M1 arrays, and simulated kinematic populations. The single-electrode datasets, EMG, leech and walking-monkey data are not in the dandiset.", "notebooks": [ { "path": "reproduce_churchland_2012.ipynb", "title": "Reproducing Churchland et al. (2012) from dandiset 000070", "executed": "notebooks/000070-churchland-2012/reproduce_churchland_2012.html" } ], "outcomes": [ { "claim": "array-dataset-composition", "statement": "The two array datasets, monkey J-array recorded 2009-09-18 and monkey N-array recorded 2010-09-23, each present 108 reach conditions and comprise 146 and 218 isolations (a mix of single and multi-unit isolations).", "source": "Methods, Recordings and task design; Figure 3e and 3f legend", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "Both sessions are in the dandiset (sub-Jenkins ses-20090918 and sub-Nitschke ses-20100923) with 108 conditions each among the selected trials. Each holds 192 units, one per electrode of the two arrays, with rates over trial time of 13.5 to 178 spikes/s, against the paper's 146 and 218 isolations. The sorted isolations are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3ef-same-direction", "statement": "In the first jPCA plane the neural state rotates in the same direction for all conditions of the J-array and N-array datasets, including reaches in opposite directions.", "source": "Results, Quasi-rhythmic responses during reaching; Figure 3e and 3f", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "102 of 108 conditions (0.944) rotate counter-clockwise in J-array and 108 of 108 in N-array; median net rotation 70.2 and 114.6 degrees over the 200 ms. Under the variants (24 ms smoothing, two other windows, 10 PCs, all successful trials) the fraction is 0.944 to 0.981 and 0.972 to 1.000. jPCA orients the plane so that the net rotation is counter-clockwise, so the fraction is also 0.963 to 0.991 after shuffles 2 and 3 and 0.926 and 0.972 for the velocity model with no lead; it shows that the conditions turn the same way, not on its own that the rotation is specific to the data.", "deviations": [ "Tested on the 192 per-electrode units, not the paper's sorted isolations.", "No PC smoothing of single-unit rates; the supplement reports it has essentially no effect.", "The analysis window is -50 to +150 ms from movement onset for both datasets, from the codepack's example; the paper chose a start per dataset, just before the rapid change in activity." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-independent-of-curvature", "statement": "The rotations do not relate directly to reach curvature; the neural state rotates the same way for clockwise-curving, counter-clockwise-curving and straight reaches.", "source": "Results, Quasi-rhythmic responses during reaching; Figure 3e and 3f", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "In N-array all conditions rotate counter-clockwise in each class (44 clockwise, 53 counter-clockwise, 11 straight reaches). In J-array 0.984 of 63 counter-clockwise and 7 of 7 straight reaches do, but 0.868 (33 of 38) of clockwise reaches, under the 0.9 of the criterion and above 0.75. Spearman correlation of heading change with net neural rotation is 0.227 (p 0.018) in J-array and -0.214 (p 0.026) in N-array; the J-array logistic slope is 0.0101 per degree. The hand paths drawn by class match the classes; the five clockwise-class conditions of J-array that turn clockwise in the plane are loops of 162 to 180 degrees. With the heading taken over the unbroken run around peak speed, or thresholds of 10 or 30 degrees, the J-array clockwise class has 38 or 41 conditions, of which 0.868 to 0.878 rotate counter-clockwise.", "deviations": [ "The paper shows this by eye in Figure 3; the classes of curvature and the thresholds were fixed here before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-phase-from-prep-state", "statement": "The rotation phase follows from the preparatory state; knowing the initial state in the jPC plane, the subsequent states are reasonably predictable.", "source": "Results, Quasi-rhythmic responses during reaching; Figure 3", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "Leave-one-condition-out R2 of the +150 ms state from the -50 ms state is 0.632 in J-array and 0.748 in N-array, both above 0.5. Shuffle 3 gives 0.633 to 0.718 (median 0.671) in J-array and 0.611 to 0.689 (median 0.656) in N-array, so the data exceed the control in N-array only. Shuffle 1, which has no rotation, scores 0.82 to 0.91 in every run, so this R2 rewards any consistent map from the first state to the last and is a weak test of the claim. With jPCA refitted leaving each condition out, the R2 is 0.615 and 0.727 against shuffle 3 medians of 0.628 and 0.649, reached by 8 of 10 shuffle 3 runs in J-array and none in N-array; several runs lie within 0.02 of the J-array value, and the round-2 verifier's copy printed 0.614 and 6 of 10, so this count moves with small numerical differences between runs. A phase score (the last phase predicted as the first plus the other conditions' mean advance) is 0.763 and 0.894 for the data, against 0.236 and -0.356 for no advance; shuffle 1 scores the same with and without an advance, and shuffle 3 keeps an advance of 65 and 99 degrees and scores a median 0.811 and 0.797, so this score also separates the data from shuffle 3 in N-array only (9 of 10 shuffle 3 runs reach the data's phase score in J-array, none in N-array).", "deviations": [ "The paper gives no measure of predictability; the complex-gain prediction and its thresholds were fixed here before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "var-captured-jpc-plane", "statement": "The first jPCA plane captures an average of 28% of the total data variance (typically 20 to 35%).", "source": "Results, Controls regarding rotational structure; Supplementary Figure 5 legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "The first jPCA plane captures 20.0% (J-array) and 23.1% (N-array), both within 18 to 38.5% (reading b, which matches). The mean, 21.6%, is outside 28 +- 2.8% (reading a). The sub-Nitschke ses-20090910 session gives 18.8%.", "deviations": [ "The paper's 28% averages nine datasets, of which the dandiset holds two; the reading of the typical range was used, as listed in the criterion.", "Tested on per-electrode units, not sorted isolations." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pc23-variance", "statement": "The plane of PC2 and PC3 captures 29% of the total variance on average, about as much as the first jPCA plane, so the jPCA plane captures patterns already present in the top PCs.", "source": "Results, Controls regarding rotational structure", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "PC2 and PC3 capture 21.6% (J-array) and 27.0% (N-array), mean 24.3%, outside 29 +- 2.9% under reading (a) and under reading (b) for J-array. The jPCA plane captures 0.93 and 0.86 times the variance of PC2 and PC3, so the comparison the claim makes holds.", "deviations": [ "Two datasets in place of the paper's nine.", "Tested on per-electrode units, not sorted isolations." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppfig4-j-array-planes", "statement": "In J-array the first three jPCA planes found within the top 10 PCs capture 22%, 19% and 12% of the variance (54% together), against 64% for the top six PCs, and each plane holds rotations coherent across conditions.", "source": "Supplementary Figure 4", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "In J-array the three jPCA planes from the top 10 PCs capture 12.3%, 14.8% and 12.8% (40.0% together) against 22%, 19% and 12% (54%); only plane 3 is within tolerance. The top six PCs capture 60.5%, within 64 +- 6.4%. The planes rotate consistently (0.926 to 0.991 of conditions counter-clockwise). The lower variance may come from the per-electrode units, which carry more noise than sorted isolations, and from the missing PC smoothing; this was not tested.", "deviations": [ "Per-electrode units in place of the paper's 146 isolations; no PC smoothing." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppfig4-planes-range", "statement": "Every dataset contains two, and usually three, planes with rotations, together capturing 50 to 70% of the variance.", "source": "Supplementary Figure 4 legend", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "The three planes capture 50.1% in N-array (within 45 to 77%) and 40.0% in J-array (below it). The first two planes have 0.954 or more of conditions rotating in their direction in both datasets. ses-20090910 gives 40.9%.", "deviations": [ "Two datasets in place of the paper's nine; per-electrode units." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6a-angle-peak", "statement": "The distribution of the angle between the neural state and its derivative in the first jPCA plane, over all conditions and times, peaks near pi/2 (rotation), not near 0.", "source": "Figure 6a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "The angle between the state and its derivative peaks at 0.528 pi (J-array) and 0.639 pi (N-array), medians 0.511 and 0.603 pi. Under the variants the peak lies between 0.528 and 0.639 pi, and with 24 or 48 bins between 0.542 and 0.646 pi.", "deviations": [ "The thresholds come from reading Figure 6a; the paper gives no number." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6b-skew-fit", "statement": "For the neural data the rotational (skew-symmetric) dynamics matrix fits the data nearly as well as the best unconstrained linear dynamics matrix, both in the 6-D space and in the first jPCA plane.", "source": "Results, Population-level quantification; Figure 6b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "R2(M_skew)/R2(M) is 0.905 and 0.845 in 6-D and 0.957 and 0.881 in the first plane (J-array, N-array). Under the variants the 6-D ratio is 0.819 or more and the plane ratio 0.879 or more. Absolute R2 of M_skew is 0.343 and 0.517.", "deviations": [ "The thresholds come from reading Figure 6b; the paper gives no number.", "M_skew is solved in closed form as in the Supplementary Derivation, where the codepack uses a gradient method for the same unique optimum." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "rotation-frequency", "statement": "The rotations are brief and fast, up to about 2.5 Hz; the largest eigenvalues of M_skew in the monkey A and B datasets are 8.8 to 13.5 radians/s.", "source": "Results, Quasi-rhythmic responses during reaching and Population-level quantification", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "The first plane rotates at 1.38 Hz (8.65 radians/s) in N-array, within 1.26 to 2.75 Hz, and 1.03 Hz (6.49 radians/s) in J-array, below it; the larger value is given as measured. No variant exceeds 1.68 Hz, so the upper bound holds. J-array reaches the range with the -100 to +100 ms window (1.45 Hz) or 10 PCs (1.68 Hz), variants that do not decide the outcome. The low J-array value is not the effect of a window starting before the rotation does (a synthetic 2 Hz rotation starting at movement onset reads 1.49 Hz from -50 ms), since windows starting at 0 and +50 ms give 1.04 and 1.13 Hz. The J-array plane's mean angular speed is about 1.3 Hz from -60 to +20 ms and 0.7 to 0.9 Hz by +100 ms, and windows starting at -150 or -100 ms give 1.31 and 1.45 Hz, so J-array rotates faster before movement onset than over the window used, which the paper chose per dataset.", "deviations": [ "The lower bound of the range comes from the eigenvalues the paper reports for monkeys A and B, whose data are not in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppfig3-shuffle-controls", "statement": "Three shuffle controls that keep preparatory activity and invert or reassign the peri-movement activity largely remove the rotational structure found by jPCA, so jPCA does not find rotations that are not there.", "source": "Supplementary Figures 2 and 3", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "Shuffle 1 removes the rotations (median R2(M_skew) 1.0% and 0.8% of the original; fraction counter-clockwise 0.565 and 0.602). Shuffle 2 leaves 71% (J-array) and 94% (N-array) of the original R2(M_skew), shuffle 3 leaves 81% and 94%, and one shuffle 3 run in N-array exceeds the original; after both the median fraction rotating counter-clockwise is 0.963 to 0.991. Only shuffle 1 meets the criterion in N-array, and shuffles 1 and 2 in J-array. The paper expected shuffles 2 and 3 to leave part of the rotational structure and to disrupt its relation to the preparatory state, which R2(M_skew) does not measure; the criterion's choice of measure, fixed before the analysis, may not capture what the paper judged by eye.", "deviations": [ "The dividing point is one time per dataset (median go cue plus 50 ms, -301 and -320 ms from movement onset) on movement-aligned rates; the paper split each condition 50 ms after its go cue on rates aligned separately to target, go cue and movement.", "The paper judged the shuffles from projections (Supplementary Figure 3); R2(M_skew) and its thresholds were fixed here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppfig5-areas-variance", "statement": "Analysed separately, the PMd and M1 arrays each show clear rotations; the jPCA plane captures 29% (PMd) and 29% (M1) in J-array and 32% and 28% in N-array.", "source": "Supplementary Figure 5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "PMd and M1 capture 23.7% and 22.8% (J-array) and 18.1% and 25.0% (N-array) against 29, 29, 32 and 28%; none within 10% (N-array M1 misses 25.2% by 0.2 points). All lie within 18 to 38.5%, with 0.917 to 0.991 of conditions rotating counter-clockwise. ses-20090910 gives 15.4% (PMd) and 21.6% (M1) against 26% and 24% for N-9-10-2010.", "deviations": [ "96 per-electrode units per array in place of the paper's isolations." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "suppfig5-m1-faster", "statement": "The angular velocity of the rotations is slightly higher for M1 than for PMd in each dataset.", "source": "Supplementary Figure 5 legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "M1 rotates faster than PMd in J-array (1.82 against 0.83 Hz) and N-array (1.54 against 1.02 Hz), and in ses-20090910 (1.70 against 0.89 Hz), under every variant shown. The paper calls the difference slight; here M1 is 1.5 to 2.4 times faster across the sessions and variants.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-velocity-model", "statement": "A simulated population of units tuned to hand velocity and speed, with preparatory activity tuned to reach endpoint, matched to the recorded data, shows no robust or consistent rotations; M_skew fits it poorly and its angle distribution peaks slightly above zero.", "source": "Results, Rotations, kinematics and EMG; Figure 4d and 4h; Figure 6a and 6b", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "The velocity model's 6-D R2 ratio is 0.361 (J-array) and 0.255 (N-array), against 0.905 and 0.845 for the data, and 0.630 and 0.778 of its conditions rotate counter-clockwise. Its angle distribution peaks at 0.806 pi and 0.361 pi, not below pi/4, so the criterion fails in both datasets. With no lead the peaks are 0.194 pi and 0.417 pi and the ratios 0.362 and 0.337. The part of the claim about the poor fit of M_skew holds under every variant (6-D ratio 0.08 to 0.55). The angle peak depends on the model's open choices. A decay toward the origin peaks near pi (0.972 pi on a synthetic decay), and the preparatory tuning decays from movement onset. With the 100 ms lead the peak lies at 0.36 to 0.86 pi over five seeds and with the preparatory tuning decaying, held or absent; with no lead and preparatory tuning it lies at 0.19 to 0.42 pi; with no lead and no preparatory tuning it is 0.028 pi in both datasets, near zero as the paper reports. The outcome follows the model fixed in the criterion.", "deviations": [ "The model is simulated here from the dandiset's condition-mean hand kinematics; its lead of 100 ms, the time course of preparatory tuning and the modulation depths are choices made here, as the Methods do not give them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-complex-kinematic-model", "statement": "A simulated population tuned to hand position, velocity, acceleration and jerk (with the Methods' sensitivities) produces multiphasic responses but no consistent rotations; M_skew fits it poorly.", "source": "Results, Rotations, kinematics and EMG; Figure 4e and 4i; Figure 6a and 6b", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_churchland_2012.ipynb", "notes": "The complex kinematic model's 6-D R2 ratio is 0.082 (J-array) and 0.132 (N-array), 0.289 and 0.207 with no lead, and 0.565 and 0.528 of its conditions rotate counter-clockwise. Its angle peaks are 0.861 pi and 0.750 pi (0.806 and 0.917 pi with no lead), not below pi/4, so the criterion fails in both datasets. The poor fit of M_skew holds as the paper reports (6-D ratio 0.06 to 0.61 across variants). With the preparatory tuning held or absent, no lead, and four more seeds, the peak lies within pi/4 of zero only in J-array with no preparatory tuning and no lead (-0.083 pi) and in one N-array seed with no lead (0.194 pi); elsewhere it lies at 0.19 to 0.97 pi or near -pi.", "deviations": [ "Simulated here with the Methods' sensitivities; the lead, the preparatory time course and hand positions read as mm are choices made here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1-leech-and-walking", "statement": "The population responses of the swimming leech and of premotor cortex in a walking monkey rotate in the jPCA plane, as expected for rhythmic movement.", "source": "Figure 1a, 1b, 1d and 1e", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The leech imaging and the walking-monkey recording are not in the dandiset, whose ten files are all maze-task array sessions, and the paper names no other archive for them.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-single-neuron-responses", "statement": "Single neurons recorded with single electrodes show multiphasic, quasi-oscillatory responses lasting about 1 to 1.5 cycles, from 469 isolations in four monkeys averaging 810 trials per neuron.", "source": "Results, Quasi-rhythmic responses during reaching; Figure 1c and Figure 2", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The 469 single-electrode isolations of monkeys A, B, J and N are not in the dandiset, and the paper names no other archive for them.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3abcd-single-electrode-datasets", "statement": "The rotations are seen in the seven single-electrode datasets (monkeys A, B, J1 to J4 and N), for example monkey B, A, J3 and N in Figure 3a to 3d.", "source": "Figure 3a to 3d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The seven single-electrode datasets (A, B, J1 to J4, N) are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-emg-no-rotation", "statement": "The recorded muscle populations (6 to 12 EMG recordings per dataset) show weak, inconsistent rotations, also when the neural population is down-sampled to their size.", "source": "Figure 4c, 4f and 4j; Figure 6a and 6b; Supplementary Figure 6", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "EMG was not recorded for the array datasets (Methods), and the EMG of the single-electrode datasets is not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-generator-model", "statement": "A generator model of two rotations of fixed frequency fits deltoid EMG with correlations of 0.97 to 0.99, and its simulated units resemble real neurons.", "source": "Figure 5; Supplementary Figures 7 to 9", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The generator model is fitted to deltoid EMG of the single-electrode datasets (J2, J3), which is not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6cd-speed-independent-frequency", "statement": "Rotations have similar angular velocity for instructed fast and slow reaches; the largest M_skew eigenvalues are 8.8 against 9.8 radians/s (monkey A) and 12.2 against 13.5 (monkey B), with larger amplitude for fast reaches.", "source": "Results, Population-level quantification; Figure 6c and 6d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The speed task of monkeys A and B is not in the dandiset, which holds sessions of monkeys J and N only.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds the paper's two array datasets but not the sorted isolations the paper analysed (146 for J-array, 218 for N-array). Its Units table has 192 units per file, one per electrode. The seven single-electrode datasets, the EMG, the leech and the walking-monkey data are not in it either, so six of the paper's main findings cannot be tested." }, { "kind": "format_error", "statement": "In nine of the ten files (all written by the first conversion) the first entry of units/spike_times_index is the true end of unit 0 modulo 65536. Unit 0 is cut short (in J-array 61030 of its 257638 spikes) and its remaining spikes open unit 1, whose times then jump from the end of the session back to its start." }, { "kind": "format_error", "statement": "In five Nitschke files (ses-20090812, 20090819, 20090910, 20090920 and 20100923) the clock restarts at recording segments after the first, as the conversion offsets only one segment. Trials overlap in time (2094 overlapping pairs in N-array), and every unit's spike times go backwards at each restart, so spikes cannot be placed in trials by time; they can be placed by their storage order, which the notebook shows decodes reach direction in every segment." }, { "kind": "metadata_error", "statement": "Hand position is stated in metres (with conversion NaN); its values span about -220 to +165 on the scale of the target positions (up to 145) and the median speed peaks at 600 to 730 per second during a reach, so they are in mm." }, { "kind": "metadata_insufficient", "statement": "The hand position ends a median 35 mm (Jenkins) and 52 to 53 mm (Nitschke) below the reached target in y, while the cursor lands on the target; the offset between hand and screen coordinates is not described in the files." }, { "kind": "metadata_insufficient", "statement": "The Units table carries only the default description (\"Autogenerated by NWBFile\") and does not say whether its units are sorted neurons, multi-unit activity or threshold crossings. Their number (one per electrode) and rates (8.8 to 300 spikes/s over trial time in the three sessions analysed) are consistent with channel-level activity." }, { "kind": "metadata_insufficient", "statement": "The dandiset does not say which of its ten sessions are the paper's datasets. Two match the J-array and N-array dates; the other eight (27-condition and two-condition maze sessions, and one 108-condition session) are not described." }, { "kind": "other", "statement": "The first conversion's code sets the year of every session date to 2009. The file sub-Nitschke ses-20090910 has 108 conditions with the same reached target as N-array (2010) for all of them, and is consistent with the N-9-10-2010 dataset of Supplementary Figure 5; if so, its date is a year early. The other 2009 Nitschke dates may be affected in the same way." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the PMC author manuscript and the publisher's Supplementary Information. The verifier tested helper functions on synthetic inputs and read the archive's asset metadata and one file for the blocked claims. Its report had no attempt record and gave its own outcome for each claim; all 22 agree with the record.", "agreed": 22, "of": 22, "disagreements": [] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the first revision, with its conclusions and summary, the README, the helper module, the claims file and the attempt record. The verifier did not download the paper this round and relied on its round-1 reading for what the paper says. All 22 outcomes agree with the record. It also noted that the README gave a run time of about 13 minutes against 14.4 minutes printed; the README now says 10 to 15 minutes (this re-run took 9.6).", "agreed": 22, "of": 22, "disagreements": [] } ] }, { "id": "000114-carcea-2021-01", "dandiset": "000114", "dandiset_version": "0.230602.1643", "paper": "10.1038/s41586-021-03814-7", "paper_title": "Oxytocin neurons enable social transmission of maternal behaviour", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000114-carcea-2021", "entry_title": "PVN units and maternal behaviour in co-housed virgin mice (Carcea et al. 2021)", "description": "Tests the findings of Carcea et al. (2021) that dandiset 000114 can support. The dandiset holds PVN single units and video annotations from virgin mice co-housed with a dam and litter, and fibre photometry from virgins watching dam retrievals. The entry tests the fraction of units activated during nest entry, shepherding and dam retrieval, the firing after shepherded against voluntary nest entries, and the rates of shepherding and dam retrieval. OT-PVN identity, the behavioural cohorts and the auditory cortex data are not in the dandiset.", "notebooks": [ { "path": "reproduce_carcea_2021.ipynb", "title": "Reproducing Carcea et al. (2021) from dandiset 000114", "executed": "notebooks/000114-carcea-2021/reproduce_carcea_2021.html" } ], "outcomes": [ { "claim": "label-link", "statement": "The dandiset's behaviour labels can be named through the paper's code; \"Mom agressing\" is shepherding, \"Virgin in rest\" is nest entry (a nest dwell) and \"Mom retrieval\" is spontaneous pup retrieval by the dam.", "source": "Methods (Spike train analysis); Extended Data Fig. 7b; shepNestPup_xCorr_ForNature.m at GitHub commit 2db2a75", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_carcea_2021.ipynb", "notes": "In V116 03122018, the one file with both naming schemes, all 7 \"Mom agressing\" intervals coincide with \"Shepherding\" intervals and both \"Mom retrieval\" intervals with \"Self gen retrieval\" intervals, and all 13 \"Virgin in rest\" intervals lie inside \"Virgin in nest\" intervals. Pooled over files, 366 of 499 \"Virgin in rest\" intervals (73.3%) last 40 s or less, within 70.5% +/- 7.05. By mouse the fraction is 72.2% in V110 and 89.2% in V111, but 9.9% in V116, where the label marks dwells with medians of 1103.7 to 2492.7 s, and 0 of 3 in V118 (median 64.1 s). Adding V85's \"Virgin in nest\" gives 77.3% of 639.", "deviations": [ "The names come from the paper's code, not from the dandiset; \"Mom aggressing\" in V85 is taken as the same label as \"Mom agressing\"." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "ed7a-nest-entry-fraction", "statement": "A significant fraction of virgin PVN units were activated during nest entry (6 of 21 OT-PVN and 33 of 126 PVN units; one-sided Fisher's exact test p = 0.01 and 0.0001).", "source": "Fig. 2i; Extended Data Fig. 7a (middle); Source Data Fig. 2i", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_carcea_2021.ipynb", "notes": "42 of 194 units (21.6%) are activated during nest entry, outside the tolerance of both readings (pooled 23.9 to 29.2%, PVN only 23.6 to 28.8%); the Fisher test against zero gives p = 1.9e-14, and 7 units are suppressed. By mouse, V116 has 37 of 70 (52.9%), V110 1 of 31 and V111 4 of 93. Without the 40 s cap, as in the code, 2 of 194 (1.0%, p = 0.25). Without the 20 units above 1,048,500 spikes, 42 of 174 (24.1%), inside the tolerance of both readings, so this variant would reproduce the fraction. With q = 0.01 and 0.1, 14.4% and 28.4%. The paper's statement separates OT-PVN (6 of 21) and PVN (33 of 126) units; the OT-PVN part cannot be tested. The clock shared by spikes and annotations could not be established in any session. Poisson units with each unit's spike count and no response give 2 of 194 (1.0%) on the same episodes and test. Real episodes without spikes are left out of the mean in 116 units (median 17% of their episodes); counting them as 0, as the shuffles do, gives 31 of 194 (16.0%, p = 1.3e-10). Counting V111 once gives 38 to 40 of 132 (28.8 to 30.3%; 28.8% is inside the pooled reading's tolerance, so this variant would reproduce the fraction); without V116 03102018, whose clock is not known, 25 of 168 (14.9%, p = 1.1e-08). The baselines of 3 to 20 entries per session overlap an earlier nest dwell or a shepherding episode; the largest count is in V110 03032018 (20 of 72, all an earlier dwell) and the largest share in V116 03092018 (16 of 29, all shepherding).", "deviations": [ "Units from 4 virgins and 7 sessions (194 units), against the paper's 147 units from more animals; which sessions the paper used is not stated.", "OT-PVN and PVN units are pooled and the false discovery rate is applied over each session's units, as OT identity is not in the dandiset; the Methods apply it over OT-PVN or PVN units of a day.", "The baseline ends 0.5 s before the episode, from the code; the Methods do not give it.", "V111's three sessions probably hold the same clusters (spike counts correlated 0.93 to 0.97) and are counted as separate units, as the paper counts units per day.", "As in the code, real episodes with no spike in either window are left out of a unit's mean, while shuffled ones count as 0; counting both as 0 is shown as a variant, as is counting V111 once." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "ed7a-shepherding-fraction", "statement": "A significant fraction of virgin PVN units were activated during shepherding by the dam (5 of 21 OT-PVN and 9 of 97 PVN units; p = 0.02 and 0.001).", "source": "Fig. 2e; Extended Data Fig. 7a (left); Source Data Fig. 2e", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_carcea_2021.ipynb", "notes": "With the Methods' 10 s baseline, 3 of 194 units (1.5%) are activated during shepherding, Fisher p = 0.12, against 11.9% (pooled) or 9.3% (PVN only); 10 units are suppressed and 15 have no value. With the code's equal-duration baseline, 9 of 194 (4.6%, p = 0.0018). V116 alone, 2 of 70 (p = 0.25). Sessions hold 1 to 22 shepherding episodes, so most units are tested on few events. Poisson units with no response give 3 of 194 activated, as many as the real units. Counting empty episodes as 0 gives 1 of 194, counting V111 once 2 or 3 of 132, and leaving out V116 03102018 2 of 168, none with p < 0.05.", "deviations": [ "Units from 4 virgins and 7 sessions, OT-PVN and PVN pooled, as for nest entry.", "Real episodes without spikes are left out as in the code, and V111's sessions counted separately, as for nest entry; both are also shown the other way.", "The Methods' 10 s baseline is used; the code's equal-duration baseline is shown as a variant." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "ed7a-dam-retrieval-fraction", "statement": "Spontaneous pup retrieval by the dam, in which the virgin was not involved, activated a significant fraction of virgin PVN units (5 of 17 OT-PVN and 10 of 69 PVN units; p = 0.02 and 0.0007).", "source": "Fig. 3b, c; Extended Data Fig. 7a (right); Source Data Fig. 3c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_carcea_2021.ipynb", "notes": "13 of 132 units (9.8%) are activated during dam retrieval, Fisher p = 9e-05, outside the tolerance of both readings (pooled 15.7 to 19.1%, PVN only 13.1 to 16.0%). 9 of the 13 are from V111 03032018, which has one retrieval episode; over sessions with at least 2 episodes, 4 of 101 (p = 0.061). More units are suppressed (20) than activated, and the median change is -22.4. With the code's baseline, 16 of 132 (12.1%). The OT-PVN part (5 of 17) cannot be tested. The 9 units of V111 03032018 share a median 71% of their spikes pairwise within 0.1 ms (33 to 81%), against 1.7% among the session's other 22 units, so they are probably far fewer than 9 neurons. Counting V111 once gives 11 of 101 with V111 03032018 (p = 0.00037) and 4 of 101 with V111 03062018 (p = 0.061). Poisson units with no response give 3 activated and 12 suppressed of 132, so the suppressed count is not far above the test's false-positive level. Counting empty episodes as 0 gives 12 of 132 (p = 0.00019); without V116 03102018, 12 of 106 (p = 0.00018). The baseline of the single retrieval in V111 03032018 is not a recording gap (537 population spikes, more than in 43% of the session's 10 s windows; no interval over 0.22 s within 60 s), but 7 of 31 units have no spike in it and the 9 activated units fire 0 to 2.1 Hz. During the 5.2 s episode about 16 units fire at 144 to 221 Hz together (14,346 population spikes in the first 5 s against 1,838 per 5 s over the session, a size reached in 12 of 3,325 windows), so the retrieval falls on one of the session's largest synchronous bursts. The outputs cannot tell a response from a burst that coincides with the episode; the outcome follows the criterion, which counts units as given.", "deviations": [ "Units from 2 virgins and 5 sessions with 1 to 11 retrieval episodes each; OT-PVN and PVN pooled.", "Real episodes without spikes are left out as in the code, and V111's sessions counted separately, as for nest entry; both are also shown the other way.", "The Methods' 10 s baseline is used; the code's equal-duration baseline is shown as a variant." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2j-shepherded-entry", "statement": "PVN units fired more when the virgin entered the nest after being shepherded than when she entered it voluntarily (18 units, Wilcoxon matched-pairs signed rank test, p = 0.0056).", "source": "Fig. 2j; Extended Data Fig. 7a; Source Data Fig. 2j", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_carcea_2021.ipynb", "notes": "Over 128 units in 5 sessions, the change is higher for shepherded than voluntary entries in 70, median difference 3.9, Wilcoxon p = 0.182. Sessions disagree; V110 03032018 (one shepherded entry) has 30 of 31 units higher (p = 4.66e-09) and V116 03102018 has 6 of 26 (p = 0.00669). With windows of 5 and 30 s, p = 0.37 and 0.166; over the 36 units activated during nest entry, median difference -7.3, p = 0.148; V116 alone, -6.0, p = 0.0732. Without V116 03102018, whose clock is not known, the median difference is 10.8 over 102 units and p = 0.0237; this variant does not decide the outcome under the criterion, and 31 of its units come from V110 03032018, compared on a single shepherded entry.", "deviations": [ "The paper does not say how a nest entry was classed as shepherded or which 18 units were used; the rule (entry starting from the start of a shepherding episode to 10 s after its end) and the unit set were fixed before the analysis." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1j-shepherding-rate", "statement": "Dams shepherded virgins more often than the 0.2 events per hour at which dams chased virgins without pups, at 3.5 +/- 0.9 events per hour with pups present.", "source": "Fig. 1j; Extended Data Fig. 3b", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_carcea_2021.ipynb", "notes": "Over 10 sessions from 5 mice the mean rate is 0.65 shepherding events per hour (s.e.m. 0.17), above 0.2 (t = 2.59, two-sided p = 0.0292), and far below 3.5 +/- 0.9. Averaged per mouse first, 0.63 per hour, p = 0.193 against 0.2. Session rates run from 0 (V118 03222018) to 1.58 (V85). Annotations of any label span each session with no gap over 0.81 h; the virgin labels run from within 0.61 h of the start to within 0.15 h of the end with gaps of up to 1.93 h. This is consistent with sessions scored in full but does not show that every shepherding episode was annotated.", "deviations": [ "Sessions are recordings of 2.5 to 15.8 h, not the paper's days of co-housing per dyad, and the dandiset does not say whether each session was annotated in full.", "The comparison of 3.5 per hour comes from Extended Data Fig. 3b (N = 4 dyads); its dyads are not identified." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "ed8a-dam-retrieval-rate", "statement": "About once every two hours, dams dropped and then retrieved pups during co-housing (daily means 0.34 to 0.60 retrievals per hour, N = 14 dams).", "source": "Results (Social transmission of maternal behaviour); Extended Data Fig. 8a", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_carcea_2021.ipynb", "notes": "Dams retrieve 23 times in 108.4 h, 0.21 per hour (session mean 0.21, range 0 to 0.70), below 0.31 to 0.66 and close to the 0.2 +/- 0.1 per hour (N = 5) the legend of Extended Data Fig. 8a gives for singly housed dams. Two of 10 sessions are inside the range (V116 03082018 at 0.33, V118 03222018 at 0.40). The rate depends on every retrieval being annotated, which the dandiset does not state; the annotations span each session with no gap over 0.81 h, and dam retrievals are too rare (gaps of up to 9.89 h) for their spacing to show unscored stretches.", "deviations": [ "Rates from 5 cages over 10 sessions, against the paper's 14 dams over 4 days." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "ot-pvn-units", "statement": "Optically tagged OT-PVN units (21 units) were activated by shepherding, nest entry and dam retrieval, and pairs including OT-PVN units were more correlated than PVN pairs during these behaviours.", "source": "Fig. 2b, e, g-i; Fig. 3b-d; Extended Data Figs. 5, 6a, 7a, 7d, 7e", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "OT-PVN units were identified by optical tagging at the end of each day; the tagging recordings (laser pulse times) are not in the dandiset, the units table has no label, and the paper's code reads the identities from a spreadsheet (\"Identified OXT neurons.xlsx\") that is not public. The Zenodo record 5039601 holds Blackrock .nev files of the same co-housing sessions, not the identities. The unit names in the files are the indices 0 to n-1 in every session. The pooled PVN part of these responses is tested in the three ed7a claims.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-virgin-chasing", "statement": "Units activated during shepherding fired less when the virgin chased the dam (6 units, Wilcoxon p = 0.03).", "source": "Fig. 2f; Source Data Fig. 2f", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The files have a \"Virgin Agressing\" label (32 events in 5 sessions with units), which may be the virgin chasing the dam, but neither the files, the Methods nor the code name it. It never overlaps \"Mom agressing\" and starts at least 162 s from the nearest one. Of the 3 shepherding-activated units, 2 have such episodes; one fires less over 11 episodes (change -25.3, shuffle p = 0.054), the other stops firing in its single episode. Two units cannot test the paper's 6.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6-dam-vs-pup", "statement": "During 5-minute interactions, more virgin PVN units were activated by the dam than by pups (25 of 248 against 7 of 248), and units barely responded to pup calls (1 of 71).", "source": "Extended Data Figs. 6c-e, 7c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The 5-minute interaction periods with the dam or with pups, and the pup call playback times, are not annotated in any file.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1cd-retrieval-onset", "statement": "Virgins co-housed with a dam and litter began retrieving pups earlier than virgins co-housed with pups alone (n = 14 and 10, P < 0.0001), and nest entry and shepherding on day 1 correlated with retrieval at the end of day 1 (r = 0.66 and 0.75).", "source": "Fig. 1c, d, f, k; Extended Data Fig. 2", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The daily retrieval tests of the 14 D+ and 10 D- virgins are not in the dandiset; only summary values are in the paper's Source Data, and the videos are on Databrary.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-dreadd", "statement": "Chemogenetic silencing of OT-PVN neurons delayed the onset of retrieval in co-housed virgins.", "source": "Fig. 2a; Extended Data Fig. 4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The DREADD cohort's retrieval scores are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3fg-observational-learning", "statement": "Non-co-housed virgins learned to retrieve after watching dams retrieve, with no barrier (11 of 15) or through a transparent barrier (12 of 19), but not through an opaque barrier (2 of 18) or when lacking the oxytocin receptor (3 of 10).", "source": "Fig. 3e-g; Extended Data Fig. 8c, d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The observation cohorts' retrieval scores are not in the dandiset. The photometry files of six observing virgins hold retrieval tests for two of them only.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3ij-observation-units", "statement": "PVN units of non-co-housed virgins were activated while watching dam retrievals (15 of 65), some also during the virgin's own retrievals (15 of 41), and only in virgins that went on to retrieve (learners against non-learners, P = 0.0001).", "source": "Fig. 3h-j", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "All units in the dandiset are from co-housing sessions; no unit recording from an observation session is in it.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-ac-photometry", "statement": "Auditory cortex photometry responses to pup calls increased over co-housing up to the day of retrieval onset (P = 0.003, n = 3).", "source": "Fig. 4a-c; Extended Data Fig. 10a", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No photometry file has pup call playback, and fibre location is \"unknown\" in every file; the photometry files are observation and retrieval sessions of Fig. 4g-i.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-pvn-ac-correlation", "statement": "Single-trial PVN activity correlated with pup-call responses in auditory cortex during observation (r = 0.5, P = 0.00001, n = 4).", "source": "Fig. 4d-f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No file holds PVN units together with photometry.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4i-projection-photometry", "statement": "PVN to auditory cortex projections were activated during observation of dam retrieval in virgins that learned to retrieve (P = 0.02) but not in those that did not (P = 0.5), three animals per group.", "source": "Fig. 4g-i; Source Data Fig. 4i", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The six photometry animals (ROV40, 41, 43, 44, 45, 49) match the three learners and three non-learners of the Source Data, but only ROV40 and ROV41 have retrieval-test files, in which they retrieve on Day 1 and Day 2; whether the other four learned is not in the dandiset. The response measure is also not stated; the Source Data values (-12.1 to 65.7 per animal) are on a scale the files cannot be linked to without it, so the claim is also methods_underspecified. The mean change in the 5 s after the dam's retrievals against the 5 s before is positive in all six animals on Day 1 (0.22 to 1.85%), which does not separate the groups even if ROV40 and ROV41 are taken as learners.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4jk-oxytocin-in-ac", "statement": "An oxytocin receptor antagonist in auditory cortex prevented learning by observation (2 of 10 against 7 of 9), and stimulating OT-PVN fibres in auditory cortex enhanced it (4 of 4 against 2 of 4).", "source": "Fig. 4j, k", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The infusion and optogenetic cohorts' retrieval scores are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9-colliculus", "statement": "Superficial superior colliculus projects to OT-PVN neurons, and stimulating this input replaced visual experience (4 of 5 against 1 of 6 virgins retrieving).", "source": "Extended Data Fig. 9", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Tracing histology and the stimulation cohort's retrieval scores are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The behaviour labels (\"Mom agressing\", \"Virgin in rest\", \"Mom retrieval\", \"Virgin Agressing\", \"Mother in nest\" and others) have no description; the table's description, \"events and states of pups\", the same in every file, fits none of them. Shepherding, nest entry and dam retrieval can be named only from the paper's code, and \"Virgin Agressing\" not at all. One file (V116 03122018) carries both the code's labels and the paper's names." }, { "kind": "data_missing", "statement": "The optical tagging recordings and the identity of the 21 OT-PVN units are not in the dandiset, so no oxytocin-specific result can be tested. The behavioural cohorts of Figures 1 to 4, the unit recordings during observation, and the auditory cortex photometry and units are also missing. Units are present for 4 of the paper's 17 recorded virgins." }, { "kind": "other", "statement": "Units in V110 and V111 have a median 7.0 to 9.2% of inter-spike intervals under 2 ms, and 79 to 90% of their spikes lie within 0.1 ms of a spike of another unit. The Methods say spikes violating a 2 to 3 ms refractory period and spikes recorded at once on 10 or more channels were removed. These units look like multi-unit clusters or one neuron split over several wires. In V111 03032018 the 9 units activated by the dam's retrieval share a median 71% of their spikes pairwise within 0.1 ms, and the retrieval falls on a synchronous burst of about 16 units at 144 to 221 Hz, one of the 12 largest of the session's 3,325 windows of 5 s." }, { "kind": "metadata_error", "statement": "Session start times disagree with the dates in the session ids; V116 03082018 and 03102018 start in May 2018, V116 03092018 on 11 March, and V118 03182018 on 23 March, after V118 03192018." }, { "kind": "format_error", "statement": "In V116 03102018 the raw voltage lasts 4.46 h, but spike times and annotations run to 13.4 h; in V118 03222018 annotations run to 2.52 h against 2.27 h of voltage. The spikes and events of these files cannot all come from the recording they are stored with." }, { "kind": "metadata_insufficient", "statement": "The units table holds spike times and a name only, with no channel, waveform, quality or cell type, and every electrode location is \"unknown\". V111's three sessions hold 31 units each with spike counts correlated 0.93 to 0.97 across days, and nothing says whether they are the same units." }, { "kind": "metadata_error", "statement": "Every subject is described as \"Virgin female co-housed with dam and pups\", including the six photometry animals of the observation experiment. Photometry fibre location, fluorophore, wavelengths and gain are \"unknown\" or NaN; the trace is stated in watts with values near 1000; the commanded_voltage series, described as the LED command, varies from 0.07 to 482 within sessions and is not a command signal." }, { "kind": "metadata_insufficient", "statement": "Which photometry animals learned to retrieve is in the dandiset for 2 of 6 (ROV40 and ROV41, from their retrieval-test files), so the learner and non-learner groups of Fig. 4i cannot be formed." }, { "kind": "other", "statement": "No test here established that spikes and annotations share a clock; the firing change at annotation onsets was not larger at the stated times than at shifts of up to 2 minutes in any session." }, { "kind": "code_mismatch", "statement": "The Methods cut nest entry episodes at 40 s and use the 10 s before shepherding and dam retrieval as baseline; the paper's significance code has the cap commented out and uses an equal-duration baseline for every behaviour. On this data the cap changes the fraction of units activated during nest entry from 1.0% to 21.6%." }, { "kind": "selection_undocumented", "statement": "The dandiset holds units from 4 virgins (228 units in 8 sessions), no units for V85, V116 03122018 and three V118 sessions, and annotations limited to \"Mother in nest\" in two V118 files, against 17 recorded virgins and 541 units in the paper. It does not say which recordings were deposited or why." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier tested helper functions on synthetic inputs and checked the archive's file list for the blocked claims. Its report had no attempt record and gave its own outcome for each claim; all 19 agree with the record.", "agreed": 19, "of": 19, "disagreements": [] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the first revision, with its conclusions and summary, the helper module, the claims file, the attempt record and the entry README, with the paper. The verifier checked each conclusion, the summary, the README table and the record notes against the printed outputs, and whether the record gave its round-1 reasons in its own words. It agreed with all 19 outcomes.", "agreed": 19, "of": 19, "disagreements": [] } ] }, { "id": "000121-even-chen-2019-01", "dandiset": "000121", "dandiset_version": "0.220124.2156", "paper": "10.1371/journal.pcbi.1006808", "paper_title": "Structure and variability of delay activity in premotor cortex", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000121-even-chen-2019", "entry_title": "Structure and variability of delay activity in premotor cortex (Even-Chen et al. 2019)", "description": "Tests the findings of Even-Chen, Sheffer, Vyas, Ryu and Shenoy (2019) on dandiset 000121, which holds 12 sessions of delayed center-out reaching with Utah arrays in two monkeys (all 7 of R, 5 of the 16 of J). It checks the sessions and trial counts, the behaviour, the low-dimensional structure of PMd delay activity (PCA, the spatial plane, its time course, the speed axis), the variability of single-trial neural states on and off the reach axis, and SVM decoding of reach direction and distance.", "notebooks": [ { "path": "reproduce_even_chen_2019.ipynb", "title": "Reproducing Even-Chen et al. (2019) from dandiset 000121", "executed": "notebooks/000121-even-chen-2019/reproduce_even_chen_2019.html" } ], "outcomes": [ { "claim": "session-configurations", "statement": "The sessions are those the Methods list for each target configuration; for monkey R, ring on 2017-01-24 and 25, horizontal on 2017-01-17 and 18, vertical on 2017-01-15 and 16, and 3-rings on 2017-01-19; for J, ring, vertical and 3-rings on the dates listed.", "source": "Materials and methods, Experimental design; Figure 1b", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "8 of 12 sessions have the configuration the Methods give for their date. R's 2017-01-15 and 16 hold horizontal targets (Methods vertical) and 2017-01-17 and 18 vertical targets (Methods horizontal); all four mismatches are horizontal and vertical exchanged. 2017-01-17 also holds 69 successful trials to six ring targets outside its layout. The dandiset holds all 7 of R's sessions and 5 of J's 16.", "deviations": [ "The configuration is inferred from the target positions, as the files' task_id is 2 in every trial." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "r-trial-counts", "statement": "Monkey R performed 3577 ring trials over two sessions, 3699 horizontal over two, 4040 vertical over two, and 912 3-rings trials in one session.", "source": "Materials and methods, Experimental design", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Grouped by the Methods' dates, ring 3584 (paper 3577) and vertical 3842 (4040) are within 10% under all three readings, horizontal 4156 (3699) and 3-rings 1340 (912) are not. Measured values are reading (a), successful delayed center-out trials; readings (b) and (c) differ by at most 26 trials per configuration. Grouped by the file geometry, three of four are within 10% (horizontal 3842 against 3699, vertical 4156 against 4040), which fits the exchange of dates found in session-configurations. The 3-rings session holds 47% more successful delayed trials than the paper used, and no reading explains the difference. Reading (b) leaves out failed trials without a go cue; counting them gives ring 4568, horizontal 5250, vertical 5033 and 3-rings 1671, none within 10%.", "deviations": [ "Which trials the paper counted is not stated; three readings were tested." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "j-sessions-complete", "statement": "Monkey J contributed 6161 ring, 5017 horizontal, 6110 vertical and 7722 3-rings trials, over four sessions each.", "source": "Materials and methods, Experimental design", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds 5 of the 16 sessions the Methods list for J (2015-10-01, 10-02, 10-15, 2016-01-27, 01-28). The 11 missing include all four horizontal sessions, three of four ring sessions and two of four in each of vertical and 3-rings. The data link in the paper (stanford.edu/~shenoy/Data/Even-ChenEtAlPLoSCompBio2019.zip) returns HTTP 403, and no other dandiset of this paper was found.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "delays-and-times", "statement": "Delays were uniform from 300 to 700 ms for J and 400 to 900 ms for R, 10% of trials had no delay; average reaction time was 346 ms (J) and 311 ms (R), average reach time 582 ms (J) and 482 ms (R), and reaction time was negatively correlated with delay (p < 1e-4 for both).", "source": "Materials and methods, Experimental design", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Reaction times (J 332, R 305 ms) and reach times read as acquisition minus go cue (J 587, R 486 ms) are within tolerance; read as acquisition minus movement onset they are 255 and 181 ms. R's mean reaction time includes the 5.9% of its trials whose onset precedes the go cue; its median (361 ms) and its mean over 100 to 800 ms (362 ms) are outside tolerance, and with onset searched only after the go cue the means are 342 ms (J, within tolerance) and 340 ms (R, just inside its bound of 342 ms). J's delays span 300 to 700 ms as stated; R's span 400 to 1000 ms, beyond the widened bound of 990 ms. No-delay trials are 19.8% of J's and 0.2% of R's successful center-out trials (26, all on 2017-01-19), not 10%. Reaction time falls with delay in R (r = -0.264, p = 1.8e-205) but not in J (r = -0.013, p = 0.21; with onset at 5% of peak speed r = -0.034, p = 1.5e-03; with onset after the go cue r = -0.029, p = 7.9e-03). J is 5 of its 16 sessions.", "deviations": [ "Movement onset (10% of peak speed) and maximum speed are defined here; the paper does not define them. Onsets at 5% and 20%, and onset searched only after the go cue, are shown.", "Reach time is undefined in the paper; two readings were tested and (b) matches." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "channels-task-correlated", "statement": "Of the 96 PMd electrodes, 74 for J and 80 for R had activity significantly correlated with the x and y location of the target (p < .05, Bonferroni over 96).", "source": "Materials and methods, Neural recording and signal preprocessing", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "72 of 96 channels (J) and 80 of 96 (R) regress on target x and y at p < 0.05/96. Per session the counts are lower (J 39 to 70, R 30 to 70). On the units the file labels PMd (0 to 95) the counts are 74 (J) and 40 (R); R's labelled array has 29 silent channels.", "deviations": [ "PMd is taken as units 96 to 191, from the data check, against the units' electrode_group labels.", "J is 5 of its 16 sessions." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pca-variance", "statement": "The top six PCs of the condition-averaged delay activity explain cumulatively 58, 82, 88, 92, 94 and 95% of the variance for J (120 conditions) and 81, 89, 92, 94, 95 and 96% for R (132 conditions).", "source": "Materials and methods, Dimensionality reduction", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "R has the paper's 132 conditions. Twelve of thirteen values are within tolerance; R's PC1 is 72.8% against 81 +- 8.1%, outside by 0.14 points. The criterion's partial case needs all R values within tolerance, so by its letter the result is not reproduced. With the day's mean taken over the analysed delay windows R's PC1 is 80.5%, and without day-mean subtraction 80.6%. Spikes exist only within trials (99.93 to 99.95% of PMd spikes inside a trial in every session), so the main day mean is the rate over trial time. J's values are within tolerance on 96 of its 120 conditions.", "deviations": [ "The day's average rate is the session's rate over its recorded time; the paper does not say how it was computed. The other choice is shown.", "J is 5 of its 16 sessions and 96 of its 120 conditions." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "spatial-plane-variance", "statement": "The spatial plane captures a large part of the variance of the condition-averaged activity for the ring, horizontal, vertical and 3-rings tasks; 66.8, 64.4, 47.7 and 68.2% for J and 33.7, 30.7, 31.0 and 30.1% for R (p < 1e-4).", "source": "Results, Structure of neural activity during delay period; Figure 2a", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Measured values are reading (a) with tasks by the Methods' dates (R ring, horizontal, vertical, 3-rings; J ring, vertical, 3-rings). No pairing of readings puts more than three of the seven values within tolerance. R's shares (29.5 to 36.9%) lie near the paper's (30.1 to 33.7%); J's are lower (40.2 to 54.4% against 47.7 to 68.2%) on 5 of 16 sessions without the horizontal task. The shares exceed those of planes fit to targets shuffled across conditions with p = 0.005 to 0.16 (shuffle medians 11.5 to 24.8%), so the stated p < 1e-4 does not hold against this null; the paper's null is not stated. 1000 shuffles cannot give p below 1.0e-03, but the observed p values lie well above that.", "deviations": [ "J's plane is fit on 96 of its 120 conditions and its horizontal task is absent.", "Two definitions of the share and two namings of R's horizontal and vertical tasks were tested." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "plane-timecourse", "statement": "After target onset the neural state in the spatial plane starts at the center, diverges after 50 ms (R 75 ms) and converges to the steady delay state after 300 ms (R 400 ms).", "source": "Results, Structure of neural activity during delay period; Figure 2c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Divergence (D below 0.9) at 70 ms (J) and 90 ms (R) after target onset; convergence (D below 0.1) at 270 ms (J) and 350 ms (R). All four are within tolerance, so by the letter of the criterion the result is reproduced; partially_reproduced is a judgment beyond the criterion, made because R's divergence cannot be told from baseline noise. Other thresholds move divergence between 10 and 150 ms and convergence between 230 and 390 ms, so both monkeys' times depend on the threshold; J diverges at 150 ms with threshold 0.8 and converges at 390 ms with threshold 0.05, outside tolerance. J's times hold under the two added checks (pre-onset D SD 0.03; with the converged state taken from trials whose delay window starts after the bin, 70 and 250 ms). R's D lies below 0.9 in 6 of the 10 bins before target onset (SD 0.09), and with the non-overlapping converged state it diverges at 10 ms and converges at 310 ms, both outside tolerance. The pre-target state sits at x -2.1, y -30.4 mm (J) and 17.6, -13.1 mm (R) in the plane's target coordinates, so \"starts at the center\" is not borne out.", "deviations": [ "The thresholds, bins and smoothing are chosen here; the paper reads the times from a figure." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "onoff-predicts-kinematics", "statement": "On single trials, on-axis and off-axis deviations of the neural state in the spatial plane are positively correlated with the on-axis and off-axis deviations of the hand position at maximum speed (on-axis p = 1e-3 J, 4e-3 R; off-axis p = 4e-4 J, 2e-4 R).", "source": "Results, Structure of neural activity during delay period; Figure 2d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Over all tasks (reading a), on-axis J r = 0.091 (p = 1.7e-17), R r = 0.022 (p = 1.3e-02); off-axis J r = 0.102 (p = 1.3e-21), R r = 0.072 (p = 2.2e-16). In the 3-rings task alone R's on-axis correlation is not significant (p = 6.5e-02). R's on-axis correlation is positive with p < 0.05 in one of seven sessions and negative in one (2017-01-16, r = -0.044, p = 4.9e-02). With deviations from session by condition means the correlations are nearly unchanged (R on-axis r = 0.020, p = 2.3e-02; off-axis 0.083, p = 3.0e-21; J on 0.092, off 0.101), so offsets between sessions do not produce them.", "deviations": [ "The position of maximum speed comes from hand positions smoothed here (Gaussian, SD 20 ms)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "speed-axis-within-distance", "statement": "The speed axis of delay activity varies with maximum speed for reaches to the same target distance, for 11 of 12 distances in J and 11 of 12 in R (p < 0.05), so it encodes speed independently of distance.", "source": "Results, Structure of neural activity during delay period; Figure 2e and 2f", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "R 11 of 12 distances under both readings and with cross-validated projections; the exception is the nearest distance. J 6 of 12 under both readings (4 and 5 cross-validated), on 3211 trials of its two vertical sessions; its horizontal sessions are not in the dandiset. Each distance rank pools both line tasks and both sessions of each. Split by task and session, R has 1, 4, 10 and 7 of 12 and J 1 and 3, so the counts rest on pooling sessions.", "deviations": [ "J has only vertical sessions here, against horizontal and vertical in the paper.", "R's horizontal targets lie at 5.2 + 10.4 k mm, so distances are matched by rank (1 to 12) within each task." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "distance-after-speed", "statement": "After regressing out speed from the neural activity, a positive correlation with target distance remains (p < 1e-4 for J and R).", "source": "Results, Structure of neural activity during delay period", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Cross-validated predictions of target distance from speed-residualised activity correlate with distance, J r = 0.123 (p = 1.2e-30), R r = 0.233 (p = 7.1e-158); in-sample r = 0.182 and 0.257. Within 3-rings the cross-validated r is 0.154 (J) and 0.265 (R).", "deviations": [ "The paper does not say how the correlation was tested; a 10-fold cross-validated linear regression was chosen." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "speed-distance-projection", "statement": "Projected onto the top PCs, the distance dimension is about half as large as the speed dimension.", "source": "Results, Structure of neural activity during delay period", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "The distance axis projects onto the top PCs as much as the speed axis for J (ratio 1.01) and more for R (1.68). With the plane projected out of the distance axis the ratios are 0.73 and 1.14.", "deviations": [ "The paper does not define the distance dimension or the projection; both are defined here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "single-trial-variance", "statement": "Across all single trials the speed dimension explains 2% (J) and 1% (R) of the variance of the neural state, and the spatial plane 20% (J) and 10% (R).", "source": "Results, Structure of neural activity during delay period", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Only R's speed value (0.86% against 1%) is within tolerance. All four values are below the paper's and keep its order, J above R. Within single sessions the plane explains 11.2 to 20.7% (J) and 6.5 to 14.2% (R).", "deviations": [ "J is 5 of its 16 sessions." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ellipse-orientation", "statement": "The distributions of single-trial neural states for each condition are elliptical, and for most conditions their major axis points along the direction of the mean neural state from the origin.", "source": "Results, Neural state variability during delay; Figure 3a and 3c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Major axis within 45 degrees of the condition mean's direction for 69 of 96 conditions (J, median 21.0 degrees, Wilcoxon p = 4.1e-08) and 99 of 132 (R, median 19.3 degrees, p = 8.0e-10). Median ratio of major to minor axis 1.35 (J) and 1.56 (R).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "on-greater-than-off", "statement": "The mean absolute on-axis (distance) deviation of the neural state is larger than the off-axis (direction) deviation, in each task (J p = 9e-7 ring, 4e-7 horizontal, 1e-8 vertical, 3e-14 3-rings; R 8e-3, 4e-7, 2e-7 and 0.19).", "source": "Results, Neural state variability during delay; Figure 3", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "On-axis exceeds off-axis with p < 0.05 in 5 of 6 task and monkey pairs under readings (a) paired over targets and (c) Welch over trials, 4 of 6 under (b). The exception is J's ring task, one session of four here (13 of 24 targets with on > off, paired p = 0.69). R's 3-rings task is not significant (paired p = 0.38), as in the paper (0.19).", "deviations": [ "J's ring task is 1 of 4 sessions.", "The test is not named; three readings were tested." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "relative-deviation-decreases", "statement": "Relative deviations of the neural state (deviation as a fraction of reach distance), on and off axis, decrease with reach distance.", "source": "Results, Neural state variability during delay; Figure 3b and 3d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Spearman rho of relative deviation with distance, on axis J -0.389 and R -0.404, off axis J -0.378 and R -0.402, all p below 1e-290. Absolute deviations grow slightly with distance (rho 0.073 to 0.103), so the decrease comes mainly from dividing by distance, and the test discriminates little.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "svm-ring-and-distance", "statement": "Direction classification of the ring targets reaches 32.2% for J (24 targets) and 16% for R (36 targets); distance classification over 12 targets reaches 18.9% (J) and 21.4% (R).", "source": "Results, Accuracy of endpoint prediction from delay activity; Figure 4a and 4b", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "All four accuracies are below the paper's (32.2, 16, 18.9, 21.4%) and well above chance (4.2, 2.8, 8.3%). With hyperparameters chosen on the 3-rings trials they are 24.3, 13.8, 16.0 and 18.3%. J's ring value comes from 1020 trials of one session against four in the paper, and its distance value from the vertical task only.", "deviations": [ "SVM hyperparameters are sklearn's defaults; the paper's tuned values are not reported. A tuned variant is shown.", "The tolerance is 10%, not the paper's SEM over folds (see the claims file).", "J ring is 1 of 4 sessions; J distance is the vertical task only." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "svm-3rings-by-ring", "statement": "Classifying the 16 directions of each ring of the 3-rings task separately, accuracy increases with ring distance; 23, 36 and 43% for J and 22, 28 and 29% for R.", "source": "Results, Accuracy of endpoint prediction from delay activity; Figure 4c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Accuracy rises with ring distance in both monkeys. J's values are within tolerance; R's are below it (paper 22, 28, 29%). With tuned hyperparameters R gives 20.2, 22.9 and 27.8%.", "deviations": [ "SVM hyperparameters are sklearn's defaults." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "arc-error-distance-independent", "statement": "Angular errors of direction classification decrease with ring distance, but errors measured as arc length are not significantly different between rings (F test, p > .05 for J and R).", "source": "Results, Accuracy of endpoint prediction from delay activity; Figure 4c and 4d", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Angular errors fall with ring distance (J 41.0, 24.3, 18.3 degrees; R 52.0, 42.4, 36.7), but arc errors grow (J 2.87, 3.40, 3.84 cm; R 3.63, 5.92, 7.69 cm), and the one-way ANOVA finds the rings different (J F = 22.15, p = 2.7e-10; R F = 52.16, p = 1.5e-22). Restricted to errors within the 4 cm ring's range, J's rings do not differ (p = 0.23) and R's do (p = 1.3e-03); the paper's Figure 4d inset uses that restriction for its means, so J matches there.", "deviations": [ "The paper's \"F test\" was read as a one-way ANOVA of per-trial arc errors; a variance test (Levene) and the restricted ANOVA are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "distance-error-and-plane-projection", "statement": "Mean distance-classification error is slightly but significantly lower than the arc-length error of direction classification, and projecting the activity onto the spatial plane before classification raises it (J 2.64 to 3.03 cm; R given as 2.78 and 3.27 cm), to the level of the direction errors.", "source": "Results, Accuracy of endpoint prediction from delay activity; Figure 4d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_even_chen_2019.ipynb", "notes": "Under reading (a) all four values are within tolerance and projection raises the error (Welch J p = 2.7e-07, R p = 4.3e-41; paired over trials J p = 4.9e-12, R p = 1.2e-62). R's full value is inside its bound (2.502 cm) by 0.001 cm, so the match is fragile. The full-activity distance error is lower than the arc error of every ring in both monkeys (p at most 3.1e-05). After projection it equals the arc error only for J's 4 cm ring (p = 0.46), so the claim that projection brings it to the level of the direction errors holds for 1 of 6 rings. With arc errors restricted to the 4 cm ring's range, as in the Figure 4d inset, the full error is still lower than every ring's (p at most 3.1e-05), and the projected error equals the arc error for J's 4 and 8 cm rings (p = 0.46 and 0.11) but not J's 12 cm ring (p = 5.3e-03) or any of R's (p at most 1.0e-04), 2 of 6 rings.", "deviations": [ "The paper prints R's values in an order that contradicts its text; two readings were listed and (a) matches.", "J's distance classification uses the vertical task only.", "The plane is fit on all trials, including the test folds of the plane-projected classifier." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "In every file the units' electrode_group labels are swapped. Units 0 to 95 are labelled PMd but their electrodes column points to electrode rows of group 1 (M1), and units 96 to 191 are labelled M1 but point to rows of group 2 (PMd), the rows the PMd LFP uses. The data agree with the electrodes column; in R the array labelled PMd has 29 silent channels and carries almost no target information (at most 6 significant channels per session in the delay window and decoding at most 0.03 above chance), though 40 of its 96 channels regress on target position when R's sessions are pooled; this is as expected of the M1 array the paper calls unusable. The conversion code assigns electrode_group by the order of a dictionary of groups." }, { "kind": "format_error", "statement": "In every J file the boundary between units 0 and 1 in units/spike_times_index is misplaced. Unit 0 stops 1323 to 3120 s into sessions of 3083 to 8106 s, and unit 1 holds two to five times the median number of spikes, with spike times that run to the session's end and restart near 0." }, { "kind": "metadata_error", "statement": "Hand, cursor, eye and decoded positions are stated in meters with conversion NaN; the values are in mm (targets at up to 120, hand reaching them at about the same values)." }, { "kind": "metadata_insufficient", "statement": "task_id is 2 in every trial and version_id is one value per monkey, so the files do not say which target configuration a session used; it must be inferred from target_pos, which has no unit. Electrode positions are NaN and impedances -1." }, { "kind": "metadata_error", "statement": "The trials column is_successful is described as \"if monkey started before the mandatory delay period after target shown\"; it holds the rig's trial success flag." }, { "kind": "metadata_error", "statement": "The dandiset description says the files hold sorted spikes; the units are threshold crossings of each electrode (one unit per electrode, built from the rig's spike rasters)." }, { "kind": "metadata_error", "statement": "The archive's assetsSummary for version 0.220124.2156 gives 15 files and 187.5 GB; the version holds 12 files and 39.5 GB." }, { "kind": "data_missing", "statement": "The dandiset holds 5 of the 16 sessions the paper uses for monkey J. All four horizontal sessions, three of four ring sessions and two of four in each other configuration are missing; the paper's own data link returns HTTP 403." }, { "kind": "other", "statement": "The files place R's horizontal targets on 2017-01-15 and 16 and vertical targets on 2017-01-17 and 18; the Methods give these dates the other way round. Grouped by the files' geometry, R's trial counts match the Methods' counts for horizontal and vertical better (within 4% and 3%) than grouped by date (12% and 5%)." }, { "kind": "other", "statement": "R's horizontal targets lie at 5.2 + 10.4 k mm from the center, not 1 cm apart as stated, and R's 2017-01-17 session holds 69 successful trials to six ring targets outside its layout." }, { "kind": "other", "statement": "R's delays run from 400 to 1000 ms, against 400 to 900 ms in the Methods, and R has only 26 trials without a delay (all on 2017-01-19), against 10% in the Methods; J has 19.8%." }, { "kind": "selection_undocumented", "statement": "R's 3-rings session holds 1340 successful delayed center-out trials where the paper used 912; neither the paper nor the dandiset says how the trials were selected." }, { "kind": "other", "statement": "In R's 2017-01-19 the cursor differs from the hand by more than 1 m in over 1% of samples; in the other sessions they agree to within 3 mm in 99% of samples." }, { "kind": "paper_inconsistency", "statement": "The Results give J's distance errors as \"3.03 cm v.s. 2.64 cm\" (projected, then full) and R's as \"2.78 cm v.s. 3.27 cm\", while stating that projection raises the error in both; the R values are printed in the reverse order or contradict the text." }, { "kind": "methods_unavailable", "statement": "The paper names no analysis code, does not report its SVM hyperparameters or the nulls of its p-values, and its data link returns HTTP 403." } ], "verifications": [ { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run (commit d455c0d) with the conclusion cells and the summary removed, the helper module and the claims file.", "agreed": 19, "of": 20, "disagreements": [ { "claim": "pca-variance", "outcome": "not_reproduced", "reason": "All 6 J values and R PCs 2-6 are within tolerance, but R PC1 is 72.8 against a lower bound of 72.9. The criterion's partial case requires all R values within, so by its letter this is not reproduced. It is a 0.14-point miss, and the result depends on the day-mean choice (the trial-window variant gives 80.5). The day mean is n_spikes / recorded_s, and recorded_s is the total in-trial hand time, while unit spans run to about 8300 s against 6520 s recorded; whether spikes exist between trials is never checked." } ] }, { "date": "2026-10-16", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the revised run (commit 57c6966) with its conclusions and summary, the helper module, the claims file and this attempt record.", "agreed": 20, "of": 20, "disagreements": [] } ] }, { "id": "000127-chowdhury-2020-01", "dandiset": "000127", "dandiset_version": "0.220113.0359", "paper": "10.7554/elife.48198", "paper_title": "Area 2 of primary somatosensory cortex encodes kinematics of the whole arm", "date": "2026-10-13", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code", "model": "not recorded", "protocol": "pilot-0" }, "tier": "agent_verified", "entry": "000127-chowdhury-2020", "entry_title": "Active and passive arm movements in somatosensory area 2 (Chowdhury et al. 2020)", "description": "Tests the active/passive findings of Chowdhury, Glaser and Miller (2020) on dandiset 000127, which holds one of the paper's twelve sessions. It compares hand and arm kinematics between active reaches and passive bumps, measures how well single neurons tell the two apart, and fits hand-only and whole-arm models of each neuron's firing. The paper's two-workspace experiment cannot be tested because those sessions are not in the dandiset.", "notebooks": [ { "path": "reproduce_chowdhury_2020.ipynb", "title": "Reproducing Chowdhury, Glaser & Miller (2020) from dandiset 000127", "executed": "notebooks/000127-chowdhury-2020/reproduce_chowdhury_2020.html" } ], "outcomes": [ { "claim": "fig4-whole-arm-fits-better", "statement": "In the two-workspace experiment, the whole-arm model predicted neural activity better than the hand-only model for 238 of 288 neurons, with no significant difference for the other 50.", "source": "Figure 4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds one session of the active/passive experiment. None of the eight two-workspace sessions is in it.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-consistent-across-workspaces", "statement": "A whole-arm model trained on both workspaces explained as much neural variance as models trained within a single workspace.", "source": "Figure 5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The two-workspace sessions are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-tuning-curves", "statement": "The whole-arm model predicted the shape of directional tuning curves in the two workspaces better than the hand-only model for 138 of 288 neurons, and worse for 2.", "source": "Figure 6", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The two-workspace sessions are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-pd-shift", "statement": "The whole-arm model predicted the shifts of preferred direction between workspaces better than the hand-only model, with a circular variance accounted for of 0.75 against 0.57.", "source": "Figure 7", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The two-workspace sessions are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig8-hand-speed-similar", "statement": "In the 120 ms after movement onset, average hand speed was similar in active reaches and passive bumps.", "source": "Figure 8B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chowdhury_2020.ipynb", "notes": "The speed traces of active and passive trials overlap in the 120 ms window and separate afterwards. Passive movements are 13% faster on average (0.207 against 0.183 m/s), half a standard deviation, which is statistically clear; the paper's \"similar\" is qualitative.", "deviations": [ "One session from one monkey; the paper has four sessions from two." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig8-arm-kinematics-separable", "statement": "A linear discriminant classifier predicted whether a movement was active or passive 89% of the time from whole-arm kinematics in the analysis window.", "source": "Results, active/passive section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chowdhury_2020.ipynb", "notes": "A linear discriminant tells active from passive trials 90% of the time from joint angles and velocities, against 58% from hand kinematics and 53% by chance. The paper reports 89% averaged over four sessions.", "deviations": [ "One session from one monkey; the paper has four sessions from two.", "Joint angles and velocities stand in for the hand and elbow marker kinematics, which are not in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig8-neurons-separable", "statement": "Many neurons had an above-chance separability index, the accuracy of a linear discriminant predicting the trial type from that neuron's firing.", "source": "Figure 8E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chowdhury_2020.ipynb", "notes": "20 of 50 neurons have a separability index above chance at p < 0.05, with a median of 0.56 and a highest value of 0.80.", "deviations": [ "One session from one monkey; the paper has four sessions from two.", "Neurons firing below 1 Hz in the window (15 of 65) are left out; the paper states no criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig9-whole-arm-fits-better", "statement": "In the active/passive experiment the whole-arm model again tended to out-perform the hand-only model, but for many more neurons than in the two-workspace experiment the difference was not significant.", "source": "Figure 9", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chowdhury_2020.ipynb", "notes": "The whole-arm stand-in is significantly better than the hand-only model for 15 of 50 neurons and worse for none; 35 (70%) show no significant difference, against 17% in the paper's two-workspace experiment. That comparison uses the paper's number.", "deviations": [ "One session from one monkey; the paper has four sessions from two.", "The whole-arm model is hand plus joint kinematics; the marker positions the paper's model uses are not in the dandiset.", "The hand-only model is two-dimensional, the fits carry a small ridge penalty, neurons below 1 Hz are left out, and no Bonferroni correction is applied." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig10-inconsistent-across-conditions", "statement": "Unlike in the two-workspace experiment, many neurons had no consistent relationship with arm kinematics across active and passive movements, shown by negative pseudo-R2 for the model trained on both conditions.", "source": "Figure 10", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chowdhury_2020.ipynb", "notes": "19 of 50 neurons scored on active trials and 23 of 50 on passive trials have negative pseudo-R2 for the model trained on both conditions, but about as many (17 and 25) are negative when trained within one condition. Only 5 and 3 neurons are positive within a condition and negative across both. Training on both costs a little on active trials and nothing on passive trials.", "deviations": [ "One session from one monkey; the paper has four sessions from two.", "The whole-arm model is hand plus joint kinematics, as for fig9-whole-arm-fits-better.", "Pseudo-R2 for one trial type is computed on a repeat's pooled held-out predictions, against that type's own mean firing; the paper does not say which mean it used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig11-separability-vs-consistency", "statement": "The consistency of the whole-arm model, its pseudo-R2 when trained on both conditions, correlated negatively with a neuron's separability index.", "source": "Figure 11", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chowdhury_2020.ipynb", "notes": "Scored on active trials, model consistency correlates negatively with separability (Spearman -0.38, 95% interval -0.60 to -0.11). Scored on passive trials the correlation is -0.13 and on all trials together 0.14; neither can be told apart from zero.", "deviations": [ "One session from one monkey; the paper has four sessions from two.", "The whole-arm model is hand plus joint kinematics, as for fig9-whole-arm-fits-better." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds one of the twelve sessions analysed in the paper, and none from the two-workspace experiment, so four of the paper's main findings cannot be tested from it." }, { "kind": "data_missing", "statement": "The positions of the arm markers, which the paper's whole-arm model is built on, are not included. Joint angles and muscle lengths derived from them are." }, { "kind": "metadata_error", "statement": "The text descriptions of hand position and hand velocity give centimetres while the stated unit is metres. The stated unit, with the file's conversion factor, is correct." }, { "kind": "selection_undocumented", "statement": "The dandiset's metadata names the paper without saying which part of it the data covers. It was packaged for the Neural Latents Benchmark, not as the paper's data release." } ], "verifications": [ { "date": "2026-10-13", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "First draft, with the author's conclusions withheld. Only the six claims that were tested.", "agreed": 5, "of": 6, "disagreements": [ { "claim": "fig8-hand-speed-similar", "outcome": "reproduced", "reason": "The author's draft said partially reproduced because passive movements are 13% faster. The verifier judged the paper's qualitative \"similar\" to hold, as the traces overlap in the window. The author adopted that." } ] }, { "date": "2026-10-13", "kind": "agent", "by": "The same independent agent, second round", "reviewed": "The revised notebook with the author's conclusions. For the four blocked claims the verifier checked the dandiset's file list and metadata on the archive itself and found two files, the training and test splits of one active/passive session of one monkey.", "agreed": 10, "of": 10, "disagreements": [] } ] }, { "id": "000130-sohn-2019-01", "dandiset": "000130", "dandiset_version": "0.241017.1448", "paper": "10.1016/j.neuron.2019.06.012", "paper_title": "Bayesian computation through cortical latent dynamics", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "000130-sohn-2019", "entry_title": "Bayesian computation through cortical latent dynamics (Sohn et al. 2019)", "description": "Tests the findings of Sohn, Narain, Meirhaeghe and Jazayeri (2019) on dandiset 000130, the Neural Latents Benchmark's DMFC_RSG set, which holds one session of monkey H performing the Ready-Set-Go task with 54 units from dorsomedial frontal cortex. It tests the behaviour and the Bayesian observer model, single-unit sensitivity to the prior and elapsed time, the geometry and speed of population trajectories, the alternative mechanisms, and single-trial GPFA trajectories. Monkey G and the recurrent network models are not in the dandiset.", "notebooks": [ { "path": "reproduce_sohn_2019.ipynb", "title": "Reproducing Sohn et al. (2019) from dandiset 000130", "executed": "notebooks/000130-sohn-2019/reproduce_sohn_2019.html" } ], "outcomes": [ { "claim": "beh-slopes", "statement": "Regression slopes of tp on ts are positive and less than one in every condition, so the animals estimated ts and their responses were biased toward the mean of the prior.", "source": "Results, Task and behavior; Figure 1E and S1; Table S1", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Six of 8 weighted slopes of tp on ts lie between 0 and 1 (0.50 to 0.90) and 5 of 8 have 95% intervals excluding 0 and 1. The Short prior slopes with the eye are 1.11 (Eye Right, interval 1.01 to 1.21) and 1.01 (Eye Left). All 8 are positive, so the animal estimated ts; the part of the statement about bias toward the mean fails in the two eye Short conditions.", "deviations": [ "One session of monkey H; the paper's slopes come from 17 sessions of H and 12 of G.", "Outliers removed with the file's `is_outlier` flag, which a refit of the Methods' mixture model does not reproduce (see findings)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "beh-overlap-prior", "statement": "At the overlapping ts of 800 ms, biases were in opposite directions for the two priors (rank-sum test, p < 1e-43 in animal H over 17 sessions).", "source": "Results, Task and behavior; Figure 1E; Table S2", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "At ts = 800 ms the median bias is +28.3 ms for Short (93 trials) and +47.6 ms for Long (107 trials), both positive; rank-sum p = 0.073. The Long tp is the longer in 2 of 4 datasets (Hand Right p = 0.00099, Hand Left p = 0.069, where the Short bias is -61.6 ms); in the eye datasets the Short tp is the longer (Eye Left +79.1 against +18.6 ms, p = 0.051).", "deviations": [ "One session; the paper's p < 1e-43 pools 17 sessions of monkey H." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "beh-sigmoid-increments", "statement": "Increments of tp between neighbouring ts are smaller at the extremes of the prior than near its mean, as the sigmoidal Bayesian estimator predicts (signed-rank test, p < 1e-11 in animal H).", "source": "Results, Task and behavior; Figure 2E and 2F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The middle increment of mean tp exceeds the extreme one in 7 of 8 conditions (median difference 31.3 ms), two-sided signed-rank p = 0.0156. Hand Left, Short is the exception (-10.7 ms).", "deviations": [ "The test is over the 8 conditions of one session; the paper's is over sessions and conditions of both animals." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "beh-long-more-bias", "statement": "Biases are larger for the Long prior than for the Short prior, as scalar variability predicts; regression slopes are smaller for Long.", "source": "Results, Task and behavior; Figure 2G and 2H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The Long slope is below the Short slope in all 4 datasets (mean 0.716 against 0.898), weighted or unweighted.", "deviations": [ "One session." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "beh-bayes-model", "statement": "A Bayesian observer model with scalar measurement and production noise fit to the behaviour captures the bias and the variance of tp in all conditions.", "source": "Results, Task and behavior; Figure 2C and 2D; Table S3", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The predicted SD of tp correlates positively with the observed one in all 4 datasets (r = 0.28 to 0.91), but the bias R2 reaches 0.8 in 2 of 4 (0.12, 0.67, 0.87, 0.98). The poorly fit datasets are the eye ones, whose Short slopes exceed 1, with wm = 0.013 and 0.025. All fits converged. Table S3 was not available, so the fitted wm (0.013 to 0.117) and wp (0.090 to 0.106) are not compared.", "deviations": [ "Fit to one session per effector and direction; the paper pools sessions.", "The prior is taken as continuous uniform over each range, as the Results describe; the task used 5 discrete values.", "The bias R2 threshold of 0.8 is a choice made here; the paper shows the fit graphically." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "glm-prior-ts", "statement": "About 30% of neurons were modulated by elapsed time (27% in monkey H) and more than 60% were sensitive to the prior (65% in monkey H), by a Poisson GLM of spike counts before Set compared by BIC.", "source": "Results, Single-neuron response profiles; Figure 3E; Methods, Generalized linear model", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "36 of 48 units are prior-dependent (75.0%, 95% interval 61.2 to 85.1%) and 22 of 48 are ts-dependent (45.8%, interval 32.6 to 59.7%), against 65% and 27% for monkey H. Both are outside tolerance and higher; the interval of the prior fraction includes 65%, that of the ts fraction excludes 27%. A likelihood-ratio test gives higher fractions still (prior 77.1 to 87.5%, ts 66.7 to 77.1% at p < 0.01 and 0.05). Chance levels by the same BIC rule are far lower; prior labels shuffled within effector and direction give 0 to 8.3% and labels shifted along the session by 50 to 200 trials, which keeps the prior blocks, 2.1 to 14.6%; time points shuffled within trials give 0 to 2.1% ts-dependent. The ts test in the Short prior alone gives 31.2% and in the Long prior alone 33.3%, both above 27 +/- 2.7%.", "deviations": [ "48 units from one session, where the paper's fractions use 536 units of monkey H over 17 sessions.", "The GLM design with attrition (rows for every trial whose Set comes after each time point) is read from the Methods; the paper's code was not available.", "The Long prior's ts test uses the Long ts as time points (800 to 1200 ms after Ready); Eq. 3 of the paper does not say which time points were used, and a unit counts as ts-dependent when either prior's test finds it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dfr-overlap-support", "statement": "At the overlapping ts of 800 ms, firing rates differ between priors, with the largest difference during the support of the prior, between 480 and 800 ms after Ready.", "source": "Results, Single-neuron response profiles; Figure 3C and 3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The mean RMS rate difference at ts = 800 ms is largest at 480 to 640 ms after Ready (6.86 spikes/s), above the 95th percentile of the shuffled maximum (3.11). Before Ready it is at the shuffle level. Per dataset the largest bin is 480-640 (2 datasets), 640-800 and 800-960 ms, and the mean is also high just after Set (6.07 at 800 to 960 ms). Over 200 bootstrap samples of trials the peak is in 480 to 640 ms in 192 and in 800 to 960 ms in 8 (96% within 480 to 800 ms).", "deviations": [ "The time range (320 ms before Ready to 640 ms after Set) and the shuffle reference are chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pca-dimensionality", "statement": "Population activity is low dimensional; 3 to 4 principal components in the estimation epoch and 5 to 10 in the production epoch explain about 75% of the variance.", "source": "Results, Geometry and dynamics of population activity; Figure S3", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Two components reach 75% of the variance in the estimation epoch in all 4 datasets (3 explain 86 to 90%), and 2, 2, 5 and 4 in the production epoch; 1 of 8 values is in range. The count depends on normalisation, which the Methods do not mention; with rates z-scored per unit (a variant) the counts are 3 or 4 and 6 to 10, all 8 in range, and with soft normalisation (range plus 5 spikes/s) 6 of 8 are in range. The outcome is judged on unnormalised rates, as the claims file fixed.", "deviations": [ "48 simultaneously recorded units, where the paper's trial-averaged PCA pools units over 17 sessions; more units can add dimensions.", "Rates not normalised before PCA; the Methods do not say." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "encoding-r2", "statement": "Projections of estimation-epoch neural states onto the encoding axis match the Bayesian estimates from the model fitted to the behaviour (R2 = 0.993 for the Short prior, 0.996 for the Long prior, monkey H, Hand Left).", "source": "Results, Encoding Bayesian estimate along curved trajectory; Figure 4C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Both readings match. (a) Hand Left R2 = 0.998 (Short) and 0.996 (Long), given as measured; (b) the mean of 4 datasets 0.959 and 0.989. With only 2 PCs in the estimation epoch, random unit axes also fit te well (median R2 0.73 to 0.98); the R2 on u exceeds 95% of random axes in 3 of 8 dataset-priors (Hand Right Long and both Hand Left), so the paper's statement that the match is specific to u (Figure S5) holds only for those. With normalised rates (3 or 4 PCs) R2 stays above 0.94 in every dataset-prior, and u beats 95% of random axes in 2 of 8 (soft normalisation) and 0 of 8 (z-scored).", "deviations": [ "te comes from the observer model fitted to this session.", "The encoding axis averages difference vectors up to the middle of the support, a choice made here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "encoding-bayes-beats-linear", "statement": "Neural projections are better explained by the Bayesian model than by a linear function of ts with the same number of parameters, for both priors (signed-rank test on RMSE, p = 0.008 for each prior).", "source": "Results, Encoding Bayesian estimate along curved trajectory; Figure 4D top", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The Bayesian RMSE is lower in 4 of 4 datasets for Long and 3 of 4 for Short (Hand Right Short 0.99 against 0.80). Where the Bayesian model wins it is better by 0.045 to 0.573 spikes/s; in Hand Right Short it is worse by 0.186. With the RMSE weighted by trial counts, as in the fit, the counts are the same. In the matched control period of the Long prior (short-in-long-control) the Bayesian model is also better in 3 of 4 datasets, so in this session the advantage is not specific to the support of the prior.", "deviations": [ "4 datasets, where the paper had 8; a signed-rank test over 4 cannot reach p < 0.05, so the criterion counts datasets." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "short-in-long-control", "statement": "In the Long prior during the period matched to the support of the Short prior (\"Short In Long\"), there is no sigmoidal representation; the Bayesian model is not better than the linear one (signed-rank test, p = 0.74).", "source": "Results, Encoding Bayesian estimate along curved trajectory; Figure 4D top", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Judged on the paper's test as the claims file fixes; signed-rank p = 0.25 over 4 datasets, where the smallest attainable p is 0.125, so the test could not have found an effect. The effect sizes do not show the control's contrast; the Bayesian model is better in 3 of 4 datasets with a median relative RMSE difference of -0.089, at least as large as in the Short prior (-0.060). This outcome carries no evidence for the absence the paper reports.", "deviations": [ "4 datasets, where the paper had 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "neural-long-more-bias", "statement": "Neural projections show more bias for the Long prior than for the Short prior, as a smaller regression slope of Xu on ts (signed-rank test, p = 0.008).", "source": "Results, Encoding Bayesian estimate along curved trajectory; Figure 4D bottom", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The Long slope of Xu on ts is below the Short slope in 4 of 4 datasets (ratios 0.55, 0.63, 0.34, 0.97).", "deviations": [ "4 datasets, where the paper had 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "speed-vs-projection", "statement": "Larger projections on the encoding axis at Set are followed by slower neural trajectories in the production epoch (Pearson correlation, rho Short = -0.74, rho Long = -0.51).", "source": "Results, Controlling speed based on Bayesian estimate; Figure 4E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Both correlations are negative and significant (Short p = 6.2e-10, Long p = 3.7e-07) and stronger than reported, outside tolerance. Within datasets -0.75 to -1.00; with Xu z-scored per dataset -0.759 and -0.779, and the speed divided by mean tp gives -0.917 and -0.923. Both quantities change with ts; with the residuals of each on ts within dataset and prior the correlation is -0.195 (Short) and +0.069 (Long), so the pooled relation is carried by the common dependence on ts. The paper's control (z-scoring within ts) is on single-trial GPFA states of the production epoch, not computed here.", "deviations": [ "20 points per prior (4 datasets), where the paper had 40.", "Speed is the mean step between 20 ms states up to the shortest tp; the Methods' division by the Set to Go duration is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "initial-speed-biased", "statement": "The initial speed of production trajectories (Set to Set + 400 ms) is biased toward the middle of the prior; its dependence on ts is shallower than the unbiased profile proportional to 1/ts (signed-rank test, p < 1e-3 over conditions and animals).", "source": "Results, Controlling speed based on Bayesian estimate; Figure 4F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The initial speed falls with ts in 8 of 8 dataset-priors and is shallower than the 1/ts profile in 7 of 8 (Eye Right Long is the exception), two-sided signed-rank p = 0.039. No trial had tp below 400 ms.", "deviations": [ "8 dataset-priors of one animal, where the paper's test combines 16 over two animals." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "speed-predicts-tp", "statement": "The speed of neural trajectories in the production epoch predicts the mean tp (Pearson correlation, rho Short = -0.58, rho Long = -0.52).", "source": "Results, Controlling speed based on Bayesian estimate; Figure 4G", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Faster trajectories go with shorter mean tp in both priors (Short p = 0.00024, Long p = 0.00017), more strongly than reported and outside tolerance. Within datasets -0.80 to -0.99. The Neural Latents Benchmark's trial-by-trial variant gives r = -0.195 to -0.740 (mean -0.519), 7 of 8 conditions with p < 0.05. With speed and tp z-scored within each ts trial by trial, as in the paper's control, r = -0.317 (Short, 481 trials, p = 1.1e-12) and -0.201 (Long, 502 trials, p = 5.5e-06), negative in 8 of 8 dataset-priors and p < 0.05 in 6. A Poisson null at constant rates with each trial's own duration gives mean null r of -0.071 (Short) and -0.033 (Long) over 20 simulations, and the observed values are below every null value, so the shorter averaging of short trials accounts for a small part. Residuals on ts of the 20 condition means give +0.084 and -0.283.", "deviations": [ "20 points per prior, where the paper had 40." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "alt-speed-unmodulated", "statement": "Instantaneous speed of neural trajectories in the full neural space is not modulated during the support of each prior (signed-rank test for zero regression slopes, p = 0.64 for Short, p = 0.08 for Long).", "source": "Results, Alternative mechanisms (speed hypothesis); Figure 5B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Judged on the paper's test as the claims file fixes; signed-rank p = 0.125 for each prior, the smallest a test over 4 datasets can give, so the outcome carries no evidence for the absence of modulation. All 8 slopes are positive, but noise produces slopes of this size, as later bins average fewer trials. For Poisson units at constant rates with the same trials and Set times, the mean null slope is above the observed one in 8 of 8 and no observed slope exceeds the null's 95th percentile. With only the trials of the longest ts, which last the whole support, slopes are -0.106 to +0.529 per 100 ms and outside the null's 95% range in 1 of 8 (below it). The bootstrap intervals over trials are biased upward (the point estimate is below the interval in 2 of 8) and are not used. The observed slopes are below the null mean in 8 of 8 with all trials and in 8 of 8 with fixed trials, while the null's mean speed over the support is below the observed one in 7 of 8 (null / observed 0.65 to 1.18), so the null is not noisier than the data. This points to a speed that falls during the support, if the units' noise is no larger than Poisson; it was not tested further. The session shows no speed increase beyond what noise produces.", "deviations": [ "4 datasets, where the paper had 8.", "Speed from smoothed trial-averaged rates with attrition in 20 ms bins of 48 units; the paper's smoothing for this measure is not stated." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "alt-transient-parallel", "statement": "In the first 200 ms after Set, trajectories for different ts run parallel; their distance to the middle ts trajectory does not change (signed-rank test for zero slopes, p = 0.92 for the shortest ts, p = 0.13 for the longest).", "source": "Results, Alternative mechanisms (transient hypothesis); Figure 5D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "For the longest ts the distance to the middle trajectory falls in the first 200 ms after Set in 6 of 8 dataset-priors (median -15.3% of the mean distance per 100 ms), signed-rank p = 0.039; for the shortest ts p = 0.078 (6 of 8 rising, median +26.7%). The PCA kept 1 to 4 components, one in Eye Left. For the longest ts p = 0.016 with 60% of the variance, 0.039 with 90%, 0.023 in the full space and 0.039 with z-scored rates; with soft-normalised rates 0.055.", "deviations": [ "8 dataset-priors of one animal, where the paper's test used 16.", "Rates smoothed over 100 ms before to 300 ms after Set and cut to the first 200 ms, a choice made here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "alt-threshold-monotonic", "statement": "Aligned to the response, distances between trajectories for different ts decrease steadily up to movement initiation, without the converging then diverging pattern a ts-dependent threshold would produce.", "source": "Results, Alternative mechanisms (threshold hypothesis); Figure 5F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "With the components reaching 60% of the variance (1 to 3), the median time of the minimum distance is 210 ms before Go; 6 of 32 curves have their minimum in the last 40 ms and 14 in the last 200 ms. Distances do fall overall (the distance at Go is below that 800 ms earlier in 26 of 32). With 75% of the variance the median minimum is 80 ms before Go and in the full space 40 ms, which would meet the criterion, so the outcome depends on the number of components. With one component (eye datasets, 16 curves) the signed difference changes sign at the minimum in 12, so those minima are crossings; 4 have the minimum at Go (3 of them not crossings), and the distance at Go is more than 10 times the minimum in 5. With at least 2 components the median minimum is 230 ms before Go, with at least 3 it is 70 ms before Go.", "deviations": [ "The paper's test (one-tailed signed-rank, p = 1.5e-4) cannot be read unambiguously; the criterion on the median time of the minimum was fixed before the analysis.", "The 60% of variance follows the figure legend; the 75% of the Methods is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gpfa-variance-inverted-u", "statement": "The variance across single trials of the GPFA neural state at Set projected on the encoding axis has an inverted-U profile over ts, lower at the extremes of each prior (one-tailed signed-rank test on quadratic coefficients, p = 0.0273, monkey H).", "source": "Results, The curved manifold hypothesis captures the variance; Figure 6C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "The quadratic coefficient is negative in 5 of 8 dataset-priors; one-tailed signed-rank p = 0.125 (paper 0.0273). Cross-validation chose 8 latent dimensions in all 4 datasets, the larger candidate. 12 latents, scored on the same folds as a variant, beat 8 in all 4 datasets; with them the coefficient is negative in 5 of 8, p = 0.125. After 100 EM iterations the training log-likelihood still rose by 0.064 to 0.085% over the last 25 iterations.", "deviations": [ "Latent dimensionality chosen only from 4 and 8, with 100 EM iterations, to keep the run short; the paper's cross-validation range is not stated.", "One GPFA per effector and direction with both priors; the paper does not say how trials were grouped." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gpfa-mean-sigmoid", "statement": "The mean of the single-trial GPFA projections is sigmoidal (signed-rank test on increments, p = 0.0078) and has a higher slope for the Short prior (one-tailed signed-rank, p = 0.0625).", "source": "Results, The curved manifold hypothesis captures the variance; Figure 6D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sohn_2019.ipynb", "notes": "Middle increments of the mean projection exceed the extreme ones in 8 of 8 (two-sided signed-rank p = 0.0078) and the Short slope is the higher in 4 of 4 datasets (one-tailed p = 0.0625), the paper's values; the mean rises with ts in 8 of 8. With 12 latents, 8 of 8 (p = 0.0078) and 4 of 4.", "deviations": [ "As for gpfa-variance-inverted-u." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "rnn-curved-manifold", "statement": "Recurrent neural networks trained on the two-prior task with scalar measurement noise behave like a Bayesian observer and show curved trajectories during the support of the prior, like DMFC.", "source": "Results, Recurrent network models; Figure 7A to 7C and S7", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The claim is about recurrent networks trained in silico. The dandiset holds only the two NWB files of spikes and trials, and the trained networks and the training code are not public (the code is available from the corresponding author on request). Training new networks from the Methods would be a new study, not a test against this data.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "rnn-perturbation", "statement": "In trained networks, compressing states along the encoding axis increases the regression to the mean of tp, and translating them shifts tp.", "source": "Results, Recurrent network models; Figure 7D and 7E", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As for rnn-curved-manifold; the perturbation experiments are on the trained networks.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "monkey-g", "statement": "The behavioural and neural results hold in monkey G as in monkey H.", "source": "Results throughout; Figures 1 to 6 and S1 to S6", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds one session of monkey H. A search of the DANDI archive for Jazayeri, Sohn, DMFC and Ready-Set-Go finds no other dandiset with these recordings (only 000620, 000897 and 001275 of the same lab, on other tasks). The paper says the data are in the article and the code is available on request.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds one recording session (2016-12-11) of monkey H, with 54 units, where the paper analyses 17 sessions of H and 12 of monkey G (617 and 741 units recorded, 536 and 636 kept for analysis). The dandiset's description does not say that it holds one session of the paper's 29 or which one. The 48 units that pass the paper's rate rule match its count for the single session of H used for GPFA." }, { "kind": "data_missing", "statement": "Following the Neural Latents Benchmark design, 283 trials of the session are in the test file without ts, tp, prior, effector or direction and without 14 of the 54 units, on a separate clock. These trials cannot be used for any analysis of the paper." }, { "kind": "metadata_error", "statement": "The description of the `iti` column says 500 ms after Short prior trials and 1220 ms after Long ones; the values are the reverse (Short 1220, Long 500), as the paper states." }, { "kind": "metadata_insufficient", "statement": "`tp` is described as the time between Set and Go, but is a median 17.9 ms longer than go_time minus set_time (5th to 95th percentile 1.1 to 29.8 ms, up to 200.6 ms in used trials). `ts` is the nominal interval, within 23.5 ms of ready_time minus set_time. Neither difference is documented." }, { "kind": "selection_undocumented", "statement": "The `is_outlier` flag is described only as a probabilistic mixture model. It flags 46 completed trials (4.47%); a refit of the Methods' Gaussian and uniform mixture per prior, ts, effector and direction flags 10 of these and no others, and the other 36 have tp from 0.53 to 1.60 times ts." }, { "kind": "metadata_insufficient", "statement": "Units carry no single-unit or multi-unit label and no electrode or probe; the electrode table has no positions or impedances and gives the filtering as unknown. The paper distinguishes 456 single units from 902 multi-units." }, { "kind": "methods_unavailable", "statement": "The paper's analysis code is available only on request. The code the dandiset links (nlb_tools) loads the data and scores benchmark models, and holds none of the paper's analyses." }, { "kind": "paper_inconsistency", "statement": "For the single high-yield session of each monkey used for GPFA, the Results give the number of neurons as N = 48 for monkey H and N = 107 for monkey G, the Methods as N = 48 in H and 96 in G." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's accepted manuscript (PMC6805134). The verifier checked the archive's asset list and metadata for the blocked claims and ran synthetic checks of weighted_slope, PCA, encoding_axis, increments, BayesObserver and attrition_rates.", "agreed": 23, "of": 23, "disagreements": [] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The second executed notebook in full, with its conclusion cells and summary, the README and this attempt record. The verifier could not get the paper's text (PMC's BioC service returned 429 and Europe PMC 500), so the figures taken from the paper were not checked against it.", "agreed": 23, "of": 23, "disagreements": [] } ] }, { "id": "000147-guan-2022-01", "dandiset": "000147", "dandiset_version": "0.221122.2256", "paper": "10.7554/elife.74478", "paper_title": "Stability of motor representations after paralysis", "date": "2026-10-13", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code", "model": "claude-opus-5-5", "protocol": "pilot-2" }, "tier": "agent_verified", "entry": "000147-guan-2022", "entry_title": "Finger representations in human posterior parietal cortex after paralysis (Guan et al. 2022)", "description": "Tests the findings of Guan, Aflalo et al. (2022) that dandiset 000147 can support. It checks online and offline finger decoding, single-unit tuning and whether the cue location can be decoded, builds the cross-validated finger RDMs of the ten sessions, compares them with the able-bodied fMRI models from the authors' repository, and tests whether the representation changed across sessions and runs. The calibration and control tasks, the component model RDMs and sorting quality metrics are not in the dandiset, so the claims that need them are blocked.", "notebooks": [ { "path": "reproduce_guan_2022.ipynb", "title": "Reproducing Guan, Aflalo et al. (2022) from dandiset 000147", "executed": "notebooks/000147-guan-2022/reproduce_guan_2022.html" } ], "outcomes": [ { "claim": "recording-counts", "statement": "Over 10 sessions the recordings yielded 95.8 (SD 6.7) sorted neurons and 408 (SD 40.8) trials of the main finger task per session.", "source": "Results, \"Intracortical recordings during finger flexion\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "The ten files hold 95.8 units per session (SD 6.7) and 408.0 trials per session (SD 40.8), 4080 trials in all, as reported.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1b-online-accuracy", "statement": "Online BCI classification of the cued finger was 86% accurate (SD 4% across sessions, weighted by trials) over 4016 trials in 10 sessions, against a chance level of 17%. No-Go trials of the first session are excluded because the classifier could not output No-Go that day.", "source": "Figure 1b, Figure 1-figure supplement 3, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "The recorded decoder outputs match the cued finger on 85.96% of the 4016 scored trials, with a trial-weighted SD across sessions of 3.6%. Shuffling the outputs gives 16.9%, the paper's chance level of 17%.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1b-errors-middle-ring-pinky", "statement": "Most (70%) of the online classification errors were middle-ring or ring-pinky confusions.", "source": "Results, \"Representational structure did not trend toward task optimum\"; Figure 1b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "Of the 379 online errors between two fingers, 69.7% confuse middle with ring or ring with pinky. Counting errors that involve No-Go, the fraction is 46.8% of 564 errors, or 59.2% of the 446 errors on finger trials.", "deviations": [ "The paper does not say which errors form the denominator. Only errors between two fingers, leaving out No-Go, give the paper's 70%." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1s4a-offline-accuracy", "statement": "Offline classification of the cued finger from sorted firing rates in the window 0.5 to 1.5 s after the cue, with diagonal LDA and leave-one-out cross-validation within each session, was 92% accurate (SD 2% across sessions) over 4080 trials.", "source": "Figure 1-figure supplement 4a, Results, Methods \"Finger classification\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "Diagonal LDA with leave-one-out cross-validation within sessions gives 93.4% (weighted SD 1.6%) over 4080 trials. The classifier and eight stratified folds of the authors' code give 92.4% (SD 1.7%).", "deviations": [ "The paper's methods say leave-one-out; the authors' code uses eight folds, a mean-count cutoff of 0.5, z-scoring and LDA with identity covariance. Both are reported, and the measured value is the leave-one-out one." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1s4b-calibration-accuracy", "statement": "In the calibration task, offline cross-validated finger classification was 96% accurate (SD 3%) over 530 trials in nine sessions.", "source": "Figure 1-figure supplement 4b, Results", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds only the main finger task. The calibration task, recorded at the start of each day, is not in any of the ten files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1s5-tuned-fraction", "statement": "Most (89%) neurons were significantly tuned to at least one finger movement, by a two-tailed t-test of each finger's firing rate in the 0.5 to 1.5 s window against No-Go trials, p < 0.05 after FDR correction, with neurons below 0.1 Hz excluded and neurons pooled across sessions.", "source": "Results, Figure 1-figure supplement 5, Methods \"Single-unit tuning to finger flexion\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "With FDR correction over all units and fingers pooled, 87.9% of 958 units are tuned to at least one finger. FDR within each session gives 87.5%, within each unit 83.9%, and no correction 91.7%. No unit fell below the 0.1 Hz cutoff, whether the rate is taken in the window over all trials (lowest 0.113 Hz) or over the whole recording (lowest 0.147 Hz).", "deviations": [ "The FDR family is not stated in the paper; the measured value pools all units and fingers.", "Student's t-test with equal variances; the paper does not say which form of the t-test." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1s6a-gaze-regression", "statement": "Linear regression could not decode the cue's screen coordinates from neural activity in the attempted-movement window; cross-validated r2 was close to 0 in every session.", "source": "Figure 1-figure supplement 6a", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": "reproduce_guan_2022.ipynb", "notes": "The trials table gives the cue location as an index from 1 to 12 on the grid of three rows and four columns, described only as a screen location index, with no map to the grid or to screen coordinates. As a check, the coordinates were regressed on spike counts under the two plain orders of the index. Ordinary least squares gives a cross-validated r2 below 0 for both coordinates in all ten sessions under both orders. Ridge regression gives r2 up to 0.097 for x and 0.104 for y, with both coordinates at or below 0.05 in 5 (row order) or 6 (column order) of the ten sessions. The result depends on the regression as well as on the unknown layout.", "deviations": [ "The check assumes the index runs along the rows or down the columns; neither is documented.", "The paper does not say whether its regression was regularised, so both ordinary least squares and ridge regression are shown, each with eight unshuffled folds per session." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1s6b-gaze-classification", "statement": "A diagonal LDA classifier could not classify the cue location from neural activity in the attempted-movement window.", "source": "Figure 1-figure supplement 6b", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "Diagonal LDA classifies the 12 cue locations at 11.5% against a chance level of 8.3% (binomial p = 1e-12), above all 500 label shuffles across trials (highest 10.0%) and all 500 shuffles within finger (highest 10.2%). The authors' classifier gives 11.2%, and removing each finger's mean activity first gives 11.7%. Five of the ten sessions are above chance at p < 0.05. With folds that never split a screen the accuracy is 11.1%, above all 200 shuffles of location within screens (highest 9.8%), and with folds that never split a run it is 11.3%. Every screen cues each location once; location and position within the screen are weakly associated over all trials (chi-square p = 0.037). The cued finger is classified at 93.4% from the same features. With folds that never split a run, 11.3% is above all 200 shuffles of location within runs (highest 9.8%). Position within the screen is itself decoded at 10.5%, above all 200 shuffles within screens (highest 9.5%), but after removing each position's mean activity location is still classified at 11.1%.", "deviations": [ "Eight stratified folds within each session; the paper does not say how this classifier was cross-validated, and the authors' code uses eight folds for its classifiers.", "The paper shows a confusion matrix without an accuracy or a test, so the comparison is with its statement that the location could not be classified." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1s6c-control-task", "statement": "Fingers could not be classified from neural activity during the control task, in which the participant viewed the cues without attempting movements.", "source": "Figure 1-figure supplement 6c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The no-movement control task is not in the dandiset; every file is described as the main task and contains only its trials.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-rdm-structure", "statement": "In the session-averaged representational dissimilarity matrix (cross-validated Mahalanobis distance, window 0.5 to 1.5 s, No-Go excluded), the thumb is distinct, while the middle, ring and pinky fingers are close.", "source": "Figure 2d and 2e, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "In the session-averaged RDM, max-scaled, the distances among middle, ring and pinky are 0.21 to 0.48 and every distance involving the thumb is 0.64 or more. This holds in 9 of the 10 sessions on their own.", "deviations": [ "The noise covariance uses OAS shrinkage, as in the authors' code; the paper names Ledoit-Wolf." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-able-bodied-over-unstructured", "statement": "The measured RDMs match the able-bodied PC-IP fMRI model better than the unstructured (pairwise-equidistant) model, by whitened unbiased cosine similarity (WUC), p = 5.7e-5.", "source": "Figure 2f, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "Mean WUC is 0.881 with the able-bodied PC-IP model and 0.781 with the unstructured model. The PC-IP model is higher in all 10 sessions; the bootstrap 95% interval of the difference is 0.074 to 0.127, and the bootstrap t-test gives p = 4.4e-5 (paper 5.7e-5).", "deviations": [ "The model RDMs are read from the authors' code repository at the commit archived with the paper, not from the dandiset.", "The p-value comes from 1000 resamples of the sessions (mean difference over its bootstrap SD, nine degrees of freedom); the paper used rsatoolbox's bootstrap t-test." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig2s5-mc-over-pcip", "statement": "The measured RDMs match the able-bodied motor cortex (MC) fMRI model better than the able-bodied PC-IP fMRI model (p = 1.9e-6), and the WUC with the MC model is close to the noise ceiling.", "source": "Figure 2-figure supplement 5a, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "Mean WUC with the MC model is 0.969, higher than with the PC-IP model in all 10 sessions (difference 0.088, bootstrap 95% interval 0.060 to 0.112, p = 7.9e-5; paper 1.9e-6). It is 0.015 below the lower noise ceiling of 0.984, and at or above its own session's ceiling in 1 of 10 sessions.", "deviations": [ "The model RDMs are read from the authors' code repository, as for fig2f-able-bodied-over-unstructured.", "The criterion's margin of 0.05 below the noise ceiling is a choice; the paper says only \"close to\"." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig2-typical-among-individuals", "statement": "Compared with the RDMs of individual able-bodied fMRI participants, participant NS's average PC-IP RDM was statistically typical (permutation test, p = 0.55).", "source": "Results, Figure 2-figure supplement 4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The test needs the RDMs of the 36 individual able-bodied fMRI participants. Neither the dandiset nor the authors' code repository holds them; the repository has only the group means.", "deviations": [], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "rdm-consistency", "statement": "The finger RDMs were consistent across sessions, with an average pairwise correlation between session RDMs of r = 0.90 (SD 0.04, min 0.83, max 0.99).", "source": "Results, \"Representational structure did not trend toward task optimum\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "The 45 pairs of session RDMs correlate at a mean Pearson r of 0.928 (SD 0.041, min 0.817, max 0.990), against 0.90 (SD 0.04, min 0.83, max 0.99). The mean is 0.028 above the paper's, inside the tolerance of 0.03.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-no-trend-to-unstructured", "statement": "Over sessions the model fit did not trend from the able-bodied model toward the unstructured model (session by model interaction t(6) = 0.50, one-tailed p = 0.32).", "source": "Figure 3a, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "The session by model interaction is t(16) = 1.47, one-tailed p = 0.080 toward the unstructured model (paper t(6) = 0.50, p = 0.32). The WUC with the PC-IP model alone declines across sessions (slope -0.009 per session, p = 0.038); the slopes for the unstructured and MC models are not significant (p = 0.20 and 0.23). In other specifications the trend is also not significant. The same t read with 6 degrees of freedom gives p = 0.096; the difference between the unstructured and PC-IP fits regressed on session gives t(8) = 1.30, p = 0.116; with the MC model in place of PC-IP the slope is negative (p = 0.84).", "deviations": [ "Ordinary least squares on the twenty session-by-model WUC values, with sixteen residual degrees of freedom. The paper's t(6) implies a different model or degrees of freedom, which it does not describe, and its code for this test is not in the repository.", "Three specifications are shown, since the paper's t(6) is not explained.", "No Bayes factor is computed." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig3b-confused-pairs-no-increase", "statement": "The distances between the most confused finger pairs (middle-ring and ring-pinky) did not increase across sessions (one-tailed p > 0.99) or across runs within sessions (one-tailed p = 0.67).", "source": "Figure 3b, Results, Methods \"Measuring changes in the representational structure\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "For the middle-ring and ring-pinky distances of 85 per-run RDMs, the session term is t(8) = -3.56 (paper -4.5) and the run term t(83) = -1.05 (paper -0.45). In all six estimates the coefficients are negative and the one-tailed p for an increase is 0.73 or more.", "deviations": [ "The paper's code for this regression is not in its repository. The regression follows the methods' formula on per-run RDMs, with degrees of freedom of sessions minus two for the session term and runs minus two for the run term, as the paper's t(8) and t(82) suggest.", "The dandiset has 85 runs; the paper's t(82) implies 84.", "Per-run RDMs use five folds of eight trials each, so a fold's noise covariance rests on one or two trials per finger and inflates the distances (mean 5.06 against 0.68 for session RDMs). A variant with the session's noise covariance (mean 0.76) is reported.", "No Bayes factors are computed." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3s1-all-pairs-small-decrease", "statement": "Across all finger pairs the inter-finger distances did not increase; they decreased slightly across sessions (t(8) = -4.0, two-tailed p = 0.004) and across runs within sessions (t(82) = -2.4, p = 0.019), with very small effect sizes (Cohen's f2 of 0.008 and 0.005).", "source": "Figure 3-figure supplement 1, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_guan_2022.ipynb", "notes": "Over all ten pairs the session and run coefficients are negative in all six estimates, and Cohen's f2 is 0.006 for session and 0.012 for run in the main regression, and 0.017 and 0.013 with the session's noise covariance (paper 0.008 and 0.005). In the main regression the session decrease is t(8) = -2.28, p = 0.052, and the run decrease t(83) = -3.12, p = 0.0025. With the session's noise covariance they are t(8) = -3.76, p = 0.0055, and t(83) = -3.29, p = 0.0015, against the paper's t(8) = -4.0, p = 0.004, and t(82) = -2.4, p = 0.019.", "deviations": [ "The same regression and choices as fig3b-confused-pairs-no-increase.", "The session decrease is significant at 0.05 only in the variant with the session's noise covariance; the pre-registered criterion asks for negative coefficients and small effect sizes, not significance. The per-run fold covariance inflates the distances of the main regression, so the variant with the session's covariance is the better estimate of the session term." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-muscle-before-somatotopy", "statement": "In a time-resolved decomposition of the RDM into muscle and somatotopy component models, the muscle model emerged 170 ms before the somatotopy model (two-sided Wilcoxon signed-rank test across sessions, p = 0.002).", "source": "Figure 4e, Figure 4-figure supplement 2", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The decomposition needs the muscle and somatotopy model RDMs of Ejaz et al. (2015). They are not in the dandiset, and the authors' code repository loads them from a models folder that holds only the two fMRI models and the unstructured model at the archived commit.", "deviations": [], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig4s1-model-selection", "statement": "Among combinations of the hand-usage, muscle and somatotopy models, the hand usage plus somatotopy and muscle plus somatotopy combinations matched the data best.", "source": "Figure 4-figure supplement 1, Results", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The hand-usage, muscle and somatotopy model RDMs are not in the dandiset or the authors' code repository.", "deviations": [], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig4s4-well-isolated-units", "statement": "The able-bodied match and the representational dynamics hold when only well-isolated units (lowest third of L-ratio) are used.", "source": "Figure 4-figure supplement 4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The units table has spike times, observation intervals, electrodes and electrode groups only, the same in every file. There are no waveforms, features or L-ratio values from which to select well-isolated units, and the representational dynamics part also needs the missing component models.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds only the main finger task. The calibration task (nine sessions) and the no-movement control task (six sessions) analysed in the paper are not included." }, { "kind": "data_missing", "statement": "The model RDMs that the paper's main comparisons rest on are not in the dandiset. The two able-bodied fMRI group RDMs and the unstructured model are in the authors' code repository; the muscle, hand-usage and somatotopy models and the individual fMRI participants' RDMs are in neither." }, { "kind": "data_missing", "statement": "The units have no waveforms or sorting quality metrics, so the paper's selection of well-isolated units by L-ratio cannot be repeated." }, { "kind": "other", "statement": "Spike times are not in ascending order within units. In nearly every unit the spikes of the first seconds of each run are stored before the rest of the previous run (590 to 1016 backward jumps per file). No trial's analysed range meets an affected span, so sorted spike times give the same counts, but tools that assume ascending spike times could be misled near run boundaries." }, { "kind": "other", "statement": "The cue location is an index from 1 to 12, described as the screen location index of the cue, with no map to the grid of three rows and four columns or to screen coordinates. The trials table's Run and TrialNumber columns read \"no description\", and the start time has only the NWB default description. Decoding the finger over time is consistent with a start time at the cue onset, but does not pin it to the cue within a few hundred milliseconds." }, { "kind": "other", "statement": "Electrode coordinates and impedances are missing (NaN), and the participant is identified as P1 in the files and as NS in the paper." }, { "kind": "other", "statement": "The paper says the first session had 84 No-Go trials. The file has 64, and the paper's own total of 4016 scored trials (4080 minus the first session's No-Go trials) implies 64." }, { "kind": "selection_undocumented", "statement": "The two published versions hold the same ten files. The earlier version, which the authors' download script pins, names the bioRxiv preprint; the later one names the eLife paper. Neither says which of the paper's tasks the data cover." } ], "verifications": [ { "date": "2026-10-13", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module, the claims file and the paper's full text (PMC9555862). For the blocked claims the verifier checked the archive's asset list and metadata and the authors' repository.", "agreed": 20, "of": 20, "disagreements": [] }, { "date": "2026-10-13", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run, with its conclusion cells and summary, the helper module, the README and this attempt record, against the verifier's round-1 points.", "agreed": 20, "of": 20, "disagreements": [] } ] }, { "id": "000207-zheng-2022-01", "dandiset": "000207", "dandiset_version": "0.220216.0323", "paper": "10.1038/s41593-022-01020-w", "paper_title": "Neurons detect cognitive boundaries to structure episodic memories in humans", "date": "2026-10-13", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code", "model": "not recorded", "protocol": "pilot-1" }, "tier": "agent_verified", "entry": "000207-zheng-2022", "entry_title": "Cognitive boundaries and human medial temporal lobe neurons (Zheng et al. 2022)", "description": "Tests the findings of Zheng et al. (2022) that can be tested on dandiset 000207, which holds spike times of medial temporal lobe neurons and the behaviour of 19 patients in a task with video clips that contain no boundary, a soft boundary or a hard boundary. It compares memory for temporal order and for scenes across the three kinds of clip, looks for boundary cells and event cells with the paper's definitions, counts neurons that respond to clip onsets, and measures how far the population state moves after a boundary. Eleven of the paper's twenty findings cannot be tested, because the dandiset has no local field potentials, no neurons outside the medial temporal lobe, no labels for the paper's cell classes, and no way to link test trials with soft or hard boundaries to the clips they came from.", "notebooks": [ { "path": "reproduce_zheng_2022.ipynb", "title": "Reproducing Zheng et al. (2022) from dandiset 000207", "executed": "notebooks/000207-zheng-2022/reproduce_zheng_2022.html" } ], "outcomes": [ { "claim": "fig2a-order-accuracy", "statement": "In the time discrimination task, subjects chose the frame that was shown first in 73% of trials when the two frames were separated by no boundary or by a soft boundary, and in 53% of trials, significantly fewer, when they were separated by a hard boundary.", "source": "Figure 2a; Results, paragraph 3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zheng_2022.ipynb", "notes": "Time discrimination accuracy is 0.528 across a hard boundary, 0.728 with no boundary and 0.720 with a soft boundary (paper 0.53, 0.73, 0.73). It is lower across a hard boundary in 18 of 19 subjects (paired p < 1e-6 against both).", "deviations": [ "19 of the paper's 20 subjects; the twentieth is not in the dandiset.", "Trials without a response are kept as coded in the file; leaving them out moves no mean by more than 0.01.", "Paired tests over subjects are added to the paper's one-way ANOVA." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-order-reaction-time", "statement": "Reaction times in the time discrimination task were longer when the two frames were separated by a hard boundary (2.10 s) than by no boundary (1.62 s) or a soft boundary (1.59 s).", "source": "Figure 2b; Results, paragraph 3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zheng_2022.ipynb", "notes": "Mean reaction time is 2.05 s across a hard boundary, 1.62 s with no boundary and 1.54 s with a soft boundary (paper 2.10, 1.62, 1.59 s), longer across a hard boundary in 18 of 19 subjects. The file's RT column is used, which runs from the disappearance of the frames.", "deviations": [ "19 of the paper's 20 subjects.", "Trials without a response have an RT of 0 in the file and are kept; leaving them out gives 2.08, 1.64 and 1.56 s." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-order-confidence", "statement": "Confidence ratings in the time discrimination task were lower when the two frames were separated by a hard boundary (1.95 on a scale of 1 to 3) than by no boundary (2.52) or a soft boundary (2.59).", "source": "Figure 2c; Results, paragraph 3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zheng_2022.ipynb", "notes": "Mean confidence is 1.98 across a hard boundary, 2.45 with no boundary and 2.51 with a soft boundary (paper 1.95, 2.52, 2.59), lower across a hard boundary in 18 of 19 subjects.", "deviations": [ "19 of the paper's 20 subjects.", "Trials without a response have a confidence of 0 in the file and are kept; leaving them out gives 2.00, 2.48 and 2.55." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "edfig2a-recognition-similar", "statement": "Scene recognition accuracy did not differ between frames from clips with no boundary (76%), a soft boundary (75%) and a hard boundary (75%).", "source": "Extended Data Figure 2a; Results, paragraph 4", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zheng_2022.ipynb", "notes": "Scene recognition accuracy over targets and foils is 0.738, 0.739 and 0.718 for clips with no, a soft and a hard boundary (paper 0.76, 0.75, 0.75), with no difference in a one-way ANOVA (F(2, 54) = 0.38, p = 0.69). Accuracy for hard-boundary clips is the lowest in every variant, by 0.01 to 0.05, without reaching significance.", "deviations": [ "19 of the paper's 20 subjects.", "The paper does not say whether foils are counted. Targets and foils are; targets alone give 0.737, 0.718 and 0.688 (p = 0.59)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2def-recognition-vs-boundary-distance", "statement": "Recognition accuracy for a target frame fell with the time between the frame and the boundary before it, for soft boundaries (r = -0.61) and hard boundaries (r = -0.44), but not for clips with no boundary (r = 0.085).", "source": "Figure 2d-f", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The dandiset does not give the position of a tested frame within its clip. Its name says frameA or frameB, which by the paper's Methods (one frame from each half) is probably the first or the second half; no column states it. For clips with soft or hard boundaries the frame names also do not identify the clip.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-boundary-cells", "statement": "42 of 580 medial temporal lobe neurons (7.24%) were boundary cells, which changed their firing in the second after soft and hard boundaries but not in the middle of clips with no boundary; 2.11% were expected by chance.", "source": "Figure 3a-c; Results, section 2; Methods, Boundary cell", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_zheng_2022.ipynb", "notes": "The analysis was run, but the procedure behind the paper's count could not be determined. 1 of 549 units (0.18%) meets the Methods' definition of a boundary cell, against 42 of 580 (7.24%) in the paper. The paper's chance level is 2.11%; the literal definition gives 0.03% here, alpha = 0.10 gives 0.10% and a looser pooled reading 0.55%, and the verifier found in simulation that the five-test definition stays at or below about 1% for every response profile it tried. No reading tried here produces the paper's chance level, so the paper's count came from a different procedure. Under the pooled reading there are 15 boundary cells (2.73%), more than in any of 300 shuffles. The authors' published code contains no cell selection. Recorded as not_reproduced before verification.", "deviations": [ "549 units from 18 sessions against the paper's 580 from 19. Subject 19 is left out because its spike times are not on the clock of the trial tables, and the dandiset's units differ from the paper's in number and in their split by region.", "The paper's \"permutation t-test\" is implemented as a sign-flip test for before against after and a one-sided label-permutation test between conditions, with 1000 permutations.", "Soft-boundary trials are every soft boundary of a session, in SB clips and in HB clips (75 per session). The Methods do not say; this follows the authors' published plotting code (B01_raster_psth_encoding_BAligned_BSep_NWB.m, lines 29 to 37). The first soft boundary of each SB clip, used before that code was read, is kept in the notebook as an alternative.", "Each condition is tested on its own, five tests per class, which is the literal reading of the Methods. The authors' published code has no cell selection to check this against.", "300 label shuffles for the chance level instead of 1000." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-event-cells", "statement": "36 of 580 medial temporal lobe neurons (6.20%) were event cells, which changed their firing in the second after hard boundaries but not after soft boundaries or in the middle of clips with no boundary; 2.26% were expected by chance.", "source": "Figure 3e-g; Results, section 2; Methods, Event cell", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_zheng_2022.ipynb", "notes": "As fig3c-boundary-cells. 7 of 549 units (1.28%) meet the Methods' definition of an event cell, more than in any of 300 label shuffles (mean 1.22, maximum 6), but about a fifth of the paper's 36 of 580 (6.20%). At alpha = 0.10 there are 12 (2.19%, above all 300 shuffles) and under the pooled reading 10 (1.82%, 4 of 300 shuffles as many). The chance levels of these readings are 0.22%, 0.72% and 0.65%, against the paper's 2.26%. Recorded as partially_reproduced before verification.", "deviations": [ "The same as for fig3c-boundary-cells." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-cell-regions", "statement": "Boundary cells were most common in the parahippocampal gyrus (18 of 68 neurons, 26%, against 7% in the amygdala and 3.5% in the hippocampus), and event cells in the hippocampus (27 of 343, 7.9%, against 4.3% in the amygdala and 2.9% in the parahippocampal gyrus).", "source": "Results, section 2; Supplementary Table 4", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_zheng_2022.ipynb", "notes": "Depends on the cell selections of fig3c-boundary-cells and fig3g-event-cells, whose procedure could not be determined. With the literal definition there is no boundary cell among 53 parahippocampal units (paper 18 of 68), and event cells are 2 of 267 in the hippocampus, 3 of 229 in the amygdala and 2 of 53 in the parahippocampal gyrus. The dandiset's split of units by region also differs from the paper's. Recorded as not_reproduced before verification.", "deviations": [ "The same as for fig3c-boundary-cells." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3dh-no-onset-response", "statement": "Boundary cells and event cells did not change their firing at clip onsets or offsets during encoding, nor at image onsets or offsets in the two memory tests.", "source": "Figure 3d,h; Extended Data Figures 3 and 4", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The dandiset does not say which units the paper classified as boundary or event cells, and the Methods' definitions select 1 and 7 units here, fewer than the 10 of each that the claim's criterion requires. The authors' published code does not select or list the cells. The notebook reports that none of the 8 responds to clip onsets or offsets.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "edfig5-clip-onset-cells", "statement": "76 of 580 medial temporal lobe neurons (13.1%) changed their firing at clip onsets and 4 of 580 (0.7%) at clip offsets, and none of them was a boundary cell or an event cell.", "source": "Extended Data Figure 5; Results, section 2", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zheng_2022.ipynb", "notes": "98 of 549 units (17.9%) fire more after clip onset, against 13.1% in the paper; the gap of 4.8 points is just inside the tolerance of 5, and 98 is more than a proportion of 13.1% would plausibly give (p = 9e-4). 26 units (4.7%) fire more after clip offset, the chance level, against 0.7% in the paper. Seven sessions hold 82 of the 98 onset-responsive units; the other eleven have 16 of 359 (4.5%), about chance, so the overall proportion averages over sessions that differ widely. The spike clock is shown to be aligned for ten of those eleven; for subject 3 (1 of 31 units responsive) it could not be established. None of the 8 boundary and event cells found responds to onsets or offsets, which is too few to judge that part of the claim.", "deviations": [ "549 units from 18 sessions against the paper's 580 from 19.", "The paper's one-tailed test does not state its direction; an increase is tested. A decrease is found in 3.1% of units at onset.", "The permutation test is a sign-flip test with 1000 permutations." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3j-response-latency", "statement": "Boundary cells responded to hard boundaries about 100 ms earlier than event cells; their firing peaked 197 ms after the boundary, against 301 ms for event cells.", "source": "Figure 3i-j", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the paper's boundary and event cells, which the dandiset does not label; 1 and 7 are found here, fewer than the 10 of each that the claim's criterion requires.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-outside-mtl", "statement": "Of 405 neurons recorded outside the medial temporal lobe, 8 were boundary cells and 9 were event cells, so boundary responses are largely confined to the medial temporal lobe.", "source": "Results, section 2; Supplementary Tables 2 and 4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "All 565 units in the dandiset are in the hippocampus, amygdala or parahippocampal gyrus. The paper's 405 units from other areas are not included.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-boundary-cells-predict-recognition", "statement": "Boundary cells fired more after soft and hard boundaries during encoding when the frame that followed the boundary was later recognised than when it was forgotten; there was no such difference for clips with no boundary, for the time discrimination task, or for event cells.", "source": "Figure 4a-c; Extended Data Figures 6 and 7", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Scene recognition trials with soft or hard boundaries cannot be linked to the clip they test. Their frame names carry 10 distinct numbers, with up to 12 trials per number, where the clips are numbered 1 to 30. The authors' published code links nothing either; it groups test trials only by boundary type. The paper's boundary cells are not labelled.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-event-cells-phase-predicts-order", "statement": "Event cells' spikes were locked more strongly to the phase of the theta-band local field potential after soft and hard boundaries when the temporal order of the clip was later remembered than when it was not; boundary cells showed no such effect.", "source": "Figure 4e-h", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds spike times only. There are no local field potentials from which to compute theta phase.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5d-state-shift", "statement": "The state of the population of all medial temporal lobe neurons changed abruptly in the first 300 ms after soft and hard boundaries, and only slowly in clips with no boundary, measured as the distance in principal-component space from the state at the boundary.", "source": "Figure 5a-d", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_zheng_2022.ipynb", "notes": "After a hard boundary the distance from the state at the boundary is larger than in clips with no boundary (9.03 against 7.42, p = 0.0001) and larger than before the boundary (after minus before 0.84 against 0.04, p = 0.004); 12 of 18 subjects show it alone. After a soft boundary the distance is larger than without a boundary (8.15, p = 0.003) but equally large before the boundary (after minus before 0.00, p = 0.55). That the shift completes within 300 ms was not shown.", "deviations": [ "549 units from 18 sessions against the paper's 580 from 19.", "Pseudo-trials are matched across subjects by clip name; the paper does not say how.", "Principal components are fitted on the three condition averages from 1 s before to 1.5 s after the boundary, giving 22 components for 99% of the variance against the paper's 55. The averages are of the same trials that are then compared.", "A trial is z-scored from 1 s before to 8 s after clip onset; the paper says \"the entire trial\".", "Clips with soft boundaries are aligned to their first soft boundary, one pseudo-trial per clip. The authors' published code does not cover this analysis.", "The comparison with the second before the boundary is this attempt's; the paper shows curves.", "Two SB clips have their first soft boundary less than 1 s after onset. Leaving them out gives the same result (SB after minus before -0.03, p = 0.59; HB 0.84, p = 0.003)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5ij-state-shift-predicts-memory", "statement": "The distance the population state travelled in the second after a boundary correlated positively with later recognition accuracy for soft (r = 0.65) and hard (r = 0.57) boundaries, and negatively with time discrimination accuracy for hard boundaries (r = -0.68).", "source": "Figure 5i-j", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the memory outcome of each clip with a soft or hard boundary. Test trials of those conditions cannot be linked to clips, in either memory test, and the authors' published code contains no mapping.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-reinstatement", "statement": "During scene recognition, population activity correlated with the activity during encoding shortly after the soft or hard boundary of the tested clip, for correctly recognised targets and for foils wrongly called old, but not for forgotten targets or correctly rejected foils.", "source": "Figure 6a-h", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs each scene recognition trial paired with the encoding of its clip. That is possible only for clips with no boundary, which are the control condition of the claim.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6i-reinstatement-timing", "statement": "The reinstated state was most similar to the state about 1.2 s after the boundary that preceded the tested frame, and 1.5 to 1.7 s before the tested frame itself was shown.", "source": "Figure 6i", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As fig6-reinstatement. The time of the tested frame within its clip is not given either.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6jm-reinstatement-confidence", "statement": "Reinstatement after soft and hard boundaries was stronger for old decisions made with high confidence than with low confidence.", "source": "Figure 6j-m", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As fig6-reinstatement.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6no-false-alarm-similarity", "statement": "For foils wrongly called old, reinstatement was stronger when the foil was highly similar to its target; for correctly rejected foils it did not vary with similarity.", "source": "Figure 6n-o", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The similarity ratings of targets and foils, collected from a separate group of raters, are not in the dandiset. The trials could not be linked to clips either.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "In the most recent published version (0.230530.1822) the spike times of subjects 13, 17 and 18 are shifted by 191.5, -16.8 and 9.3 s against the encoding trials, which did not move, so spikes and clips no longer line up. The version the paper cites (0.220216.0323) does not have this shift." }, { "kind": "metadata_error", "statement": "The spike times of subject 19 are near -7.02e12 s while its events run from 0 to 2892 s, in both versions read. Its 16 units cannot be aligned to the task." }, { "kind": "identifier_missing", "statement": "Scene recognition and time discrimination trials with soft or hard boundaries cannot be linked to the clips they test. Their frame names are numbered differently from the clips (10 distinct numbers in recognition, 1 to 60 in time discrimination, against clips 1 to 30). The position of a tested frame within its clip is not given." }, { "kind": "identifier_missing", "statement": "The dandiset does not say which units the paper classified as boundary cells or event cells, so the paper's selection cannot be compared with a new one cell by cell." }, { "kind": "data_missing", "statement": "The dandiset has no local field potentials, no units outside the medial temporal lobe (the paper has 405), no similarity ratings and no stimuli, and it lacks the behaviour of one of the paper's 20 subjects." }, { "kind": "selection_undocumented", "statement": "The dandiset has 565 medial temporal lobe units where the paper analyses 580, with a different split by region (hippocampus 279 against 343, amygdala 233 against 169, parahippocampal gyrus 53 against 68). Nothing says how the two sets relate." }, { "kind": "metadata_error", "statement": "Several column descriptions do not match the values. stimCategory holds 0, 1, 2 and is described as 1, 2, 3. A missing second or third boundary is stored as the clip's start time and described as 0. The accuracy code 0 for \"no response\" is never used; trials without a response are coded incorrect, or, in 20 time discrimination trials, correct. resp_value is 1 for those trials and described as -1. RT is measured from the disappearance of the frames, which its description does not say, and is negative in 151 time discrimination trials." }, { "kind": "metadata_error", "statement": "The events series holds 43 entries with a code 0 that its description does not list, with timestamps as low as -7.0e12 s. The spike times have no stated unit." }, { "kind": "methods_unavailable", "statement": "The paper's Methods do not specify the permutation test, which soft boundaries are used, or how trials are matched across subjects for the pseudopopulation. The definitions of boundary and event cells, read literally, give a chance level about seventy times lower than the paper reports." }, { "kind": "methods_unavailable", "statement": "The code the dandiset links to (github.com/rutishauserlab/cogboundary-zheng, commit 60f7ece) is four scripts that plot rasters from the NWB files. It contains none of the paper's analyses, no cell selection, chance level, statistics, state-space or reinstatement analysis, and nothing that links a tested frame to its clip." }, { "kind": "metadata_error", "statement": "The authors' plotting code drops missing boundaries by testing for a stored time above 0. In version 0.220216.0323 a missing boundary is stored as the clip's start time, so the code would keep 150 soft-boundary rows where 75 exist and its fixed row ranges for the three conditions would be wrong. In version 0.230530.1822 missing boundaries are NaN and the code works, but that version has the shifted spike times." }, { "kind": "other", "statement": "Methods and published code disagree on the firing-rate traces. The Methods give a 200 ms window moved in 2 ms steps; the code uses 10 ms bins smoothed with a Gaussian window of 20 bins. The code shows 0.5 s before and 1 s after a boundary. It also treats every soft boundary, including those inside hard-boundary clips, as a soft-boundary trial (75 per session), which the Methods do not state." }, { "kind": "other", "statement": "Four hard-boundary clips (HB_7, HB_11, HB_14, HB_15) drive strong population activity in the half second before the hard boundary; all contain a soft boundary between 2.75 and 3.40 s. This raises the baseline of a before-against-after test of the hard boundary." } ], "verifications": [ { "date": "2026-10-13", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1, the notebook at commit 8284b56 executed, with the author's conclusions and summary withheld, the helper module and the claims file. Outcomes below are compared with those recorded before verification.", "agreed": 17, "of": 20, "disagreements": [ { "claim": "fig3c-boundary-cells", "outcome": "blocked", "reason": "Blocked by methods_underspecified. In simulation the five-test conjunction under label shuffling stayed at or below about 1% chance for every response profile tried, so the paper's 2.11% cannot come from the procedure as written, and failing to match 42 cells does not show the effect is absent." }, { "claim": "fig3g-event-cells", "outcome": "blocked", "reason": "As fig3c-boundary-cells." }, { "claim": "fig3-cell-regions", "outcome": "blocked", "reason": "Follows from fig3c-boundary-cells and fig3g-event-cells." } ] }, { "date": "2026-10-13", "kind": "agent", "by": "The same independent agent as round 1", "reviewed": "Round 2, the notebook executed after the round-1 changes, with the conclusions and summary, the helper module, the entry README and this record. Its other findings were a header that still counted the outcomes from before verification, a summary sentence on chance levels that covered only four readings, and round-1 reasons recorded in words it had not used. All were corrected.", "agreed": 20, "of": 20, "disagreements": [] } ] }, { "id": "000213-tingley-2018-01", "dandiset": "000213", "dandiset_version": "0.250624.0438", "paper": "10.1016/j.neuron.2018.04.028", "paper_title": "Transformation of a Spatial Map across the Hippocampal-Lateral Septal Circuit", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000213-tingley-2018", "entry_title": "Spatial phase coding in the lateral septum (Tingley and Buzsaki 2018)", "description": "Tests the findings of Tingley and Buzsaki (2018) on dandiset 000213, which holds 67 sessions of simultaneous hippocampal and lateral septum recordings from five rats running on alternation mazes and a linear track. It decodes position from the spike rate and the spike theta phase of each LS and hippocampal unit, finds place fields, measures spatial information, relates phase coding to recording depth, and measures hippocampal-LS theta coherence and theta-gamma coupling, and detects hippocampal-LS cell assemblies on a random sample of pairs.", "notebooks": [ { "path": "reproduce_tingley_2018.ipynb", "title": "Reproducing Tingley and Buzsaki (2018) from dandiset 000213", "executed": "notebooks/000213-tingley-2018/reproduce_tingley_2018.html" } ], "outcomes": [ { "claim": "ls-neuron-count", "statement": "A total of 1,647 LS neurons were recorded from five animals, in 62 sessions.", "source": "Results, third paragraph; Figure 2G (N = 62 sessions)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "1,696 units are labelled ls (DT2 375, DT5 480, DT7 60, DT8 296, DT9 485), 3.0% more than 1,647, in 62 sessions, and all five rats hold LS units. 43 units of DT7 20170317 carry no region label and are not counted.", "deviations": [ "The criterion was written after the counts had been seen in the data check." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "hpc-unit-count", "statement": "The hippocampal recordings hold 2,297 isolated CA1 units and 654 CA3 units (2,951 in all, Figure 3A).", "source": "Results, first paragraph; Figure 3A legend", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "2,593 units are labelled hpc (+12.9% on 2,297 CA1 units, outside tolerance) and 624 ca3 (-4.6% on 654, within); the sum, 3,217, is 9.0% above 2,951. 36 sessions hold hpc units and 11 ca3 units, where Figure 6A gives 63 CA1 and 19 CA3 sessions.", "deviations": [ "The labels hpc and ca3 are read as CA1 and CA3; the dandiset does not define hpc.", "The criterion was written after the counts had been seen in the data check." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ls-active-neurons", "statement": "Of the LS neurons, 840 fired at least 1.5 action potentials per trial on average.", "source": "Results, third paragraph; STAR Methods, position prediction analysis", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "793 LS neurons pass (-5.6% on 840), over 3,694 neuron-condition pairs against the paper's 4,393; 1,630 of 1,696 LS units have a condition with at least 10 trials. With 1.0, 2.0 and 3.0 spikes per trial the count is 932, 707 and 563.", "deviations": [ "Conditions are formed from trial type, direction and start and end site, as the paper's trial conditions are not in the dandiset; the count depends on them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-ls-phase-vs-shuffle", "statement": "The majority of LS neurons (751 of 840, 89%) showed position encoding in their spike theta phase, compared with shuffled data, in at least one condition.", "source": "Results, third paragraph; Figure 2C and 2D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "408 of 783 decoded active LS neurons (52.1%) decode position from phase better than chance at p < 0.01 in at least one condition, against 89%; 66.0% at p < 0.05 and 43.3% at p < 0.001. Per rat 39% (DT2) to 63% (DT9). 23.2% of conditions pass. The rate code passes its own chance test in 54.4% of neurons. Mean MSE over LS conditions is 6,359 for phase against 6,839 for its chance; uniform guessing over 200 bins gives 6,666. In the 37 sessions whose theta channel has more 6 to 9 Hz than 1 to 4 Hz power the fraction is 52.9%, against 51.1% in the others, so the weak theta of DT5 does not account for the gap.", "deviations": [ "Linearization (path fraction, 200 bins), conditions and the theta channel are rebuilt; the paper's are not in the dandiset.", "The binning of spike phases (bz_phaseMap2Bins) is not public; the circular mean per bin is used.", "10 active LS neurons of DT2 20160217, which has no hippocampal channel, are not decoded." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-ls-phase-beats-rate", "statement": "Spike-phase decoding outperformed rate decoding of the rat's position for 786 of 840 LS neurons, 3,046 of 4,393 conditions, and 62 of 62 sessions.", "source": "Results, third paragraph; Figures 2F and 2G", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Phase beats rate at p < 0.01 in 662 of 783 neurons (84.5%, paper 93.6%), 1,762 of 3,660 conditions (48.1%, paper 69.3%) and 58 of 58 sessions (paper 62 of 62). The neuron and condition fractions are outside tolerance and fewer than half the conditions pass, so the criterion gives not reproduced; the direction holds in every rat (neurons 72% to 95%) and session, and rate beats phase in 5.3% of conditions. At p < 0.05, 89.5% of neurons and 60.1% of conditions; in the 37 sessions with a theta ratio above 1, 87.5% and 52.8%; with whole trials held out, 72.9% and 35.4%. Samples are split at random as in the paper's per-cell decoder (randperm over all trial-by-bin samples in scratch_07_11_17_spatialBinnedMaxCorr.m).", "deviations": [ "As for fig2-ls-phase-vs-shuffle.", "58 sessions are decoded, not 62; DT2 20160217 has no theta reference, and three sessions have no LS condition that passes." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-ls-phase-lower-mse", "statement": "Across LS neurons the spike-phase code is stronger than the rate code (two-sample t tests; N = 4,393 conditions, p < 1e-100; N = 62 sessions, p < 1e-10).", "source": "Results, third paragraph; Figure 2E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Over 3,660 LS conditions phase MSE is 6,359 and rate MSE 7,404 (t = -33.8, p = 2.5e-232); over 58 sessions 6,349 and 7,481 (p = 2.9e-23). Each rat gives phase lower (DT7 p = 0.018, others below 1e-38). In the 37 sessions with a theta ratio above 1, p = 2.9e-147. With whole trials held out, 6,527 against 7,920.", "deviations": [ "As for fig2-ls-phase-vs-shuffle." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2fg-mse-difference", "statement": "The mean phase minus rate MSE is about -1,000 for LS conditions and -33 for hippocampal place fields, and -1,024 and -25 for LS and hippocampal sessions.", "source": "Figure 2F and 2G legends", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "The LS condition mean, -1,045, is within tolerance of -1,000; the LS session mean, -1,132, is just outside -1,024 plus or minus 102; the hippocampal place field mean (-234) and session mean (-126) are far from -33 and -25. LS values are larger in magnitude than the hippocampal ones at both levels. Per rat the LS mean runs from -565 (DT7) to -1,428 (DT2).", "deviations": [ "MSE is in bins squared with 200 bins of about 1.1 cm; the paper's bin count is not given.", "Only 531 hippocampal place fields are found against 1,820 (see ls-few-place-fields)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1i-hpc-rate-phase-equivalent", "statement": "For hippocampal place fields the distributions of rate and phase decoding errors are statistically equivalent (two-sample KS test; 1,820 place fields, p = 0.19; 45 sessions, p = 0.61).", "source": "Results, first section; Figure 1I", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Changed from reproduced in revision, after the place fields were found on the Gaussian rate map the paper's code uses. The two-sample KS test finds a difference between phase and rate MSE over 531 place fields (D = 0.085, p = 0.044), so the claim of absence fails; over 42 sessions it finds none (D = 0.167, p = 0.61). The mean phase minus rate MSE is -234 bins squared (fields) and -126 (sessions). Per rat only DT2 differs (KS p = 0.001; DT5, DT7, DT9 p = 0.51 to 0.79). With the 318 fields of the 5-bin box map, p = 0.097. Over all 5,045 included hippocampal conditions the distributions differ (p = 7.4e-48); with whole trials held out the fields differ too (KS p below 0.001); and without the rule dropping peaks whose SD across trials exceeds their mean, 2,320 fields differ (D = 0.104, p below 0.001).", "deviations": [ "531 fields in 42 sessions, against 1,820 in 45; the field detector finds fewer fields than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ls-few-place-fields", "statement": "Only 5.3% (232 of 4,393) of LS rate maps showed place fields by the criteria applied to hippocampal units, where 31.7% (1,820 of 5,735) did.", "source": "Results, third paragraph", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Changed from not reproduced in revision, after the place fields were found on the Gaussian rate map the paper's code uses. 198 of 3,694 LS rate maps have a field (5.4%, within tolerance of 5.3%) and 531 of 5,045 hippocampal maps (10.5% against 31.7%, outside); the LS fraction is lower (chi-squared p = 8.9e-18), the partial outcome of the criterion. The hippocampal fraction is 8.0% to 13.6% per rat. With a Gaussian of SD 5 bins the fractions are 4.9% and 11.6%; with the 5-bin box map 5.8% and 6.3% (p = 0.40); with the 1% threshold of the code's default 0.4% and 4.6%. Without the rule dropping peaks whose SD across trials exceeds their mean they are 20.0% and 46.0%, so that rule accounts for most of the hippocampal shortfall, and no setting matches both of the paper's fractions.", "deviations": [ "Per-trial rate maps are smoothed with a Gaussian of SD 4 bins (FMAToolbox Smooth in bz_firingMap1D rateMaps, with tau = round(nBins/50) as in scratch_07_25_17_calc_firingMaps.m); the paper's bin count is not known. The Methods' widths (8 and 120 cm) are converted to 5 and 80 bins at the paper's 1.5 cm per bin, and the 2 Hz peak and 20% threshold of the Methods are used; the code's 1% default is shown as a variant.", "Per-trial rate maps come from a linearization by path fraction with about one position sample per bin and trial, which probably makes the code's rule dropping peaks whose SD across trials exceeds their mean strict." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "hpc-place-field-properties", "statement": "711 of 1,425 hippocampal neurons had at least one place field (1.27 fields per neuron on average); the median peak in-field rate was 8.5 Hz and the median field width 38 bins.", "source": "STAR Methods, place field definition", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "301 of 1,314 active hippocampal neurons have a field (22.9% against 49.9%, outside tolerance), with 0.47 fields per neuron against 1.27; the median peak rate, 8.4 Hz, and the median width, 39 bins over 614 fields, are within tolerance of 8.5 Hz and 38 bins. The peak rate is the RMS-smoothed peak, as bz_getPlaceFields1D reports it. Under the variants of the map and threshold the fraction is 12.4% to 24.1% (14.7% with the 5-bin box map), and 62.3% without the rule dropping peaks whose SD across trials exceeds their mean.", "deviations": [ "As for ls-few-place-fields." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ls-place-fields-unstable", "statement": "The few LS rate maps with a place field were less stable across trials than CA1/CA3 place fields (median coefficient of variance 41.5 against 10; two-sample t test, p < 1e-20).", "source": "Results, third paragraph", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Changed from partially reproduced in revision, after the place fields were found on the Gaussian rate map the paper's code uses (makeFig2.m also takes the SD from that map). Under reading (a), the SD at the peak that makeFig2.m computes, the LS median (3.5 Hz) is below the hippocampal one (6.4 Hz, t = -7.76, p = 2.8e-14), the reverse of the claim. Under reading (b), SD over mean, the medians are 86.2% and 83.6% and do not differ (t = 1.56, p = 0.12). No reading has LS higher at p < 0.05.", "deviations": [ "The paper does not define its coefficient of variance; two readings are shown.", "198 LS and 531 hippocampal fields, against 232 and 1,820." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-phase-info-smaller-scale", "statement": "Hippocampal place fields reach their peak information at smaller smoothing scales for phase than for rate (medians 15 and 29 bins; two-sample t test, p < 1e-40).", "source": "Results, first section; Figure 1E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Peak information is reached at a median smoothing of 10 bins for phase and 17 for rate (paper 15 and 29), t = -11.18, p = 1.9e-27, over 525 and 493 fields kept of 531. Phase is below rate in each rat (medians 7 to 15 against 16 to 19).", "deviations": [ "The information function of the paper (olypherInfo) is not public; the measure is built from the Methods' formula with choices fixed in the claims file.", "Bins are about 1.1 cm against the paper's 1.5 cm, which shrinks the medians in bins.", "At the same nominal span the rate and phase smoothings differ slightly (MATLAB smooth drops an even span by one; circ_smoothTS uses 2 ceil(w/2) + 1 bins), as in the paper's code." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-phase-more-info-fine-scale", "statement": "At smoothing below 6 cm (about one theta cycle) phase carries more spatial information than rate in hippocampal place fields, and above 10 cm rate carries more.", "source": "Results, first section; Figure 1G", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "At 7 to 50 bins rate carries more information than phase at p < 0.05 in 42 of 44 smoothings (95%; difference -0.008 at 7 bins to -0.033 at 50). At 2 bins phase is higher (+0.018, p = 2.1e-5); at 3 bins it is higher by +0.006, not significantly (p = 0.16). Neither reaches the criterion's p < 1e-5.", "deviations": [ "As for fig1e-phase-info-smaller-scale. Spans of 3 and 4 bins give the same smoothing, and so do 5 and 6; for rate because MATLAB smooth reduces even spans by one, for phase because circ_smoothTS uses 2 ceil(w/2) + 1 bins." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-depth-gradient", "statement": "The strength of phase coding relative to rate coding increases with recording depth within the LS, within sessions and across animals.", "source": "Results, fourth paragraph; Figures 4A to 4D", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "With depth and session value centred within rat, r = -0.365 (p = 0.005, 58 sessions). Per rat r = -0.70 (DT2, p = 0.034), -0.43 (DT5, p = 0.10), -0.62 (DT9, p = 0.024) and +0.24 (DT8, p = 0.36); DT7 has three sessions. Without centring r = -0.10 (p = 0.45). With the second depth of the name the per-rat signs are the same, and the pooled centred r is -0.268 (p = 0.042). The within-session part could not be tested, as the dandiset gives no recording site per unit.", "deviations": [ "The LS depth is the first number in the session name, an assumption; the dandiset does not describe the depths. It rests on DT9, where units are labelled ca3 exactly when the second depth is 828 um or more; in DT5 the hpc and ca3 files alternate at second depths of 2232 to 2448 um, and DT8 does not settle it.", "Session depth only; the paper adds the site of each unit on the shank." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-onset-depth", "statement": "The theta phase at the onset of LS phase fields varies with recording depth (DT5 r = 0.38, DT9 r = 0.25, DT2 r = 0.27; circular-linear correlation, p < 0.001).", "source": "Results, fourth paragraph; Figure 4E", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Circular-linear r between onset phase and LS depth is 0.082 (p = 0.57, 169 neurons) in DT5, 0.072 (p = 0.78, 98) in DT9 and 0.118 (p = 0.65, 62) in DT2, against 0.38, 0.25 and 0.27 at p < 0.001. Using every significant condition gives r = 0.06 to 0.16, p above 0.27. Keeping only the sessions whose theta channel has the rat's most common label (hpc in DT5 and DT9) gives r = 0.027 (p = 0.96) and 0.170 (p = 0.37).", "deviations": [ "As for fig4d-depth-gradient. The theta channel is chosen per session and may sit in a different layer from session to session, which shifts phases between sessions.", "Neurons are selected by this attempt's phase test (52% of neurons pass, against 89%)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-ca3-coherence-increases", "statement": "Theta phase coherence between LS and the CA3 pyramidal layer increases from the beginning to the end of the run, while coherence between LS and CA1 stays relatively flat.", "source": "Results, sixth paragraph; Figure 6C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "In 11 CA3 sessions (DT5 6, DT9 5) the median slope of LS-hippocampal theta phase locking on position segment is 0.0026 (signed-rank p = 0.83, 7 of 11 positive); in 36 CA1 sessions -0.0018 (p = 0.35). CA3 slopes are not above CA1 slopes (Mann-Whitney p = 0.35), nor within DT5 (p = 0.18) or DT9 (p = 0.91). Mean locking is 0.74 to 0.76 (CA3) and 0.78 to 0.81 (CA1) over the ten segments. With the 19 sessions without hippocampal units counted as CA1, as in the first version, p = 0.24.", "deviations": [ "Phase locking value of the 4 to 12 Hz phase difference in 150 ms windows, not multitaper coherence.", "The hippocampal channel is the chosen theta channel, labelled ca3 in the CA3 sessions and hpc (or unknown, in DT2) in the CA1 sessions; no session has both labels, where the paper's Figure 6A implies sessions with both a CA1 and a CA3 site. The sessions without hippocampal units (17 DT8, 2 DT7) are left out, as the criterion groups sessions by their unit labels." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-cfc-stronger-ca3", "statement": "Coupling between hippocampal theta phase and LS gamma amplitude increases along the run for both CA1 and CA3, and is stronger for CA3-LS than for CA1-LS.", "source": "Results, sixth paragraph; Figure 6D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Changed from reproduced in revision. The first version put the 19 sessions without hippocampal units in the CA1 group, against the criterion; with the criterion's grouping (36 CA1 sessions) theta-gamma coupling is not higher in CA3 than CA1 sessions at p < 0.05 (medians 0.059 and 0.051, Mann-Whitney p = 0.089), which the criterion needs for a full or a partial outcome. Coupling rises along the run in both groups (CA3 slope 0.0036 per segment, p = 0.002, 10 of 11 positive; CA1 0.00125, p = 0.001, 24 of 36). Within DT5 CA3 coupling is higher (p = 0.011); within DT9 it is not (CA3 0.049 against CA1 0.057, p = 0.88). Per rat the CA1 medians span 0.027 (DT2) to 0.090 (DT7); the CA3 group is two rats.", "deviations": [ "As for fig6c-ca3-coherence-increases for the channel and grouping." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs7-ensemble-ls-phase-best", "statement": "The firing phases of ensembles of simultaneously recorded LS neurons read out position better than the firing phases or rates of an equal number of hippocampal neurons (p < 0.001 at 15 to 25 neurons).", "source": "Results, third paragraph; STAR Methods, ensemble position prediction", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "In 65 conditions from 13 sessions (DT2, DT5, DT9) with at least 15 active LS and 15 hippocampal units, ensembles of 15 give MSE 4,738 for LS phase, 4,597 for hippocampal phase and 3,119 for hippocampal rate; LS phase is worse than both (one-sided p for LS phase higher = 5.8e-04 and 3e-186). At 20 units (7 conditions) the same (differences +290 and +1,668). At 25 units (3 conditions) LS phase MSE is below hippocampal phase (3,459 against 3,746, one-sided p = 0.0075, which treats the ensemble draws within a condition as independent and so overstates the evidence) but not below hippocampal rate (2,259).", "deviations": [ "The Methods' Poisson naive Bayes on discretized phases is followed with choices fixed in the claims file (20 equal-width levels, 10 ensembles per size); Figure S7 was not read." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-assemblies", "statement": "Spike trains of hippocampal neurons predicted LS firing in 18.5% (2,087 of 11,264) of hippocampal-LS pairs, with a median optimal timescale of 25 ms.", "source": "Results, fifth paragraph; Figure 5D to 5F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Changed from blocked in revision, at the verifier's request, by testing a random sample of pairs. Of 670 sampled pairs (of 70,898 hippocampal-LS pairs active in the same condition, counted per condition; 20,979 pairs of active units recorded together, against the paper's 11,264), 35 form an assembly of strength at least 4 (5.2%, 95% interval 3.7% to 7.2%), against 18.5%, and the median best window of the assemblies is 20 ms, against 25. Both are outside the criterion. The real gain beats all ten shuffles in 35.4% of pairs; this has no 1 in 11 reference, as the window is chosen on the real fit and the shuffles run only at that window. With thresholds of 1.5, 2 and 8 the fractions are 19.4%, 12.7% and 1.8%. Per rat 0% (DT7, 5 pairs) to 10.2% (DT5). With the LS unit's rate map at the current position added as a covariate, 5.5% (95% interval 3.9% to 7.5%), so the linear coding of position does not account for the low fraction.", "deviations": [ "A random 1% of the pairs, as all pairs need about 12 process-hours at about 0.6 s per pair measured in this run (1.2 s in the previous run).", "The bin size (1 ms), the Gaussian kernel, the window grid (13 windows from 1 to 150 ms) and the covariate coding are choices made here; the Methods do not give them and the paper's assembly code is not public. Shuffles are run at the best window only.", "Pairs are counted once per condition in which both units are active, as the Methods imply (one strength per pair and block of trials)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5g-assembly-neurons-stronger-phase", "statement": "LS neurons that take part in at least one predictive assembly carry a stronger spatial phase code than those that do not (p < 1e-20).", "source": "Results, fifth paragraph; Figure 5G", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "Needs to know which LS neurons take part in any assembly, which needs the assembly strength of every pair; at about 0.6 s per pair measured under fig5-assemblies in this run (1.2 s in the previous run), the 70,898 pairs take about 12 process-hours, beyond the time limit. A 1% sample leaves most LS neurons with no sampled pair. A sample of LS neurons with all of their pairs (about 89 each) would fit and was not run in this attempt.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6e-assembly-position", "statement": "CA3 place fields form progressively stronger gamma assemblies with LS along the track (r = 0.34) while CA1 coupling decreases (r = -0.11), and the two are anti-correlated (r = -0.88).", "source": "Results, sixth paragraph; Figure 6E", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "Needs the assembly strengths of all CA1 and CA3 place cells paired with LS units, which needs every pair (about 12 process-hours, as for fig5g-assembly-neurons-stronger-phase).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "speed-independent", "statement": "Only 2.8% (125 of 4,393) of LS conditions showed a significant correlation between running speed and the rate of phase precession, and 10.7% of LS rate maps were modulated by running speed.", "source": "Results, third paragraph", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The paper does not define the rate of phase precession, how it is correlated with running speed, or the test of speed modulation of rate maps, and no code for it is in the repositories read. The data needed (positions, spikes, LFP) are in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ls-information-lower", "statement": "LS rate maps have lower peak information rates than hippocampal place field maps (0.4 against 1.7 bits/cm; p < 1e-100).", "source": "Results, third paragraph", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2018.ipynb", "notes": "Changed from blocked in revision, after the verifier noted that the direction could be tested; the criterion was added then. LS rate maps carry less peak information than hippocampal place-field maps (means 0.632 and 1.490 bits/cm over 2,873 and 301 maps, t = -40.3, p = 6.0e-287, below the paper's 1e-100), but neither value is within tolerance under either reading (medians 0.556 and 1.435). Per rat the LS means are 0.52 to 0.66 and the hippocampal means 1.06 to 1.60.", "deviations": [ "The paper does not say how its per-bin information becomes bits per cm, at which smoothing the maps were compared, or how its information function normalizes; the measure of fig1e-phase-info-smaller-scale on the place-field map, divided by the bin size, is used, so the scale of the values is uncertain.", "DT2 is left out, as its positions are in pixels." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs6-reference-frame", "statement": "After maze rotation many LS neurons kept their phase precession related to distal room cues, so the phase shift is a spatial code.", "source": "Discussion; Figure S6; STAR Methods, reference frame analysis", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No file, trial or interval marks a maze rotation; the trials carry only type (central or wheel alternation) and direction. processing/behavior/allocentric_frame_tracking holds one series, a head-orientation quaternion with timestamps, in every file of DT5, DT7, DT8 and DT9 (the data check prints it), but which sessions or trials follow a rotation cannot be told. Figure S6 was not read.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-dynamic-weighting-model", "statement": "In a spiking model, CA1 and CA3 inputs weighted dynamically as the measured assemblies give a rate-independent phase code in the LS neuron, which static or random weights, or the loss of theta sequences, do not.", "source": "Figure 7; Results, last paragraph", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "A simulation that uses no recorded data from the dandiset (its weights come from a file in the paper's code repository), so it says nothing about the dandiset. It was not run.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The paper's processed behaviour is not in the dandiset; the linearized position, the trial conditions used for every rate and phase map, and the CA1 pyramidal layer channel used as the theta reference in each session must be rebuilt, and several outcomes depend on how." }, { "kind": "data_missing", "statement": "Units have no waveform, recording site or channel of largest amplitude, so the within-session depth analyses of Figure 4 (unit site on the shank) cannot be repeated." }, { "kind": "metadata_insufficient", "statement": "The two depths in each session name (for example 1944um and 2232um) are not described; which is the LS probe and what the zero is cannot be told from the metadata. The `hpc` unit label is not defined as CA1." }, { "kind": "metadata_error", "statement": "Eight DT8 files state position in mm but hold values spanning about 1.1 to 1.3, which are metres." }, { "kind": "format_error", "statement": "In all 67 files the third column (z) of position is a copy of the second (y)." }, { "kind": "format_error", "statement": "In eight of the eleven DT2 files the position timestamps repeat or go back; the time per sample (33.3 ms) can only be taken from the session span." }, { "kind": "format_error", "statement": "11 units in six files hold spike times that are not in increasing order." }, { "kind": "metadata_insufficient", "statement": "Every DT2 electrode, and those of two DT9 files, is labelled `unknown`; DT2 positions are in pixels with no scale; DT7 20170317 has 43 units with no region or group; DT7 20170324 has no units." }, { "kind": "metadata_insufficient", "statement": "Trials on the linear track, and in two DT8 alternation files (20170207 and 20170224), carry no type or direction." }, { "kind": "other", "statement": "In DT9 20170501 the trials do not match the positions (speed inside the trial windows does not change when they are shifted by up to 3 s), and in DT2 20160221 speed peaks with the trials shifted by 1 s, which suggests an offset of up to a second." }, { "kind": "selection_undocumented", "statement": "The dandiset holds 1,696 LS units and 3,217 hippocampal units (2,593 hpc, 624 ca3) against the paper's 1,647 LS and 2,951 hippocampal units, and 20,979 pairs of active hippocampal and LS units against 11,264 examined; which units the paper left out is not documented." }, { "kind": "methods_unavailable", "statement": "The functions the paper's figure scripts call to bin spike phases (bz_phaseMap2Bins), compute information (olypherInfo) and detect assemblies, and the parameters of its place-field call, are not in the public repositories; the session files they read (behavior.mat, sessionInfo) are not in the dandiset." }, { "kind": "metadata_error", "statement": "The head-orientation quaternion in processing/behavior/allocentric_frame_tracking states its unit as meters." }, { "kind": "metadata_insufficient", "statement": "In every session the hippocampal channels and units carry one label, hpc or ca3, so no session has both a CA1 and a CA3 site labelled, where the paper's Figure 6A counts 63 CA1 and 19 CA3 sessions, more than the 67 files, so some of its sessions had both; the paper's per-session CA1 and CA3 channels cannot be recovered." }, { "kind": "code_mismatch", "statement": "In scratch_07_25_17_calc_firingMaps.m (DavidTingley/scratch at 2f80453), the place-field file that the figure scripts load is named for a 20% threshold, but the call that fills it passes no threshold, so bz_getPlaceFields1D's default of 1% applies; the Methods state 20%." }, { "kind": "other", "statement": "42 files chunk the LFP as 500 samples by all channels, so reading one channel of a session means reading the whole LFP; chunks along time per channel would make single-channel access practical." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run (commit 1775fd8) with the conclusion cells and the summary removed, the helper module and the claims file.", "agreed": 25, "of": 25, "disagreements": [] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the first revision (commit 984db9b), with its conclusions and summary, the helper module, the claims file and the attempt record.", "agreed": 25, "of": 25, "disagreements": [] } ] }, { "id": "000218-tingley-2019-01", "dandiset": "000218", "dandiset_version": "0.250624.0439", "paper": "10.1016/j.neuron.2019.10.012", "paper_title": "Routing of Hippocampal Ripples to Subcortical Structures via the Lateral Septum", "date": "2026-10-16", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "runs", "entry": "000218-tingley-2019", "entry_title": "Lateral septum HFOs and hippocampal ripples (Tingley and Buzsaki 2019)", "description": "Tests the findings of Tingley and Buzsaki (2019) on dandiset 000218, which holds LFP, sorted units, sleep states and trials from simultaneous recordings of the lateral septum and hippocampus in 6 rats. LS high-frequency oscillations and CA1 ripples are detected from the LFP, as the files hold no detected events, and the notebook tests their properties, their coupling and state dependence, the phase locking and co-activation of LS neurons, and which ripple features predict LS firing. The optogenetic experiments are not in the dandiset.", "notebooks": [ { "path": "reproduce_tingley_2019.ipynb", "title": "Reproducing Tingley and Buzsaki (2019) from dandiset 000218", "executed": "notebooks/000218-tingley-2019/reproduce_tingley_2019.html" } ], "outcomes": [ { "claim": "dataset-composition", "statement": "LS was recorded in 6 rats, with 1989 LS neurons; 37 recordings had CA1 and LS and 25 had CA3 and LS recorded simultaneously; LS HFO rates come from 89 recordings and CA1 ripple rates from 53.", "source": "Results, first paragraph; Figure 1C legend; Figure 5B legend; STAR Methods, Experimental model and subject details", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "The animal count matches (6). LS neurons number 2448 labelled `ls`, and 2046 with more than 50 spikes in high-power epochs, within 10% of 1989. Files with LS and `hpc` units number 37, as in the paper; files with LS electrodes 94 (paper 89). Files with LS and CA3 units number 10 against 25, and the CA1 recording count is 40 (units), 72 (electrodes) or 43 (electrodes and states) against 53. Three of five counts beyond the animals are within tolerance.", "deviations": [ "The paper's recordings cannot be matched to files one by one; counts are compared under the readings the criterion lists." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-hfo-each-animal", "statement": "Transient 120-180 Hz HFOs occur in LS in each of the 6 animals, with a robust increase in the firing probability of LS neurons at the events.", "source": "Results, first paragraph; Figure 1A to C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Median event frequency is 152 to 158 Hz in every animal. LS firing within 10 ms of the events exceeds firing at random times by more than 3 SEM only in DT1 (6.0 SEM); DT2 and DT5 are higher by 1.3 and 1.4 SEM, and DT7, DT8 and DT9 are lower (-3.4, -4.6, -1.4 SEM). In variants, NREM events pass in DT2 (3.3) and DT9 (3.9), and ripple-coupled events in DT9 (4.2). On the LS channel re-referenced within its shank no animal passes (largest 1.5 SEM, DT2). Random times mix states; against each neuron's firing 50 to 100 ms before and after the same events, firing at the events is higher in DT1, DT2, DT5 and DT9 and lower in DT7 and DT8, and exceeds 3 SEM only in DT1 (5.2 SEM; DT2 1.6, DT5 1.7, DT9 0.5). In DT2 and DT5 the differences are large (0.024 and 0.037 spikes) but vary widely across neurons. The test does not show raised LS firing at the events outside DT1, and does not show that the events lack it.", "deviations": [ "Events are detected here on one LS channel per recording chosen by a fixed rule (highest 120-200 Hz SD in a 300 s NREM sample); the paper does not say which channels it used.", "The paper's noise channel is replaced by the EMG estimated from the LFP, which the Methods allow when no noise channel exists." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-event-count", "statement": "Across 6 animals, 29,955 LS HFO events were analysed.", "source": "Figure 1C legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Under reading (b), recordings with LS units, 31,984 events are detected, within 10% of 29,955. Reading (a), all 94 recordings with LS electrodes, gives 67,186, of which 38,008 come from DT7. More events fall in WAKE (27,676) than in NREM (20,019). The count matching does not show that the same events were found, and is probably a coincidence, as DT7 contributes most events and the count depends on the channel; on the re-referenced LS channel the recordings with LS units give 66,458 events.", "deviations": [ "Detection channels and noise exclusion differ from the paper's (see fig1c-hfo-each-animal)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-participation", "statement": "On average 16% of LS neurons take part in a given HFO, firing an average of 0.23 spikes per event.", "source": "Results, first paragraph (Figure S1A, B)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Pooled over 31,984 events, 2.7% of LS neurons fire in an HFO, with 0.051 spikes per neuron per event; the mean over 76 recordings gives 3.5% and 0.068. The paper reports 16% and 0.23. The fraction is 0.17 (pooled) to 0.22 (recordings) of the paper's, the spike count 0.22 to 0.30. The highest recording reaches 18.2%; the median recording 1.7%. On the re-referenced LS channel the pooled values are 4.5% and 0.060.", "deviations": [ "Spikes are counted between event start and stop; the paper does not give its window." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-phase-locking", "statement": "The vast majority of LS neurons (1840 of 1989, 92%) are significantly phase-locked to the 120-200 Hz band (Rayleigh P < 0.05), with a strong preference for the trough of each cycle.", "source": "Results, first paragraph; Figure 1D, E; STAR Methods, Phase locking analysis", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "1151 of 2046 tested LS neurons (56.3%) are significantly locked (47.0% of all 2448), against 92.5%. The trough preference holds, with preferred phases centred on 189 degrees (resultant 0.755). By animal the fraction is 5.7% (DT7) to 70.4% (DT5). Median resultant 0.124 against 0.048 with the phase shifted. With the phase taken on an LS channel on another shank than the unit's, 1048 of 2003 tested neurons (52.3%) are locked, centred on 189.7 degrees (resultant 0.743), and 44 have a resultant above 0.6, so the trough preference does not come from the units' own spikes. Locking is stronger for units on the detection shank (76.4%) than on other shanks (51.4%).", "deviations": [ "The phase is taken on the recording's detection channel, not on a channel near each unit; the paper does not say which channel it used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-shorter-than-ripples", "statement": "LS HFOs are shorter than CA1 ripples from the same animals (27 +- 9 against 31 +- 14 ms; rank-sum P < 0.01).", "source": "Results, first paragraph; Figure 1F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "LS HFOs last 33.9 +- 25.0 ms and CA1 ripples 38.3 +- 23.7 ms (medians 23.2 and 32.0), inside the tolerances of the paper's SDs, and LS HFOs are shorter (rank-sum p underflows to 0). The means are 6.9 (LS) and 7.3 ms (CA1) above the paper's. DT8 shows no difference (27.5 against 28.0 ms, p = 0.83). With NREM events only, the means are 38.0 and 38.4 ms, and on the re-referenced LS channel 38.2 and 38.3 ms. With 56,871 and 230,161 events the rank-sum p is small for any difference.", "deviations": [ "The tolerances are the paper's stated SDs, as the protocol asks, which makes them wide.", "The `hpc` channel is taken as CA1." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-slower-than-ripples", "statement": "LS HFOs are slower in frequency than CA1 ripples (147 +- 5.7 against 159 +- 8 Hz; rank-sum P < 0.01).", "source": "Results, first paragraph; Figure 1G", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "LS HFOs average 153.6 +- 8.3 Hz and CA1 ripples 150.8 +- 9.2 Hz; LS events are faster, the reverse of the claim, in four of five animals, and both means are outside tolerance. With NREM events only, LS are slower by 0.8 Hz (150.3 against 151.1 Hz). On the re-referenced LS channel LS events are faster (156.3 against 150.8 Hz).", "deviations": [ "The instantaneous-frequency estimator pulls towards the band centre (the verifier measured 145 Hz for a 140 Hz burst and 167 Hz for 170 Hz); this compresses differences but cannot reverse their order." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1h-no-amplitude-frequency-correlation", "statement": "LS HFOs show no significant correlation between event amplitude and peak frequency.", "source": "Results, first paragraph; Figure 1H", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Over 67,186 events, Pearson r = 0.056 (p = 2.4e-47), Spearman rho = 0.123. By animal r is -0.009 to 0.080, significant in four of six; NREM events only give r = 0.028 (p = 7.3e-05). The outcome follows the criterion's test; the correlation is negligible in size (0.3% of the variance) and significant because of the event count.", "deviations": [ "The paper names no test; a Pearson test over all events was fixed in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-confined-to-ls", "statement": "HFO events are seen only at recording sites within LS, not at sites in neighbouring structures.", "source": "Results, second paragraph; Figure 2A to C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Of 5 DT7 recordings with at least 20 HFOs in the 30 min block, LS channels have the highest HFO-triggered power ratio in 2 (2017-03-18, 5.38 against 5.31 for cingulate cortex; 2017-03-21, 8.25 against 8.05 for medial septum). Medial septum (6.05 against 5.18), corpus callosum (50.1 against 42.0) and fimbria (72.1 against 64.8) channels are higher in the other three. The test rests on one animal, DT7, the only one whose files label electrodes outside LS and the hippocampus. With each channel re-referenced to the median of its shank and the re-referenced LS events as triggers, 4 recordings have at least 20 events and LS is highest in 2; medial septum channels are higher in the other 2 (4.00 against 3.09, 4.21 against 3.65).", "deviations": [ "Tested on the DT7 recordings with channels in other regions, over up to 30 min of all channels, in place of the paper's depth series of Figure 2C." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2ef-intermediate-ls", "statement": "HFO power and the proportion of phase-locked neurons are highest in intermediate LS and taper towards its dorsal and ventral borders.", "source": "Results, second paragraph; Figure 2D to F; Figure S1C, D", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The claim needs each recording's depth relative to the dorsal and ventral borders of LS, which the paper estimated from implant depths, drive turns and histology. The files give only the drive depths in the session names and a region label per channel; the borders, the histology and the relative depths are not in the dandiset, and the names do not say which of their two depths is the LS drive. For the record, the notebook shows the HFO band SD and the locked fraction against each depth within each animal (rank correlations -0.61 to 0.41 and -0.84 to 0.36); the band SD is largest at the shallowest or deepest recording in 9 of 11 series.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-travelling-waves", "statement": "LS HFOs are travelling waves, posterior to anterior at 1.01 m/s (4 animals), medial to lateral at 0.53 m/s (1 animal) and dorsal to ventral at 2.19 m/s (4 animals).", "source": "Results, second paragraph; Figure 3", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The speeds need the positions of the electrodes along the anterior-posterior, medial- lateral and dorsal-ventral axes. The electrode x, y and z are NaN in every file, and the probe layouts are named only in the device descriptions, without their orientation in the brain. The electrode groups are described only as \"GroupN electrodes.\", and the devices give the layout (shanks by sites) without site pitch or orientation.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-pre-post-unchanged", "statement": "The co-activation of LS neuron pairs during HFOs (excess correlation) is not modulated by waking experience on a familiar maze (PRE against POST, rank-sum P = 0.36).", "source": "Results, third paragraph; Figure 4B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "PRE and POST excess correlations do not differ (medians 0.0062 and 0.0059, rank-sum p = 0.81; within animals p = 0.49 to 0.88). Only 106 pairs in 10 recordings pass the inclusion rule, against 7,172 in 53 sessions, so the test has much less power than the paper's.", "deviations": [ "The CCG normalization, the smoothing at the window edges and the reading of the 5-spike inclusion rule were fixed in the criterion; the Methods do not give them.", "HFO spikes are those inside this attempt's detected events, which hold few LS spikes." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-hfo-above-behav", "statement": "Excess correlations during HFOs (PRE and POST) are higher than during maze traversal (rank-sum P < 0.001), and those of PRE and POST HFOs exceed chance from spikes jittered by +-200 ms (P < 0.01).", "source": "Results, third paragraph; Figure 4B; Figure S3A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "HFO excess correlations exceed BEHAV (median 0.0003; PRE p = 9.1e-24, POST p = 3.8e-25) and their jittered values (p = 3.6e-31 and 7.8e-35); BEHAV is slightly above its jitter (p = 0.0022). 106 pairs in 10 recordings.", "deviations": [ "As for fig4b-pre-post-unchanged." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-sessions-few-change", "statement": "Only 7 of 53 sessions have significantly different excess correlations in PRE and POST (rank-sum P < 0.01), three with PRE below POST and four with PRE above.", "source": "Results, third paragraph", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Too few recordings under the claim's own rule; decided after the pair selection. The shortfall comes from this attempt's HFO detection, whose events hold few LS spikes, not from the dandiset, which holds the spikes, epochs and trials. 7 recordings have at least 5 pairs, against 53 sessions in the paper; at the paper's rate of 7 in 53 about one significant recording would be expected, so the count cannot test the claim. For the record, none of the 7 has p < 0.01 (smallest p = 0.050).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-temporal-bias", "statement": "The temporal ordering of LS spike pairs during HFOs before and after the maze correlates with the ordering during traversal to a similar degree (P = 0.85).", "source": "Results, fourth paragraph; Figure 4C", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Too few recordings under the claim's own rule; decided after the pair selection, for the reason given under fig4-sessions-few-change. 4 recordings have at least 10 pairs, against 53 in the paper, too few for a t-test over recordings. For the record, the mean correlations are 0.042 (PRE-BEHAV) and 0.084 (BEHAV-POST), t-test p = 0.81.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-compression", "statement": "Cross-correlograms of LS pairs during HFOs correlate with those during traversal above chance up to about 20-fold temporal compression (P < 0.01), similarly for PRE and POST (P > 0.01 for all compression factors).", "source": "Results, fourth paragraph; Figure 4D; Figure S3B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "PRE correlations exceed chance (p < 0.01) at factors 1 and 2 only, and POST at 1, 2, 4 and 20, against up to about 20 in the paper. PRE and POST do not differ at any factor (smallest p = 0.038), as the paper reports. Pairs with a defined correlation fall from 59 (PRE) and 77 (POST) at factor 1 to 5 and 11 at factor 50, so the higher factors rest on few pairs; PRE at factor 4 rests on 24 pairs (p = 0.18).", "deviations": [ "Interpolation and chance by circular shift were fixed in the criterion; the Methods describe the warping but not the chance procedure in detail. One shift per pair is used for all factors." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2-post-rate-increase", "statement": "Firing rates increase during post-behavior NREM sleep in CA1, CA3 and LS.", "source": "Results, fifth paragraph (Figure S2A, B)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "LS units fire more in POST NREM than in PRE NREM (median ratio 1.06, Wilcoxon p = 8.4e-07, 1326 units). The `hpc` units (ratio 1.00, p = 0.52, 2552 units) and the `ca3` units (1.03, p = 0.22, 466 units) do not.", "deviations": [ "The paper's supplementary figure was not available; the test was fixed in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-nrem-and-rates", "statement": "LS HFOs occur primarily during NREM sleep, and their rates are lower than those of hippocampal SPW-Rs.", "source": "Results, sixth paragraph; Figure 5A, B", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "LS HFO rates in NREM are far below CA1 ripple rates (medians 0.006 and 0.461 per s, lower in 34 of 39 recordings, Wilcoxon p = 3.1e-06). The detected LS events are not more frequent in NREM than in WAKE (NREM higher in 18 of 49 recordings, lower in 29, p = 0.44), while CA1 ripples are (about 9 times). On the re-referenced LS channel the same holds (NREM higher in 17, lower in 31, p = 0.73; below CA1 in 35 of 39, p = 6.7e-06).", "deviations": [ "Detection as in fig1c-hfo-each-animal; 4 recordings without NREM or WAKE time are left out." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5d-lag", "statement": "LS HFOs are reliably coupled to CA1 ripples, with a median peak-to-peak lag of 6.4 +- 4.2 ms, CA1 leading LS.", "source": "Results, sixth paragraph; Figure 5D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "The coupling holds; the pooled CA1-LS correlogram peaks at 0 ms, 166 SD above its flanks. The lag is 0.00 ms under both readings, outside 6.4 +- 4.2 ms, because 35% of LS HFOs within 50 ms of a ripple fall on the same sample (DT8 71%, DT2 62%, DT9 7%). Without the pairs within 1 ms the pooled median is 3.2 ms with LS after CA1 in 55%, but by animal it is -3.2 (DT2), -5.6 (DT5), -6.4 (DT7), 1.6 (DT8) and 8.0 ms (DT9), so LS leads in three animals. Over all pairs, DT9's median of recording medians is 3.8 ms, inside the tolerance (2.2 to 10.6 ms); the other animals give 0.0 ms. On the LS channel re-referenced within its shank, 4.1% of pairs fall on the same sample, the correlogram still peaks at 0 ms (53.4 SD above the flanks), and the lag is 0.00 ms (a) and 0.80 ms (b), LS after CA1 in 52%. The criterion requires both the lag and the correlogram peak and defines no partial outcome, so the claim is not reproduced; the coupling part holds and the lag part does not. Changed from partially reproduced after round 3.", "deviations": [ "Detection as in fig1c-hfo-each-animal; event times are the troughs of the filtered signal." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5e-state-coupling", "statement": "HPC-LS coupling is stronger in NREM sleep than in waking; the fraction of LS HFOs within +-25 ms of a CA1 ripple is 0.3 in NREM and 0.15 in WAKE (P < 6.6e-6).", "source": "Results, sixth paragraph; Figure 5E and inset", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Over 25 recordings with at least 10 HFOs in each state, 0.199 of LS HFOs have a CA1 ripple within 25 ms in NREM and 0.116 in WAKE (t-test p = 0.089); pooled, 0.088 and 0.041. The direction matches, the difference is not significant, and both are below the paper's values. With ripple times shifted by 1 s the fractions are 0.019 and 0.005. On the re-referenced LS channel, over 16 recordings, 0.118 and 0.085 (p = 0.43).", "deviations": [ "Detection as in fig1c-hfo-each-animal." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-ripple-triggered-firing", "statement": "LS firing around CA1 ripples is higher during NREM than during waking.", "source": "Results, sixth paragraph; Figure 5F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Over 978 LS neurons (paper 1,313), the rate within 25 ms of CA1 ripples is 1.39 Hz in NREM and 1.33 Hz in WAKE (paired t-test p = 0.24). Relative to each neuron's rate in the state, WAKE is higher (1.56 against 1.34, p = 0.00016). By animal, DT5, DT7 and DT9 are higher in NREM and DT2 is lower.", "deviations": [ "A window of +-25 ms and a single test over neurons were fixed in the criterion; the figure tests each bin of the correlogram." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-no-phase-coherence", "statement": "CA1-LS phase coherence in the 120-180 Hz band around CA1 ripples does not differ from that of randomly jittered windows, so LS does not inherit the ripple wave by wave.", "source": "Results, seventh paragraph; Figure 5F inset", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "The CA1-LS 120-180 Hz phase-locking value at ripple times is 0.405 against 0.202 +- 0.007 for jittered windows (31 SD above), higher in 70 of 71 recordings, and 90 of 125 lags within 50 ms exceed the bound. The jittered value is itself high. With a median of 1722 ripples per recording random phases would give about 0.021, and the jittered value per recording is 0.030 to 0.602 (median 0.134), so the two channels keep a phase relation outside ripples. On the LS channel re-referenced within its shank, the value at ripples is 0.164 against 0.074 +- 0.004 jittered (23.9 SD above, higher in 60 of 71 recordings), so the excess remains.", "deviations": [ "The coherence measure (phase-locking value of the phase difference across ripples) was fixed in the criterion; the paper does not define it.", "The LS channel is the detection channel; the paper does not say which channel it used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-optogenetic-hfos", "statement": "Optogenetic activation of LS GABAergic neurons with a Gaussian light waveform induces local oscillations of about 140 Hz.", "source": "Results, seventh paragraph; Figure 6", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The two rats used for optogenetics are not in the dandiset, whose 6 subjects are the recording rats, and no file holds an optogenetic series (notebook, fig6-optogenetic-hfos cell). Archive searches for \"Tingley\" and \"lateral septum\" find only 000213, 000218 and 000233; 000213 and 000233 are named for other papers.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-ca1-spikes", "statement": "The number of CA1 spikes in a SPW-R significantly predicts the number of spikes of 38% of LS neurons.", "source": "Results, eighth paragraph; Figure 7D, E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "The number of CA1 spikes predicts 79.4% of 880 LS neurons under reading (a) (chance 4.7%) and 88.4% under (b) (chance 40.5%); above chance and far above 38%. Counting from ripple start to stop makes the LS and CA1 counts both grow with duration; with a fixed +-25 ms count window, 24.7% under (a) (chance 5.6%). Reading (b) is miscalibrated by construction (chance about 40%) and is not used.", "deviations": [ "The paper does not state its model; a linear regression with cross-validated MSE and shuffles was fixed in the criterion. Under reading (b), the paper's t-test wording, the chance rate is about 40%.", "The `hpc` units are taken as CA1." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-state", "statement": "Brain state (WAKE or NREM) in which a SPW-R occurs significantly predicts the spike count of 26% of LS neurons.", "source": "Results, eighth paragraph; Figure 7E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "State predicts 34.3% of 813 LS neurons under (a) (chance 5.4%) and 67.4% under (b) (chance 41.7%), above chance and above 26 +- 2.6%. With a fixed window, 34.9% under (a) (chance 6.0%).", "deviations": [ "As for fig7e-ca1-spikes." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-duration", "statement": "The duration of hippocampal SPW-Rs significantly predicts the spike count of about 20% of LS neurons.", "source": "Results, eighth paragraph; Figure 7E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_tingley_2019.ipynb", "notes": "Duration predicts 86.0% of 880 LS neurons under (a) (chance 5.9%) and 93.2% under (b), far above about 20%. Counting spikes from ripple start to stop makes the count grow with duration; with a fixed +-25 ms window it is 17.8% under (a) (chance 7.2%), just below the tolerance of 18 to 22%, shown as a variant.", "deviations": [ "As for fig7e-ca1-spikes; the count window (ripple start to stop) was fixed in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-ca1-depth", "statement": "The mean depth within the CA1 pyramidal layer of the neurons active in a SPW-R predicts the spike count of 23% of LS neurons.", "source": "Results, eighth paragraph; Figure 7D, E; STAR Methods, Relative anatomical depth within CA1", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The depth of a CA1 neuron is estimated from its waveform amplitude on the three channels where it is largest. The units carry no waveforms and no channel, only a shank; the units table holds clu_id, group_id (the shank) and location, or only ids in nine files. The notebook's fig7e-ca1-depth cell lists the wide-band data. 20 kHz wide-band series are in 27 of the 98 files (all 12 DT1 files, all 13 DT2 files and two DT9 files, which take 1.15 TB). Twelve of them (10 DT2, 2 DT9) hold hippocampal units, 1.00 TB of wide-band data, from which waveforms could be re-extracted; streaming them within the 30 min run limit would need about 556 MB/s, so for these recordings the block is the run time (not_runnable). The other 1579 of 2778 hippocampal units, including all of DT5 and DT7, have no wide-band data, so their waveforms are missing, which is the main reason given.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-replay", "statement": "The sequential content of SPW-Rs, by three replay scores, predicts the firing of only 7.9, 6.6 and 7.1% of LS neurons.", "source": "Results, ninth paragraph; Figure 7D, E", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The three replay scores need place-field decoding of the CA1 units on the tracks (bin size, smoothing, trial selection, cell inclusion, and the shuffles for the scores) and the model that relates the scores to LS firing. Neither the paper nor any published code fixes them; the paper's repository holds no code for this figure. The files do hold positions and trials; 74 files in DT2, DT5, DT7, DT8 and DT9 have a position series, covering all trials except in DT7 (93%).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-seqnmf", "statement": "Template sequences extracted from SPW-Rs without supervision predict the firing of only 8.1% of LS neurons.", "source": "Results, tenth paragraph; Figure 7E; Figure S5", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The seqNMF decomposition is described only by its reference and the 40 templates; its lag, regularization, binning and the test against LS firing are not given, and no code for this paper is published.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-content-independent", "statement": "All spike-content-independent ripple features predict LS firing above chance, while all spike-content-based features do not.", "source": "Results, eleventh paragraph; Figure 7E, bottom row", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Depends on fig7e-replay, fig7e-seqnmf (methods underspecified) and fig7e-ca1-depth (data missing). The three content-independent features tested here are all above chance (see their outcomes).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig8-model", "statement": "In a model HPC-LS circuit, forward, reverse and scrambled compressed sequences evoke nearly identical responses of the LS neuron.", "source": "Results, twelfth paragraph; Figure 8", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "A simulation of a model circuit, not a finding about the recorded data, so the dandiset cannot test it. The model's code is in https://github.com/DavidTingley/papers (notebook dynamicWeightingModel-ripple.ipynb) and was not run here.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The files hold no detected LS HFOs or hippocampal ripples, nor the detection channels and parameters, which the Methods say are stored with each event structure. Every analysis of events has to detect them anew, and the detection channels cannot be matched to the paper's." }, { "kind": "metadata_insufficient", "statement": "Nine files (DT5 2016-10-07, DT7 2017-03-14, -16, -17, -19, 2017-04-07, -10, DT9 2017-04-28, 2017-05-26) store units without a location column, so their 268 units cannot be assigned to LS or hippocampus." }, { "kind": "metadata_insufficient", "statement": "Hippocampal electrodes and units are labelled `hpc` or `ca3`; `hpc` does not say whether a site is in CA1, which the paper's analyses distinguish. Four DT7 files label all electrodes `unknown`." }, { "kind": "data_missing", "statement": "The paper's CA3 recordings used a CA1 reference electrode to detect ripples. The 10 files with `ca3` electrodes hold 64 `ca3` and 32 `ls` channels and no CA1 channel, and the paper reports 25 CA3 and LS recordings against 10 here." }, { "kind": "metadata_insufficient", "statement": "Electrode x, y and z are NaN in every file. The probe geometry and its orientation in the brain, needed for the travelling-wave analysis of Figure 3, are not given, and the relative depth of each recording within LS (Figure 2) is not given." }, { "kind": "data_missing", "statement": "The units carry no waveforms, no channel and no quality metric (the Methods compute isolation distance), so the CA1 depth of each neuron (Figure 7) cannot be estimated and single units cannot be told from multi-unit clusters; 11 units fire above 50 Hz on average. Wide-band data, from which waveforms could be re-extracted, are in 27 of the 98 files (DT1, DT2 and two DT9 files); 1579 of 2778 hippocampal units have none." }, { "kind": "data_missing", "statement": "The two rats of the optogenetic experiments (Figure 6) are not in the dandiset." }, { "kind": "format_error", "statement": "25 units in 10 files have spike times out of order (1 to 2782 inversions each), against the NWB rule that spike times are sorted." }, { "kind": "methods_unavailable", "statement": "The paper's Key Resources point to github.com/DavidTingley/papers for scripts that recreate each main figure, but the repository holds only the network model of Figure 8 and the code of the 2018 paper; the analyses of Figures 1 to 7 are not published." }, { "kind": "paper_inconsistency", "statement": "The HFO band is given as 120-180 Hz in the Summary and the legends of Figures 1, 2 and 5 and as 120-200 Hz in the Results and Methods. The Methods call the 62-recording dataset that of Figure 6, which shows optogenetics, where Figure 7 is meant, and cite Figure 3A and 3B (travelling waves) for the jitter control and the state of phase-locking epochs, which appear to be Figure S3A and Figure 5." }, { "kind": "other", "statement": "In this attempt's detection, 35% of LS HFOs within 50 ms of a CA1 ripple fall on the same 0.8 ms sample as the ripple (71% in DT8, 62% in DT2, 7% in DT9), and the CA1-LS 120-200 Hz phase difference is consistent even at random times (median phase-locking value 0.134 against about 0.021 for random phases). Re-referencing the LS channel to another LS channel on its shank lowers the same-sample share to 4.1%. This points to a signal common to the LS and hippocampal channels, such as the reference, which the files do not document; some files list a device of \"reference sites a few millimeters dorsal\" without saying which channels use it." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. The attempt record was not among its materials.", "agreed": 30, "of": 31, "disagreements": [ { "claim": "fig5d-lag", "outcome": "not_reproduced", "reason": "The median lag is 0.00 ms under both readings, against 6.4 +- 4.2; 35% of pairs fall on the same sample. The CCG peak criterion holds (166 SD above the flanks, at 0 ms). Problem 1, that the LS detection channel carries the hippocampal or a common-reference 120-180 Hz signal (same-sample pairs, 0 ms lag, jittered PLV of 0.20), and no local re-referencing was tried." } ] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run, with its conclusions, figures and summary, the helper module, the claims file and the attempt record.", "agreed": 30, "of": 31, "disagreements": [ { "claim": "fig5d-lag", "outcome": "not_reproduced", "reason": "Not reproduced, as in round 1. The criterion defines no partial outcome. The part of the claim that can be measured, a lag of 6.4 ms with CA1 leading, fails on both channels, 0.00 ms on the detection channel and 0.00 or 0.80 ms re-referenced. A correlogram peak at 0 ms does not show CA1 leading. Also, cell 61 and the notes say \"DT9 gives 3.8 ms\" without those pairs, but the 3.8 ms comes from all pairs, as the median of DT9's per-recording medians, and it is inside the tolerance (2.2 to 10.6 ms), which neither text says." } ] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The proposed change of outcome for fig5d-lag only, with the full executed notebook of the final revision (cells 60, 61 and 68), the claims file and the attempt record. No paper text was downloaded this round. Report in transcripts/000218/verifier-3-report.md.", "agreed": 1, "of": 1, "disagreements": [] } ] }, { "id": "000226-severson-2017-01", "dandiset": "000226", "dandiset_version": "0.230607.1747", "paper": "10.1016/j.neuron.2017.03.045", "paper_title": "Active Touch and Self-Motion Encoding by Merkel Cell-Associated Afferents", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000226-severson-2017", "entry_title": "Merkel and other whisker afferents during active touch and whisking (Severson et al. 2017)", "description": "Tests the findings of Severson, Xu, Van de Loo, Bai, Ginty and O'Connor (2017) on dandiset 000226, which holds 56 trigeminal afferent recordings with high-speed whisker video and 4 EMG sessions. It checks the recordings against the paper's Table S1, the spike rates during non-whisking, whisking in air and touch, the classes of afferents, direction selectivity, the statistical and viscoelastic models of touch responses, phase tuning during whisking in air, the nasolabialis motor units and the curvature noise. The cutting conditions of the progressive cutting experiment, the intrinsic protractor EMG and the optogenetic tagging data are not in the dandiset.", "notebooks": [ { "path": "reproduce_severson_2017.ipynb", "title": "Reproducing Severson et al. (2017) from dandiset 000226", "executed": "notebooks/000226-severson-2017/reproduce_severson_2017.html" } ], "outcomes": [ { "claim": "table-s1-link", "statement": "The dandiset's recordings can be matched one to one to the recordings of Table S1, and the matched records agree on mouse, sex, mouse line and date.", "source": "Table S1 (Supplemental Information)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "All 60 files match a distinct Table S1 recording, 58 by recording id (the NWB identifier without \"KS\" and leading zeros) and 2 (KS0125_ and KS0128_, matched to 125B and 128D) by number and mouse. All 60 agree on mouse, sex, mouse line and date. Groups - 33 touch, 13 progressive cutting, 5 cut-whisker, 4 EMG, 3 excluded touch, 2 whisking-only. No Table S1 recording lacks a file. The transcription of Table S1 agrees with the table parsed from the supplement on all 60 rows and every column used.", "deviations": [ "The criterion's rule of removing \"KS0\" was applied as removing \"KS\" and leading zeros, so that the EMG files KS0007A to KS0011A match 7A to 11A." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "video-frames", "statement": "The initial dataset of 33 touch afferents comprises 54,647,500 video frames with simultaneous single-unit recordings, and the paper analyses 65,257,500 frames (2,175 min) in total.", "source": "Results, first section; Quantification and Statistical Analysis", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "The 33 touch recordings hold 54,660,000 frames (paper 54,647,500, 5 trials more). The 53 analysed afferents hold 65,710,000 frames, 2,190 min (paper 65,257,500 and 2,175 min, 181 trials more). The other readings are also within 10% - 68,455,000 (53 afferents and EMG), 68,005,000 (56 afferents), 70,750,000 (all files).", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "merkel-minutes", "statement": "Identified Merkel afferents account for 823 minutes of the initial dataset and 846 minutes (25,365,000 frames) overall, against 999 minutes for unidentified afferents in the initial dataset.", "source": "Results, first section; Quantification and Statistical Analysis", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Merkel touch recordings 823.8 min (paper 823), unidentified touch recordings 998.2 min (paper 999), the 17 analysed Merkel afferents 846.4 min (paper 846). All 20 identified Merkel afferents hold 922.9 min, also within tolerance. Merkel identity is from Table S1; the minutes are from the dandiset's trials, and they agree with the paper's.", "deviations": [], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig2c-baseline-rate", "statement": "During non-whisking periods most afferents spiked at low rates (0.0 plus or minus 0.2 Hz, median and IQR, n = 33).", "source": "Results, first section; Figure 2C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Median non-whisking rate 0.03 Hz, IQR 0.20 Hz, over the 33 touch afferents (paper 0.0 and 0.2). Range 0.00 to 34.39 Hz; 221B fires at 34.4 Hz without whisking.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2c-touch-rate", "statement": "All afferents responded with increased spike rates during whisker-pole contact (48.0 plus or minus 96.3 Hz, median and IQR, n = 33).", "source": "Results, first section; Figure 2C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Median contact rate 47.9 Hz, IQR 94.8 Hz (paper 48.0 and 96.3), range 3.6 to 239.2 Hz. All 33 afferents are touch-sensitive by the Glossary rule, with bootstrap CIs over trials and with Poisson CIs. The median is also within 10% of the paper's value, so the outcome does not rest on the wide tolerance.", "deviations": [ "The Methods do not say what the bootstrap resamples; trials were resampled (1,000 times)." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2c-wt-star", "statement": "A subset of 13 of the 33 touch afferents (WT*) spiked especially strongly during whisking in air (19.1 plus or minus 58.2 Hz, median and IQR), and the other afferents divide into those sensitive to whisking and touch (WT) and to touch only (T).", "source": "Results, first section; Figure 2C; Glossary; Table S1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Under reading (b), spikes during whisking in air, 13 afferents are WT*, the same set as Table S1's (5 Merkel, 7 other SA, 1 RA), with a median whisking-in-air rate of 19.0 Hz and IQR 57.4 Hz (paper 19.1 and 58.2). Classes agree with Table S1 for 31 of 33; 223B and 243B are WT in Table S1 and T here (whisking-in-air rates 0.23 and 0.38 Hz, CIs overlapping the non-whisking rate). Under reading (a), all spikes, 15 are WT* (median 7.1 Hz) and 29 of 33 agree; 227A and 145B (1.05 and 1.26 Hz) have more than 1,000 spikes in all but 393 and 233 during whisking in air. With Poisson CIs, 15 are WT* and 29 of 33 agree.", "deviations": [ "The Glossary's \"at least 1,000 spikes\" can be read as spikes in the recording (a) or during whisking in air (b); only (b) matches the paper's count and Table S1's classes." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3a-direction-selective", "statement": "Merkel and SA afferents responded to contact in a dramatically direction-selective manner, far more strongly to contacts in either the protraction or the retraction direction.", "source": "Results, second section; Figure 3A, E, H, I", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "17 of 26 Merkel and SA afferents (65%) have a direction index of 0.5 or more (criterion 80%); 21 of 26 have 0.33 or more and 11 of 26 have 0.67 or more. Median index 0.65 over Merkel and SA, 0.59 over the 14 Merkel afferents, 0.23 over the 7 RA afferents, none of which reaches 0.5. 18 of 26 prefer protraction contacts. Contacts are classified by the sign of their mean M0; in 77% to 93% of contacts per recording that sign matches the whisker velocity at onset.", "deviations": [ "The paper shows direction selectivity in examples and tuning surfaces without a measure or threshold; the index and the 0.5 threshold were chosen before the analysis." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig3d-gam-full", "statement": "A full statistical model of ten mechanical and kinematic variables strongly predicted ongoing spike rate during touch (r = 0.71 plus or minus 0.16, mean and SD, n = 33).", "source": "Results, second section; Figure 3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Mean r 0.708, SD 0.141 (paper 0.71 and 0.16), median 0.726, range 0.363 to 0.919, 33 afferents. With lambda 100 the mean is 0.687. All 1,617 spline fits converged. Fits used a median of 60,000 frames per recording (at least 47,342) of a median 288,418 clean contact frames.", "deviations": [ "Penalized cubic B-splines (10 per variable, lambda 1) fitted as a binomial model with two trials per 2 ms frame replace mgcv GAMs on 1 ms bins with UBRE smoothing.", "At most 60,000 randomly chosen contact frames per recording." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3d-gam-single", "statement": "Models fitted to moment or its rate of change alone explained spiking relatively poorly (r = 0.45 plus or minus 0.19 and 0.42 plus or minus 0.21).", "source": "Results, second section; Figure 3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "M0 alone mean r 0.441 (SD 0.178; paper 0.45), M0' alone 0.415 (SD 0.217; paper 0.42). With lambda 100, 0.415 and 0.398.", "deviations": [ "Spline models in place of mgcv GAMs, as for fig3d-gam-full." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3d-gam-best-pair", "statement": "M0 and its rate of change together explained spiking (r = 0.63 plus or minus 0.20) better than any other pair of variables, and better than a model of M0, Fax and Flat (r = 0.48 plus or minus 0.19).", "source": "Results, second section; Figure 3D; Figure S2C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "M0 and M0' mean r 0.622 (paper 0.63); M0, Fax and Flat 0.475 (paper 0.48), lower than M0 and M0' in 31 of 33 (Wilcoxon p = 4.8e-08). Of the 45 pairs, M0 and omega (velocity) has the highest mean r, 0.633, and M0 and M0' is second; per afferent M0 and M0' is higher than M0 and omega in 19 of 33 (median difference 0.003). Flat and omega (0.620), Flat and M0' (0.606) and M0 and Flat' (0.605) follow. The values are within tolerance, but M0 and M0' is not the single best pair. The rank holds in two variants - with lambda 100 M0 and M0' is second (0.589 against 0.600 for M0 and omega, higher in 17 of 33), and fitted on a random half of the frames and evaluated on the other half it is second (0.620 against 0.630, higher in 20 of 33).", "deviations": [ "Spline models in place of mgcv GAMs; the ranking of close pairs may depend on the smoothing method." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig4c-viscoelastic", "statement": "A simple viscoelastic model of moment and its rate of change predicted spike rates of Merkel and SA afferents during touch at levels comparable to the statistical model based on M0 and its rate of change (25 of 26 afferents fitted).", "source": "Results, third section; Figure 4C; STAR Methods, Viscoelastic model", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Over 25 Merkel and SA afferents (Table S1's fitted set), mean r 0.656 for the viscoelastic model against 0.686 for the spline model of M0 and M0' on the same frames, difference -0.030 (95% bootstrap CI -0.061 to -0.006); viscoelastic higher in 10 of 25; Merkel afferents alone -0.034. The optimizer reported success for all 25, but 6 of 25 fits end with a parameter at a bound (eps_lim in 4, E in 1, eta in 2), so some fits may be local optima, which would only lower the viscoelastic r. These values differ slightly from the previous run (-0.029, 9 of 25, 7 at a bound) with the same code, data and locked packages; the cause was not established. With three other sets of random starts the mean difference is -0.037, -0.040 and -0.017, so the outcome holds, but single recordings change by up to 0.555 in r. Different parameter sets give nearly the same prediction, so the fitted parameter values are not interpreted.", "deviations": [ "Fitted with L-BFGS-B from 8 starts, with the rate of change of moment scaled by its 80th percentile inside the fit; the Methods used fmincon. During development an unscaled version found worse optima for the same model, so the result depends on the optimizer.", "Fitted and evaluated on the same at most 60,000 contact frames as the spline models, which also exclude frames that are outliers on the other nine variables." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig5-phase-modulation", "statement": "All 15 WT* afferents (13 touch WT* and 2 whisking-only) were dramatically modulated by whisk phase, with rates at non-preferred and preferred phases of 2.1 plus or minus 3.4 and 51.2 plus or minus 105.7 Hz (median and IQR).", "source": "Results, fourth section; Figure 5A to C; Figure S3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Over the 15 WT* afferents, non-preferred phase median 2.43 Hz, IQR 3.16 (paper 2.1 and 3.4); preferred phase median 51.1 Hz, IQR 96.6 (paper 51.2 and 105.7). All 15 fire at least 9.5 times more at the preferred than the non-preferred phase. Both medians are within the claim's tolerances (the paper's IQRs). Against a 10% band, which is not the criterion, the non-preferred median (16% above the paper's) would be outside and the preferred inside.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig5e-phase-span", "statement": "Across the population of WT* afferents, preferred phase spanned the whisk cycle.", "source": "Results, fourth section; Figure 5D, E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Preferred phases occupy all four quarter cycles (7, 4, 1 and 3 of 15), but the Rayleigh test finds a preferred direction (R = 0.448, p = 0.047, just below 0.05). The outcome sits at the threshold and depends on the estimator of preferred phase, which the criterion fixes as the bin of highest rate of 30 - with the circular mean of the tuning curve p = 0.062 (which would be reproduced), with the highest of 20 or 60 bins, computed on the outlier-free frames kept for figs6-kinematic-gam, p = 0.023 and 0.046; all four quarters are occupied under every estimator. At the preferred phase the mean whisker velocity is negative for 11 of 15. Whether this agrees with the paper's slight abundance in retraction (Figure 7G, on 28 afferents) is not established, since the stored phase is negated and the paper's phase convention for the figure is not known.", "deviations": [ "The paper gives no test for spanning the whisk cycle; the quarter-cycle and Rayleigh criterion was chosen before the analysis." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "figs3-phase-invariance", "statement": "The preferred phase of each WT* afferent was largely invariant across whisk cycles of different amplitudes, frequencies and setpoints.", "source": "Results, fourth section; Figure S3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Median absolute circular difference between the preferred phases of the two halves 0.37 rad (amplitude), 0.59 (frequency), 0.48 (setpoint), against pi/4 = 0.785. 4, 6 and 5 of 15 afferents differ by more than pi/4.", "deviations": [ "The paper shows invariance with tuning surfaces only; the median split and the pi/4 threshold were chosen before the analysis." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "figs6-kinematic-gam", "statement": "Statistical models fitted to whisker position, velocity, acceleration and jerk during whisking in air predicted phase tuning curves nearly perfectly (r = 0.97 plus or minus 0.04, n = 28), while single kinematic variables performed poorly.", "source": "Results, fifth section; Figure S6A, B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "On the 15 WT* afferents, the full model's mean r between predicted and observed phase tuning curves is 0.975, SD 0.013 (paper 0.97 and 0.04, on 28). Single-variable models give 0.524 (jerk) to 0.724 (acceleration); velocity and acceleration together give 0.960. No fit failed to converge.", "deviations": [ "Tested on 15 of the paper's 28 afferents; the intact condition of the 13 progressive cutting recordings cannot be separated.", "Spline models in place of mgcv GAMs, fitted on 60,000 frames and evaluated on up to 400,000 whisking-in-air frames per afferent." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig7g-phase-span-28", "statement": "Preferred phases of all 28 WT* afferents spanned the whisk cycle, with a slight abundance in the retraction phase.", "source": "Discussion, fourth paragraph; Figure 7G", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the intact condition of the 13 progressive cutting recordings, whose trials are all labelled intact (see fig6-cut-eliminated). The 15 other WT* afferents are tested in fig5e-phase-span.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig6-cut-eliminated", "statement": "Progressive whisker cutting eliminated spiking during whisking in air in 6 of 13 afferents (from 50.1 plus or minus 42.3 Hz intact to 0.9 plus or minus 0.7 Hz after the final cut, mean and SD).", "source": "Results, fifth section; Figure 6B, E", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Every trial of the 13 progressive cutting recordings has cuttingGroup \"intact\" and each file has one MOI value, so the intact, sham and cut conditions cannot be told apart. The whisking-in-air rate falls over most sessions (last fifth below half the first in 10 of 13, below 10% in 5 of 13), so the files appear to hold the cut conditions under the intact label. Splitting by trial order would be a guess.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig6-cut-remained", "statement": "In 7 of 13 afferents self-motion responses remained after cutting (86.1 plus or minus 71.5 Hz intact against 70.3 plus or minus 58.5 Hz after the final cut).", "source": "Results, fifth section; Figure 6C to E", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As fig6-cut-eliminated.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig6a-final-length", "statement": "Cutting shortened the whisker to near its base (final length 0.37 plus or minus 0.43 mm, mean and SD, n = 13).", "source": "Results, fifth section; Figure 6A", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The remaining whisker length after each cut is not in the dandiset; the trial table's MOI has one value per file, the same for all trials.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7d-cut-emg", "statement": "After whisker trimming, phase tuning curves of the 7 afferents that kept spiking were correlated with intrinsic protractor or nasolabialis EMG (r = 0.66 plus or minus 0.27).", "source": "Results, sixth section; Figure 7D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the intrinsic protractor EMG, which is not in the EMG files 7A, 8A and 9A (they hold tracked whisker series only, with no spike times and nothing in acquisition), and the cut condition of each trial (metadata insufficient, see fig6-cut-eliminated). The EMG is given as the main reason because no labelling of the trials would supply it.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig7e-lost-rate-kinematics", "statement": "The spike rate lost after cutting was correlated with positive acceleration, negative acceleration or jerk (r = 0.71 plus or minus 0.19, n = 13).", "source": "Results, sixth section; Figure 7E", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the intact and fully cut conditions of the 13 progressive cutting recordings, which the trial tables do not distinguish (see fig6-cut-eliminated).", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig7f-precut-emg", "statement": "In 5 afferents recorded with the whisker already cut near its base, phase tuning was strongly correlated with intrinsic protractor or nasolabialis EMG (r = 0.76 plus or minus 0.06).", "source": "Results, sixth section; Figure 7F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The 5 cut-whisker recordings and the nasolabialis motor units (11A) are in the dandiset, but the best match is chosen between the intrinsic protractor and the nasolabialis curves, and the intrinsic protractor EMG is not in the dandiset. The nasolabialis curve alone gives no useful bound - 4 of the 5 afferents are anticorrelated with it (mean r -0.277, SD 0.559), and only 305A correlates (0.695). As a stand-in that is not the criterion, the better of each afferent's correlations with its own positive and negative velocity curves has mean 0.753 (0.680 to 0.848), with positive velocity, which the paper relates to the intrinsic protractor, the better for 4 of 5.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "figs4-nasolabialis", "statement": "Motor unit activity of m. nasolabialis was phase modulated and correlated with negative whisker velocity (r = 0.93) and anti-correlated with positive velocity (r = -0.75) within whisk cycles.", "source": "Figure S4F to H; Figure 7A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "The spike times of 11A, taken as motor unit spikes, give r = 0.924 with negative velocity (paper 0.93) and -0.716 with positive velocity (paper -0.75) across 30 phase bins of 23.3 min of whisking; the rate ranges 0.7 to 37.6 Hz and peaks where velocity is negative. The raw EMG is not in the file.", "deviations": [ "The file does not say that its spike times are motor units of m. nasolabialis; this is taken from Table S1." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "figs4-intrinsic-protractor", "statement": "Intrinsic protractor EMG was correlated with positive whisker velocity within whisk cycles (r = 0.94, 0.97 and 0.96 in three mice).", "source": "Figure S4B to D; Figure 7A", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Files 7A, 8A and 9A hold the tracked whisker series of the EMG sessions (position, velocity, Mi, dMi and others) but no EMG signal, no spike times and nothing in acquisition, analysis or stimulus. The archive's variableMeasured for them lists only BehavioralTimeSeries and ProcessingModule, and their size per trial (0.31 MB) equals that of 11A and of the progressive cutting files. The undescribed Mi (N*m) and dMi (N*m/s) do not follow positive velocity by phase - r -0.026 to 0.002 for Mi and -0.570 to -0.534 for dMi in 7A, 8A and 9A, close to the medians in every group of afferent files (-0.026 to -0.014 and -0.536 to -0.485) - so neither is the intrinsic protractor EMG.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "sigma-kappa", "statement": "The noise level of curvature estimates, curvature change during whisking in air as a percentage of that during contact, was 7.8 plus or minus 5.0% (mean and SD) across 33 sessions.", "source": "STAR Methods, Video analysis, whisker baseline curvature; Figure S7", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_severson_2017.ipynb", "notes": "Mean 10.01%, SD 6.97, range 4.23 to 39.89 over the 33 touch recordings (paper 7.8 and 5.0). The mean is within the paper's stated spread but 28% above its mean value, outside a 10% band; 243B (39.89%) and 265A (28.49%) are high. Both readings of contact frames give the same values.", "deviations": [ "The Methods give no rule for frames with a missing distance to the pole; these are treated as far from the pole." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "figs1-optotag-latency", "statement": "Identified Merkel afferents spiked at short latency (4.9 plus or minus 1.3 ms) and low jitter (SD of first-spike latency 0.91 plus or minus 0.29 ms) after brief light pulses.", "source": "STAR Methods, Optogenetic identification; Figure S1C, D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The light pulse times and the optogenetic stimulation trials are not in the dandiset; no file has a member in stimulus, acquisition or analysis, or an optogenetic neurodata type.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-labelling-specificity", "statement": "In TrkC-CreER;Rosa-Ai9 mice, 99.2% of classified labelled afferent endings in whisker follicles were Merkel cell-associated (1,045 of 1,053).", "source": "STAR Methods, Histology quantification; Figure S1B", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The histology (confocal stacks and their scoring) is not in the dandiset, and was not found in another public archive.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "contact-classifier", "statement": "Automatic contact classification agreed with manual curation for 99.5 plus or minus 0.2% of frames, with a false positive rate of 0.3 plus or minus 0.1%.", "source": "STAR Methods, Video analysis, contact detection", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The files hold the final contact classification only, not the manually curated frames the classifier was tested against.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The files do not say which experiment each recording belongs to (touch, progressive cutting, cut-whisker, whisking-only, EMG), the afferent type (RA or SA), which afferents were identified as Merkel afferents by optogenetic tagging, or the whisking and touch class. All of these are in the paper's Table S1, whose recording ids match the NWB identifiers." }, { "kind": "selection_undocumented", "statement": "The paper excludes three touch recordings (227C, 214A, 271A) from all analyses except Figure S1. The dandiset holds them without saying so." }, { "kind": "metadata_error", "statement": "In the 13 progressive cutting recordings every trial has cuttingGroup \"intact\" and the trial table's MOI has one value per file, although the whisking-in-air rate falls over most of these sessions (last fifth below half the first in 10 of 13). The cutting conditions (intact, sham, cut 1 to 3) and the moment of inertia after each cut are missing, which blocks Figure 6 and parts of Figure 7." }, { "kind": "data_missing", "statement": "The EMG files of the intrinsic protractor recordings (7A, 8A, 9A) hold the tracked whisker series but no EMG signal; the nasolabialis file (11A) holds spike times but not the EMG. The optogenetic tagging data, the histology, the whisker geometry and the manually curated contact frames are not in the dandiset." }, { "kind": "metadata_error", "statement": "Velocity, acceleration and jerk are stated in degree/s, degree/s^2 and degree/s^3, and dM0, dFaxial and dFlateral in N*m/s and N/s, but the values are per millisecond; each is close to half the change of its variable per 2 ms frame (median ratios 0.467 to 0.502 over files)." }, { "kind": "metadata_insufficient", "statement": "The stored whisk phase is the negative of the Hilbert phase of the band-passed whisker position; its sine is anticorrelated (median -0.9999 over files) and its cosine correlated (median 0.9999) with those of the Hilbert phase, and position peaks at phase 0 in all 60 files. So phases from -pi to 0 are retraction, the reverse of the convention the paper cites. Neither the files nor the paper describe the convention." }, { "kind": "metadata_insufficient", "statement": "Every series has the description \"no description\". distanceToPoleCenter has unit \"unknown\"; its median in frames with contact = 1 is between -0.08 and 0.09 in every file but one (209A, a cut-whisker recording with almost no contact), which fits the Methods' distance from whisker to pole in mm, not a distance to the pole's centre. Series not used here (Mi, dMi, Fnorm, thetaAtContact, follicleCoordsX and Y) are not explained; Mi and dMi have units N*m and N*m/s and values below 3e-8 in absolute size, in every file including the EMG files." }, { "kind": "metadata_error", "statement": "Trial stop_time is 6.998 s after start_time in every trial of every file, while each trial's series hold 2,500 frames at 500 Hz (5 s), as the Methods describe." }, { "kind": "format_error", "statement": "The spike times of file sub-KSm31 (KS0277A) are not sorted." }, { "kind": "metadata_error", "statement": "Two identifiers, KS0125_ and KS0128_, lack the unit letter of their Table S1 recordings (125B and 128D). All session start times are 12:00, so only the dates carry information." }, { "kind": "other", "statement": "Some series hold extreme values, likely tracking errors, such as whisker position from -985 to 596 degrees, whisk frequency from -250 to 250 Hz and M0 down to -0.52 N m. The Glossary's percentile outlier removal excludes them, but they are not flagged in the files." }, { "kind": "metadata_insufficient", "statement": "Two recordings made with the whisker cut before recording (199B and 209A) hold distance-to-pole series and frames with contact = 1 (5,014 and 32); in 209A the distance at those frames is 5.6 to 6.5. The files do not say whether a pole was presented in these sessions or what these frames are." }, { "kind": "methods_unavailable", "statement": "The paper's MATLAB and R analysis code is available only on request; no public repository was found, so the GAM and viscoelastic fits had to be reimplemented." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper (PMC5528144). The verifier queried the archive metadata and tested helper functions on synthetic inputs. Its report gave its own outcome for each claim; all 28 agree with the record. It listed ten problems (B1 to B10), three marked as affecting a conclusion, and outputs it could not check. B7 (contact requires whisking, as the claims file fixes) needed no change. The cell numbers in the reasons below refer to the round-1 notebook.", "agreed": 28, "of": 28, "disagreements": [] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, the helper module, the claims file and the attempt record, with the paper (PMC5528144). The verifier checked every conclusion cell, the README and the record against the printed outputs and reviewed the round-1 responses. It agreed with all 28 outcomes, found seven statements not fully supported by the outputs, and said the Table S1 transcription had still not been checked by a verifier. The cell numbers in its reasons refer to the round-2 notebook; this revision adds code cells at positions 19, 47 and 64, so later cells move. Outside the claims, the velocity column of the data check (cell 11) was labelled degrees/s although the notebook's own ratio check shows per millisecond; the label now says so.", "agreed": 28, "of": 28, "disagreements": [] } ] }, { "id": "000232-chang-2023-01", "dandiset": "000232", "dandiset_version": "0.240510.2038", "paper": "10.1101/2023.08.21.554194", "paper_title": "Preprint for: Rule-based modulation of a sensorimotor transformation across cortical areas", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000232-chang-2023", "entry_title": "Rule-based modulation of a sensorimotor transformation across cortical areas (Chang et al. 2023)", "description": "Tests the findings of Chang, Finkel, Xu and O'Connor (bioRxiv 2023, version 2) on dandiset 000232, which holds silicon-probe recordings from S1, S2, MM, ALM and AMM of mice performing a cross-modal sensory selection task, and the behaviour of optogenetic inhibition sessions in that task and in a tactile detection task. It covers behavioural performance, single-neuron rule and stimulus discrimination, population decoding of the rule, neural trajectories and subspaces, coding dimensions, rule transitions and the effects of optogenetic inhibition.", "notebooks": [ { "path": "reproduce_chang_2023.ipynb", "title": "Reproducing Chang et al. (2023) from dandiset 000232", "executed": "notebooks/000232-chang-2023/reproduce_chang_2023.html" } ], "outcomes": [ { "claim": "fig1e-recording-counts", "statement": "Single units were recorded with 64-channel probes in S1 (6 mice, 10 sessions, 177 neurons), S2 (5 mice, 8 sessions, 162 neurons), MM (7 mice, 9 sessions, 140 neurons) and ALM (8 mice, 13 sessions, 256 neurons), one area per session, and in AMM (110 neurons).", "source": "Results, first section; Figure 1E and 1G; Figure S1K", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Sessions, mice and units per area match exactly; S1 10, 6, 177; S2 8, 5, 162; MM 9, 7, 140; ALM 13, 8, 256; AMM 110 units in 9 sessions from 7 mice. The units are those left after the paper's quality filter.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-session-counts", "statement": "The optogenetic experiments in the cross-modal task comprise S1/S2 (4 mice, 10 sessions), MM (4, 11), ALM (4, 10), sham (7, 28), AMM (7, 21) and PPC (7, 21); in the tactile detection task sham (5, 9), S1/S2 (3, 3), MM (3, 5), ALM (3, 4), AMM (3, 4) and PPC (3, 4).", "source": "Figure 6 legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "All 24 counts of sessions and mice per optogenetic condition match the Figure 6 legend. The code's performance check, ported here, passes 27 of the 28 cross-modal sham sessions and all other cross-modal sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-performance", "statement": "Performance was about 75% correct under both rules (respond-to-touch 74 plus or minus 1%, respond-to-light 75 plus or minus 1%, mean and SEM over 12 mice), with no difference between them (paired t-test, p = 0.56).", "source": "Results, first section; Figure 1D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Reading (a), trials as deposited, gives 73.6 plus or minus 0.8% (touch) and 74.8 plus or minus 1.5% (light) over 12 mice, paired t-test p = 0.561, matching the reported 74, 75 and p = 0.56. Reading (b), without the last 20 trials, gives 72.8 and 74.2% (p = 0.558), with the touch value outside tolerance.", "deviations": [ "The Methods remove the last 20 trials of each session and the code does not; the files may already lack them. Both readings are shown and reading (a) matches." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-outcome-fractions", "statement": "The fractions of trial outcomes were similar under the two rules (touch against light; hit 36 against 35%, correct rejection 38 against 40%, miss 13 against 14%, false alarm 13 against 12%).", "source": "Figure 1D legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Under reading (a) all eight fractions are within the paper's SEM (touch against light; hit 35.6 and 35.2, correct rejection 38.1 and 39.6, miss 13.0 and 13.6, false alarm 13.3 and 11.6%). Reading (b) puts 6 of 8 within. Gaps between rows, which mark removed trials, separate 4.5% of consecutive rows within the last 20 rows of a session against 12.7% earlier; this is consistent with the last rows being the end of the session but does not show it.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1h-thit-tcr-selective", "statement": "18 to 33% of neurons discriminate tactile hits from tactile correct rejections in the first 150 ms after the stimulus (S1 28.8%, S2 17.9%, MM 32.9%, ALM 23.4%), and most of these respond more in tactile hits (AUC above 0.5).", "source": "Results, first section; Figure 1H", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "S1 30.5, S2 16.7 and ALM 23.0% are within tolerance; MM is 36.4% against 32.9 plus or minus 3.29, and above the stated range widened by 10%. Over four other seeds MM gives 35.0 to 36.4%, S1 28.2 to 30.5, S2 17.9 to 19.1 and ALM 21.9 to 25.0%. MM is within tolerance in 3 of the 5 seeds, and the five-seed means (S1 29.7, S2 18.1, MM 35.6, ALM 23.1%) are all within tolerance, so the partial outcome depends on the bootstrap draw; it is judged on the main seed. 165 of 191 selective neurons (86.4%) have mean AUC above 0.5, as the claim states.", "deviations": [ "The bootstrap resamples are shared by all units and bins of a session; the code draws them separately. Each unit's interval depends only on its own resamples." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-rule-prestim-units", "statement": "Before the stimulus (-100 to 0 ms), fewer than 5% of neurons in S1 and S2 discriminate the rule, while about 10 to 20% do in MM and ALM (S1 4.5%, S2 2.5%, MM 21.4%, ALM 10.2%).", "source": "Results, second section; Figure 2C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "S2 2.5, MM 20.0 and ALM 9.8% are within tolerance; S1 is 5.6% (10 neurons) against 4.5% (8 neurons). Over the main seed and four others S1 gives 3.4 to 5.6% and is within tolerance in none (9 neurons, 5.1%, is just above it); ALM is within tolerance in 2 of 5. The five-seed means (S1 5.0, S2 2.8, MM 20.7, ALM 9.9%) are all within tolerance. The outcome is judged on the main seed. MM and ALM each exceed S1 and S2, as the claim states.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-stimulus-prestim-units", "statement": "As a negative control, almost no neuron discriminates tactile from visual trials before the stimulus (S1 0%, S2 0%, MM 0%, ALM 0.8%).", "source": "Results, second section; Figure 2D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "0% in S1, S2 and MM and 0.8% (2 neurons) in ALM, as in the paper.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-stimulus-poststim-units", "statement": "After the stimulus (0 to 100 ms), more than 35% of neurons in S1 and S2 and about 15% in MM and ALM discriminate tactile from visual trials (S1 37.3%, S2 35.2%, MM 15%, ALM 14.1%).", "source": "Results, second section; Figure 2E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "All four within tolerance of 37.3, 35.2, 15 and 14.1%.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-prestim-predicts-touch-response", "statement": "Among neurons with significant rule discrimination before the stimulus, the pre-stimulus rule preference predicts the rule modulation of the early touch response (0 to 50 ms); Pearson r = 0.93 in MM (30 neurons) and 0.83 in ALM (26 neurons), both p < 0.001 (S1 r = 0.69, 8 neurons, p = 0.056; S2 r = 0.91, 4 neurons, p = 0.093).", "source": "Results, second section; Figure 2F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "MM r = 0.958 over 28 neurons and ALM r = 0.841 over 25 neurons, both p < 0.001 (paper 30 and 26 neurons). S1 r = 0.681 (10 neurons, p = 0.030) and S2 r = 0.902 (4 neurons, p = 0.0985), against the paper's 0.69 (8 neurons, p = 0.056) and 0.91 (4, p = 0.093).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-rule-decoding", "statement": "The rule can be decoded from pre-stimulus population activity (-100 to 0 ms) in each area; median LDA accuracy over sessions, true against shuffled, S1 0.61 against 0.5, S2 0.62 against 0.53, MM 0.7 against 0.52, ALM 0.68 against 0.55.", "source": "Results, third section; Figure 3B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Shuffled medians are 0.564, 0.532, 0.526 and 0.535; 37 of 40 sessions exceed their shuffled value. The S1 sessions differ from shuffled at Wilcoxon p = 0.055, the others at p below 0.01. The shuffled medians (0.526 to 0.564) are about equal to the larger block's share of correct trials (medians 0.529 to 0.556 by area).", "deviations": [ "The Methods name LDA; the code's diagonal LDA is used. The Methods' soft normalization and the code's z-score give the same diagonal LDA predictions." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-rule-decoding-motor-stronger", "statement": "Rule decoding is robust in the motor areas, whose bootstrap 95% CIs of mean accuracy do not overlap those of shuffled data (MM 0.60 to 0.73 against 0.48 to 0.53; ALM 0.56 to 0.66 against 0.49 to 0.54), and limited in the sensory areas, whose true CIs are above 0.5 but overlap the shuffled ones (S1 0.52 to 0.61 against 0.49 to 0.55; S2 0.53 to 0.63 against 0.49 to 0.54).", "source": "Results, third section; Figure 3C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Bootstrap 95% CIs, true against shuffled; MM 0.601 to 0.731 against 0.472 to 0.523; ALM 0.560 to 0.655 against 0.495 to 0.544 (no overlap); S1 0.530 to 0.614 against 0.493 to 0.545; S2 0.528 to 0.619 against 0.488 to 0.539 (overlap). These are within 0.012 of the paper's bounds.", "deviations": [ "200 resamples per area; the code's header sets 100 and its saved file names say 1000." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3de-stimulus-decoding-controls", "statement": "Population activity discriminates tactile from visual trials after the stimulus (0 to 100 ms) but not before it (-100 to 0 ms).", "source": "Results, third section; Figure 3D and 3E; Figure S3C and S3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Before the stimulus true means 0.495 to 0.509 with CIs overlapping shuffled in all areas; after it 0.642 (MM) to 0.805 (S2), no overlap in any area.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs3-svm-rf-decoding", "statement": "Support vector machines and random forests decode the rule from pre-stimulus activity about as well as LDA (median accuracy true against shuffled; SVM S1 0.6 against 0.53, S2 0.61 against 0.51, MM 0.71 against 0.51, ALM 0.65 against 0.52; random forests S1 0.59 against 0.52, S2 0.6 against 0.52, MM 0.65 against 0.49, ALM 0.7 against 0.5).", "source": "Results, third section; Figure S3A and S3B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "All eight within 10% and above their shuffled medians. With the code's z-score the SVM medians are 0.575, 0.603, 0.701 and 0.642.", "deviations": [ "scikit-learn's SVC and random forest stand in for MATLAB fitcsvm and TreeBagger with their defaults." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-prestim-distance-predicts-divergence", "statement": "Sessions with a larger pre-stimulus distance between tactile hit and correct rejection trajectories (top 50% of 40 sessions) show a larger distance after the stimulus than the bottom 50% (permutation test, p < 0.001).", "source": "Results, fourth section; Figure 4B and 4C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Top 20 sessions 1.171 against bottom 20 0.966 mean post-stimulus distance, permutation p = 0.004. With the code's normalization (range without the offset 5) p = 0.001. Pre- and post-stimulus mean distances correlate over sessions (Spearman 0.54, p = 0.0004).", "deviations": [ "The code's windows are offset by one 10 ms bin from the stated ones; the stated windows are used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-subspace-overlap", "statement": "In all four areas the subspace overlap of tactile correct rejections with tactile hits (0 to 150 ms) is lower than that of held-out tactile hits (tCR minus control tHit; S1 -0.23, 8 sessions, p = 0.0016; S2 -0.23, 7 sessions, p = 0.0086; MM -0.36, 5 sessions, p < 0.001; ALM -0.35, 11 sessions, p < 0.001; paired t-test).", "source": "Results, fifth section; Figure 4E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Negative in all four areas with p = 0.0007, 0.025, 0.003 and below 0.0001 (8, 7, 5 and 12 sessions), but only S2 is within 10% of the paper. MM and ALM are larger in magnitude than the reported -0.36 and -0.35; the code's single-split procedure repeated 200 times gives 95% ranges of -0.497 to -0.376 (MM) and -0.473 to -0.359 (ALM), which exclude the reported values.", "deviations": [ "Sessions with at least 10 units (Methods), 12 ALM sessions; the code keeps more than 10, 11 ALM sessions, as the paper reports. Both are shown and give the same result.", "Overlaps average 100 random equal splits with offset 5 throughout; the code uses one split drawn separately for each neuron and offsets 5 and 0.01, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-prestim-overlap-predicts-poststim", "statement": "Across sessions, the tCR subspace overlap before the stimulus (-100 to 0 ms) correlates with that after it (Pearson r = 0.68, p < 0.001, 31 sessions).", "source": "Results, fifth section; Figure 4F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "r = 0.688 over 32 sessions (p = 1.3e-05); 0.686 over the code's 31 sessions; the code's single-split procedure gives 0.573 to 0.734 over 200 runs.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4ef-coding-dimensions", "statement": "Stimulus coding dimensions are aligned between the two rules in S1, S2 and MM but not in ALM, while choice coding dimensions (lick against no lick) are not aligned in any area (dot product magnitudes, true against shuffled, with 95% CIs).", "source": "Results, sixth section; Figure S4E and S4F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Seven of eight judgements match. The MM stimulus CD is not aligned (0.366, CI 0.218 to 0.521, shuffled 0.150 to 0.441), where the paper reports 0.48 against 0.24 with non-overlapping CIs; with the code's sessions of more than 10 units it is 0.295 and also not aligned. S1, S2 and ALM values are close to the paper's (0.557, 0.620, 0.348 against 0.5, 0.62, 0.33).", "deviations": [ "All sessions are used, as the paper's session counts state; the code keeps sessions with more than 10 units, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4h-choice-right-left", "statement": "Choice coding dimensions computed from right against left lick trials are still not well aligned between the two rules (true against shuffled; S1 0.39 against 0.2, S2 0.32 against 0.2, MM 0.35 against 0.18, ALM 0.28 against 0.21).", "source": "Results, sixth section; Figure S4H", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "All four below 0.5; S1, MM and ALM within 0.1 of the paper, S2 0.422 against 0.32. All four CIs overlap the shuffled ones. Over the main seed and four others the S2 mean is 0.420 to 0.425, within 0.1 of the paper in 1 of 5 (0.420); the outcome is judged on the main seed.", "deviations": [ "The criterion's \"needed condition\" first read as each of the four rare categories left 1 of 10 S1 sessions, none in S2 and MM and 1 of 13 in ALM, so it could not decide; following the code's nanmean over stimuli, right- and left-lick trials are pooled over stimuli (at least 2 each, all 40 sessions). The first reading is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-first-hit-switches", "statement": "Mice switched before or immediately after the cue on the 9th trial; there were 88 switches into respond-to-touch blocks and 91 into respond-to-light blocks.", "source": "Results, seventh section; Figure 5B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Non-first blocks with a hit, as the criterion and the code's GetFirstHitInfo define them, number 63 (touch) and 75 (light), against 88 and 91. Both counts fail, so two of the three conditions fail and the outcome is not reproduced (round 1 recorded partially reproduced, which the criterion does not allow). The third condition holds; first hits at or before the trial after the cue are 57.1% (touch) and 65.2% (light) of blocks with a cue row, counted in rows of the file, and 55.4% and 62.1% in trial numbers estimated from the gaps between rows. All blocks, including the first of each session, number exactly 88 and 91, and blocks with a hit including first blocks 87 and 91. The code's GetFirstHitInfo returns one entry per block, NaN for first blocks and blocks without a hit, so a count of its entries gives the number of blocks.", "deviations": [ "The code numbers trials by the behavioural system, including trials the files lack; first hits are placed relative to the cue row in the files, and as a variant in trial numbers estimated from the gaps between rows (xm.estimated_trial_numbers)." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5de-motor-states-track-switch", "statement": "Over a rule transition, the fraction of trials classified as respond-to-touch from pre-stimulus activity changes progressively in MM and ALM (Kendall's tau, mean and 95% CI; touch to light MM -0.39 [-0.67, -0.11], ALM -0.29 [-0.54, -0.04]; light to touch MM 0.37 [0.07, 0.63], ALM 0.27 [0.03, 0.49]).", "source": "Results, seventh section; Figure 5D and 5E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Touch to light MM -0.401 [-0.667, -0.111], ALM -0.302 [-0.538, -0.051]; light to touch MM 0.382 [0.074, 0.630], ALM 0.268 [0.026, 0.513]; all within 0.04 of the paper's values and bounds.", "deviations": [ "LDA with Ledoit-Wolf shrinkage stands in for the code's optimized LDA; 500 resamples (code 1000)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5-sensory-states-no-tracking", "statement": "Classification of trials in S1 and S2 shows no clear trend across block transitions (Kendall's tau touch to light S1 -0.16 [-0.43, 0.1], S2 -0.15 [-0.54, 0.21]; light to touch S1 0.21 [-0.07, 0.5], S2 0.25 [-0.17, 0.63]).", "source": "Results, seventh section; Figure S5", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "S1 -0.163 [-0.433, 0.117] and 0.219 [-0.067, 0.500]; S2 -0.140 [-0.500, 0.250] and 0.259 [-0.105, 0.620]; all include 0. The 10-fold estimates without resampling are as large in S1 and S2 as in MM and ALM (S2 to touch 0.583, MM 0.519), so the absence rests on wide CIs from 10 and 8 sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-pre-inhibition-tactile", "statement": "Inhibiting MM or ALM before the stimulus reduces tactile detection sensitivity in respond-to-touch blocks, while inhibiting S1/S2, AMM or the sham does not (95% CI of the change; S1/S2 [-0.47, 0.08], MM [-0.65, -0.12], ALM [-0.68, -0.02], sham [-0.12, 0.13], AMM [-0.19, 0.06]).", "source": "Results, eighth section; Figure 6C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "MM -0.390 (CI -0.658 to -0.123) is below 0; ALM -0.373 has a CI of -0.707 to 0.005 when false-alarm trials are also resampled (Methods). S1/S2, sham and AMM include 0. With the code's resampling, which keeps the observed false-alarm rate, ALM is -0.682 to -0.018 and every CI is within 0.03 of the paper's, which would make the claim reproduced. The outcome is judged on the main seed; the ALM upper bound is at the edge of 0. Over ten other seeds it averages -0.001 (SD 0.003, range -0.006 to 0.001) and is below 0 in 7 of 10; with the code's resampling it is below 0 in all ten (mean -0.018). No other Methods-resampling bound of the optogenetic CIs checked over seeds changes side; the figs6b ALM interval with the code's resampling does (upper bound 0.002 on the main draw, below 0 in 9 of 10 other seeds), and the fig6ij laser-only calls keep their side in all ten seeds.", "deviations": [ "Hit and false-alarm trials are both resampled; the code resamples hits only, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs6b-pre-inhibition-hit-rate", "statement": "The loss of tactile sensitivity with pre-stimulus inhibition is mainly a fall in the tactile hit rate (95% CI of the change; S1/S2 [-0.31, 0.01], MM [-0.49, -0.15], ALM [-0.46, -0.07]).", "source": "Results, eighth section; Figure S6B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "MM -0.318 (-0.492 to -0.152), ALM -0.227 (-0.463 to -0.007), S1/S2 -0.147 (-0.303 to 0.010). The ALM upper bound is close to 0. Over ten other seeds it is below 0 in all ten (mean -0.004, SD 0.002). The code's resampling is the same procedure here, as there is no false-alarm group; its draw gives 0.002 and is below 0 in 9 of 10 other seeds.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-post-inhibition-tactile", "statement": "Inhibiting S1/S2, MM or ALM from the stimulus onset reduces tactile sensitivity (95% CI S1/S2 [-0.67, -0.08], MM [-0.6, -0.34], ALM [-0.55, -0.27]).", "source": "Results, eighth section; Figure 6D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "S1/S2 -0.389 (-0.699 to -0.080), MM -0.487 (-0.612 to -0.327), ALM -0.402 (-0.568 to -0.253).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs7gh-visual-sensitivity", "statement": "Visual detection sensitivity in respond-to-light blocks falls with pre-stimulus inhibition of MM [-0.6, -0.18] and AMM [-0.35, -0.08] but not of ALM [-0.5, 0.04] or S1/S2 [-0.27, 0.05]; with inhibition from the stimulus onset it falls for MM, ALM and AMM but not for S1/S2 [-0.44, 0.04].", "source": "Results, eighth section; Figure S7G and S7H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "All eight judgements match; pre MM -0.603 to -0.173, AMM -0.356 to -0.082, ALM -0.494 to 0.050, S1/S2 -0.282 to 0.070; post MM -0.839 to -0.518, ALM -0.870 to -0.385, AMM -0.725 to -0.353, S1/S2 -0.460 to 0.045.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-ppc-inhibition", "statement": "Inhibiting PPC before or after the stimulus onset reduces both tactile and visual detection sensitivity (tactile pre [-0.4, -0.06], post [-0.43, -0.04]; visual pre [-0.31, -0.05], post [-0.54, -0.07]).", "source": "Results, eighth section; Figure 6C and 6D; Figure S7G and S7H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Tactile pre -0.408 to -0.052, post -0.466 to -0.009; visual pre -0.333 to -0.031, post -0.555 to -0.070. The tactile post upper bound is below 0 in all ten other seeds (mean -0.011, SD 0.003).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6fg-detection-task", "statement": "In a simple tactile detection task without rule switching, inhibiting S1/S2, MM or ALM after the stimulus onset reduces sensitivity, but inhibiting them before it does not (pre S1/S2 [-0.34, 0.18], MM [-0.23, 0.06], ALM [-0.28, 0.07]; post S1/S2 [-0.59, -0.31], MM [-0.59, -0.25], ALM [-0.45, -0.1]); AMM and PPC have no effect in either window.", "source": "Results, eighth section; Figure 6F and 6G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "Pre-stimulus CIs include 0 for S1/S2, MM and ALM; post-stimulus S1/S2 -0.643 to -0.251, MM -0.628 to -0.233, ALM -0.471 to -0.065. AMM and PPC include 0 in both windows.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6ij-laser-only-licks", "statement": "Lick probability on laser-only trials does not change during S1/S2, MM or ALM inhibition in either task, so the behavioural effects are not due to an inability to lick (cross-modal S1/S2 [-0.18, 0.24], MM [-0.31, 0.03], ALM [-0.24, 0.16]; detection S1/S2 [-0.13, 0.31], MM [-0.06, 0.45], ALM [-0.18, 0.34]).", "source": "Results, eighth section; Figure 6H, 6I and 6J", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chang_2023.ipynb", "notes": "11 of 12 CIs include 0. On short laser-only trials of the detection task, MM inhibition raises the right-lick probability from 0.333 in the inter-trial window to 0.553 in the response window (change 0.258, CI 0.045 to 0.483; 141 trials, 5 sessions, 3 mice); over ten other seeds the lower bound is 0.040 to 0.053, and the other eleven CIs include 0 in every seed. All cross-modal CIs and all long- laser CIs include 0; the paper gives one CI per area and task (MM detection -0.06 to 0.45), without saying which laser duration. The windows are the code's (GetBehavInfo, GetBehavInfo_tDetection). In the cross-modal task, licks on short laser-only trials are scored 0 to 2 s after the laser offset, in the detection task -0.8 to 1.2 s from it, which covers the laser. The paper's cross-modal CIs match the long-laser rows (MM -0.312 to 0.030 against -0.31 to 0.03), so the criterion's twelve CIs test more than the paper reports. Its detection CIs match neither the short, the long nor the pooled rows (the code's \"all laser trials\"; pooled MM 0.020 to 0.274 also excludes 0). A rise in licking does not bear on the paper's point that inhibition does not prevent licking.", "deviations": [ "The paper reports one CI per area and task; short and long laser-only trials were tested apart, as the code computes them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-probe-locations", "statement": "The probe locations were reconstructed histologically and lie in S1, S2, MM and ALM.", "source": "Figure 1E; Methods, Electrophysiology", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The files give the recorded area only as a label; electrode x, y and z are NaN, electrode locations are \"unknown\", and no histology images or reconstructed coordinates are in the dandiset or the code repository.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "selection_undocumented", "statement": "The ephys files hold only the trials and units the paper analysed. No trial has a lick between -1 and 0.1 s of the stimulus (the Methods remove about 25%; gaps of 8 to 64 per session remain in the trial times), and the units are those passing the quality filter and the 50 Hz cut (unit counts per area equal the paper's). The dandiset does not say that trials or units were removed." }, { "kind": "metadata_insufficient", "statement": "Units carry only spike times and observation intervals; there are no quality metrics, waveforms, channel or depth, and unit ids run from 0, so units the paper names by cluster number (for example unit 127 of YT084, 2020-02-01) cannot be identified." }, { "kind": "data_missing", "statement": "Electrode x, y and z are NaN in all 49 ephys files and electrode locations \"unknown\"; the probe locations of Figure 1E (histology) are not in the dandiset." }, { "kind": "metadata_insufficient", "statement": "The trials table columns have no descriptions. `response` (1 right lick, 2 left, 0 none, 3 on trials without a stimulus), `blockType` (\"Whisker\", \"Visual\", and \"Change\" for the cue trial), the opto trial types and the TTT to VVN indicator columns are explained only by the paper's code." }, { "kind": "metadata_error", "statement": "In the 130 behaviour files `start_time` equals the stimulus onset (or laser time on laser-only trials), so trial intervals overlap and do not delimit trials; licks before the stimulus are stored in the trial's lists." }, { "kind": "metadata_error", "statement": "In the tactile detection files, trials without a whisker stimulus are labelled \"Stim_Vis\" and \"Stim_Vis_NoCue\" with a visual stimulus type, though no visual onset is given." }, { "kind": "other", "statement": "Two laser trials start 1.6 and 2.7 s before the reference time and one lasts 9.5 s, outside the stated 0.8 s pre-stimulus and 2 s post-stimulus inhibition; the code counts them as pre-stimulus." }, { "kind": "paper_inconsistency", "statement": "Figure 5B gives 88 and 91 block switches; the 40 recording sessions hold exactly 88 touch and 91 light blocks when the first block of each session is counted, and 63 and 75 non-first blocks with a hit, so the reported numbers appear to count blocks, not switches. The code's GetFirstHitInfo returns one entry per block, NaN for first blocks and blocks without a hit, which a count of entries would give." }, { "kind": "code_mismatch", "statement": "The Methods describe soft normalization (x - mean) / (range + 5) for population analyses; the code's trajectory distance divides by the range alone, its subspace overlap uses offset 5 for the reference and 0.01 for compared data, the coding dimensions use 0.01, and decoding uses a z-score. The Methods exclude sessions with fewer than ten units from the subspace analysis; the code requires more than ten." }, { "kind": "code_mismatch", "statement": "The code's hierarchical bootstrap of optogenetic sensitivity draws resampled false-alarm trials but computes the false-alarm rate from the original trials, so only hits are resampled." }, { "kind": "code_mismatch", "statement": "The coding-dimension code keeps sessions with more than ten units (S1 8, S2 7, MM 5, ALM 11), while Figure S4 reports 10, 8, 9 and 13 sessions." }, { "kind": "other", "statement": "The shared clock of spike times and trial times could not be established by the stimulus-decoding check for three sessions, YT084 2020-02-02 and 2020-02-03 (AMM, 2 and 5 units) and YT086 2020-03-20 (MM, 5 units, accuracy 0.63 before and 0.65 after the onset). They are kept." }, { "kind": "other", "statement": "The cross-modal sham session set includes one session (of 28) that fails the code's own performance check as ported here; it is kept, as deposited." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. The attempt record was not among its materials. It checked the archive's file list and metadata for the blocked claim.", "agreed": 28, "of": 29, "disagreements": [ { "claim": "fig5b-first-hit-switches", "outcome": "not_reproduced", "reason": "Under the criterion (non-first blocks with a hit) the counts are touch 63 and light 75, against 88 and 91. Both counts fail; the before-or-at-cue+1 condition holds (0.57, 0.65). The all-block counts are exactly 88 and 91, and the paper says \"total number of block switches\", so the criterion's definition is probably not the paper's. Problem 2, that the count of blocks with a hit including first blocks is never printed, and that `rel` is counted in file rows, so `rel <= 1` can cover trials several positions after the cue, which biases the fraction upward." } ] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run (89 cells), the helper module, the claims file and the attempt record. Report in transcripts/000232/verifier-2-report.md. Points not tied to one claim were also answered. The introduction said 141 optogenetic behaviour sessions where the dandiset holds 130; corrected. The README said the run takes about 15 minutes, a quarter of it streaming, where streaming took 131 s of 14.7 min; it now gives the new run, 162 s of 8.7 min. The summary's \"no other optogenetic call changes\" and \"with other seeds\" were reworded (see fig6c, figs6b, fig6ij and fig1h). The clock part of round-1 problem B11 (three sessions, among them YT086 2020-03-20 in MM, where the stimulus-decoding check does not establish a shared clock), which was recorded only in the notebook, is now a finding. The re-run gives the same numbers as the second run in every cell that existed before.", "agreed": 29, "of": 29, "disagreements": [] } ] }, { "id": "000239-xu-2022-01", "dandiset": "000239", "dandiset_version": "0.230607.1752", "paper": "10.1038/s41586-022-04478-7", "paper_title": "Cortical processing of flexible and context-dependent sensorimotor sequences", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000239-xu-2022", "entry_title": "Cortical processing of flexible sensorimotor sequences (Xu et al. 2022)", "description": "Tests the findings of Xu, Dong, Chen, Delgado, Hughes, Zhang and O'Connor (2022) on dandiset 000239, which holds the trial tables, tongue tracking and sorted spikes of mice performing a sequence licking task. It decodes tongue kinematics, sequence identity and sequence time from S1TJ, M1TJ, ALM and S1BF populations, classifies backtracking and zigzag sequence context, and checks the behavioural measures and unit counts. The optogenetic and control experiments cannot be tested, as the files do not say which region was inhibited or which condition each session was.", "notebooks": [ { "path": "reproduce_xu_2022.ipynb", "title": "Reproducing Xu et al. (2022) from dandiset 000239", "executed": "notebooks/000239-xu-2022/reproduce_xu_2022.html" } ], "outcomes": [ { "claim": "ephys-unit-counts", "statement": "Silicon probe recordings gave 1537 single units and 303 multi-units from 57 recording sessions.", "source": "Results, \"Sequence tiling of single-unit responses\"; Extended Data Fig. 4a-d", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "The 57 files described as ephys ALM, M1TJ, S1TJ, S1BF, M1B, S1L and ZZ hold 1917 units, within 10% of the paper's 1840. With an ISI violation rate (2.5 ms) of at most 1% and a contamination of at most 15%, 1578 are single units (1537 in the paper, within tolerance) and 339 multi-units (303, outside 272.7 to 333.3). Other thresholds give 1490 to 1732 single units; three variants put the multi-units inside the tolerance, the contamination criterion alone at 15% (331), the RPV criterion alone at 0.5% (309) and both criteria with a 20% contamination threshold (295). Other estimates of the contamination at 15% give 341 multi-units (0.5 ms censored period) and 478 (spikes inside the trial span only, T the whole span). On synthetic units the estimate is 0.163 for a true contamination of 0.15 and 0.233 for 0.20, so 85% of units at 0.15 are called multi-units. Multi-units range from 0 to 21 per session. The 22 \"ephys others\" sessions (742 units) and 14 opto efficiency recordings (414 units) are not among the 57.", "deviations": [ "The contamination estimate (Hill et al. 2011) uses a censored period of 0 and the mean rate over 1 s bins of the trial span holding a spike, with all of a unit's spikes in the count; the Methods give none of these.", "Units recorded outside the target structure were excluded in the paper; the files do not say which these are, so all units are counted." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-session-counts", "statement": "The population analyses of Figure 3 use 8 S1TJ, 9 M1TJ, 13 ALM and 5 S1BF sessions.", "source": "Figure 3b legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Counted from the session descriptions, the only place the files name the recorded area. The sessions come from 4, 4, 8 and 3 mice, and every one holds units and at least 13 selected standard trials per direction.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-units-per-session", "statement": "Regressions used the simultaneously recorded units of each session, 32 plus or minus 13 units (mean and SD).", "source": "Results, \"Hierarchical population coding\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Reading (b), all 57 recording sessions, gives 33.6 and 13.0 units, both within tolerance. Reading (a), the 35 Figure 3 sessions the claim refers to, gives a mean of 32.0 and an SD of 14.4, just outside 11.7 to 14.3. Single units alone give 26.4 and 13.2. Unit counts do not depend on a random seed, so the SD of reading (a) is 14.4 under every seed.", "deviations": [ "The reading that matches, all 57 sessions, is wider than the sessions the Results describe." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-trial-count", "statement": "Figure 3a averages 2684 trials of standard and backtracking sequences.", "source": "Figure 3a legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "The Methods' trial selection gives 2169 standard and 717 backtracking trials over the 35 sessions; together 2886 (reading a), within 10% of 2684. Standard trials alone are 2169. The count is a third of the candidates (at least 10) and does not depend on the search. The greedy search finds the best subset in 43 of 70 exhaustive checks on 16 candidates (at most 8.4% above the best mean distance); a swap search improves on it by at most 4.9% on the full sets, sharing a median of 97% of the trials.", "deviations": [ "The subset of most similar trials is found by a greedy search; the Methods do not say how it was searched." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-length", "statement": "Tongue length L is decoded from population activity best in S1TJ and M1TJ and poorly in ALM and S1BF (R2 0.56, 0.42, 0.11 and 0.04).", "source": "Figure 3b,c; Results, \"Hierarchical population coding\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Mean R2 by area (S1TJ, M1TJ, ALM, S1BF) are each within the SD the figure prints, and S1TJ and M1TJ exceed ALM and S1BF. With folds that keep each trial in one fold, 0.551, 0.392, 0.087 and 0.016, same order. Decoding L with spikes shifted by 25 to 100 ms lowers R2 in S1TJ.", "deviations": [ "The inter-lick-interval standardisation of the Methods is not applied before the fits.", "Fits use scikit-learn's elastic net path (l1 ratio 0.1, 30 penalties, standardised predictors, one-SE rule), not MATLAB's lasso; samples are assigned to folds at random, as MATLAB does by default. Random folds let the autocorrelation within a trial into the test folds; R2 values are higher than with folds that keep trials together, the orderings the same.", "The fitting window is -0.5 to 0.5 s from the middle touch, read from the Methods' remark that 0.5 to 0.8 s of the decoding was new data; the paper does not state it.", "The expected values were read from the figure image, as the text does not give them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-velocity", "statement": "Tongue velocity L' is decoded best in S1TJ and M1TJ and poorly in ALM and S1BF (R2 0.35, 0.32, 0.07 and 0.01).", "source": "Figure 3b,c; Results, \"Hierarchical population coding\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "All four means within tolerance of 0.35, 0.32, 0.07 and 0.01, and the order holds with either fold scheme. L' is the derivative of L where the tongue is out.", "deviations": [ "As for fig3c-length." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-angle", "statement": "Tongue angle theta is encoded comparably in S1TJ, M1TJ and ALM, but not in S1BF (R2 0.59, 0.57, 0.54 and 0.12).", "source": "Figure 3b,c; Results, \"Hierarchical population coding\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "All four means within tolerance of 0.59, 0.57, 0.54 and 0.12. S1TJ, M1TJ and ALM differ by 0.049 and S1BF is below each. With trial folds the spread is 0.059. theta is the angle of the tongue base-to-tip vector, used where L exceeds 1 mm.", "deviations": [ "As for fig3c-length. The sign of theta (left or right) cannot be fixed from the files; R2 does not depend on it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-identity", "statement": "Sequence identity I is encoded most strongly in ALM, then progressively less in M1TJ, S1TJ and S1BF (R2 0.67, 0.42, 0.23 and 0.14).", "source": "Figure 3b,c; Results, \"Hierarchical population coding\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Means (S1TJ, M1TJ, ALM, S1BF) within tolerance of 0.23, 0.42, 0.67 and 0.14, in the order ALM > M1TJ > S1TJ > S1BF. With trial folds 0.188, 0.323, 0.657 and 0.049, same order.", "deviations": [ "As for fig3c-length." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-time", "statement": "Relative sequence time tau is encoded most strongly in ALM, then progressively less in M1TJ, S1TJ and S1BF (R2 0.60, 0.45, 0.17 and 0.08).", "source": "Figure 3b,c; Results, \"Hierarchical population coding\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Means within tolerance of 0.17, 0.45, 0.60 and 0.08, in the stated order; with trial folds 0.145, 0.381, 0.601 and 0.063, same order.", "deviations": [ "As for fig3c-length. tau is the time from the middle touch without lick standardisation." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed5b-variables-uncorrelated", "statement": "Any pair of the five behavioural variables (L, L', theta, I, tau) is uncorrelated.", "source": "Results, \"Hierarchical population coding\"; Extended Data Fig. 5b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Mean absolute correlations of the ten pairs range from 0.000 (I-tau, zero by the balanced design) to 0.118 (theta-I); the largest single-session value is 0.368 (L-theta).", "deviations": [ "The bound of 0.3 is a choice; the paper gives no threshold." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed5e-variance-explained", "statement": "Across regions, the summed variance explained by the five coding axes reached about half that of the top five principal components.", "source": "Results, \"Hierarchical population coding\"; Extended Data Fig. 5e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "The median ratio over 35 sessions is 0.454 (mean 0.490, IQR 0.387 to 0.544), inside 0.45 to 0.55 but close to its lower bound; per area medians are 0.433 to 0.476. One coding axis of 175 had all weights zero. With seeds 3, 11, 12 and 13 the median is 0.453 to 0.455, inside the range each time.", "deviations": [ "VE is computed on -0.5 to 0.8 s from the middle touch of the selected standard trials; the paper says \"during sequence execution\"." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed5f-axes-orthogonal", "statement": "The five coding axes were largely orthogonal to each other.", "source": "Results, \"Hierarchical population coding\"; Extended Data Fig. 5f", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Nine pairs have a mean absolute cosine of 0.114 to 0.225; L' and theta have 0.302, just above the bound of 0.3 the criterion fixed. Random directions in the same sessions give 0.154. With seeds 3, 11, 12 and 13, L' and theta give 0.302 to 0.320 and are the only pair at or above 0.3 each time.", "deviations": [ "The bound of 0.3 is a choice; the paper says \"largely orthogonal\"." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-cca", "statement": "After canonical correlation, ALM trajectories in the top three PCs correlate best with the theta, I, tau coding subspace (group 2), more than with L, L', theta (group 1) or all five variables with five PCs (group 3); in S1TJ and M1TJ the correlation is high only when the coding subspace includes L and L'.", "source": "Figure 3d,e; Results, \"Hierarchical population coding\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Mean canonical correlation, groups 1, 2, 3; ALM 0.607, 0.900, 0.743; S1TJ 0.746, 0.589, 0.735; M1TJ 0.712, 0.662, 0.809. All five comparisons hold by exact sign-flip tests (ALM p = 0.0002 twice; S1TJ p = 0.023 and 0.008; M1TJ p = 0.020). The figure marks p < 0.001, which an exact paired permutation cannot reach with 8 or 9 sessions; the criterion uses 0.05.", "deviations": [ "Decoded variables come from the fits of fig3c-length, without lick standardisation." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-backtracking-svm", "statement": "ALM and M1TJ activity predicts whether the port backtracked from the initial missed lick on; S1TJ shows only an insignificant trend and S1BF no prediction.", "source": "Figure 3f; Results, \"Sequence branching signals in ALM, M1TJ\"", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Sessions with backtracking in both directions are 6 ALM (as in the paper), 9 M1TJ, 8 S1TJ and 5 S1BF. Mean accuracy in 0.2 to 0.4 s after the trigger is 0.740 (ALM), 0.734 (M1TJ), 0.595 (S1TJ) and 0.556 (S1BF), against null 95th percentiles of 0.526, 0.523, 0.516 and 0.515; before 0.1 s all are 0.487 to 0.519. ALM and M1TJ decode as stated; S1TJ and S1BF also exceed the null, which the paper reports as an insignificant trend and no prediction. In this window the classes differ in behaviour (1.854 against 0.113 missed licks, ed2e-missed-licks), which S1TJ and S1BF activity may reflect.", "deviations": [ "The paper's null and confidence intervals come from a hierarchical bootstrap; here the null is 20 label shuffles per session, averaged over sessions.", "Trials are balanced across directions by random subsampling.", "The PCA before the SVM is fitted on all trials of a session, without labels, before the cross-validation." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4g-zigzag-context", "statement": "In the zigzag task, ALM population activity predicts the sequence identity (context) during subsequences with the same licking movements, across 6 sessions from 3 mice.", "source": "Figure 4f,g; Results, \"Context-dependent coding of subsequences\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "The 6 ZZ sessions come from 3 mice with 18 to 79 perfectly executed trials per sequence. Mean accuracies of the four comparisons are 0.785 to 0.858 against null 95th percentiles of 0.510 to 0.518; the lowest session is 0.651. By mouse 0.730 to 0.916. The files do not name the recorded area of the ZZ sessions; the paper says ALM.", "deviations": [ "Subsequences are aligned on touches (the seventh touch against the third or eleventh), not on the cross-correlogram of tongue angle, and the extra selection of trials closest to the median angle is not applied.", "The null mean over bins uses every fifth 5 ms bin." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7f-target-position-alm", "statement": "During the inter-trial interval, ALM populations encode the upcoming target position more strongly than the other regions.", "source": "Extended Data Fig. 7e,f; Results, \"ALM encodes upcoming sequences\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Mean R2 of the upcoming direction in the second before the cue is 0.271 (ALM), 0.097 (M1TJ), 0.075 (S1TJ) and 0.051 (S1BF); ALM is higher than each (Mann-Whitney p = 0.0025, 0.0007, 0.0014). With trial folds 0.159 against 0.022 to 0.034 (p = 0.023 to 0.047). Per ALM mouse 0.055 to 0.642. The 13 ALM sessions come from 8 mice; with one value per mouse, p = 0.012 to 0.024.", "deviations": [ "The paper's ITI window and trial set are not fully stated; the second before the cue of every standard trial is used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7h-no-time-coding", "statement": "None of the regions, including ALM, encoded time or distance to the trial start during the inter-trial interval.", "source": "Extended Data Fig. 7h; Results, \"ALM encodes upcoming sequences\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Mean R2 of the time to the cue is 0.008 to 0.034 by region (largest session 0.091, ALM), below 0.1 everywhere; 0.004 to 0.018 with trial folds.", "deviations": [ "The paper gives no test; the bound of 0.1 was fixed in the criterion.", "Only the last second before the cue is used, where the paper may have used more of the interval." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed4m-active-neuron-counts", "statement": "Extended Data Fig. 4m counts 324 ALM, 233 M1TJ and 119 S1TJ neurons.", "source": "Extended Data Fig. 4m legend", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Single units with a maximal PETH rate of at least 10 spikes/s are 351 (ALM) and 223 (M1TJ), within 10% of 324 and 233, and 155 (S1TJ) against 119. With multi-units, 387, 261 and 251. At 5 and 15 spikes/s the single-unit counts are 387, 259, 164 and 321, 200, 140.", "deviations": [ "PETHs are not computed on standardised inter-lick intervals.", "The unit classification is that of ephys-unit-counts, with its open choices." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed4l-alm-initiation", "statement": "More ALM neurons are tuned to sequence initiation than neurons of the other regions.", "source": "Results, \"Sequence tiling of single-unit responses\"; Extended Data Fig. 4l", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "91 of 351 active ALM neurons (25.9%) peak in the initiation window, against 48 of 223 in M1TJ (21.5%, Fisher one-sided p = 0.14) and 20 of 155 in S1TJ (12.9%, p = 0.0006). S1BF, outside the criterion, has 17 of 55 (30.9%), above ALM, against the statement's \"the other regions\". The windows differ in length (0.5, 2 and 1.2 s); per second of window ALM (0.519) is still above M1TJ (0.430) and S1TJ (0.258).", "deviations": [ "The paper shows histograms of peak times without a test; the test was chosen in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed4o-rhythmicity", "statement": "S1TJ and M1TJ contain more neurons modulated by individual licks than ALM.", "source": "Results, \"Sequence tiling of single-unit responses\"; Extended Data Fig. 4n,o", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Median r_avg is 0.201 (S1TJ), 0.156 (M1TJ) and 0.093 (ALM); one-sided Mann-Whitney against ALM p = 2.5e-36 and 4.1e-24.", "deviations": [ "Without lick standardisation the rhythm of trial-averaged PETHs is blurred away from the middle touch, which lowers r in every region." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6-alm-reward-drop", "statement": "ALM contains neurons that fire during sequence execution and decrease firing abruptly when the tongue first contacts water, although licking continues.", "source": "Results, \"Reward modulation in ALM\"; Extended Data Fig. 6a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Of 351 active ALM single units, 188 decrease and 92 increase from 0.5 s before to 0.5 s after the first water touch (p < 0.01 each; binomial p = 5e-09). S1TJ 50 against 51, S1BF 16 against 15, M1TJ 96 against 74 (p = 0.054).", "deviations": [ "The paper shows example neurons and decoded tau; the test over units was chosen in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1h-sequence-duration", "statement": "Expert mice completed the 7 port positions in about a second.", "source": "Results, first section; Extended Data Fig. 1h", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Over 25438 standard trials of 17 mice (the paper's number), the median over mice from the first port-moving touch to the first touch at the last position is 0.992 s (0.890 to 1.138 s by mouse); from the cue, 1.324 s. Recording sessions alone give 1.004 s.", "deviations": [ "The paper does not list the sessions of Extended Data Fig. 1h; recording sessions (except zigzag) and the opto sessions' trials without light are used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1l-learning-curves", "statement": "Over training, 15 mice reduced their sequence initiation time and increased their sequence speed.", "source": "Extended Data Fig. 1l; Results, first section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "15 mice have learning files. Median over mice of the initiation time falls from 2.573 s (first 100 standard trials) to 0.291 s (last 100), Wilcoxon p = 0.00043, and the sequence speed rises from 4.902 to 6.038 positions/s, p = 0.0043; 14 of 15 mice improve in both. MX181003 does not; its file of 2018-10-02 was left out as a duplicate, so its other learning files may also be mislabelled. Without MX181003, 14 of 14 improve (p = 0.00012 each).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1l-proficiency-1500", "statement": "Mice reached proficiency in standard sequences after about 1500 trials of training.", "source": "Results, first section; Extended Data Fig. 1l-n", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Under reading (a) the median over mice of the trial at which sequence speed reaches 90% of its final value is 200 (150 and 250 at 80% and 95%); under reading (b), initiation time within 110% of final, 1100. Both are outside 1350 to 1650. One mouse (MX200101) reaches neither. The paper does not define proficiency, and the learning files may not start at the first day of training. Every mouse's first file holds standard sequences in both directions and almost nothing else (2 other trials in MX170903, 1 in MX180803 and 1 in MX181002), and in 3 of 15 mice (MX170903, MX180201, MX181003) the median initiation time of the first 100 standard trials is already under 1 s; if earlier training is missing, both counts are too low. In the median mouse the speed reaches 90% of its final value within 200 trials, so the result under reading (a) also reflects how proficiency was defined. MX200101 has no standard trials among its last 500 learning trials, so it has no final value.", "deviations": [ "Proficiency was defined in the criterion, as the paper gives no definition." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed2-backtracking-counts", "statement": "Backtracking analyses used 7458 standard and 2695 backtracking sequences from 47 sessions of the 9 mice trained on backtracking.", "source": "Extended Data Fig. 2c,e legends; Methods, \"Behavioural training\"", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "Reading (c) gives 55 sessions of 9 mice with 10365 standard and 3839 backtracking trials; only the number of mice matches. Readings (a) and (b) give 74 and 59 sessions. A variant outside the criterion leaves out the 8 sessions whose touches are mostly a few ms long (5th percentile 3 to 7 ms, against 14 ms or more in the others), which fits the Methods' 8 sessions \"where only touch onsets were correctly registered\"; it gives 47 sessions, the paper's number, of 8 mice, with 8891 and 3207 trials. On these 47 sessions, removing the first and last trial and trials not finished within the video (the Methods' exclusions) leaves 8627 and 3104; both above tolerance. Adding initiation under 1 s, the Figure 3 trial selection and not an exclusion the Methods give for Extended Data Fig. 2, leaves 8058 and 2894, both within tolerance. This chain was built after seeing the results and does not decide the outcome; it has 8 mice where the paper has 9.", "deviations": [ "The paper's own trial exclusions (first and last trial, unfinished videos) are not applied in the readings of the criterion; they are shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed2e-missed-licks", "statement": "After the port backtracked, mice took on average 1 to 2 missed licks before relocating it.", "source": "Results, first section; Extended Data Fig. 2e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "In 29 Figure 3 sessions with backtracking (8 mice), backtracking trials have a mean of 1.854 missed licks in the fourth interval, against 0.113 in standard trials (Mann-Whitney p printed as 0). By mouse 0.97 to 5.39. A touch tolerance of 0 or 25 ms in place of 12.5 ms gives the same mean on the same trials.", "deviations": [ "Sessions are the Figure 3 sessions with backtracking, not the paper's 47." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6b-consummatory-licks", "statement": "After the first lick that touched water, mice continued with about 5 consummatory licks.", "source": "Results, \"Reward modulation in ALM\"; Extended Data Fig. 6b", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "After the first lick touching water, the bout continues for a median of 6 video licks (mean 6.38, 6864 trials), or 4 touches (mean 3.87); counting the first water lick, 7. None is within 4.5 to 5.5. The video ended during the bout in 88 trials, which are left out. By mouse, 4 to 10 video licks and 2 to 7 touches. Under (a) the most common count is 5 (20.2% of trials; 19.6% at 6, 12.8% at 4). With the bout threshold of (b) taken from video lick intervals (238 ms, against 243 ms from touches) the median is still 4 touches.", "deviations": [ "The paper does not say whether licks or touches are counted or where the bout ends; the bout rule (1.5 times the median interval) is the Methods' rule for lick bouts." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7b-correct-side", "statement": "Expert mice usually initiated sequences from the correct side without exploring the other side.", "source": "Results, \"ALM encodes upcoming sequences\"; Extended Data Fig. 7b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_xu_2022.ipynb", "notes": "In all 11 mice of the Figure 3 sessions, 0.562 to 0.923 of standard trials start with no lick on the other side of the midline before the first touch (0.647 to 0.980 with a 5 degree margin); pooled 0.714. The paper shows 8 mice.", "deviations": [ "The side of the port is taken from the angle of the lick that made the first touch, as the files do not say which side each position is on." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-s1tj-angle-variability", "statement": "Inhibiting S1TJ increased the across-trial variability of lick angle, SD(theta_shoot), without reducing the lateral reach |theta_shoot|, and did not shorten licks.", "source": "Figure 2b; Extended Data Fig. 3j", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The 35 opto sessions at 4 mW (described \"2s 5V\") are 5 per mouse for 7 mice, one per region presumably, but no file names the inhibited region; trial tables mark only light times, and the opto1 and opto2 series give the LED drive. The 25 sessions at 2 mW are the same. Checked in all 74 opto files, in the trial columns (opto takes 0, 1, 2 or NaN, without a description), the session description (cut short in the files themselves), general (only experimenter, institution, lab and subject), acquisition (empty), stimulus (empty presentation and templates groups), and the attributes of the opto1 and opto2 series (unit \"categorical\", no description).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-almm1tj-angle-length", "statement": "Inhibiting ALM/M1TJ reduced the ability to direct licks to the sides and decreased lick length; inhibiting M1B only slightly increased angle variability; inhibiting S1BF or S1Tr changed nothing.", "source": "Figure 2b; Extended Data Fig. 3j", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As fig2b-s1tj-angle-variability; the inhibited region of each session is not stated.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-almm1tj-initiation", "statement": "Inhibiting ALM/M1TJ at sequence initiation strongly suppressed licking (licks largely absent in 4 of 7 mice), and less strongly at mid-sequence.", "source": "Figure 2c; Extended Data Fig. 3k", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As fig2b-s1tj-angle-variability.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-termination", "statement": "Inhibiting S1TJ or M1B at water consumption impaired the stopping of ongoing licking.", "source": "Figure 2c; Extended Data Fig. 3k", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "As fig2b-s1tj-angle-variability.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3lm-half-power", "statement": "With half the illumination power (2 mW) the effects were consistent with, though weaker than, those at 4 mW, and the termination deficit of S1TJ and M1B inhibition was similarly strong.", "source": "Extended Data Fig. 3l,m; Results, \"Optogenetic inhibition screen\"", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The 25 sessions at 2 mW (\"2s 2.5V\", 5 mice) do not name the inhibited region either.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3f-inhibition-efficiency", "statement": "At 4 mW, light within 1 mm reduced the spike rate of putative pyramidal cells by 91%, at about 1.5 mm by 61% and at about 3 mm by 19%; FS neurons within 1 mm increased by 739%.", "source": "Methods, \"Photostimulation\"; Extended Data Fig. 3c-f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The 14 efficiency recordings (4 mice, 414 units) hold spike times and light trials, but no spike waveforms, which the paper uses to separate putative pyramidal and FS cells, and no distance of the fibre from the recording site. The distance is also missing from the metadata (metadata_insufficient).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1i-earplug", "statement": "Hearing loss with earplugs did not increase missed licks during sequences.", "source": "Extended Data Fig. 1i; Methods, \"Hearing loss\"", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The 10 earplug sessions are two per mouse for 5 mice, as the Methods describe, but nothing in the files says which session had earplugs and which was the sham. Without the labels, the paper's test (paired one-tailed bootstrap of missed licks over mice) finds an effect under 4 of the 32 possible assignments, so the absence cannot be shown label-free. In all 5 mice the earlier session has the longer time to first touch (by 0.40 to 1.49 s), as the paper reports for earplugs; under that inferred assignment missed licks differ by +0.032 per trial (p = 0.36), no effect, as the claim says. The inferred labels do not decide the outcome.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1j-odor-masking", "statement": "Masking odours with an air flow did not change missed licks.", "source": "Extended Data Fig. 1j; Methods, \"Odor masking\"", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The 6 air sessions (6 mice) switch the air flow after the 100th trial, on first in two mice and off first in four; the files do not say which. Over the 15 possible choices of the two on-first mice, the paper's test finds an effect in one (smallest p = 0.018), so the absence cannot be shown label-free.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1k-tongue-numbing", "statement": "Numbing the tongue with lidocaine increased missed licks, so mice require tactile feedback from the tongue.", "source": "Extended Data Fig. 1k; Methods, \"Tongue numbing\"", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The 11 numbing sessions (6 mice, one with a single session) do not say which session was lidocaine and which saline. In all 5 mice with two sessions the earlier session has more missed licks in its first 30 min (0.99 to 2.74 against 0.23 to 1.07 per trial), significant in 4; the direction of the claim needs the labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1f-lick-force", "statement": "The maximal force of a lick was on average about 4 mN.", "source": "Methods, \"Two-axis optical force sensors\"; Extended Data Fig. 1f", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The force sensor series (tubeH, tubeV) are in volts; the calibration to mN of Extended Data Fig. 1d is not in the files; their conversion is 1 and offset 0, and the paper gives no slope.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed4j-nnmf-clusters", "statement": "Clustering the PETHs of all neurons by NNMF was most consistent with 13 clusters.", "source": "Methods, \"PETH and NNMF clustering\"; Extended Data Fig. 4j,k", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The consistency measure needs cluster labels matched across bootstrap iterations, and the Methods do not say how; the paper's code could not be found.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The opto sessions do not name the inhibited region; 35 sessions at 4 mW and 25 at 2 mW, five per mouse, carry only the light times and LED drive. Figure 2 and Extended Data Fig. 3j-m cannot be tested." }, { "kind": "metadata_insufficient", "statement": "The control sessions do not mark the condition; which earplug session had earplugs, which half of each air session had the air flow on, and which numbing session was lidocaine are not stated." }, { "kind": "metadata_insufficient", "statement": "The recorded area and the kind of session are given only by the session description (the name of the lab's data folder); there is no electrodes table, unit location, depth or quality label, and the area of the zigzag (ZZ) and \"ephys others\" sessions is not given." }, { "kind": "data_missing", "statement": "Spike waveforms are not included, so units cannot be classified as putative pyramidal or FS cells (Extended Data Fig. 3c-f), and the fibre distance of the efficiency recordings is not given." }, { "kind": "format_error", "statement": "1446 spike times in 35 files are duplicated within a unit, away from trial boundaries (median 2.9 s). The Methods say these Phy duplicates were removed before analysis; the deposited spike times keep them." }, { "kind": "other", "statement": "One training recording is deposited twice; the MX181003 learning file of 2018-10-02 15:30:57 repeats all 4028 touches of the MX181002 file with the same start time and then continues, so it is unclear which mouse it belongs to." }, { "kind": "format_error", "statement": "In the 574 learning files start_time and stop_time count from 0 while cue, touch, port and water times are on another clock (around 10^6 s), so trial intervals and events do not line up." }, { "kind": "format_error", "statement": "The seqId column of the learning files holds the text of an unconverted MATLAB categorical object, not a sequence identity." }, { "kind": "metadata_insufficient", "statement": "Force sensor and lick port series are in volts without a calibration, tongue landmarks are in pixels without a scale (the Methods give 32 um per pixel), and every trial column is described as \"no description\"." }, { "kind": "selection_undocumented", "statement": "The Methods leave out 8 sessions whose touch offsets were not registered; the files do not mark them. Eight sessions with backtracking have touches of a few ms (5th percentile 3 to 7 ms), and leaving them out gives the paper's 47 sessions." }, { "kind": "metadata_error", "statement": "The session description is cut short (\"... se\") in the files themselves, so the full name of the lab's data folder, the only place the area and kind of session are given, is lost." }, { "kind": "metadata_insufficient", "statement": "The trial column opto (values 0, 1 and 2) and the opto1 and opto2 series (unit \"categorical\") have no description, and no file has optogenetics metadata (light source, site, power)." }, { "kind": "methods_unavailable", "statement": "The paper says its MATLAB analysis code is available at GitHub but gives no address, and no repository was found under the authors' accounts." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (verifier-1; same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The executed notebook with the conclusion cells and the summary removed, the helper module and the claims file; the paper from PMC9109820. The archive's metadata was checked for the blocked claims.", "agreed": 39, "of": 39, "disagreements": [] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (verifier-2; same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook with conclusions and summary, the helper module, the claims file, the entry README and this record; the paper from PMC9109820. In reply the entry was corrected and re-run; the README's run time, area count and claim count were also corrected.", "agreed": 39, "of": 39, "disagreements": [] } ] }, { "id": "000350-mu-2019-01", "dandiset": "000350", "dandiset_version": "0.240822.1759", "paper": "10.1016/j.cell.2019.05.050", "paper_title": "Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000350-mu-2019", "entry_title": "Futility-induced passivity and whole-brain neuronal and glial activity in zebrafish (Mu et al. 2019)", "description": "Tests the findings of Mu, Bennett, Rubinov et al. (2019) that dandiset 000350 can test. The dandiset holds 12 light-sheet sessions of paralysed larval zebrafish swimming fictively in virtual reality, with swim bouts, stimulus signals and, in 8 of them, segmented neuronal or neuronal and glial traces. The entry measures passive and active epochs, swim intervals and vigor in closed and open loop, and whole-brain neuronal and glial activity around passivity onset. The perturbation and noradrenergic imaging experiments of Figures 4 to 6 are not in the dandiset.", "notebooks": [ { "path": "reproduce_mu_2019.ipynb", "title": "Reproducing Mu et al. (2019) from dandiset 000350", "executed": "notebooks/000350-mu-2019/reproduce_mu_2019.html" } ], "outcomes": [ { "claim": "fig1h-epoch-durations", "statement": "In prolonged open loop, fish cycle between passive epochs lasting 24.4 +/- 2.5 s and active epochs lasting 36.1 +/- 4.2 s (mean +/- SEM, n = 74 fish), swimming 29 +/- 6 times per active epoch.", "source": "Figure 1H; Results, first section; STAR Methods, Futility-induced passivity behavioral analysis", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "Under reading (a), epochs from the swim bouts in open loop, the mean over 12 fish is 20.47 s for passive epochs (within 24.4 +/- 4.9) and 19.06 bouts per active epoch (within 29 +/- 11.8), but 22.36 s for active epochs (outside 36.1 +/- 8.2). Reading (b), the ActivityStates table, gives 18.19 and 15.77 s; reading (c), pooled epochs, 18.81 s, 19.66 s and 15.99 bouts; neither puts any value within tolerance. Active epochs range from 7.3 to 64.1 s over fish. With a pause threshold of 6 s the means are 21.46 and 25.31 s. Keeping the epochs cut by the edges of an open-loop period (a variant) gives 20.87 s, 21.20 s and 18.06 bouts, again 2 of 3 within tolerance.", "deviations": [ "12 imaged fish, where the paper's numbers come from 74.", "Pauses are measured from the end of one bout to the start of the next; the Methods say only that the fish did not swim for 5 s.", "Open loop is read from the gain signal (gain 0, grating moving); epochs cut by the edges of an open-loop period are left out, as the protocol alternates closed and open loop in 8 fish.", "The tolerance is 1.96 times the stated SEM, not the SEM." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "methods-isi", "statement": "In closed loop fish swim in discrete bouts about once per second (inter-swim interval 1.2 +/- 0.05 s, n = 74), and within active epochs of open loop the interval is 1.19 +/- 0.047 s against 24.4 s in passive epochs.", "source": "STAR Methods, Futility-induced passivity behavioral analysis", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "Read as start to start over intervals under 5 s, the closed-loop interval is 1.143 s (within 1.2 +/- 0.098) and the interval within open-loop active epochs is 1.332 s (outside 1.19 +/- 0.092). End-to-start intervals give 0.981 and 0.881 s, and all closed-loop intervals 2.886 s (start to start); no reading puts both values within tolerance.", "deviations": [ "The paper does not say how the interval is measured or which closed-loop intervals count; four readings are shown and one matches the closed-loop value.", "12 fish, against 74." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1j-open-loop-passivity", "statement": "Fish spend much more time in the passive state when swimming produces no visual feedback (open loop) than in closed loop with a naturalistic gain, where passivity is rare.", "source": "Figure 1J; Figure 1C to E; Results, first section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "Over all closed-loop time the median fraction of time in pauses of 5 s or more is 0.546, against 0.551 in open loop; open loop is higher in 7 of 12 fish (Wilcoxon p = 0.285), and the closed-loop median is far above the 10% the criterion allowed. Closed-loop passivity is high in blocks that follow open loop and at some gain levels (for example 0.937 at gain 0.030 in 20170127-1). Restricted to closed loop before the first open loop, a variant, the median is 0.104 and open loop is higher in 8 of 10 fish (p = 0.0137). By gain level, closed-loop passivity has a median of 0.183 before the first open loop and 0.825 after it, and it is lower at the highest gain than at the lowest in 2 of 7 fish before and 3 of 7 after (2 fish tied at 0.000 before). The gain is in arbitrary units, and no level can be identified as the paper's naturalistic gain. The outcome rests on the choice of closed-loop time; the closed-loop blocks after the first open loop decide it. The variant with closed loop before the first open loop is closer to the paper's comparison and meets the criterion for partially reproduced. The main reading was fixed before the analysis and is kept.", "deviations": [ "The paper's Figure 1J varies the gain in 6 dedicated fish; here closed loop is all time with gain above 0 in the imaging sessions, which includes closed-loop blocks between open-loop blocks.", "The dandiset's gain units cannot be mapped to the paper's, so closed loop is not restricted to a naturalistic gain." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-vigor-open-loop-onset", "statement": "When switched from closed to open loop, fish first swim with higher vigor, then stop swimming.", "source": "Figure 1C; Results, first section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "In 9 fish with a usable switch, bouts after the switch to open loop are more powerful than the closed-loop bouts of the 30 s before in 7, median ratio 3.49 (0.78 to 10.30), Wilcoxon p = 0.0195. Requiring 30 s of uninterrupted closed loop before the switch leaves 4 fish (median ratio 4.87, p = 0.125). 3 fish have no usable switch. The bouts counted after a switch are limited to that open-loop period, a correction made after the first verification round that left every number unchanged.", "deviations": [ "The paper shows this with example traces; the measure (power ratio of bouts) and its test were fixed here before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1i-isi-before-passivity", "statement": "Before the switch to passivity the inter-swim interval increases progressively, and fish swim more vigorously and less frequently in the seconds before passivity.", "source": "Figure 1I (n = 61 fish); Results, first section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "In active epochs of 10 or more bouts ending in passivity (11 fish), the last interval (1.506 s) is longer than the seventh from last (1.312 s) in 8 fish, Wilcoxon p = 0.103. The Spearman rho of k against the mean is -0.536, but only k = 1 stands out; the means for k = 2 to 7 lie between 1.274 and 1.357 s with no trend. The last 3 bouts are not more powerful than bouts 8 to 10 back (0.636 against 0.575, 6 fish, p = 0.16). The outcome depends on the minimum epoch length, which the paper does not state; with 8 or more bouts both parts hold (p = 0.00806, rho = -0.286; power p = 0.0269), and with 15 or more the interval part holds (p = 0.00195) and the power part does not (p = 0.423). Keeping the epochs cut by either edge of an open-loop period (a variant) gives p = 0.0874 for the intervals and p = 0.139 for the power.", "deviations": [ "The minimum of 10 bouts per epoch and the comparison of k = 1 with k = 7 were chosen here; the paper plots the interval against the number of swims before passivity for 61 fish." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2bc-neurons-lower-in-passivity", "statement": "Whole-brain average neuronal activity is higher during active behavior than during passivity, and decays after passivity onset.", "source": "Figure 2B and 2C; Results, second section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "The whole-brain neuronal signal is lower in open-loop passive epochs than in active epochs in all 8 fish (Wilcoxon p = 0.00391), by 0.64 to 1.96 SD of each fish's trace, and falls 5 to 10 s after passivity onset with p < 0.05 in 7 of 8 fish. The ActivityStates rows give 8 of 8.", "deviations": [ "The whole-brain signal is the mean of the stored DfOverF over 8 to 15% of ROIs, in units of the stored series, which is not \u0394F/F as the Methods define it.", "The paper shows this in one example fish; it was tested here over 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-glia-rise-at-passivity", "statement": "Whole-brain average radial astrocyte calcium increases before passivity onset and peaks soon after it.", "source": "Figure 2B and 2C (one example fish, 64 events); Figure 2G and 2I; Results, second section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "The whole-brain glial signal rises before passivity onset and peaks after it in 2 of 4 two-colour fish (20170228-3 and 20170228-4; 1 to 4 s after onset 0.61 and 0.53 SD above baseline, p = 8.0e-13 and 1.1e-14; 2 to 0 s before, p = 1.7e-11 and 3.6e-17; peaks 3.5 and 2.5 s after onset). In 20161109-2 and 20170203-1 it falls after onset (-0.91 and -0.64 SD, p = 1 for an increase). The criterion needed 3 of 4. 20170228-3 has 67 onsets, close to the 64 events of the paper's example fish (Figure 2B), so it may be that fish. All 26 onsets of 20161109-2 and 42 of the 46 of 20170203-1 fall in code 32, prolonged open loop with the grating moving. The ActivityStates variant gives the same split, and so does keeping the epochs cut by the edges of an open-loop period, which adds 1 or 2 onsets per fish. Over the first five onsets after the start of each open-loop period the glial response is -1.13 and -0.62 SD in 20161109-2 and 20170203-1, and 0.83 and 1.36 SD in the other two. In 20161109-2 and 20170203-1 the glial trace has an SD of 0.0016 and 0.0011 (0.0097 and 0.0072 in the other two) and correlates with the neuronal trace at 0.58 and 0.59 (0.06 and 0.15). In 20170203-1 the neuronal trace also has a low SD (0.0016, against 0.0069 to 0.0180 in the other fish) and rises after onset (+0.28 SD, p = 0.0023), unlike the other three two-colour fish, so there the low SD affects both channels. The data here do not show why these two files differ.", "deviations": [ "Whole-brain average of glia, as in the paper's Figure 2C, not the L-MO component of Figure 2G and 2I, which needs the cross-fish clustering and template registration.", "The glia of these fish carry jRGECO1b; the paper's component analysis used GCaMP6f." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2a-open-loop-higher", "statement": "Whole-brain average neuronal and glial calcium are higher and fluctuate more strongly in open loop than in closed loop.", "source": "Results, second section; Figure S2A (not read)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "For neurons the whole-brain signal is higher in open than closed loop in 6 of 8 fish (Wilcoxon p = 0.0195, median difference 0.17 SD) and fluctuates more in 7 of 8 (p = 0.00781, median SD ratio 2.98). For glia both hold in 3 of 4 fish (median difference 0.73 SD, SD ratio 3.06), not in all 4 as the criterion required; 20170203-1 is the exception for both. With the SD taken within each continuous period, raw or detrended (a variant), it is higher in open loop in 8 of 8 neuron fish (p = 0.0039, median ratios 3.72 and 5.15) and in 4 of 4 glia fish (median ratios 5.04 and 6.11). These periods differ in length (in 20170228-3, 10 closed-loop periods over 213 frames against 2 open-loop periods over 5477), so slow fluctuations count only in the long ones. With the SD in 10 s windows in both conditions (a variant), it is higher in open loop in 7 of 8 neuron fish (p = 0.0195, median ratio 2.52) and 3 of 4 glia fish (median ratio 2.07), with 20170203-1 the exception.", "deviations": [ "Figure S2A was not read; the claim is taken from the Results text.", "Switches are those between closed and open loop; stationary-grating periods carry the label of the condition before them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2h-glia-weaker-closed-loop-pauses", "statement": "When fish in closed loop stop swimming because the stimulus stops moving, glial calcium signals are weaker than during futility-induced passivity.", "source": "Figure 2H and 2M; Results, second section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_mu_2019.ipynb", "notes": "The glial response to closed-loop pauses is smaller than to open-loop passivity onsets in 2 of 4 fish (20170228-3 and 20170228-4, Mann-Whitney p = 1.1e-05 and 5.0e-11), the two whose glia rise at passivity. In 20161109-2 and 20170203-1 the glia fall after passivity onset, and the pause response is not smaller (p = 0.78 and 0.98). 26 to 54% of the pauses start during a stationary grating. Requiring the gain above 0 over the whole window from 10 s before to 4 s after the pause, keeping the edge epochs, or both (variants) give the same 2 of 4.", "deviations": [ "Closed-loop pauses include those with the grating moving, as the dandiset gives no stimulus labels beyond the velocity signal and stationary periods are 2 to 18 s long." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2dg-nmf-components", "statement": "Non-negative matrix factorization of neurons and radial astrocytes gives components consistent across fish; glial component 1, in the lateral medulla oblongata (L-MO), is the most reliable, rising before and peaking after passivity onset (n = 5 neuron fish, 6 glia fish).", "source": "Figure 2D to 2G", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The claim is that components are consistent across fish, and the paper's clustering of components across fish was tuned by hand, with no code or parameters published. The paper's glial components come from 6 fish with glial GCaMP6f; the dandiset holds 3 such fish, with raw images only (8499 to 9000 volumes, 0.39 to 0.42 TB per file), and repeating the segmentation on them does not fit the time limit (too_large). The 4 two-colour files hold full glial DfOverF tables (jRGECO1b), so an NMF per fish could be run on them, but without the cross-fish clustering or a registration to a reference brain it would not test the claim.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2kl-lmo-glia-most-consistent", "statement": "Of all brain regions, radial astrocytes in L-MO show the most consistent increases at passivity onset, with ramping signals before it.", "source": "Figure 2K, 2L and 2M", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The ROIs have voxel masks in each fish's own image space, with no registration to a reference brain, no region labels and no stated orientation of the axes, so L-MO cannot be located without the paper's template.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1k-passive-unresponsive", "statement": "Passive fish are less responsive to visual motion than active fish (p = 4.2e-7, n = 11).", "source": "Figure 1K", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The protocol of a brief static stimulus followed by brief forward motion (11 fish) cannot be identified. The protocol codes are not described. Code 33, in 10 files, is a 0.3 to 0.5 s speed-up of the grating within open loop (faster in 390 of 462 blocks, never stationary), which is not the paper's static then forward stimulus; code 12 occurs once, for 3.4 s. Whether the paper's probe sessions are absent or present without labels cannot be told.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-replay", "statement": "Replaying in open loop the visual motion recorded in closed loop also induces passivity.", "source": "Figure 1F", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "A replay would show as open loop whose grating velocity follows an earlier closed-loop session. Only the baseline velocity is usable, which takes a few fixed levels; the TotalStimulusVelocitySignal stays between -0.002 and 0.008 and does not hold the velocity it describes. No protocol code is described, so a replay, if recorded, cannot be recognised. Code 52 has a randomised gain, not a replay. No separate behavioural dataset is on the archive.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-glia-necessary", "statement": "Ablating radial astrocytes, or blocking their IP3 receptors, halves futility-induced passivity, while random neuronal ablation does not change it.", "source": "Figure 4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The ablation, nitroreductase and xestospongin experiments are not in the dandiset, and no other dandiset of this paper was found on the archive.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-glia-sufficient", "statement": "Activating radial astrocytes with TRPV1, CoChR or Opto-alpha1-AR suppresses swimming, and astrocyte activation drives GABAergic neurons at the edge of L-MO.", "source": "Figure 5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The TRPV1, CoChR, Opto-alpha1-AR and GABAergic activation experiments are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6a-ne-ramp", "statement": "The neuronal population whose activity rises fastest before passivity overlaps the noradrenergic neurons of the medulla oblongata (NE-MO).", "source": "Figure 6A", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The neuronal traces are there (4 fish with processed GCaMP6f traces of the paper's 5), but locating NE-MO needs the registration to a reference brain and the noradrenergic labels, neither of which is in the files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-ne-drives-glia", "statement": "NE-MO activity precedes astrocyte activity at passivity, NE-MO ablation reduces passivity, and NE-MO stimulation activates radial astrocytes through alpha1B receptors.", "source": "Figure 6B to 6N", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No session images noradrenergic neurons (Tg(th-P2A-Gal4); Tg(UAS:GCaMP6s)) or stimulates NE-MO, and the ablation and pharmacology experiments are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-ne-mismatch", "statement": "NE-MO neurons respond to swims without visual feedback, encoding sensory-motor mismatch.", "source": "Figure 7A to 7G", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Code 52, in 20170113-4 and 20170127-1 (neuronal GCaMP6f), has 16 and 22 gain levels and is consistent with the randomised gain of Figure 7C, but the code is not described, and NE-MO cannot be located without a registration to a reference brain or noradrenergic labels. The paper's NE imaging in Tg(th-P2A-Gal4); Tg(UAS:GCaMP6s) fish is not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-glia-accumulate", "statement": "Radial astrocyte calcium grows with the number of consecutive failed swims and with the probability that a swim fails.", "source": "Figure 7H to 7K", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Figure 7H uses open loop for 1, 2, 4, 8 or 16 bouts before a return to closed loop. No protocol code is described as ending open loop after a number of bouts. In the two-colour files, switches from closed to open loop followed by 16 or more bouts number 7 in 20170203-1, 2 in 20170228-3 and 3 in 20170228-4, so an analogue of Figure 7H (glia against the number of bouts since the switch, within long open-loop periods) could be run in three fish, two of them with 2 and 3 events. It was not run, as the claims file fixes no criterion for it and it would test only half of the claim; it is left for a new attempt. Figures 7J and 7K need to know which bouts produced visual flow. Codes 51 and 53 in 20170228-3 and 20170228-4 alternate with the gain at 0 in both, which may be the probabilistic task, but the codes are not described and TotalStimulusVelocitySignal does not hold the feedback of each bout, so the task cannot be identified.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds the 12 light-sheet sessions behind Figure 2 and its supplement, with behaviour, but none of the perturbation or noradrenergic imaging experiments of Figures 4 to 6, nor the behavioural recordings of the other 62 of the 74 fish of Figure 1. Some sessions hold undescribed protocols (randomised gain, brief grating speed-ups) that may belong to Figures 1K and 7, but they cannot be identified. No other dandiset of the paper was found." }, { "kind": "data_missing", "statement": "Four files have raw images only and no cell traces, among them the only three glia-only GCaMP6f recordings (the paper's glial NMF used 6). Raw images cover only part of 20170113-4 (3065 of 12050 volumes present) and 20170228-4 (5776 of 7200 present), and 20170113-2 holds 7616 imaging volumes against 9751 camera triggers." }, { "kind": "metadata_error", "statement": "The glial imaging plane of the four two-colour files is labelled GCaMP6f but excited at 561 nm and detected at 660 nm, the jRGECO1b channel of the Methods (Tg(gfap:jRGECO1b)). The raw images are typed TwoPhotonSeries and the archive lists two-photon microscopy, though the microscope is a one-photon light sheet; the device is described as Zeiss confocal microscopes." }, { "kind": "metadata_error", "statement": "The DfOverF series are not \u0394F/F. In the four single-colour files each ROI trace is divided by its mean (float64, mean 1); in the four two-colour files traces are centred near 0 (float32) with the first 60 s held constant. The Fluorescence series vary by about 1e-6 per frame or not at all, consistent with baselines, and carry the same description as DfOverF." }, { "kind": "metadata_insufficient", "statement": "The ActivityStates table is described only as classified periods of activity. It does not follow the Methods' definition (many active rows of 5 s or less), its transient rows are undefined and duplicate active rows, it holds 3 rows in the glia-only files, and it does not say which condition each row belongs to." }, { "kind": "metadata_insufficient", "statement": "The stimulus signals have no units or descriptions beyond their names, and the protocol codes in StimulusParameterSignals (12, 22, 23, 32, 33, 51, 52, 53) are not described. Closed and open loop can be read only from the gain signal. From the signals, code 33 is a 0.3 to 0.5 s speed-up of the grating in open loop, code 52 a randomised gain, and codes 51 and 53 alternate closed and open loop in six files but both have the gain at 0 in 20170228-4." }, { "kind": "metadata_error", "statement": "TotalStimulusVelocitySignal is described as the drift speed minus the motosensory gain times the swim power, but its values lie between -0.002 and 0.008 in every file, against baseline velocities of 0.5 to 2. The visual feedback each bout produced is not recorded." }, { "kind": "other", "statement": "In two of the four two-colour files (20161109-2 and 20170203-1) the whole-brain glial trace has an SD of 0.0016 and 0.0011, against 0.0097 and 0.0072, correlates with the neuronal trace at 0.58 and 0.59 (0.06 and 0.15 in the others), and falls after passivity onset. In 20170203-1 the neuronal trace also has a low SD (0.0016, against 0.0069 to 0.0180 in the other fish), so there the low SD affects both channels. The files do not allow the cause to be checked." }, { "kind": "metadata_insufficient", "statement": "The ROIs are in each fish's own image space, with no registration to a reference brain and no region labels, so the paper's region-level results (L-MO, NE-MO) cannot be located." }, { "kind": "other", "statement": "The two groups of files were processed differently (trace scaling, data type, censoring, chunking), and the volume rate is 1.6 to 2.9 Hz against the 3 volumes per second of the Methods." }, { "kind": "metadata_error", "statement": "The SwimIntervals width column is described as the estimated width spanned by the swim event but equals the bout duration in seconds." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text (main text and STAR Methods; the Supplemental Information was not read). The verifier tested helper functions on synthetic inputs and read the archive's file list for the blocked claims. Its report had no attempt record and gave its own outcome for each claim; all 19 agree with the record on the outcome, and for five blocked claims it gave a different reason for the block.", "agreed": 19, "of": 19, "disagreements": [] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the first revision, with the conclusions and the summary, the helper module, the claims file and the attempt record. The verifier could not download the paper text this round (cell.com returned 403, the lab-site URL 404) and did not check the record's description of the Figure 7H protocol against the paper. It agreed with all 19 outcomes and listed sentences the outputs do not support.", "agreed": 19, "of": 19, "disagreements": [] } ] }, { "id": "000409-ibl-2025-01", "dandiset": "000409", "dandiset_version": "0.260309.1324", "paper": "10.1038/s41586-025-09235-0", "paper_title": "A brain-wide map of neural activity during complex behaviour", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "runs", "entry": "000409-ibl-2025", "entry_title": "The IBL brain-wide map of neural activity (International Brain Laboratory et al. 2025)", "description": "Tests the findings of the IBL brain-wide map paper (Nature 2025) on dandiset 000409, which holds 459 sessions of Neuropixels recordings from 139 mice performing the IBL decision-making task. It checks the dataset's composition and inclusion counts, the behavioural results of Figure 1, and, on a fixed set of regions, the decoding of stimulus, choice and feedback, single-cell selectivity, the latencies of stimulus trajectories and the feedback oscillations related to licking, and over all canonical regions the number with significant stimulus trajectories.", "notebooks": [ { "path": "reproduce_ibl_2025.ipynb", "title": "Reproducing the IBL brain-wide map (2025) from dandiset 000409", "executed": "notebooks/000409-ibl-2025/reproduce_ibl_2025.html" } ], "outcomes": [ { "claim": "dataset-sessions-mice-labs", "statement": "The data come from 459 sessions of 139 mice recorded in 12 laboratories.", "source": "Abstract; Methods, Sessions and insertions", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "The pinned version holds 459 sessions of 139 mice from 12 labs, one processed and one raw file per session.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dataset-probes-units", "statement": "699 Neuropixels insertions yielded 621,733 units, an average of 889 per probe.", "source": "Abstract; Results, Recordings; Methods", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "699 insertions and 621,733 units, 889.5 per probe.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "well-isolated-neurons", "statement": "Stringent quality metrics identified 75,708 well-isolated neurons, an average of 108 per probe.", "source": "Results, Recordings; Methods, Neurons and brain regions", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "75,708 units have ibl_quality_score 1, 108.3 per probe. Recomputing the three metrics gives 75,708 with a noise cutoff below 5 and 95,430 with the Methods' 20. The criterion's side check, that the score is the fraction of the three metrics passed with the Methods' cutoff of 20, holds for 540,399 of 621,733 units; with a cutoff of 5 it holds for every unit.", "deviations": [ "The files hold spike sorting revision 2025-05-06; the paper's code loads revision 2024-05-06. The counts are identical." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "canonical-regions", "statement": "The main analyses use a canonical dataset of 201 regions with at least 2 sessions of 5 well-isolated neurons and at least 20 neurons in total, 62,857 neurons.", "source": "Results, Neural analyses; Methods, Neurons and brain regions", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Every inclusion step gives the counts of the code's inclusion table: 75,708 well-isolated units in 268 regions, 65,336 in grey matter, 63,357 with 5 per session (245 regions), 62,990 with 2 sessions (210), and 62,857 neurons in 201 regions over 454 sessions. The region table region_info.csv marks 210 regions canonical, those left before the 20-neuron step.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "brain-areas-279", "statement": "The probes covered 279 brain areas.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Units fall in 279 Beryl regions other than void and root (266 with a well-isolated unit).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "mice-sex", "statement": "The 139 mice were 94 male and 45 female.", "source": "Results, Behavioural task; Methods, Animals", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "94 male and 45 female mice; each mouse has one sex in all its files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "mice-age-weight", "statement": "On the day of recording the mice were aged 13 to 178 weeks (mean 44.96, median 27.0) and weighed 16.1 to 35.7 g (mean 23.9, median 23.84).", "source": "Methods, Animals", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Weight holds under every reading (reading a gives 16.1 to 36.2 g, mean 24.19, median 24.00). Age does not under any reading. At the first session the mice were 13.1 to 63.1 weeks old, mean 28.09, median 26.00; over all sessions at most 65.9 weeks, against the paper's 178 and mean 44.96. The files give each mouse one weight for all its sessions. The paper's code takes age and reference weight from the IBL database, not from the recording day, which may explain the age difference.", "deviations": [ "Age is session start minus date of birth in the files, which the Methods describe; the paper's code uses the database's age field. Measured values are reading (a)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "probe-versions", "statement": "The insertions used Neuropixels 1.0 probes of versions 3A (109) and 3B2 (586), and Neuropixels 2.4 probes (4).", "source": "Methods, Materials and apparatus", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "586 insertions use PRB_1_4_0480_1 (403) or PRB_1_4_0480_1_C (183), 109 NP1010 and 4 NP2010.", "deviations": [ "The files name imec models, not versions; NP1010 is read as 3A (its devices have no PXI port or slot) and NP2010 as the 2.x probes. The counts match under this reading." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "trials-per-session", "statement": "Recorded sessions lasted on average 645 trials (median 602, range 401 to 1,525).", "source": "Results, Behavioural task", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Mean 645.1, median 601, range 401 to 1,525 trials per session.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "rf-mapping", "statement": "Receptive-field mapping after the task (504 of 699 insertions) found a relatively small fraction of cells with significant receptive fields, with large fractions in VISp, VISl and SCs.", "source": "Results, Representation of visual stimulus; Methods, RF mapping; Supplementary Fig. 5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No session lists receptive-field mapping among its passive phases (428 sessions have spontaneous activity and task replay, 31 none), and the stimulus groups of all 459 processed files are empty. The paper used the mapping in 504 of 699 insertions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "behav-performance", "statement": "After training, mice made correct choices on 81.4 +/- 0.4% (mean +/- s.d.) of trials.", "source": "Results, Behavioural task", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Reading (c), the mean over 459 sessions, gives 81.58% correct, within 81.4 +/- 0.4. The mean over mice is 80.76% (all trials) and 84.62% (analysed trials); all trials pooled give 81.94%. Across mice the s.d. is 5.12 and the s.e.m. 0.43. On the 454 sessions of the canonical set the mean over sessions is 81.59% and over mice 80.77%.", "deviations": [ "The paper does not say how the mean is taken; four readings are shown and only the mean over sessions is within tolerance." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "behav-zero-contrast", "statement": "On 0% contrast trials mice were rewarded on 58.7 +/- 0.4% (mean +/- s.e.m. across mice) of trials, better than chance (t138 = 20.18, P = 5.2e-43).", "source": "Results, Behavioural task; Fig. 1d legend", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Over all trials the mean over 139 mice is 58.26% (s.e.m. 0.42), t138 = 19.68, P = 6.9e-42. The t statistic is within tolerance and the mean is 0.44 points below 58.7, just outside the 0.4 tolerance. Over analysed trials the mean is 59.29% and t138 = 16.21, both outside tolerance. On the 454 canonical sessions, which the Fig. 1d legend names, the values are 58.27% with t138 = 19.68 (all trials) and 59.31% with 16.23 (analysed trials). No reading puts both values within tolerance, and the criterion defines no partial case. Mice are clearly above chance, so the effect in the claim's statement holds.", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "behav-early-movements", "statement": "22.8% of first wheel-movement times occurred under 80 ms after stimulus onset.", "source": "Fig. 1c legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "22.75% of all 296,090 trials (reading a); 22.99% of trials with both times (b); 22.49% as a mean over sessions (c). 12.06% of trials with both times have the first movement before stimulus onset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-contrast", "statement": "Mice performed better and faster on trials with high visual contrast.", "source": "Fig. 1d; Results, Behavioural task", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Median over mice of percent correct rises at every step, 59.2% at 0% to 96.8% at 100% (higher in 139 of 139 mice, p = 1.5e-24); median first movement time falls at every step, 196 to 137 ms (shorter in 133 of 139 mice, p = 5.9e-24).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1ef-end-of-session", "statement": "Towards the end of the sessions, performance decreased and first wheel-movement times increased.", "source": "Fig. 1e,f; Results, Behavioural task", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Last 50 trials against trials 51 to 300 from the end, median over mice of percent correct 80.0 against 85.0 (lower in 105 of 139 mice, p = 7.9e-13), median first movement time 279 against 165 ms (longer in 131 of 139 mice, p = 2.6e-22).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-block-switch", "statement": "After a block switch, mice took around 5 to 10 trials to adjust their behaviour, as shown by the fraction of correct choices on 0% contrast trials after the switch.", "source": "Fig. 1g; Results, Behavioural task", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Over 395 sessions with valid blocks and 16,447 zero-contrast trials, the fraction correct starts at 0.338 after the switch. Fitted tau is 3.86 trials, outside reading (a); 90% of the change is covered at 9.9 trials, within reading (b), on the point estimate. Resampling mice (1000 resamples) gives a 95% interval of 2.79 to 5.30 trials for tau and 7.4 to 13.2 trials for reading (b), with 75.9% of resamples within 4.5 to 11. Per-mouse tau has a median of 3.88 (interquartile 1.86 to 11.30, 125 mice).", "deviations": [ "The 64 sessions whose probability_left alternates on every trial are left out.", "The paper gives no measure of the adjustment time; two readings were fixed before the analysis and the claim holds under reading (b) only." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1h-block-bias", "statement": "For all contrast values mice chose the side of the block's likely stimulus more often, responding right more often in right blocks than in left blocks.", "source": "Fig. 1h; Results, Behavioural task", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "In 395 sessions with valid blocks (125 mice) the right-block fraction of right choices is higher at all nine signed contrasts, median differences 0.013 to 0.333, every p below 1e-8. With all sessions the differences are smaller at every contrast (0.012 to 0.314).", "deviations": [ "The 64 sessions whose probability_left alternates on every trial are left out." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dec-stim-restricted", "statement": "The visual stimulus side, decoded from the first 100 ms after stimulus onset, was represented in a narrower set of regions than choice or feedback, with strong signatures in visual cortex such as VISp.", "source": "Fig. 4a,i; Results, Representation of visual stimulus; Discussion", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "4 of 10 tested regions are significant for stimulus (CL, GRN, IRN, VISp), against 5 for choice and 7 for feedback. VISp is significant (35 sessions, Fisher p = 1.3e-08, effect 0.039, paper table 0.02). Significance agrees with region_info.csv in 10 of 10 regions and the effects correlate with the paper's (Spearman 0.91, p = 0.00025). With BH at q = 0.05 the counts are 4, 7 and 9. The paper reports 40 of 201 regions for stimulus. With the full nested search for each null (30 nulls in each of the 35 VISp sessions) VISp stays significant, Fisher p 1.8e-05 against 2.8e-05 with the reused C on the same nulls, 13 sessions below 0.05 under each, and significant with BH at q = 0.01 among the 10 regions. The decoder fits an L1 penalty (scikit-learn 1.9.1; at C = 0.01 no coefficient of 13 is nonzero in one VISp session, against 12 with L2).", "deviations": [ "The tested regions are VISp, GRN, IRN and seven drawn at random (ACAv, CL, HATA, LDT, PA, PVT, TR), each with all its canonical sessions, not all 201 regions; the Benjamini-Hochberg correction runs over these 10 regions.", "One run of nested cross-validation (paper 10) and 100 null sessions (paper 200); each null reuses the C chosen for the real labels in each outer fold. On three example sessions the full nested null has a higher 95th percentile in 6 of 9 comparisons (0.555 to 0.622 against 0.531 to 0.598), so per-session p-values here can be smaller than the paper's procedure would give.", "The trial mask follows the Methods and the code's truncation, without the saturation intervals of the IBL aggregate trials table, which are not in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dec-choice-widespread", "statement": "Choice, decoded from the 100 ms before the first wheel movement, was represented in a larger number of regions than the visual stimulus, with strong effects in hindbrain regions such as GRN.", "source": "Fig. 5a,i; Results, Representation of choice", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "GRN is significant for choice (14 sessions, Fisher p = 6e-15, effect 0.277, paper table 0.28); 5 tested regions are significant for choice against 4 for stimulus, a margin of one region. Significance agrees with region_info.csv in 9 of 10 regions (LDT, 2 sessions, p = 0.0154, is significant in the paper). Effects correlate with the paper's (Spearman 0.98). The paper reports 172 of 201 regions. The margin over stimulus rests on one region; CL's choice result (2 sessions, Fisher p = 0.0010) sits at the 2-session floor, and the full nested null was run only for VISp stimulus. With 100 nulls the per-session p cannot go below 1/101, so a region of 2 sessions cannot have a Fisher p below about 0.0010; LDT's result may be partly this limit.", "deviations": [ "The tested regions are VISp, GRN, IRN and seven drawn at random (ACAv, CL, HATA, LDT, PA, PVT, TR), each with all its canonical sessions, not all 201 regions; the Benjamini-Hochberg correction runs over these 10 regions.", "One run of nested cross-validation (paper 10) and 100 null sessions (paper 200); each null reuses the C chosen for the real labels in each outer fold. On three example sessions the full nested null has a higher 95th percentile in 6 of 9 comparisons (0.555 to 0.622 against 0.531 to 0.598), so per-session p-values here can be smaller than the paper's procedure would give.", "Synthetic choices and feedback come from an action-kernel model fitted per session with a logistic choice policy, written here; the paper uses the companion paper's model package.", "The trial mask follows the Methods and the code's truncation, without the saturation intervals of the IBL aggregate trials table, which are not in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dec-feedback-nearly-all", "statement": "Whether the trial was correct could be decoded from the 200 ms after feedback onset in nearly all recorded regions, almost perfectly in many.", "source": "Fig. 6a,i; Results, Representation of feedback", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "7 of 10 tested regions are significant, including IRN (27 sessions, effect 0.407, paper table 0.42); HATA (Fisher p = 0.0255), PA (0.1455) and TR (0.0227) are not. The paper's table marks 8 of these 10 significant (HATA yes, PA and TR no). With BH at q = 0.05, 9 are significant. 23 of 111 region-sessions have a balanced accuracy above 0.9; median accuracy 0.913 in GRN and 0.905 in IRN. Effects correlate with the paper's (Spearman 0.96). The paper's own table has 8 of these 10 regions significant, so this region set could not reach the criterion's 9 with the paper's own results.", "deviations": [ "The tested regions are VISp, GRN, IRN and seven drawn at random (ACAv, CL, HATA, LDT, PA, PVT, TR), each with all its canonical sessions, not all 201 regions; the Benjamini-Hochberg correction runs over these 10 regions.", "One run of nested cross-validation (paper 10) and 100 null sessions (paper 200); each null reuses the C chosen for the real labels in each outer fold. On three example sessions the full nested null has a higher 95th percentile in 6 of 9 comparisons (0.555 to 0.622 against 0.531 to 0.598), so per-session p-values here can be smaller than the paper's procedure would give.", "Synthetic choices and feedback come from an action-kernel model fitted per session with a logistic choice policy, written here; the paper uses the companion paper's model package.", "The trial mask follows the Methods and the code's truncation, without the saturation intervals of the IBL aggregate trials table, which are not in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "sc-stim-fraction", "statement": "Single-cell tests controlling for choice and block found few stimulus-selective neurons (0.5% of all neurons); even in the regions with the largest fractions, such as visual cortex, the fraction did not exceed about 10%.", "source": "Fig. 4b; Results, Representation of visual stimulus", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_ibl_2025.ipynb", "notes": "The test ran on 5,228 units in 200 region-sessions of 14 regions. The null run (pseudo-session sides and blocks) selects 14 units (2.7e-3, 95% interval 1.5e-3 to 4.5e-3), far above the paper's 5e-5, so by the criterion the procedures differ. Under the null the simple test alone passes 7.1e-3 and the combined test 6.9% of units. The regional fractions agree with region_info.csv (14 of 14 within 0.02; largest 5.9% in CL with 17 units; visual regions 2.1% to 3.8%), and the pooled 1.82% is above the paper's 0.41% because the tested regions over-represent visual areas. Were it not for the false-positive check the claim would be reproduced. With the stimulus side shuffled over the tested trials (one permutation per region-session) the test selects 4 units (7.7e-4, interval 2.1e-4 to 2.0e-3), while the product of the two tests' single rates is 4.7e-5. So the dependence of the two tests alone puts the rate above the paper's, and the pseudo-session null is about 3.5 times higher again.", "deviations": [ "The 64 sessions whose probability_left alternates on every trial are left out. Here 19 region-sessions and 381 units.", "Regions are the 14 loaded for the neural claims, not all canonical regions.", "The paper does not state which trials enter the simple Mann-Whitney test; the same trials as the combined test are used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "sc-choice-fraction", "statement": "More neurons responded to choice than to the visual stimulus (4% of all neurons), with the largest fractions in hindbrain, midbrain and thalamic regions.", "source": "Fig. 5b; Results, Representation of choice", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_ibl_2025.ipynb", "notes": "The null run with synthetic choices selects 13 of 5,228 units (2.5e-3, interval 1.3e-3 to 4.2e-3), far above 5e-5. Otherwise the pattern holds: pooled 5.64% choice-selective against 1.82% for stimulus (270 against 70 units selective for one only, p = 3.8e-29); largest fractions CL 35%, GRN 22%, IRN 14%; regional fractions correlate with the paper's (Spearman 0.84, p = 0.00016). With the choices shuffled over the tested trials the test selects 3 units (5.7e-4, interval 1.2e-4 to 1.7e-3), against a product of the two tests' single rates of 3.3e-5.", "deviations": [ "The 64 sessions whose probability_left alternates on every trial are left out.", "Regions are the 14 loaded for the neural claims.", "Synthetic choices and feedback come from an action-kernel model fitted per session with a logistic choice policy, written here; the paper uses the companion paper's model package." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "traj-latency-visual", "statement": "The latency of the stimulus trajectory separation ordered the visual regions as LGd < VISp, which is about equal to LP, < VISpm < VISam, at about 34, 42, 42, 57 and 78 ms.", "source": "Fig. 4d,l,m; Results, Representation of visual stimulus", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Latencies (Methods' definition) LGd 31.7, VISp 46.5, LP 48.6, VISpm 61.3, VISam 59.2 ms. LGd is first and VISp and LP are within 10 ms, but VISam is not later than VISpm, and VISp, LP and VISam are outside 10% of 42, 42 and 78 ms. The code's significance condition and its 0 to 100 ms window change the values by less than 1 ms. The paper's results table (meta/Results/stim.pkl) gives 34.0, 44.7, 46.8, 59.6 and 66.0 ms, closer to these values than the text is for VISp, LP, VISpm and VISam, and also has VISam later than VISpm. All five distances are significant (p = 0.001). With the 16 region-sessions of invalid blocks included the five latencies are unchanged. The code's canonical-window variant now keeps the full window's baseline, as the code does, and gives 31.9, 46.8, 48.9, 61.7 and 59.6 ms.", "deviations": [ "The 64 sessions whose probability_left alternates on every trial are left out. Here 16 region-sessions.", "Trials follow the mask here, without the saturation intervals the code uses.", "The Methods define latency as the first crossing of 70% of the range; the code adds point-wise significance. The Methods' definition decides; the code's is a variant and gives the same values here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "traj-latency-late", "statement": "The early visual wave was followed by later stimulus encoding in the MRN, SCm, PRNr, IRN and GRN, with latencies of about 100 to 120 ms.", "source": "Fig. 4d,l,m; Results, Representation of visual stimulus", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "IRN 118.3 ms and GRN 109.9 ms, both within 90 to 132 ms, both distances significant (p = 0.001). MRN, SCm and PRNr were not tested; the paper's results table gives 89.4 ms for IRN and GRN in its 0 to 100 ms window, in which IRN has no latency here and GRN 100.0 ms. With the window extended to 0 to 200 ms the latencies are 117.9 and 109.5 ms; the IRN distance is still rising at 190 ms. The outcome rests on the criterion's 0 to 150 ms window.", "deviations": [ "Only IRN and GRN of the five regions named are tested.", "The 64 sessions whose probability_left alternates on every trial are left out." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "traj-stim-regions", "statement": "The stimulus trajectory distance was significant in 104 regions.", "source": "Results, Representation of visual stimulus; Fig. 4c", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "Tested after the first verification round. Of 201 canonical regions, 195 have 20 or more units in sessions with valid blocks. The distance is significant in 46 regions with Benjamini-Hochberg at q = 0.01 (reading a) and 62 at P < 0.01 (reading b), against 104 +/- 10.4; 42 regions reach the smallest attainable p of 0.001. With the 64 sessions of invalid blocks 51 and 70; with the code's permutation classes 47 and 67, and 53 and 76 with all sessions. The code's Benjamini-Yekutieli correction at 0.05 gives the same counts as reading (a). Only an uncorrected P < 0.05 comes near (91 to 98). Significance agrees with stim_euc_sig of region_info.csv in 133 of 201 regions (41 in both, 5 here only, 63 in the paper only). The cause of the difference is not found here; the trial mask lacks the saturation intervals the code uses.", "deviations": [ "The 64 sessions whose probability_left alternates on every trial are left out; CL, LING, MH, P5, PC5 and SOC then have fewer than 20 units and are not tested.", "The Methods permute stimulus sides within each block and choice; the code merges the unbiased block with the 0.2 blocks. The Methods decide; the code's classes are a variant.", "One set of permutations per session, shared by its regions; the code draws them per insertion.", "Trials follow the mask here, without the saturation intervals the code uses." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fback-oscillation-licking", "statement": "During reward delivery, activity showed coherent oscillations of about 10 Hz that were missing after negative feedback and were closely related to licking.", "source": "Results, Representation of feedback; Fig. 6j-l; Extended Data Fig. 12", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ibl_2025.ipynb", "notes": "In 27 IRN sessions the population PSTH after correct feedback peaks at a median 7.08 Hz, outside the 9 to 11 Hz of the criterion. Power at the peak is higher after correct than incorrect feedback in 20 of 27 sessions (p = 0.0042), and the lick PSTH peaks at a median 7.23 Hz, within 1 Hz of the neural peak. In 4 sessions the neural peak is at 4.00 Hz, the edge of the band, and in one at 4.25 Hz. The power difference holds when each unit's PSTH is z-scored (18 of 27 sessions, p = 0.028, median peak 7.28 Hz) and when power at the peak is taken as a fraction of the 4 to 20 Hz power (26 of 27, p = 1e-07); both measure at the correct-trial peak and keep the evoked difference. With the band taken within 1 Hz of each session's lick peak, which does not use the neural correct-trial PSTH, power is higher after correct feedback in 15 of 26 sessions (p = 0.038), and in 15 of 26 (p = 0.031) after subtracting each condition's slow evoked response (Gaussian smoothing, sigma 60 ms; faster components of the evoked response remain). Each condition at its own peak after the subtraction gives 16 of 27 (p = 0.077). In the 9 to 11 Hz band there is no difference (12 of 27, p = 0.7 raw, 0.66 after the subtraction). Condition (ii) holds when the band follows the licks.", "deviations": [ "Tested in IRN only, the paper's example region; the paper's analysis is a population trajectory over regions.", "The spectral measure (Hann-windowed spectrum of the session PSTH, 4 to 20 Hz) is chosen here; the paper describes the oscillation without a measure." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "wheel-speed-decoding", "statement": "Wheel speed was decodable from 163 of the 201 regions.", "source": "Results, Representation of wheel movement; Fig. 7a", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted. It needs Lasso decoding in 20 ms bins for all 201 regions with imposter null sessions; the notebook estimates about 41 minutes on 4 processes to decode one binary variable for all 2,458 region-sessions with the reduced settings used here (30 in the previous run; the estimate varies with the run), and wheel decoding is heavier.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "encoding-feedback-largest", "statement": "In the encoding model the kernel for correct feedback explained the most variance of all kernels (mean delta R2 of 8.6e-3 over all neurons).", "source": "Results, Representation of feedback; Extended Data Fig. 13", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted. The encoding model would be fitted to each of the 62,857 neurons with its leave-one-out refits, which needs every session's spikes and wheel traces.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "video-correlates", "statement": "More than half of the neurons in most brain regions were significantly correlated with at least one behavioural variable from video (nose, paw, pupil, tongue).", "source": "Results, Representation of wheel movement; Extended Data Fig. 15", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted. It needs video pose and pupil series and every session's spikes; pose is present in 407 of 459 sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "granger-interactions", "statement": "High Granger interaction scores were found for region pairs from all major brain regions, weakly correlated with anatomical distance and mostly bidirectional.", "source": "Results, Neural analyses; Extended Data Fig. 4", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted. It needs every simultaneously recorded region pair of every session with 1,000 permutations each.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "In 64 sessions, all with the protocol name _iblrig_tasks_ephysChoiceWorld without a version (hausserlab 48, churchlandlab_ucla 13, mainenlab 2, cortexlab 1, recorded 2022-01-31 to 2023-10-19), probability_left alternates between 0.2 and 0.8 on every trial after the first 90, so block_index and block_type change on every trial. In these sessions the stimulus falls on the stated block's likely side in 47.5% to 57% of biased trials, against 75.9% to 82.8% in the other 395 sessions, so the column does not describe the blocks the mice experienced. Analyses of the block prior cannot use these sessions." }, { "kind": "data_missing", "statement": "No session holds the receptive-field mapping phase or its stimulus sequence; passive phases list only spontaneous activity and task replay, and the stimulus groups are empty. The paper ran the mapping in 504 of 699 insertions (Supplementary Fig. 5)." }, { "kind": "paper_inconsistency", "statement": "The Methods give a noise cutoff below 20 uV for a well-isolated unit, but the quality score in the files, and the paper's count of 75,708 well-isolated units, follow a noise cutoff below 5 for every unit (20 would give 95,430). The files describe the noise cutoff in standard deviations, not uV." }, { "kind": "metadata_error", "statement": "wheel_movement_onset_time is described as the first wheel movement after the go cue, but in 11.97% of trials it precedes the go cue (11.93% precede the stimulus onset)." }, { "kind": "other", "statement": "reward_volume_uL is 1.5 on every one of the 242,628 rewarded trials, while the Methods state a 3 uL reward." }, { "kind": "metadata_error", "statement": "The units table's description refers to a 'label' column that the files do not have (the column is ibl_quality_score) and describes all units as from Neuropixels 1.0 probes, though four insertions used NP2010 probes." }, { "kind": "metadata_insufficient", "statement": "Subject weight is one value per mouse, identical in all its sessions, and is not described as a reference weight; the Methods give weights on the day of recording." }, { "kind": "code_mismatch", "statement": "The Methods give age and weight on the day of recording (13 to 178 weeks), but meta/mice_info.py and print_age_weight in the paper's code take age_weeks and reference_weight from the IBL database. From the files the ages at recording are 13.1 to 65.9 weeks. print_age_weight also prints the median weight under the label mean and the mean under the label median." }, { "kind": "paper_inconsistency", "statement": "The Results give 81.4 +/- 0.4% correct as mean +/- s.d.; across mice the s.d. here is 5.12 and the s.e.m. 0.43, so the 0.4 is an s.e.m." }, { "kind": "other", "statement": "The single-cell test's false-positive rate, which the paper sets to 0.001 x 0.05 = 5e-5 in its binomial test of regional fractions, is about 2.5e-3 to 2.7e-3 when the test is run with null sessions here, and 5.7e-4 to 7.7e-4 with the labels shuffled over the tested trials, where the product of the two tests' single rates is 3.3e-5 to 4.7e-5. The two tests are not independent, so the stated rate understates false positives." }, { "kind": "code_mismatch", "statement": "region_info.csv marks 210 regions as canonical; the paper's canonical set, and the code's inclusion table, have 201 (the 9 others have fewer than 20 neurons)." }, { "kind": "paper_inconsistency", "statement": "The Results give visual trajectory latencies of 34, 42, 42, 57 and 78 ms for LGd, VISp, LP, VISpm and VISam; the paper's own results table (meta/Results/stim.pkl) gives 34.0, 44.7, 46.8, 59.6 and 66.0 ms." }, { "kind": "code_mismatch", "statement": "For the stimulus trajectories the Methods permute stimulus sides among trials of the same block and choice and call a region significant at P < 0.01 with Benjamini-Hochberg at q = 0.01, while state_space_bwm.py merges the unbiased block with the 0.2 blocks and applies Benjamini-Yekutieli at 0.05. Here neither choice brings the count of significant regions near the paper's 104 (46 to 53)." }, { "kind": "other", "statement": "The files hold IBL spike sorting revision 2025-05-06, while the paper's code loads revision 2024-05-06; the unit and inclusion counts are identical." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier tested helper functions on synthetic inputs and checked the archive for the blocked claims. Its report gave its own outcome for each claim; 29 of 30 agree with the record, and behav-zero-contrast does not.", "agreed": 29, "of": 30, "disagreements": [ { "claim": "behav-zero-contrast", "outcome": "not_reproduced", "reason": "Under reading (a) t = 19.68 is within tolerance, but the mean of 58.26% misses 58.7 +/- 0.4 by 0.04. Reading (b) fails both. A narrow miss; the 454-session subset was never tried." } ] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the first revision, with its conclusions and summary, the helper module, the claims file, the README and this record. The verifier did not download the paper this round and checked against the notebook's outputs and the criteria. It agrees with 29 of 30 outcomes and not with behav-zero-contrast. Its points outside the claims were also fixed, the README's run time now matches the printed timings of the new run, and the summary no longer says the dandiset holds the released dataset completely.", "agreed": 29, "of": 30, "disagreements": [ { "claim": "behav-zero-contrast", "outcome": "not_reproduced", "reason": "The criterion defines only the reproduced case, both values within tolerance under one reading. Every other criterion in the file with two parts defines a partial case explicitly, and this one does not. Neither reading meets it (cell 48). With the 454 canonical sessions the mean is still 58.27%, so the miss of 0.04 points beyond the tolerance stands." } ] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 3. Only the proposed change of outcome for behav-zero-contrast, with the analysis behind it in cells 2, 48 and 49 of the executed notebook of the final revision, the helper module and the claims file. The verifier did not download the paper for this check.", "agreed": 1, "of": 1, "disagreements": [] } ] }, { "id": "000552-huszar-2022-01", "dandiset": "000552", "dandiset_version": "0.230630.2304", "paper": "10.1038/s41593-022-01138-x", "paper_title": "Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000552-huszar-2022", "entry_title": "Birthdated CA1 pyramidal neurons in freely moving mice (Huszar et al. 2022)", "description": "Tests the findings of Huszar, Zhang, Blockus and Buzsaki (2022) that can be tested on dandiset 000552, which holds sleep states, sharp-wave ripples, spike-sorted units and position from 17 mice electroporated at E13.5 to E16.5. It checks the description of the dataset and tests the findings on all pyramidal neurons on familiar and novel mazes (population-vector decorrelation, firing rates, spatial information and ratemap correlations). The units carry no light-responsiveness label and no optogenetic pulse times are stored, so the comparisons of same- and different-birthdate neurons are blocked.", "notebooks": [ { "path": "reproduce_huszar_2022.ipynb", "title": "Reproducing Huszar et al. (2022) from dandiset 000552", "executed": "notebooks/000552-huszar-2022/reproduce_huszar_2022.html" } ], "outcomes": [ { "claim": "cohort-birthdates", "statement": "Chronic recordings were made from 17 adult mice (12 males, 5 females) electroporated at E13.5 (n = 4), E14.5 (n = 3), E15.5 (n = 6) and E16.5 (n = 4).", "source": "Results, first section; Methods, Implantation and recording", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "17 mice, with E13.5 4, E14.5 3, E15.5 6 and E16.5 4, as the paper states. With each mouse's sex taken from most of its files, 12 males and 5 females, as the paper states. The sex field differs between files of two mice (e13_1f1 Female in 3 files and Male in 2; e13_1m1 Male in 9 and Female in 3), so reading only each mouse's first file gives 13 and 4. The ids, which carry f or m, also give 12 and 5.", "deviations": [ "The criterion took sex from the subject metadata without saying how to combine files that disagree; the value in most of a mouse's files is used, chosen after the per-file values were seen (the first round of this attempt read the first file and gave 13 and 4)." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "sessions-durations", "statement": "The recordings comprise 92 sessions lasting 113.7 to 475.6 min (median 309.1 min), each including a homecage period of sleep and wake.", "source": "Methods, Implantation and recording", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "104 processed files, within 10% of the 96 sessions of Figure 1e and Figure 7f but not of the 92 of the Methods. Median duration 319.6 min (paper 309.1), range 113.7 to 494.2 min, all inside the widened range of 102.3 to 523.2 min; two files last exactly the paper's bounds (113.7 and 475.6 min). Without e15_13f1 and e16_3m2 there are 96 sessions with per-birthdate counts equal to Figure 1e (30, 24, 24, 18), range 113.7 to 475.6 min and median 309.9 min. Two files of e13_1f1 (200305, 200307) hold one Awake interval for the whole session and no scored sleep, so the statement that each session includes sleep fails for them; that part makes the outcome partial.", "deviations": [ "Session duration is the end of the last sleep-state or ripple interval; in 57 files the last spike falls 1.2 to 5.2 s later.", "The criterion named the sleep condition without saying which outcome its failure gives; with the count, median and range holding and the sleep condition failing in 2 of 104 files, the outcome is taken as partial.", "The session count was judged under two readings (92 and 96), as the paper gives both." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "spwr-duration", "statement": "SPW-Rs were detected with duration limits of 20 to 200 ms, and their median duration across all recordings was 36.4 ms.", "source": "Figure 2b legend; Methods, SPW-R detection", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "Median duration 36.0 ms over all 494,578 ripples pooled and 36.0 ms as the median of the 104 session medians (paper 36.4). All ripples last 20.0 to 199.2 ms, within the 20 to 200 ms limits. Per-mouse medians run from 29.6 to 40.0 ms.", "deviations": [ "Uses the ripples stored in the files; detection was not repeated." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "unit-count", "statement": "The dataset includes 9,471 well-isolated units, 7,411 putative pyramidal cells and 2,060 putative interneurons.", "source": "Methods, Unit isolation and classification; Extended Data Figure 2a", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "8,201 units in 65 of 104 files, below the tolerance of 8,524 to 10,418. Six mice (e13_1f1, e13_1m1, e14_1m1, e15_4m1, e15_4m2, e15_5m1; 39 files) have no units. Files with units hold 34 to 376 (median 99). The 5 Hz rule classes 87.8% as putative pyramidal cells, against the paper's 78.3%.", "deviations": [ "The pyramidal fraction uses a firing-rate rule, as the files hold no cell type." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "maze-cohort", "statement": "Nine mice (E13.5 n = 2, E14.5 n = 2, E15.5 n = 2, E16.5 n = 3) ran a spatial alternation task on a familiar figure-eight maze, and a cohort of three mice also explored novel environments.", "source": "Results, SBD pyramidal neurons exhibit overlapping place tuning; Methods, Behavior", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "11 mice have figure-eight trials. Under reading (b), the maze mice without e15_13f1 and e16_3m2 are nine, at E13.5 2, E14.5 2, E15.5 2 and E16.5 3, and three mice (e13_26m1, e15_13f1, e16_3m2) have novel recordings, so e13_26m1 is in both cohorts. Reading (a), disjoint cohorts of 12 mice, does not hold.", "deviations": [ "The paper calls the novel cohort separate; the reading that matches takes the overlap from the paper's code, recorded as an ambiguity." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "maze-task", "statement": "On the figure-eight maze each trial was 205 cm long, position was tracked at 30 Hz, and animals ran at least ten trials along each arm in every session.", "source": "Methods, Behavior", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "Median trial length 204.1 cm and tracking at 30.00 Hz in all 65 familiar recordings, both within tolerance. Only 38 of 65 sessions have at least ten trials on each visited arm (22 of 65 by expected arm), and 6 sessions have fewer than 20 trials (fewest 12), so neither the full nor the partial condition holds. The requirement may have applied to training, not to every recorded session.", "deviations": [ "Two readings of \"trials along each arm\" (visited and expected) were used; neither holds." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "novel-explorations", "statement": "The novel-environment cohort of three mice made 16 novel environment explorations in six distinct environments (two linear tracks, three open fields and one figure-eight maze).", "source": "Results, SBD pyramidal neurons exhibit overlapping place tuning; Methods, Behavior", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "Three mice with 9 novel explorations that have trials and position (3 T-maze runs of about 164 cm, 3 linear-track runs of 110 cm and 3 of 100 cm), against 16. The novel-cohort sessions also hold 7 epochs of 10 to 50 min without position that are not a session's last epoch, and the files hold no other position or video series for them. They are not counted; they would bring the count to 16, but they were picked after the data were seen and nothing in the files marks them as explorations. No open field has position.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5e-pv-decorrelation", "statement": "Population firing-rate vectors at the same linearized position decorrelate between left and right trials once the animal leaves the common stem of the figure-eight maze (median correlations stem 0.93, turn 1 0.412, arm 0.372, turn 2 0.394).", "source": "Figure 5e", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "57 sessions of nine mice (the paper's bin counts, 4,218 stem bins, imply the same 57), with 28 to 242 putative pyramidal cells per session. Kruskal-Wallis H = 7632.7 (paper 7278.3), p = 0, stem highest. Stem 0.937 is within tolerance; turn 1 0.547, arm 0.492 and turn 2 0.465 are above the paper's 0.412, 0.372 and 0.394. The stem is the most correlated segment in every mouse. The medians depend strongly on the cell rule; at most 2 Hz gives 0.925, 0.387, 0.288, 0.306; at most 10 Hz gives 0.966, 0.787, 0.771, 0.746; all units 0.988, 0.948, 0.94, 0.921; no speed threshold 0.924, 0.589, 0.522, 0.492. With a 2.59 Hz rule, which classes the paper's fraction of units (0.783) as pyramidal, the medians are 0.928, 0.436, 0.343 and 0.357, all four within tolerance; the criterion fixed the 5 Hz rule, so this variant does not change the outcome. 51 of 11,685 bins had no value.", "deviations": [ "Putative pyramidal cells by session mean rate (at most 5 Hz), not by waveform and autocorrelogram; the files hold no cell type or waveforms.", "Speed from smoothed linearized position, not a Kalman filter." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-theta-rate-preserved", "statement": "Individual pyramidal neurons preserve their theta-related firing rates between the familiar and novel environments (Spearman rho = 0.7378, n = 2,544 neurons).", "source": "Figure 6c, top", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "Spearman rho = 0.726 over 2,038 putative pyramidal cells with a familiar and a novel rate (paper 0.7378 over 2,544), p = 0; per mouse 0.711 to 0.745, per session 0.586 to 0.826. Variants with all units, a 10 Hz rule or a 1.5 cm/s running threshold give 0.754 to 0.802. 679 cells of the 3 sessions without a novel maze have no novel rate. The running rate now ends each running stretch at the end of its trial (round 1 gave 0.734 with stretches that could span the gap between trials).", "deviations": [ "The rate is the firing rate while running at 5 cm/s or faster inside maze trials, in place of the rate in LFP theta cycles; the LFP is in the raw files of 8 of the 9 novel sessions but was not used.", "Novel mazes are only those with position; the open fields are not in the data.", "Putative pyramidal cells by firing rate." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-novel-ratemap-corr-higher", "statement": "Pairwise spatial ratemap correlations between pyramidal neurons are higher in novel environments (median 0.048) than in the familiar environment (median -0.045).", "source": "Figure 6c, bottom", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "Median familiar -0.0530 over 327,656 pairs (within tolerance) and novel -0.0364 over 242,655 pairs (outside 0.018 to 0.078); rank-sum p = 0.67. Within each of the 9 sessions with a novel maze the novel median is higher than the familiar one (sign test p = 0.0039; rank-sum p < 0.05 within 7 of the 9 sessions), so the direction holds session by session; the pooled test, which the criterion names, is weighted by the sessions with most pairs; with familiar pairs only from those sessions the pooled test gives p = 0.1. Variants with all units (p = 0.38) or a 10 Hz rule (p = 0.66) agree; including the stem gives p = 3.5e-50 with novel higher. Per maze kind, novel medians run from -0.0548 to 0.0073.", "deviations": [ "All pairs of putative pyramidal cells, where the paper's pairs each include a light-responsive neuron (not identifiable in the files).", "Novel mazes are only the T-maze and linear tracks with position; the paper's novel pairs also come from open fields with two-dimensional maps." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-info-lower-novel", "statement": "Spatial information is lower in novel environments than in the familiar one (median 0.39 against 0.88 bits/s).", "source": "Figure 6d, right", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "Familiar median 0.631 bits/s over 2,709 cells and novel 0.270 over 2,028 cell-maze values, rank-sum p = 1.5e-59, so information is lower in novel mazes as stated, but both medians are below the tolerances (0.792 to 0.968 and 0.351 to 0.429). The code's unweighted measure gives 0.646 and 0.285. By mouse, familiar 0.617 to 0.645; novel 0.083 to 0.337 on linear tracks and 0.282 to 0.608 on the T-maze.", "deviations": [ "Skaggs information over left and right maps of the whole linearized track, with putative pyramidal cells by firing rate; no open fields." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-rate-lower-novel", "statement": "Theta-related firing rates are slightly lower in novel environments than in the familiar one (median 0.69 against 0.77 Hz).", "source": "Figure 6d, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_huszar_2022.ipynb", "notes": "Familiar median 0.794 Hz over 2,717 cells and novel 0.714 Hz over 2,038, both within tolerance of the paper's 0.77 and 0.69 Hz; rank-sum p = 0.041 (paper 3.3e-3). The difference is weak. The paired signed-rank test gives a median ratio of 0.942, p = 0.19; familiar from the sessions with a novel maze only gives p = 0.09; the variants (all units, 10 Hz rule, 1.5 cm/s threshold) give lower novel rates with p = 0.075 to 0.11. Novel is lower in two mice (0.722 against 0.883, 0.680 against 0.835) and slightly higher in e15_13f1 (0.734 against 0.729). Round 1 gave 0.958 and 0.799 Hz, p = 7e-06, with running stretches that could span the gap between trials and count its spikes but not its time; in 371 of 698 pairs of consecutive trials the animal was running at the end of one and the start of the next.", "deviations": [ "Running rate in place of the rate in LFP theta cycles.", "Putative pyramidal cells by firing rate; no open fields." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed2-light-responsive-count", "statement": "664 of 7,411 putative pyramidal neurons (8.96%) were light-responsive, that is, birthdated.", "source": "Extended Data Figure 2a", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No unit is labelled light-responsive and no optogenetic pulse times are stored in the processed or raw files (stimulus and acquisition are empty in the processed files; a listing of every dataset in all 13 raw files finds only the ElectricalSeries, the LFP and the electrodes table). The paper's labels come from CellExplorer optoTag fields and pulses.events.mat files on the lab server, which the paper's data link reaches only through the lab databank and Globus, at no pinned identifier. The Methods say the pulses were given at the end of each session, in blocks of five 200 ms apart, and that the raw data were clipped out from 0.15 ms before to 0.8 ms after each pulse; they give no interval between blocks and do not say what the clipped samples hold. In the raw file of e16_3m2_211213 the wideband signal ends 2 s after the processed session, and ten 2 s windows over its last 30 min hold no flat or zeroed stretch on eight channels; if clipped samples are flat or zero, the stimulation period is not in the deposited recording. The other 10 wideband files (54 to 184 GB each) were not scanned.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-labelled-fraction", "statement": "The fraction of light-responsive pyramidal cells per session follows a bell-shaped wave over birthdates, peaking at E15.5 (E13.5 5.39%, E14.5 11.16%, E15.5 14.74%, E16.5 9.16%; ANOVA p = 4e-4).", "source": "Figure 1e", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the light-responsive units of each session; see ed2-light-responsive-count.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-radial-depth", "statement": "Neurons born on later days lie more superficially in the pyramidal layer (median normalized depth 0.71, 0.48, 0.28 and 0.19 for E13.5 to E16.5).", "source": "Figure 1c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Histology (tdTomato and DAPI images) is not in the dandiset and was not found elsewhere.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-rem-shift", "statement": "Earlier-born light-responsive neurons more often shift their preferred theta phase in REM sleep (30.89% at E13.5 to 19.7% at E16.5; regression slope -3.42% per day).", "source": "Figure 1f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs light-responsive units by birthdate; see ed2-light-responsive-count. It also needs the LFP, which is in the raw files of only 12 sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-rate-by-birthdate", "statement": "Earlier-born light-responsive pyramidal neurons have higher firing rates (medians 1.57, 1.63, 1.62 and 1.16 Hz; Kruskal-Wallis p = 0.016).", "source": "Figure 1g", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the light-responsive units; see ed2-light-responsive-count. Grouping all units by the mouse's birthdate would test a different quantity, as most units in a mouse are not birthdated.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1h-burst-by-birthdate", "statement": "Burst index is an inverted-U function of birthdate (medians 0.1167, 0.1272, 0.136, 0.1082; Kruskal-Wallis p = 0.0044).", "source": "Figure 1h", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the light-responsive units; see ed2-light-responsive-count.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-synchrony-per-animal", "statement": "Same-birthdate (SBD) pairs fire more synchronously than different-birthdate (DBD) pairs in 11 of 13 animals.", "source": "Figure 2a,b; Extended Data Figure 4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "SBD and DBD pairs cannot be formed without light-responsiveness labels; six of the homecage mice also have no units.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-theta-cofiring", "statement": "SBD pairs cofire more than DBD pairs in theta cycles (median 0.0189 against 0.0087).", "source": "Figure 2c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD and DBD pairs (no labels) and theta cycles from the LFP (raw files of 12 sessions only).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-theta-depth", "statement": "Intermediate-birthdate neurons have lower theta depth modulation in waking but not in REM sleep.", "source": "Figure 2d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs light-responsive units by birthdate and the LFP.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-ripple-firing-by-birthdate", "statement": "SPW-R firing rates and participation of light-responsive neurons are an inverted-U function of birthdate.", "source": "Figure 2f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs light-responsive units by birthdate; the ripples themselves are in the files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2g-ripple-cofiring", "statement": "SBD pairs cofire more than DBD pairs in SPW-Rs (median 0.0399 against 0.0231).", "source": "Figure 2g", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD and DBD pairs; no labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-assembly-cofiring", "statement": "Assembly members cofire more in SPW-Rs than member-nonmember pairs, and segregation from nonmembers depends nonlinearly on the members' birthdate.", "source": "Figure 3c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The member-nonmember part could be computed, but the analysis keeps only assemblies with a light-responsive member and groups them by birthdate, which needs the labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-assembly-expression", "statement": "Assemblies with intermediate-birthdate members are expressed in SPW-Rs at higher rates (E13.5 8.16, E14.5 9.25, E15.5 8.16, E16.5 6.9 Hz; ANOVA p = 0.0158).", "source": "Figure 3e", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Assemblies are grouped by the birthdate of light-responsive members; no labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-model-fit", "statement": "A model with a bell-shaped rate of neurogenesis and correlations among SBD neurons reproduces the assembly expression rates, and a uniform-neurogenesis model does not.", "source": "Figure 4c,d; Extended Data Figure 9", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The model is fitted to the assembly expression rates of fig3e-assembly-expression, which is blocked.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5b-spatial-info-by-birthdate", "statement": "Spatial information and coverage on the maze are largest in intermediate-birthdate neurons.", "source": "Figure 5b", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs light-responsive units by birthdate.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-sbd-ratemap-overlap", "statement": "SBD pairs have higher spatial ratemap correlations than DBD pairs on the familiar maze (median 0.0152 against -0.0256).", "source": "Figure 5c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD and DBD pairs; no labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5d-overlap-by-distance", "statement": "The ratemap overlap of SBD pairs depends on their anatomical distance, larger within 250 micrometres.", "source": "Figure 5d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD pairs and the shank of each unit; units have no electrode link and their group_id does not match the electrode groups in 64 of 65 files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-remap-together", "statement": "Between left and right trials, ratemaps of SBD pairs reorganize closer together than those of DBD pairs.", "source": "Figure 5f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD and DBD pairs; no labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6e-sbd-novel-overlap", "statement": "In novel environments SBD pairs have higher ratemap correlations than DBD pairs (median 0.117 against 0.046).", "source": "Figure 6e", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD and DBD pairs; no labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6f-remap-together-novel", "statement": "Ratemaps of SBD pairs remain closer together than those of DBD pairs between the familiar and novel environments.", "source": "Figure 6f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD and DBD pairs; no labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7b-sbd-convergence", "statement": "SBD pyramidal pairs converge onto the same interneurons more than DBD pairs (median convergence 0.2727 against 0.2).", "source": "Figure 7b", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs SBD pairs and putative interneurons; neither labels nor cell types are in the files.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7ce-convergence-by-birthdate", "statement": "Convergence onto interneurons and spike transmission probability are bell-shaped functions of the presynaptic neurons' birthdate.", "source": "Figure 7c-e", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs light-responsive units by birthdate and putative interneurons.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7fg-convergence-cofiring", "statement": "Of all pyramidal pairs, 65.27% share at least one postsynaptic interneuron, and cofiring in SPW-Rs, theta cycles and ratemap overlap all increase with convergence.", "source": "Figure 7f,g", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Uses all pyramidal-interneuron pairs and needs no birthdate labels. The notebook applies the rate rule (units above 5 Hz as interneurons, 1,001 in all against the paper's 2,060) and the connection test of the Methods (0.8 ms CCG bins, hollowed-Gaussian baseline of 15 ms s.d., alpha 0.001) to two sessions. In e15_13f1_220117, whose mouse is not among the 15 of Figure 7f, the test at fixed lags of 0.8 to 3.2 ms detects connections in 5,073 of 11,319 possible pairs (0.448, against 31,932 of 184,230 or 0.173 in the paper), and 96.7% of pyramidal pairs share a target (paper 65.27%). In e13_26m1_211019, inside the Figure 7f cohort, it detects 0.407, with 96.7% of pairs sharing a target. The Methods test the three bins around the CCG peak, where this test uses fixed lags; a peak-centred variant (peak sought at lags up to 4.0 ms, a range the Methods do not give, chosen after the fixed-lag results were seen) detects 0.405 and 0.394, with 95.7% and 93.4% of pairs sharing a target. With a connection rate this far from the paper's under both forms, the procedure differs from the paper's, whose connections come from the lab's CellExplorer mono_res files (not public; the paper's code reads them and does not compute them). The difference may lie in this implementation as well as in what the Methods leave unstated (lag range, hollow fraction, CCG window). Of the paper's 96 sessions (the files without e15_13f1 and e16_3m2), 39 have no units in the dandiset, and cofiring in theta cycles needs the LFP, which the processed files lack.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "No unit is labelled light-responsive (birthdated), and no optogenetic pulse times are stored in the processed or the raw files, so the paper's comparisons of same- and different-birthdate neurons and its birthdate profiles (22 of the 35 claims listed here) cannot be tested. The labels exist in the lab's CellExplorer files (optoTag, putativeCellType), which are not public at a pinned identifier." }, { "kind": "metadata_insufficient", "statement": "Units carry no putative cell type and no waveforms, though the paper classifies 7,411 pyramidal cells and 2,060 interneurons." }, { "kind": "data_missing", "statement": "Six of the 17 mice (e13_1f1, e13_1m1, e14_1m1, e15_4m1, e15_4m2, e15_5m1; 39 files) have sleep states and ripples but no units and no position. The dandiset holds 8,201 units where the paper reports 9,471." }, { "kind": "data_missing", "statement": "Of the 16 novel environment explorations, only 9 have position and trials, and no open field has position. The novel-cohort sessions hold 7 further epochs of 10 to 50 min without position or video that may be the missing explorations." }, { "kind": "metadata_error", "statement": "The subject sex differs between files of the same mouse. e13_1f1 is Female in 3 files and Male in 2; e13_1m1 is Male in 9 and Female in 3. The value in most of each mouse's files gives the paper's 12 males and 5 females." }, { "kind": "metadata_error", "statement": "The trials column is_familiar_maze is True only for the first two trials of sessions with a single maze recording, where every trial is on the familiar maze (112 True, 1,182 False)." }, { "kind": "metadata_error", "statement": "In several novel recordings (e13_26m1 211019, 211116, 211119; e15_13f1 220120; e16_3m2 211213) x and y lie between 0 and 1 though stated in cm." }, { "kind": "metadata_error", "statement": "Twelve of the 13 raw files give a session start of 2011-08-18 for sessions recorded in 2021 and 2022." }, { "kind": "metadata_error", "statement": "The processed file of e16_3m1_210201 holds a copy of the 1250 Hz LFP of the raw file, labelled with a rate of 30,000 Hz and a conversion factor of 3.05e-13 V." }, { "kind": "identifier_missing", "statement": "Units have no link to the electrodes table, and their group_id values (\"Group3\") do not match the electrode group names (\"Group 3\") in 64 of 65 files, so a unit's shank and position on the probe cannot be recovered." }, { "kind": "metadata_insufficient", "statement": "The embryonic day of electroporation, the variable the paper is about, is stored only as the prefix of each subject id (e13 for E13.5); the age is given as P3M/P6M for every mouse." }, { "kind": "other", "statement": "Two files of e13_1f1 (200305, 200307) hold a single Awake interval for the whole session, so sleep was not scored, though both hold ripples." }, { "kind": "other", "statement": "Only 38 of 65 familiar-maze sessions have ten or more trials on each visited arm, and 6 have fewer than 20 trials, where the Methods require ten per arm in every session; 19 of 1,942 trials have no start or stop time." }, { "kind": "paper_inconsistency", "statement": "The Methods give 92 sessions, while Figure 1e (30, 24, 24 and 18 sessions) and Figure 7f give 96. The dandiset's files of the 15 homecage mice are 96 sessions that match Figure 1e by birthdate and the Methods' duration bounds exactly (113.7 to 475.6 min)." }, { "kind": "paper_inconsistency", "statement": "The paper calls the novel-environment cohort of three mice separate, but one of them (e13_26m1) is also among the nine figure-eight mice, in the dandiset and in the paper's code." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text (the PMC author manuscript). The verifier tested helper functions on synthetic inputs and queried the archive's asset metadata for the blocked claims. Its report gave its own outcome for each claim; it agreed with the record on 34 of 35 outcomes, gave reproduced for cohort-birthdates, and for fig7fg-convergence-cofiring agreed on blocked but disputed the reason. Problems B6 (dependent bins and pairs treated as independent, as in the paper), B8 (skaggs_information weights by unsmoothed occupancy and divides by smoothed occupancy) and B9 (mean_rates divides by an end time 1 to 5 s short of the last spike in 57 files) it marked as not affecting a conclusion; they were left as they are, since the first follows the paper, the second follows the Methods' map definition with the occupancy probability of Skaggs et al., and the third changes rates by under 0.1%.", "agreed": 34, "of": 35, "disagreements": [ { "claim": "cohort-birthdates", "outcome": "reproduced", "reason": "17 mice and the birthdate counts 4/3/6/4 match. The notebook's 13 M / 4 F comes from taking each mouse's first file. The sex field differs between files of the same mouse; e13_1f1 is Male in 2 files and Female in 3, e13_1m1 is Male in 9 and Female in 3 (cell 7, and the DANDI asset metadata it queried). Taking each mouse's majority gives 12 M / 5 F, which matches. Problem B2 (affects a conclusion) is the same point." } ] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file and the attempt record, with the paper's full text (the PMC10807234 author manuscript). The verifier agreed with all 35 outcomes, and for fig7fg-convergence-cofiring accepted the block while calling two parts of its reasoning weak. It quoted five sentences the outputs do not support: the count of 31 sessions without units (39), the statement on stimulation channels in the raw files (1 of 13 listed), the assumption about clipped pulses in cell 16, a swapped column label in the fig6c output, and the reading of the T-maze as the novel figure-eight. Remaining points bearing on a conclusion were B4 (fig5e rate rule), the weak fig6d-rate test, fig7fg's single out-of-cohort session and detector, and B7 (raw files). The round-1 response on fig7fg also gave 31 sessions; it is left as recorded, and the notes are corrected.", "agreed": 35, "of": 35, "disagreements": [] } ] }, { "id": "000559-markowitz-2023-01", "dandiset": "000559", "dandiset_version": "0.260528.0858", "paper": "10.1038/s41586-022-05611-2", "paper_title": "Spontaneous behaviour is structured by reinforcement without explicit reward", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000559-markowitz-2023", "entry_title": "Dopamine and spontaneous behaviour in mice (Markowitz, Gillis, Jay et al. 2023)", "description": "Tests the findings of Markowitz, Gillis, Jay et al. (2023) on dandiset 000559, which holds the dLight photometry, MoSeq syllables and closed-loop optogenetic sessions of the paper. It relates DLS dopamine to velocity, syllable identity, syllable use and sequence entropy, compares DMS with DLS, and tests the reinforcement of target syllables by closed-loop dopamine release. The modelling of Figures 4 and 5 is not attempted.", "notebooks": [ { "path": "reproduce_markowitz_2023.ipynb", "title": "Reproducing Markowitz, Gillis, Jay et al. (2023) from dandiset 000559", "executed": "notebooks/000559-markowitz-2023/reproduce_markowitz_2023.html" } ], "outcomes": [ { "claim": "fig1e-velocity-timescales", "statement": "DLS dopamine fluctuations are significantly negatively correlated with translational velocity at short timescales (under 10 s), and the correlation reverses and becomes positive at longer timescales, for both dLight transient rates and binned amplitudes.", "source": "Results, first section; Figure 1e", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "Over 121 DLS sessions from 14 mice, binned dLight amplitude and transient rate are both significantly negatively correlated with 2D speed at all 20 timescales below 10 s (amplitude mean r -0.201 to -0.109, rate -0.123 to -0.062; shuffle ranges within about 0.02 of zero), and all 14 mice are negative at 0.25 s for both. The transient rate turns positive from 18.75 s and is significantly positive at 47 of 100 timescales of 10 s or more (largest 0.113 at 58.75 s). The binned amplitude is still significantly negative at 49.75 s and is significantly positive at none of the 100 longer timescales (largest 0.005). The claim holds for one of the two measures under both readings of \"short timescales\".", "deviations": [ "dLight is re-referenced and z-scored from the stored dF/F series; the paper used a pre-computed z-scored trace that is not in the files.", "100 shuffles where the paper used 1,000.", "121 sessions where the paper's code reports 216 for this panel; the dandiset holds fewer sessions, and habituation sessions are left out here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1h-syllable-dlight-differs", "statement": "Average syllable-associated dLight amplitudes differ across syllables (Kruskal-Wallis H = 209.29, P < 1e-25, n = 518 mouse-syllable pairs).", "source": "Figure 1h legend", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "The 518 mouse-syllable pairs (14 mice x 37 syllables) match the paper's n. Kruskal-Wallis P = 5.98e-37, below the paper's 1e-25, but H = 266.40 is 27 % above 209.29 and outside the 10 % tolerance. Variants give H 266.99 (target instances kept), 268.58 (pairs with at least 50 instances) and 265.62 (the 9 DLS sessions failing the quality criteria added), so neither the quality filter nor the post-session rule explains the difference. Per-mouse tests are significant in 14 of 14 mice.", "deviations": [ "Instances from 177 DLS sessions without stimulation (habituation sessions left out); the paper used more sessions per mouse." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1l-identity-not-decodable", "statement": "Random forest classifiers cannot predict which syllable is being expressed from the coincident dLight peak amplitude or waveform.", "source": "Results, second section; Figure 1l", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "Held-out accuracy for 37 syllables is 0.0271 from peak amplitude and 0.0323 from the waveform and its derivative, 1.00 and 1.20 times chance (0.0270), below the criterion of 0.0541. Shuffled labels give 0.0278 and 0.0279.", "deviations": [ "A 100-tree sklearn random forest with at least 5 instances per leaf on 1,000 instances per syllable, where the paper used cuML with 1,000 trees; the paper gives no accuracy, so \"unable to predict\" was set as below twice chance.", "One label shuffle per feature set as the null, where the paper used 100." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-dlight-usage-across-syllables", "statement": "Syllables associated on average with more DLS dopamine in an experiment tend to be used more.", "source": "Results, third section; Figure 2b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "Over 507 mouse-syllable pairs in 14 mice, held-out r = 0.165 between syllable-associated dLight and syllable count; no shuffle of 200 reached it (P < 0.005, 95th percentile 0.051). Per-mouse rank correlations are positive in 14 of 14 mice. The paper's r is shown only in its figure.", "deviations": [ "Fivefold cross-validation repeated 20 times and 200 shuffles, where the paper used 100 repeats and 1,000 shuffles." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2i-dlight-entropy-across-syllables", "statement": "Mice string together less predictable sequences after syllables associated with more dopamine; average syllable-associated dLight correlates positively with the entropy of the syllable's outgoing transitions.", "source": "Results, third section; Figure 2i", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "Held-out r = 0.271 between syllable-associated dLight and the entropy of outgoing transitions over 507 mouse-syllable pairs; no shuffle of 200 reached it (P < 0.005, 95th percentile 0.042). Positive in 14 of 14 mice.", "deviations": [ "Plain Shannon entropy of the outgoing transition probabilities per experiment, as the Methods state; the code uses a Dirichlet entropy estimate." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-dlight-predicts-future-usage", "statement": "When an instance of a syllable coincides with a higher-amplitude dopamine transient, that syllable is used more over the following minutes.", "source": "Results, third section; Figure 2c-g", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "The mean correlation between an instance's dLight and the count of the same syllable in the next n syllables is positive at every n (0.0043 to 0.0251) and significant from n = 10 to 90 (P < 0.01), 11 of 14 mice positive at n = 10. It is not significant at n = 110, 130, 150 and 170 (P = 0.09, 0.15, 0.18 and 0.05), so it holds at 6 of 10 values up to 190 and fails the criterion's \"throughout\"; it is significant again from 190 to 330. The shuffles permute only instances with a dLight peak, so the same groups enter the observed value and every shuffle (15,480 at n = 10).", "deviations": [ "Five equal time segments in place of the paper's five behavioural segments (Extended Data Fig. 2e).", "Correlations are compared with shuffles directly, not z-scored to them; 100 shuffles." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7-dms-fewer-transients", "statement": "dLight recordings in dorsomedial striatum (DMS) show less frequent dopamine transients than in DLS.", "source": "Results, third section; Extended Data Figure 7a,b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "DMS mice have a median 56.48 transients per minute against 62.12 in DLS (8 against 14 mice, U = 13, two-sided P = 0.0022); with a 1.96 threshold 22.10 against 25.21 (P = 0.0006).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7-dms-no-usage-prediction", "statement": "DMS dopamine transients do not predict future syllable usage.", "source": "Results, third section; Extended Data Figure 7", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "By the test used for fig2e-dlight-predicts-future-usage, DMS dLight predicts the later use of the same syllable. Mean r is 0.0110 to 0.0331 for n from 10 to 190, significant at 9 of those 10 values (n = 10 to 90 at P below 0.01), positive in 8 of 8 mice at n = 10, and larger than in DLS (0.0044 to 0.0251). The test is this attempt's version of the paper's (see the deviations of fig2e-dlight-predicts-future-usage). The paper's Extended Data Fig. 7 has no lagged future-usage test; it supports the claim with the encoding model (panel e) and the title \"DMS dopamine does not correlate with syllable usage or entropy\". The across-syllable count test of fig2b-dlight-usage-across-syllables run on DMS agrees with the paper (held-out r = 0.026, shuffle P = 0.170). That the lagged test finds DMS stronger than DLS suggests it differs from the paper's (equal time segments, no z-scoring to the shuffles); the outcome follows the pre-set criterion.", "deviations": [ "Same deviations as fig2e-dlight-predicts-future-usage." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-optoda-learning", "statement": "Pairing a target syllable with optogenetic dopamine release (Opto-DA) increases its use relative to baseline more than in no-opsin controls (log2 fold change in target counts, one-sided Mann-Whitney U = 197, P = 0.002, f = 0.82).", "source": "Figure 3e legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "20 Opto-DA and 12 control mice, 191 targets. Log2 fold change in target counts, Opto-DA median 0.330, control 0.081; U = 198, one-sided P = 0.0013, f = 0.82 (paper 197, 0.002, 0.82).", "deviations": [ "Stimulation, baseline and post sessions are identified from stimulation pulses, session dates and descriptions, as the files give no session number or type." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-cumulative-counts", "statement": "The cumulative increase in target counts relative to baseline is larger in Opto-DA mice than in controls (one-sided Mann-Whitney U = 184, P = 0.007, f = 0.77).", "source": "Figure 3f legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "Change in target counts, Opto-DA median 27.6, control -2.3; U = 182, one-sided P = 0.0083, f = 0.76 (paper 184, 0.007, 0.77).", "deviations": [ "As for fig3e-optoda-learning." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-learner-count", "statement": "Only a fraction of Opto-DA mice learn; nine mice exceed the largest change in target counts of any control (\"learners\").", "source": "Methods, \"Quantifying changes in target syllable counts\"; Figure 3e; Extended Data Figure 10", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "Seven of 20 Opto-DA mice exceed the largest control change (54.5, vta-nacc-ctrl-6), not nine. All seven are among the nine the paper's code printed; the other two (3442 at 47.3 and dls-ai32jr-1 at 41.7) fall below that control; their per-target changes range from -49 to 148 and -26 to 93, against -50 to 152 for vta-nacc-ctrl-6. Counting mice above the control maximum of the log2 fold change gives 10. The criterion is the count, which is outside the tolerance. The statement's first part, that only a fraction of mice learn, holds (7 of 20).", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-stim-post-correlation", "statement": "In learners, the change in target usage during stimulation predicts the change in the post-stimulation sessions (Pearson r = 0.89, P = 0.005).", "source": "Figure 3h legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_markowitz_2023.ipynb", "notes": "Among the seven learners found here, r = 0.891 between the change during stimulation and in the post sessions (one-sided shuffle P = 0.017); with the code's nine learners r = 0.888 (P = 0.001). The learner set differs from the paper's (see fig3e-learner-count), and the result holds with either. Controls also correlate (r = 0.591, one-sided P = 0.017, two-sided 0.039), where the paper reports P = 0.082.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3l-no-kinematic-effect", "statement": "Brief (250 ms) Opto-DA does not change movement at the moment of stimulation; no comparison between stimulation and catch trials in any mouse is significant.", "source": "Figure 3l legend; Results, fourth section", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": "reproduce_markowitz_2023.ipynb", "notes": "The test needs catch trials (target detections on which stimulation was withheld), which the files do not mark; the conversion kept only the stimulated detections. The criterion's substitute (online target onsets with no pulse in the next 0.5 s) is not the paper's catch set. The Methods give stimulation on 75 % of detections; with the substitute, stimulations are a median 0.593 of detections per mouse (0.521 to 0.687; 0.111 to 0.776 over sessions). It does not isolate the light's effect. In no-opsin controls, stimulation trials differ from these catch trials at P < 0.05 in 9 of 12 mice, and the controls' median difference (3.96 mm/s) exceeds the Opto-DA one (-0.07 mm/s; Opto-DA against control U = 68, P = 0.045). With catch trials at least 2 s from any pulse, controls are still significant in 9 of 12. Taken literally, the criterion gives 9 of 20 Opto-DA mice significant, which would be not reproduced (8 of 20 with the 2-s catch trials); because the controls fail, the claim is recorded as blocked.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3m-long-stim-velocity", "statement": "Extending stimulation to 3 s (pulsed, 25 Hz) makes mice increase their velocity.", "source": "Figure 3m; Extended Data Figure 10l; Results, fourth section", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": "reproduce_markowitz_2023.ipynb", "notes": "As for fig3l-no-kinematic-effect. With the criterion's substitute catch trials, stimulations are 0.302 to 0.348 of detections per mouse, and onsets during an ongoing 3-s train count as catch trials. 1 of the 3 Opto-DA mice with 3-s pulsed sessions is significant (P = 0.024; the others 0.091 and 0.053), which taken literally would be partially reproduced, and both controls are (P = 0.0002 and 0.0083), with larger differences (median 6.75 mm/s against 4.58). With catch trials at least 2 s from any pulse, 0 of 3 Opto-DA mice are significant (P = 0.10, 0.064, 0.082) and both controls still are (P = 0.0007 and 0.010). The 2-s continuous sessions give significant differences in 2 of 3 Opto-DA mice and 2 of 3 controls.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-food-reward-transients", "statement": "Spontaneous syllable-associated dopamine transients roughly match those during consumption of an unexpected chocolate chip (mean spontaneous peak 2.12 +- 0.80 z, n = 5,247; reward 2.36 +- 0.92 z, n = 10).", "source": "Figure 2a; Methods, \"Food reward experiments\"", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No session in the dandiset is described as a food-reward session, and the human-annotated consumption times are not in any file (session descriptions, NWB contents of the photometry files). The paper's code reads them from its Zenodo deposit (doi:10.5281/zenodo.7274803, one 60.8 GB zip), which was not opened here.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-syllable-vs-movement-onset", "statement": "The average syllable-associated dLight transient exceeds that associated with movement initiation (P = 0.0006, n = 14 mice).", "source": "Figure 1f", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted in this attempt, for time. The data it needs (dLight, syllable labels, 2D speed for movement initiations) are in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2k-dlight-predicts-sequence-variability", "statement": "A higher-amplitude dopamine transient at a syllable instance is followed by less predictable syllable choices over the next several seconds.", "source": "Figure 2j-l", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted in this attempt, for time. The data it needs are in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3i-optoda-entropy", "statement": "Behavioural sequences right after Opto-DA stimulation are less predictable than after catch trials.", "source": "Figure 3i", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Not attempted; it compares stimulation with catch trials, which the files do not mark (see fig3l-no-kinematic-effect).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed10d-optoda-vigour", "statement": "Opto-DA delivered on the fastest (slowest) quartile of target instances makes later instances faster (slower).", "source": "Results, fourth section; Extended Data Figure 10d", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted in this attempt, for time. The 94 velocity-conditioned files of 9 mice are in the dandiset, with \"Stim Up\" and \"Stim Down\" notes.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-endo-da-influence-consistent", "statement": "Per mouse, the influence of endogenous dopamine on syllable counts and on sequence entropy are correlated (r = 0.69, P = 0.001).", "source": "Figure 4b", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted in this attempt, for time; it builds on the per-mouse lagged analyses of Fig. 2e and 2k.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-endo-da-predicts-learning", "statement": "Mice whose syllable use is more influenced by endogenous dopamine learn more from Opto-DA (r = 0.51, P = 0.001).", "source": "Figure 4c", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted in this attempt, for time. The mice it needs have photometry and closed-loop sessions in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-catch-dlight-predicts-learning", "statement": "Syllables with higher endogenous dLight on catch trials are more reinforced by Opto-DA (r = 0.32, P < 0.001).", "source": "Figure 4f", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Not attempted; it uses dLight on catch trials, which the files do not mark.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-decoding-model", "statement": "A model in which endogenous and exogenous dopamine add predicts held-out syllable choices better than shuffled and noise controls (median r 0.20 against 0.04).", "source": "Figure 4h; Methods, \"Decoding model predicting behaviour from dLight\"", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted in this attempt, for time.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-rl-model", "statement": "A Q-learning agent rewarded by syllable-associated dLight learns a transition matrix similar to the observed one, best when dopamine also transiently raises choice variability.", "source": "Figure 5b-d", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted in this attempt, for time; the paper fitted it on a 128-CPU machine, and its code is in the repository named under inputs.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The closed-loop files mark stimulation onsets but not catch trials (target detections on which stimulation was withheld); the conversion kept only the stimulated detections. Comparisons of stimulation with catch trials (Fig. 3i, 3l, 3m, 4f) cannot be made, and a substitute selection shows stimulation-catch differences in 9 of 12 no-opsin controls." }, { "kind": "metadata_insufficient", "statement": "No file states the genotype or opsin of a mouse. Opto-DA (Ai32) and no-opsin control mice are told apart only by the stimulation site (\"snc (axon)\" or \"ctrl\"), and the dLight+ChrimsonR mice only by their subject names." }, { "kind": "metadata_insufficient", "statement": "Session type (baseline, stimulation, post) and session number are not stored; they must be inferred from free-text descriptions, dates and stimulation pulses. Five files with stimulation are described as recording sessions." }, { "kind": "metadata_error", "statement": "Every closed-loop file states a 635-nm stimulator (Opto Engine MRL-III-635), including the Ai32 (ChR2) mice, which the Methods say were stimulated with 470-nm light." }, { "kind": "metadata_error", "statement": "The dLight-only mice (C57BL/6J in the Methods) carry the subject description \"wild-type DAT-IRES-Cre and Ai32 mice\", the same as the optogenetic mice." }, { "kind": "format_error", "statement": "In 28 photometry and 547 closed-loop files the syllable timestamps are not ascending. In 573 of these 575 the rows are rotated, with one backward step, which is at least 0.95 of the session length in 558 files and 0.635 of it at the least. Sorting by timestamp restores a regular 30-Hz clock (median interval 0.03337 s in every file)." }, { "kind": "format_error", "statement": "Two closed-loop files of mouse 3155 store every syllable frame twice (53,822 and 53,862 repeated timestamps), and have two and three non-ascending steps." }, { "kind": "data_missing", "statement": "14 files of dLight+ChrimsonR mice hold empty syllable series; all list two target syllables." }, { "kind": "data_missing", "statement": "For the dLight+ChrimsonR mice only the 250-ms closed-loop sessions are present; the 2-s and pulsed sessions the Methods describe are not. The dandiset holds 224 DLS photometry files without stimulation (210 with syllables, 193 of them not habituation sessions, 177 of those passing the quality criteria), where the Methods give 379 experiments." }, { "kind": "data_missing", "statement": "The food-reward sessions and the consumption times of Fig. 2a are not in the dandiset." }, { "kind": "selection_undocumented", "statement": "The dandiset includes behaviour-only files for photometry sessions without a dLight series (111 files, among them all files of dls-dlight-6, dls-dlight-8, dms-dlight-7 and dms-dlight-9) and sessions that fail the paper's quality criteria (16 DLS and 11 DMS), with no flag saying which were excluded from the paper." }, { "kind": "other", "statement": "The re-referenced, z-scored dLight trace used by every photometry analysis is not stored; it must be recomputed from the stored dF/F and smoothed reference, whose regression fit is not stored either." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. The header still listed which claims were tested and blocked.", "agreed": 23, "of": 24, "disagreements": [ { "claim": "fig3e-learner-count", "outcome": "not_reproduced", "reason": "7 learners against the paper's 9. All 7 are in the code's list; 3442 (change 47.3) and dls-ai32jr-1 (41.7) fall below the control maximum of 54.5 (vta-nacc-ctrl-6). It asked for the per-target stimulation and baseline counts and the chosen baseline day for these two mice and for vta-nacc-ctrl-6." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run (after author-revise-1, commit 17be4c1), with the conclusion cells and the summary, the helper module, the claims file, the README and this attempt record, and the paper text.", "agreed": 24, "of": 24, "disagreements": [] } ] }, { "id": "000568-valero-2022-01", "dandiset": "000568", "dandiset_version": "0.230705.1633", "paper": "10.1126/science.abm1891", "paper_title": " Probing subthreshold dynamics of hippocampal neurons by pulsed optogenetics", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "runs", "entry": "000568-valero-2022", "entry_title": "Pulsed optogenetics in hippocampal CA1 (Valero et al. 2022)", "description": "Tests the findings of Valero, Zutshi, Yoon and Buzsaki (2022) on dandiset 000568, which holds 28 sessions of CA1 units recorded with uLED probes in four CaMKIIa-Cre::Ai32 mice. Pulse times and laps are in two sessions only, so the light responses during ripples, theta and place fields are tested on those two; the ripple modulation of firing is tested on all sessions. The intracellular recordings and the light intensity levels are not in the dandiset.", "notebooks": [ { "path": "reproduce_valero_2022.ipynb", "title": "Reproducing Valero et al. (2022) from dandiset 000568", "executed": "notebooks/000568-valero-2022/reproduce_valero_2022.html" } ], "outcomes": [ { "claim": "cohort-counts", "statement": "CA1 pyramidal neurons were recorded and probed in four CaMKIIa-Cre::Ai32 mice, 822 pyramidal neurons in all, 43.3 plus or minus 8.37 per session.", "source": "Results, second paragraph", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Under reading (a), all 28 sessions, 4 mice and 48.2 putative pyramidal cells per session (SD 12.18) match, but the total is 1351 against 822. Under reading (b), the 22 sessions naming the uLED protocol, 3 mice, 1047 cells and 47.6 per session. 822 cells at 43.3 per session would be about 19 sessions. With thresholds of 2.5 and 10 Hz the total is 1205 or 1441.", "deviations": [ "Pyramidal cells are units with a baseline rate below 5 Hz, as the files carry no cell type; the paper classified cells by other features.", "The paper does not say which sessions it used; two readings are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-pulse-protocol", "statement": "uLEDs were driven with 20 ms pulses at random sites with randomly variable 20 to 40 ms offsets, so that the stimulation of each site recurred at about 0.3 to 0.6 s intervals.", "source": "Results, second paragraph; Figure 1C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Pulses last 19.87 ms (sess9) and 19.63 ms (sess12). The median interval between pulses of one uLED is 0.281 to 0.383 s for the four uLEDs with at least 1000 pulses, within 0.27 to 0.66 s. The median offset from the end of one pulse to the start of the next is 60.4 and 80.0 ms, outside 18 to 44 ms; 31.8% and 30.2% of offsets fall within 20 to 40 ms, and the 95th percentiles are 241 and 328 ms. Most pulses are not in the files (5.76 and 7.50 deposited pulses per s in PreStim against about 17 to 25 implied by the protocol; in sess9 the offsets fall only near multiples of 20 ms), so the longer offsets span missing pulses and the protocol's offsets cannot be measured from the files.", "deviations": [ "Two sessions of 28, the only ones with pulse times.", "The files hold only part of the pulses, so the offsets between pulses are measured on the deposited ones." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-responsive-fraction", "statement": "Of 822 pyramidal neurons, 611 responded to light from the uLEDs.", "source": "Results, second paragraph; Figure 1E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Under reading (b), all stimulation epochs, 66 of 91 putative pyramidal cells (72.5%, 95% interval 62.2 to 81.4%) respond to at least one uLED. Under reading (a), the PreStim epoch, 57 of 91 (62.6%, 51.9 to 72.6%), outside tolerance. Of 364 unit and uLED tests in PreStim, 68 pass all three parts of the test; on sham onsets (jittered by up to 200 ms, or moved into BaselinePre) none of 364 passes. For reading (b), with the onsets of all stimulation epochs jittered by up to 200 ms, none of 364 tests passes either. No putative pyramidal cell on shank Group3 responds (0 of 17), and that shank's uLEDs are likely among those whose pulses are not in the files. Without Group3, 57 of 74 (77.0%) under (a), within tolerance, and 66 of 74 (89.2%) under (b), above it. The criterion lists (a) first but only (b) matches, so the measured value is that of (b).", "deviations": [ "Two sessions of one mouse (91 putative pyramidal cells), not 822 cells.", "The response test is the one in the first author's later code (HippoCookBook getuLEDResponse.m), with 500 bootstrap sets drawn on a 1 ms grid and shared across units, and a minimum of 1000 pulses per uLED in place of 2000; the paper's own test is in its unavailable Methods.", "Which pulses the paper tested is not stated; two readings are shown and the claim matches under reading (b) only.", "Cells near uLEDs whose pulses are not in the files cannot be tested for a response to them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1i-swr-decrease", "statement": "Light-induced spike responses of individual pyramidal cells decreased during sharp-wave ripples (n = 485 neurons, P < 1e-55, Wilcoxon paired signed-rank test).", "source": "Results, third paragraph; Figure 1, F to I", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "In 57 light-responsive putative pyramidal cells, light minus control rate is 0.30 Hz (median) in windows overlapping ripples and 2.68 Hz outside, lower inside in 49 of 57 (Wilcoxon p = 6.8e-09), and in each session (p = 7.8e-06 and 9.5e-07). As a ratio, 1.25 inside and 2.89 outside (53 of 56, p = 8.6e-10). The paper's n of 485 and P < 1e-55 cannot be reached with two sessions. The control windows, the 20 ms before each onset, are dark under the stated protocol, so the missing pulses do not enter them.", "deviations": [ "Two sessions of one mouse.", "Ripples are the deposited ripple intervals; a window counts as inside a ripple when it overlaps one.", "Control windows are the 20 ms before each pulse with no uLED on." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs10-swr-gain-vs-baseline-rate", "statement": "The firing-rate change of pyramidal neurons during SPW-Rs is negatively correlated with their baseline firing rate (rho = -0.19, P < 1e-7).", "source": "Results, third paragraph (figure S10)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Over 1166 putative pyramidal cells of 24 sessions, the log2 ratio of the rate inside ripples to outside is negatively correlated with the baseline rate (rho = -0.437, p = 1.8e-55). It is negative in every subject (-0.37 to -0.71) and every session, and significant in all sessions but three (fCamk1 sess13 p = 0.12, fCamk3 sess13 p = 0.29, fCamk5 sess14 p = 0.81). This is stronger than -0.19 and outside the tolerance of 0.068. The difference reading gives rho = -0.002 (p = 0.95). Without the two sessions in the analysis whose ripples fail the clock check (the third has under 50 first-epoch ripples), n = 1055 and rho = -0.468; in the 22 sessions whose first epoch is labelled BaselinePre, -0.450; against the rate outside ripples, -0.466.", "deviations": [ "The paper's measure of rate change is in the unavailable supplement; two readings were fixed before the analysis and they disagree.", "The tolerance is the sampling half-width at n = 822, not 10% of the value." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-theta-trough-gain", "statement": "During track running, the light-induced rate gain is largest at the trough of the theta cycle (P < 1e-6, Wilcoxon test).", "source": "Results, fourth paragraph; Figure 2, A and B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "In 57 light-responsive putative pyramidal cells during laps, the gain is 2.04 Hz in the trough half of theta and 2.07 Hz in the peak half (medians), higher at the trough in 22 of 57 cells (Wilcoxon p = 0.14) and significant in neither session. In 60-degree bins the gain is largest 30 degrees after the peak (2.13 Hz). The stored LFP rate is 1250 Hz from 0 s and the LFP ends with the last epoch; ripple-band power at 44 and 27 deposited ripple peaks inside the Maze epoch is 113 and 78 times its mean; spikes of putative pyramidal cells in control windows have a circular mean phase of 128 and 130 degrees, in the trough half; the theta-band LFP averaged around onsets deviates by at most 27.1 and 8.5 against a theta-band SD of 406 and 770.", "deviations": [ "Two sessions of one mouse.", "The LFP channel (largest ripple power), the theta band (6 to 10 Hz) and the half-cycle split are choices made here; the paper's are in its unavailable Methods." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs11-place-cell-fraction", "statement": "More than half of the pyramidal neurons were place cells, 73% of light-responsive and 71% of non-responsive neurons, with no difference between them (P = 0.90, chi-squared test).", "source": "Results, fourth paragraph (figure S11)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "48 of 57 light-responsive (84.2%, 95% interval 72.1 to 92.5%) and 24 of 34 non-responsive (70.6%, 52.5 to 84.9%) putative pyramidal cells are place cells; the paper's chi-squared test finds no difference (p = 0.20), as in the paper. The non-responsive fraction is within tolerance, the responsive one above it. Per session 83% against 56% (sess9) and 86% against 83% (sess12). Over all putative pyramidal cells 79.1% are place cells. With all time without a deposited pulse as control time and the earlier field rule (the round-1 analysis) the fractions are 78.9% and 52.9% with p = 0.018; the control time alone changes 5 cells, the field rule alone 1, both 11. Some non-responsive cells may respond to uLEDs whose pulses are not in the files.", "deviations": [ "Two sessions of one mouse.", "Place fields follow a port of buzcode's bz_findPlaceFields1D with its defaults, on control maps from the windows dark under the stated protocol (the 20 ms before each deposited onset and after each offset), since most pulses are not in the files; the paper's standard definition is in its unavailable Methods. The files do not follow the protocol exactly (3.2% and 3.8% of deposited offsets in PreStim are under 20 ms), so missing pulses may fall in some of these windows." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-infield-gain", "statement": "The light-induced rate increase is higher within than outside the place field (n = 553 place fields, P < 1e-115, Wilcoxon test).", "source": "Results, fourth paragraph; Figure 2, C to E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Over 80 control place fields of 48 light-responsive putative pyramidal cells, gain is 3.95 Hz in the field and 1.37 Hz outside (medians), higher in the field for 61 of 80 (Wilcoxon p = 1e-08) and in each session (p = 9.5e-07 and 0.0018). As a ratio of light to control the in-field value is lower (2.19 against 2.77, p = 4.3e-05), so the increase is larger in hertz but not relative to the control rate.", "deviations": [ "Two sessions of one mouse; 80 fields against 553.", "Control rates come from the windows dark under the stated protocol." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs12-gain-rate-correlations", "statement": "The in-field gain is positively correlated with the out-of-field firing rate (rho = 0.17, P < 1e-5) and with the home-cage firing rate of the neuron (rho = 0.25, P < 1e-7).", "source": "Results, fourth paragraph (figure S12)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Over 80 fields, rho is -0.018 (p = 0.87) for the out-of-field rate and -0.063 (p = 0.58) for the home-cage rate, both outside tolerance. With one field per cell, rho is 0.131 for the out-of-field rate (within tolerance) and -0.003 for the home-cage rate.", "deviations": [ "Two sessions of one mouse; 80 fields against 553." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-place-cells-more-excitable", "statement": "Light responses in the home cage before the track were stronger in place cells than in non-place cells (P < 1e-4, Kruskal-Wallis test).", "source": "Results, fifth paragraph; Figure 3A", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "The PreStim light response (best uLED) has a median of 1.90 Hz in 72 place cells and 1.03 Hz in 19 non-place cells, higher in place cells but not significantly (Kruskal-Wallis p = 0.19; z-scored p = 0.25). It is significant in sess9 (p = 0.027) and not in sess12 (0.94 against 1.19 Hz, p = 0.85). Within halves of the baseline rate neither difference is significant (p = 0.6 and 0.2).", "deviations": [ "Two sessions of one mouse; 19 non-place cells.", "Place cells as in figs11-place-cell-fraction." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-unmasked-fields", "statement": "Optogenetic depolarization revealed place fields in the majority of non-place cells, 289 of 417 (69.3%).", "source": "Results, fifth paragraph; Figure 3, B and C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Under reading (a), 7 of 9 light-responsive non-place cells (77.8%, 95% interval 40.0 to 97.2%) have a light field, 1.6 points above the tolerance of 69.3 plus or minus 6.9; under reading (b), 6 of 19 non-place cells (31.6%, 12.6 to 56.6%), below it and above the 15.8% found in control maps thinned at random to the time of the light maps. Reading (a) rests on 9 cells and its interval includes the paper's value. Its light maps use only each cell's own uLEDs (2.6% to 6.2% of lap time); control maps thinned to that time give a field in 31.7% of draws on average over the 9 cells.", "deviations": [ "Two sessions of one mouse; 19 non-place cells against 417.", "The paper's denominator and its rule for an induced field are in its unavailable Methods; two readings are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-ghost-fields", "statement": "The spatial location of light-induced spikes matches that of spikes without stimulation, both for place fields of place cells (P < 1e-40) and for unmasked place fields of non-place cells, whose sparse control spikes form ghost fields (P < 1e-10).", "source": "Results, fifth paragraph; Figure 3, C and E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "For 70 field directions of light-responsive place cells the light peak follows the control peak (Pearson r = 0.806, p = 3.9e-17). For 14 light field directions of 7 non-place cells r = 0.321 (p = 0.26). In the shuffle variant, 35.7% of unmasked peaks lie within 4.4 cm of the control peak against 14.6% for shuffled pairings (p = 0.014), which is closer to the paper's test against shuffles. 8 of the 14 unmasked field directions come from sess9.", "deviations": [ "Pearson correlation of peak positions in place of the paper's chi-squared test against 500 shuffles, whose details are in the unavailable Methods; a shuffle test is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-light-stability", "statement": "Place fields during light stimulation were more stable between the first and second halves of the session than during control epochs, for both true place fields and unmasked place fields (P < 1e-9 and P < 1e-19, two-way ANOVA).", "source": "Figure 3F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Light maps are not more stable than control maps between laps 11-60 and 71-120 (place fields 0.664 against 0.714, light higher in 28 of 70, p = 0.058; unmasked fields 0.187 against 0.527, 6 of 14, p = 0.39). Against control maps from as many 20 ms control windows as light windows, place fields 0.664 against 0.602 (p = 0.68) and unmasked fields 0.187 against 0.293 (p = 0.67). Control maps from stimulated laps only give the same medians (p = 0.059 and 0.39), as they must, since dark windows lie only next to deposited pulses. The two-way ANOVA finds an effect of condition (p = 0.046), with light the less stable by the medians.", "deviations": [ "Control maps use the windows dark under the stated protocol (19% to 20% of lap time); the paper's control epochs were random 20 ms intervals between pulses, shown as a time-matched variant.", "Wilcoxon tests in place of the paper's two-way ANOVA, which is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-spatial-information", "statement": "Spatial information of control and light-stimulated epochs is correlated, and the light-boosted increase is stronger for unmasked place fields of non-place cells than for place cells (P < 1e-15, Kruskal-Wallis test).", "source": "Figure 3G", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Control and light spatial information are correlated for place fields (rho = 0.655, p = 7.6e-10) and for unmasked fields (rho = 0.574, p = 0.032). The increase is larger for unmasked fields (median 0.03 against -0.03 bits/spike, Kruskal-Wallis p = 0.039), far from the paper's P < 1e-15. Against time-matched control maps both correlations hold (place rho = 0.501, p = 1e-05; unmasked rho = 0.609, p = 0.021), but the increase is negative in both groups (place -0.10, unmasked -0.17) and does not differ (p = 0.3); as a ratio it does not differ either (p = 0.14). The paper's control epochs are random 20 ms intervals between the light pulses, which the time-matched variant follows most closely, and the dark-window control maps are themselves a revision of the criterion's control (all time with no uLED on). Part 1 holds and part 2 does not. Unmasked fields are chosen for a light field and no control field, which favours a larger increase by construction; the paper defines its groups the same way. Changed from reproduced after verification round 3 agreed.", "deviations": [ "Control maps use the windows dark under the stated protocol; time-matched control windows are a variant, under which the larger increase in unmasked fields does not hold." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-swr-cofiring-place-pairs", "statement": "Cofiring of place cell pairs during SPW-Rs in the home cage is positively correlated with their spatial overlap on the track (P < 1e-27), while pairs of a place cell and a non-place cell show no such relationship (P = 0.11).", "source": "Results, sixth paragraph; Figure 4, B and C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Over 1264 place cell pairs, ripple cofiring is correlated with spatial overlap (rho = 0.060, p = 0.032), so part 1 holds, weakly and in sess9 only (0.119, p = 0.0015; sess12 0.019, p = 0.66). Over 698 place and non-place pairs the paper's test finds no correlation (rho = 0.062, p = 0.1), so part 2 holds, but the coefficient is as large as for place cell pairs. Correlation of participation per ripple gives 0.054 (p = 0.056) and 0.072 (p = 0.058).", "deviations": [ "Two sessions of one mouse.", "Cofiring as the Pearson correlation of spike counts per deposited ripple, a choice made here; the paper's measure is in its unavailable Methods." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-light-unmasked-cofiring", "statement": "With light-induced spikes, the relationship between SPW-R cofiring and spatial overlap appears for pairs that include non-place cells (P < 1e-5, Spearman correlation).", "source": "Results, sixth paragraph; Figure 4, C and D (legend panel D)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_valero_2022.ipynb", "notes": "Over 231 pairs of light-responsive place and non-place cells, cofiring is not significantly correlated with the overlap of light maps (rho = 0.075, p = 0.25; sess9 0.108, p = 0.16; sess12 -0.062, p = 0.65). With control maps the same pairs give rho = 0.110 (p = 0.094).", "deviations": [ "Two sessions of one mouse." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1j-light-intensity", "statement": "Stronger light (three intensities) decreased the light-induced response during SPW-Rs, increased the in-field gain of place cells several-fold, and increased the in-field gain of unmasked fields (Figure 1J, Figure 2F, Figure 3D; Friedman tests).", "source": "Figure 1J, Figure 2F, Figure 3D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The pulse series hold one value per uLED in each of the two sessions with pulses (19 in sess9, 62623 to 63599 in sess12, stated as watts), so no pulse has an intensity level, and the other 26 sessions have no pulse series. The paper's other named data location, the Buzsaki Lab Databank, serves data through Globus with an account and no pinned identifier.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1km-intracellular", "statement": "Intracellular recordings in which the membrane potential was varied reproduce the decreased gain during SPW-Rs (five cells in anesthetized rats and five in head-fixed mice, P = 0.002).", "source": "Results, third paragraph; Figure 1, K to M", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds extracellular recordings of four mice only; the intracellular recordings in rats and head-fixed mice are not in it. The lab's data page lists this dandiset for the paper and otherwise points to a Globus endpoint without a pinned identifier.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs9-excitatory-vs-inhibitory-swr", "statement": "During SPW-Rs, excitatory neurons increased their firing rates more than inhibitory neurons.", "source": "Results, third paragraph (figure S9)", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The units carry no cell type, and the no-raw-data files hold no waveforms. A rate threshold separates cells by the very quantity the claim compares, so it was not used for this claim. Waveforms could be taken from the raw signal, but the full files are 17 to 54 GB each and six of them have no raw signal. As a proxy shown in the notebook, units at or above 5 Hz raise their rate inside ripples less than putative pyramidal cells (median log2 ratio 0.75 against 1.19, p = 0.00065); since the ripple gain falls with baseline rate within putative pyramidal cells alone (figs10), this split would show the same without interneurons, so it does not test the claim.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-position-decoding", "statement": "Decoding of position is most accurate from light-boosted spikes of place cells, and light-induced spikes of non-place cells predict position better than control spikes of place cells (P = 0.001, Tukey test).", "source": "Results, fifth paragraph; Figure 3H", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The decoder, its spatial bins, time windows and cross-validation are described in the supplement, which could not be obtained; the main text and legend do not fix them. The data for it (two sessions with laps and pulses) are in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4ef-assemblies", "statement": "ICA assemblies of place cells in the home cage show higher spatial correlation than chance, mixed assemblies of place and non-place cells do not, and with unmasked place fields they reach the level of place-cell assemblies.", "source": "Results, sixth paragraph; Figure 4, E and F", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The ICA assembly detection (bin size, significance of components) and the chance level for spatial correlation are in the unavailable supplement. The legend gives only the member threshold of 2 SD. The data are in the dandiset for two sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4gh-replay", "statement": "Sequential firing of place cells is correlated with spike sequences during SPW-Rs, and the fraction of SPW-Rs with significant trajectories increases when unmasked place fields are included in the template (P < 1e-4, Friedman test).", "source": "Results, sixth paragraph; Figure 4, G and H", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The Bayesian decoding of ripples, the template construction and the shuffle are in the unavailable supplement; the legend gives only 500 shuffles. The data are in the dandiset for two sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "Light pulse times are deposited for 2 of 28 sessions (fCamk1 sess9 and sess12). Twenty other sessions name uLED stimulation in their epochs but hold no pulse series, so their light responses cannot be computed. Laps are also in these two sessions only." }, { "kind": "metadata_error", "statement": "The OptogeneticSeries are stated in watts but hold one value per uLED, 19 in sess9 and 62623 to 63599 in sess12, not a light power (the paper gives 0.02 to 0.1 uW). No light intensity per pulse is stored, so the paper's three intensities cannot be recovered." }, { "kind": "data_missing", "statement": "The files hold pulse series for 6 of the probe's 12 uLEDs (Site3 to Site8), two of them with only 120 to 221 pulses, and most pulses of the protocol are missing. In PreStim the deposited pulses come at 5.76 and 7.50 per s, where the stated protocol implies about 17 to 25; in fCamk1 sess9 the offsets between deposited pulses fall only near multiples of 20 ms, the gaps left by missing pulses. No putative pyramidal cell on shank Group3 responds to any deposited uLED. Time without a deposited pulse therefore cannot be taken as dark." }, { "kind": "other", "statement": "Every session is deposited twice, as a full file and a no-raw-data file; in all 28 sessions the two hold the same units, spike times, ripples and position. The full file of fCamk3 sess20 is named sub-fCamk3_behavior+ecephys+image.nwb, without its session." }, { "kind": "data_missing", "statement": "The full file of fCamk3 sess17 is 28 MB and holds 378 s of raw signal and 6850 s of LFP of a 34621 s session. The six full files of fCamk1 sess13 to sess19 hold the LFP but no raw signal." }, { "kind": "metadata_insufficient", "statement": "Units carry no cell type and the no-raw-data files no waveforms, so pyramidal cells and interneurons cannot be told apart as in the paper." }, { "kind": "metadata_error", "statement": "session_start_time is 2016-03-15 in every file, while the session ids date the recordings to 2020 and 2021." }, { "kind": "metadata_error", "statement": "The linearized position holds values from 0 to 110 cm (the track length) but has a conversion factor of 100, which would put it at 0 to 110 m." }, { "kind": "metadata_insufficient", "statement": "Six sessions (fCamk2 sess1 to sess4, fCamk3 sess13, fCamk5 sess10) name their epochs only by a time stamp, without behavioral paradigm or manipulation. fCamk2 sessions have no position and 0 to 1110 ripples." }, { "kind": "selection_undocumented", "statement": "The dandiset holds 28 sessions and 1351 units with a baseline rate below 5 Hz, where the paper reports 822 pyramidal neurons at 43.3 per session (about 19 sessions). It does not say which sessions the paper used. 14 sessions include CNO or DMSO epochs, which the paper does not describe." }, { "kind": "other", "statement": "In fCamk3 sess13, fCamk3 sess17 and fCamk5 sess10 the deposited ripple intervals mark population bursts weakly (population rate 1.2 to 1.98 times that 1 s later, against at least twice in the other 22 sessions with ripples). fCamk5 sess10 has 217 events with a median length of 109 ms." }, { "kind": "paper_inconsistency", "statement": "The paper gives randomly variable 20 to 40 ms offsets between pulses, the files' description 40 to 60 ms. Measured onset to onset, 30% to 32% of the deposited intervals fall in 40 to 60 ms; measured end to start, 30% to 32% fall in 20 to 40 ms, and most others span missing pulses." }, { "kind": "methods_unavailable", "statement": "The paper's Materials and Methods are in its supplement. This attempt could not obtain the supplement from PMC or the publisher, and the analysis code the paper names (buzcode) is a general toolbox without scripts for its figures." }, { "kind": "paper_inconsistency", "statement": "The paper reports 822 pyramidal neurons of which 73% of light-responsive and 71% of non-responsive neurons were place cells, which leaves about 230 non-place cells, but gives the unmasked fraction as 289 of 417 non-place cells." }, { "kind": "metadata_insufficient", "statement": "The units table of some files lacks the shank column (group_id); columns are spike_times, unit_name, clu_id and, in the others, group_id." } ], "verifications": [ { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper (PMC author manuscript). The verifier did not open NWB files; it tested find_fields and a simulated pulse protocol on synthetic inputs and read the archive's asset list. Its report had no attempt record and gave its own outcome for each claim; all 22 agree with the record as it then stood. The revision changed five outcomes, which round 2 reviews.", "agreed": 22, "of": 22, "disagreements": [] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file and the attempt record, with the paper (PMC author manuscript, saved as paper/PMC9632609_bioc.json and paper/PMC9632609.txt). It read the new find_fields but could not run it, as numpy was not installed. Report in transcripts/000568/verifier-2-report.md. Points not tied to one claim were also answered. The dark-window premise (round-2 remaining point 4) is now printed in the data check (3.8% and 3.2% of deposited offsets in PreStim under 20 ms) and stated in cell 12, the figs11 deviations and the summary. Point 3 (two sessions of one mouse) needs no change beyond what the notes state. Point 5 (Methods) cannot be answered, as the supplement is still unavailable.", "agreed": 21, "of": 22, "disagreements": [ { "claim": "fig3g-spatial-information", "outcome": "partially_reproduced", "reason": "Part 2 rests on p = 0.039 with dark-window control maps. Against time-matched control the increase is negative in both groups and does not differ (p = 0.3). The paper says random intervals (20 ms) between the light pulses served as control epochs, which the time-matched variant follows most closely. The criterion fixed time when no uLED is on, which the revision already replaced, so the main control maps are not the pre-registered ones either, and the selection bias still favours part 2." } ] }, { "date": "2026-10-17", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 3. The one proposed change of outcome (fig3g-spatial-information) and the analysis behind it in the executed notebook after the round-2 revision (cells 51, 59 and 60), with the paper text saved in round 2. Nothing else was reviewed. Report in transcripts/000568/verifier-3-report.md.", "agreed": 1, "of": 1, "disagreements": [] } ] }, { "id": "000582-sargolini-2006-01", "dandiset": "000582", "dandiset_version": "0.251111.2151", "paper": "10.1126/science.1125572", "paper_title": "Conjunctive Representation of Position, Direction, and Velocity in Entorhinal Cortex", "date": "2026-10-13", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code", "model": "not recorded", "protocol": "pilot-0" }, "tier": "agent_verified", "entry": "000582-sargolini-2006", "entry_title": "Grid, head-direction and conjunctive cells by entorhinal layer (Sargolini et al. 2006)", "description": "Tests three conclusions of Sargolini et al. (2006) on dandiset 000582, which holds spike times and tracked positions for 620 cell-sessions from the medial entorhinal cortex of 15 rats. For every cell it computes a grid score, head-direction tuning and speed tuning, with chance levels from time-shifted spike trains, and compares the cell types found in each cortical layer.", "notebooks": [ { "path": "reproduce_sargolini_2006.ipynb", "title": "Reproducing Sargolini et al. (2006) from dandiset 000582", "executed": "notebooks/000582-sargolini-2006/reproduce_sargolini_2006.html" } ], "outcomes": [ { "claim": "layer2-grid", "statement": "Layer II of the medial entorhinal cortex was predominated by grid cells.", "source": "Abstract", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sargolini_2006.ipynb", "notes": "Layer II has the highest grid scores (median 0.33 against 0.10 in the deeper layers). With a grid-score threshold of 0.3, 54% of layer II cell-sessions are grid cells, more than in any other layer. Against the stricter chance level from shuffled spike trains (0.61), 22 of 70 (31%) are, the same as layer III (34%) and above layers V and VI (18% each). Whether grid cells are the majority in layer II depends on the criterion, and the paper's was not available (closed access). The dandiset is described as a sample without saying how cells were selected, and most sessions last 10 minutes.", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "deep-hd-conjunctive", "statement": "In the deeper layers, grid cells colocalized with head-direction cells and with conjunctive grid x head-direction cells.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sargolini_2006.ipynb", "notes": "Head-direction tuning above chance in 58% (layer III), 91% (V) and 73% (VI) of cells against 12% in layer II, which holds within the one rat recorded in both. Conjunctive cells are 62 of 396 in the deeper layers and 2 of 43 in layer II. Uses only the 71 sessions with two tracking LEDs. Counts are of cell-sessions from few rats, so they are not independent.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "speed", "statement": "All cell types were modulated by running speed.", "source": "Abstract", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sargolini_2006.ipynb", "notes": "The correlation of firing rate with running speed has a positive median in every cell type (0.28 to 0.58) against -0.06 for time-shifted spike trains, and 20% to 33% of cells in each type pass the 95th percentile of the shuffles where 5% are expected. Tested for each type as a population, not for each cell.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "Every file's session description says the enclosure was 1 x 1 m, but in 23 of the 118 sessions the tracked positions span 1.5 to 2.5 m." }, { "kind": "metadata_error", "statement": "The session descriptions say position is given for two LEDs, but 47 of the 118 sessions have one, so head direction cannot be computed for 167 of 620 cell-sessions." }, { "kind": "identifier_missing", "statement": "No identifier links a cell across sessions, so the same cell may be counted more than once." }, { "kind": "selection_undocumented", "statement": "The dandiset is described as a sample of the paper's cells without saying how they were selected." }, { "kind": "methods_unavailable", "statement": "The paper is not open access and the dandiset does not give the analysis parameters, such as the criterion for a grid cell." } ], "verifications": [ { "date": "2026-10-13", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "First draft, before the enclosure-size fix. The author's conclusions were withheld.", "agreed": 2, "of": 3, "disagreements": [ { "claim": "layer2-grid", "outcome": "not_reproduced", "reason": "In that draft, 13 of 71 layer II cell-sessions passed the grid threshold, below layer III. The verifier also pointed out that the 1 m enclosure was assumed and never checked. That was a real error; 23 sessions used larger enclosures and the rate maps were clipping them. The attempt was corrected." } ] }, { "date": "2026-10-13", "kind": "agent", "by": "The same independent agent, second round", "reviewed": "The corrected notebook, with the author's conclusions.", "agreed": 3, "of": 3, "disagreements": [] } ] }, { "id": "000625-geiller-2020-01", "dandiset": "000625", "dandiset_version": "0.231114.0019", "paper": "10.1016/j.neuron.2020.09.013", "paper_title": "Large-Scale 3D Two-Photon Imaging of Molecularly Identified CA1 Interneuron Dynamics in Behaving Mice", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-4" }, "tier": "agent_verified", "entry": "000625-geiller-2020", "entry_title": "Molecularly identified CA1 interneurons during random foraging (Geiller, Vancura et al. 2020)", "description": "Tests the findings of Geiller, Vancura et al. (2020) that can be tested on dandiset 000625, which holds three random-foraging sessions of one mouse with 231 interneurons, 74 of them assigned one of the paper's six subtypes. It checks the imaging clock against the behaviour, then measures each interneuron's correlation with running speed, run-stop responses, spatial selectivity, position decoding and the stability of tuning curves within and across sessions. The sharp-wave ripple, novel-context, goal-oriented learning and VIP experiments are not in the dandiset.", "notebooks": [ { "path": "reproduce_geiller_2020.ipynb", "title": "Reproducing Geiller, Vancura et al. (2020) from dandiset 000625", "executed": "notebooks/000625-geiller-2020/reproduce_geiller_2020.html" } ], "outcomes": [ { "claim": "fig1-cells-per-mouse", "statement": "About 227 interneurons were imaged per mouse (226.6 \u00b1 27.3, mean \u00b1 std over 16 mice), and 121.0 \u00b1 28.4 per mouse were assigned a putative subtype.", "source": "Results, first section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "The mouse has 231 ROIs, inside 226.6 \u00b1 27.3 (199.3 to 253.9). 74 ROIs carry one of the six subtypes and 83 are not labelled UNIDENTIFIED; both are below 121.0 \u00b1 28.4 (92.6 to 149.4).", "deviations": [ "One mouse, compared with the paper's mean and standard deviation over 16 mice.", "Two readings of \"assigned a subtype\" were allowed, as the labels NOTHING and UNIDENTIFIED are not explained." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1-depth-distribution", "statement": "The layer distribution of each subtype along the CA1 depth axis is consistent with earlier anatomical studies.", "source": "Figure 1F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The files hold no depth or 3D coordinates of the ROIs. The plane segmentation has only id and pixel_mask (x, y, weight, no z); the masks lie on a strip of the 231 cropped frames side by side, and the imaging plane's origin_coords and grid_spacing are placeholders. The paper's Z-stacks and coordinates are not public as far as the dandiset and the paper's repository show.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-most-positive", "statement": "The majority of interneurons were positively correlated with running velocity, and about 10% were negatively correlated, across all subtypes (156 negative and 1429 positive in Figure 2D).", "source": "Results, locomotion section; Figure 2C, 2D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "Averaged over sessions, 90.5% of the 74 ROIs in the six subtypes are positively correlated with velocity and 0.095 negatively, inside 0.088 to 0.108. Among all 228 imaged ROIs 96.5% are positive and 0.035 negative, outside the tolerance. The claim holds under the six-subtype reading, and only because r is averaged over sessions; per session that reading gives 0.055, 0.143 and 0.164, all outside the range. Per session the all-ROI reading gives 0.065, 0.111 and 0.089, in range in session 21322 only. The sign of r changes between sessions in 17 of the 74 subtyped ROIs (7 of 15 CCKC); 18 are negative in at least one session and 7 on average. The result is at the edge of the range; 6 or 8 of 74 would fall outside it.", "deviations": [ "One mouse, three sessions, where the paper has seven mice.", "Frame rates for sessions 21324 and 21322 fitted from the data; on the stated clock 28% of ROIs in session 21322 are negatively correlated.", "Velocity smoothed with a Gaussian of 0.5 s, a width the paper does not give; 0 and 1 s change the averaged fractions by no more than 0.005 under either reading, and a per-session fraction by at most 0.014.", "Correlations averaged over sessions on the assumption that the ROI index is the same cell, which the data are consistent with but do not show.", "The denominator can be read two ways; the six-subtype reading matches and the all-ROI reading does not." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-cck-negative", "statement": "Negatively correlated cells were significantly enriched in CCKC, where nearly half of cells were more active during immobility.", "source": "Results, locomotion section; Figure 2B, 2C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "6 of 15 CCKC (0.40) are negatively correlated against 1 of 59 cells in the other five subtypes, one-sided Fisher exact p = 0.00017. By session the CCKC fraction is 0.13, 0.50 and 0.43.", "deviations": [ "One mouse, 15 CCKC, where the paper has 44 from seven mice.", "The threshold of 0.35 for \"nearly half\" is ours." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-subtypes-differ", "statement": "The correlation with velocity differs between the six subtypes (one-way ANOVA, p < 1e-10, with Tukey's post hoc test).", "source": "Figure 2C legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "One-way ANOVA across the six subtypes gives p = 0.0015. Tukey's test places the difference with CCKC, lower than PVBC (p = 0.0009) and IvC/NGFC (p = 0.005). Per session the ANOVA is significant in one session of three. The paper's p < 1e-10 rests on seven mice and is not reached here.", "deviations": [ "One mouse; significance threshold 0.05 in place of the paper's reported p-value." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-ngfc-less-modulated", "statement": "IvC/NGFC were less modulated by locomotion than other subtypes.", "source": "Results, locomotion section; Figure 2C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "Averaged over sessions IvC/NGFC have a mean correlation of 0.511 against 0.484 for PVBC, SomC, BiC and AAC pooled (one-sided Mann-Whitney p = 0.58), and the same for the absolute correlation. Session 21324 alone shows a lower correlation for IvC/NGFC (0.368 against 0.525, p = 0.005); the other two sessions do not.", "deviations": [ "One mouse with 13 IvC/NGFC, where the paper has 119.", "The comparison group (PVBC, SomC, BiC and AAC pooled) and the test are ours." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-negative-cells-in-oriens", "statement": "Negatively correlated cells were enriched in stratum oriens and positively correlated cells in stratum pyramidale.", "source": "Figure 2D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the depth of each ROI, which the files do not hold.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "s2-lags", "statement": "The activity of positively correlated cells followed changes in velocity by up to several seconds, while the activity of negatively correlated cells was more tightly linked in time to changes in velocity.", "source": "Results, locomotion section (Figure S2)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "Positively correlated ROIs lag velocity (median -1.67 s), as stated. The 8 negatively correlated ROIs have a larger median absolute lag (2.06 s against 1.67 s, one-sided p = 0.60), and the same direction holds in each session taken alone. Lags are averaged over sessions even where the sign of r changes; keeping only ROIs with the same sign in every session leaves 1 negatively correlated ROI, too few to test. Figure S2 itself was not available.", "deviations": [ "One mouse; the paper's Figure S2 was not available, so the criterion rests on the Results text.", "Lags depend on imaging and behaviour starting together at time 0, which the files state and which could not be checked independently." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "s2-cck-run-stop", "statement": "Run-start and run-stop responses show that immobility-triggered activation is specific to CCKC.", "source": "Results, locomotion section (Figure S2)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "At run stops the other five subtypes drop by 0.06 to 0.10 dF/F while CCKC stay flat on average (-0.003), a significant difference (one-sided Mann-Whitney p = 0.0009 at separations of 3, 5 and 10 s). CCKC do not rise on average, which the criterion requires. The 6 negatively correlated CCKC rise (0.084) and the other 9 fall (-0.061). By session the mean CCKC response is -0.005, 0.024 and -0.023, while every other subtype falls in every session (-0.021 to -0.173); the CCKC negatively correlated in a session rise in all three (0.019, 0.123 and 0.102).", "deviations": [ "One mouse; event separation of 5 s chosen for \"several seconds\", with 3 and 10 s shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "s3-subtype-classification", "statement": "A deep network classified PV-expressing, SOM-expressing, CCK and IvC/NGFC cells from dF/F, velocity and depth with accuracies of 64, 71, 60 and 59%.", "source": "Results, machine-learning section (Figure S3)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The reported accuracies come from a network trained on cells pooled from the paper's mice with depth as a feature. The dandiset holds one mouse (74 identified cells, 13 to 33 per merged class) and no depth. A dF/F-only network could be trained on this mouse, but it would not test the reported accuracies. The code is public (TensorFlow 2.1, Keras 2.3.1); its data files are not.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-swr-pvbc-vs-somc", "statement": "During sharp-wave ripples PVBC were generally strongly modulated while most SomC were not.", "source": "Figure 3D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The ripple experiments used LFP and 40 Hz imaging of about 30 cells in four other mice. The dandiset holds no LFP and no 40 Hz sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-swr-bimodal", "statement": "AAC and BiC showed bimodal modulation during sharp-wave ripples, and all subtypes but CCKC and IvC/NGFC split into a modulated and a non-modulated group.", "source": "Figure 3E, 3F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As for fig3-swr-pvbc-vs-somc.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-fraction-spatial", "statement": "17.5 \u00b1 6.4% (mean \u00b1 sem over 6 mice, 3 sessions each) of interneurons, blind of subtype, passed the test for significant spatial selectivity.", "source": "Results, spatial section; Figure 4", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "With the paper's rule, including a peak above 100% dF/F, 1.0% of ROIs are selected on average over sessions, since only 1.1% of ROIs have a tuning curve reaching 1.0 dF/F. Without the peak rule 69.8% are selected, against 8.6% on a surrogate with dF/F rotated against behaviour. Neither reading is within 17.5 \u00b1 6.4%. A peak rule of 50% dF/F gives 13.0%, but that threshold is not the paper's. The paper states no false-positive rate for the rule.", "deviations": [ "One mouse, three sessions, where the paper has six mice with three sessions each.", "Fields may wrap around the end of the belt (not stated in the paper); without wrapping the rule without the peak selects 66.0%.", "The belt is 2.11 m long in the data, divided into 100 bins of 2.11 cm, where the paper has 2 m and 2 cm bins.", "The dF/F in the files may not be scaled as the paper's was; this cannot be checked." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-fraction-negative", "statement": "12.7 \u00b1 8.3% of interneurons (mean \u00b1 sem) had negative spatial selectivity, slightly fewer than had positive selectivity.", "source": "Results, spatial section (Figure S5)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "On average 66.4% of ROIs have a negative field (47.0%, 74.5% and 77.7% by session), against 10.8% on the surrogate and 12.7 \u00b1 8.3% in the paper. Under the paper's rule the two kinds of field are coupled, as a strong field raises the rotated shuffles at every bin. On synthetic cells, a cell with only a positive field is also flagged negative, and a cell with only a negative field is flagged positive under the rule without the peak. With the positive rule without the peak, 55.8% of ROIs on average have both kinds, 10.6% only a negative field and 13.9% only a positive one. The coupling explains part of the 66.4%, not all of it; 78.4% of ROIs with a positive field have a negative field, and so do 37.7% of ROIs without one, about 3.5 times the surrogate rate. Counting only ROIs with a negative field and no positive field gives 10.6%, inside the paper's range, but that variant depends on the positive rule without the peak (65.3% with the peak rule), excludes real negative cells flagged positive, and was chosen after the result, so the outcome is kept.", "deviations": [ "As for fig4-fraction-spatial." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-decoding", "statement": "Position decoded from the small subset of spatially selective interneurons was about as accurate as from all interneurons, and more accurate than from as many randomly chosen interneurons or with position shuffled.", "source": "Figure 4D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "The criterion holds in one session of three. In 21324 the 162 selected ROIs give an error of 13.8 cm, against 13.2 cm from all ROIs, 14.4 cm from random subsets and 48.7 cm with position shuffled. In 21333 the 118 selected ROIs do no better than random subsets (25.2 against 24.8 cm). In 21322 the 6 peak-rule ROIs give 30.3 cm against 15.4 cm from all ROIs. Shuffling position brings the error to about chance (49 to 53 cm, chance 52.7 cm) in every session, and all ROIs decode position with errors of 13 to 21 cm.", "deviations": [ "The selected subset is not small in two sessions (118 and 162 ROIs), because the peak rule selects fewer than 5 ROIs there and the rule without the peak is used.", "A one-vs-one linear SVM (scikit-learn SVC, C = 1); the paper names a linear SVM without the multi-class scheme or penalty.", "Shuffled position made by rotating dF/F against position by at least 60 s, three draws; ten random subsets." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-bic-recurrence", "statement": "BiC had a higher probability than other subtypes of being spatially modulated again in other sessions.", "source": "Figure 4E", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The dandiset has 3 BiC, below the 5 the criterion requires; the paper had 50.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-selectivity-no-difference", "statement": "The selectivity index of spatially selective cells did not differ between subtypes (one-way ANOVA, p = 0.35).", "source": "Figure 4F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "One-way ANOVA across the six subtypes of the selectivity index of selected cells gives p = 0.17, so no difference is found. Subtype means range from 0.012 to 0.033 with a standard deviation of 0.020 across cells. The tuning curves of the selected subtyped cells have a median minimum of 0.158 dF/F and a median maximum of 0.255; subtracting each curve's minimum raises the median index from 0.016 to 0.307. The test compares near-flat curves and has little power.", "deviations": [ "Selection without the peak rule in two sessions, as for fig4d-decoding, so the cells are many more than the paper's spatially selective cells." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-pvbc-more-stable", "statement": "Spatially selective PVBC had a more stable within-session recruitment (odd-even lap correlation of tuning curves) than spatially selective SomC.", "source": "Figure 4H", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "For 22 spatially selective PVBC and 9 SomC, the mean odd-even correlation is 0.678 and 0.736 (unpaired t-test p = 0.42); SomC are higher in each session where both are present.", "deviations": [ "Selection as for fig4d-decoding.", "Each cell's correlation averaged over the sessions in which it was selected." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "s6-within-session-order", "statement": "Within-session stability of tuning curves differed between subtypes, PVBC showing the highest and CCKC the lowest odd-even correlations.", "source": "Results, spatial section (Figure S6A, S6B)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "CCKC have the lowest mean odd-even correlation (0.500). PVBC (0.598) are second to SomC (0.606). The one-way ANOVA across the five subtypes with at least 5 cells gives p = 0.56, so the statement that subtypes differ does not hold here.", "deviations": [ "One mouse; Figure S6 was not available, so the criterion rests on the Results text." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "s6-later-lower-above-chance", "statement": "Tuning curve correlations of the same cells after 1 hour and after 24 hours were lower than within-session correlations, and still higher than chance.", "source": "Results, spatial section (Figure S6I)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_geiller_2020.ipynb", "notes": "Across-session correlations are lower than within-session ones in every pair (0.22 against 0.61 for the same-day pair, Wilcoxon p = 4e-07; 0.06 and 0.14 for the two-day pairs). Above chance holds only for the same-day pair with identities shuffled among all cells (p = 0.047), not with shuffles within subtype (p = 0.10), and for neither two-day pair (p = 0.075 and 0.53).", "deviations": [ "Sessions 2.5 h and 54 to 56 h apart stand in for 1 h and 24 h. The order rests on the stated start times, which put 21333 first although its id is the highest; nothing else in the files dates the sessions.", "The ROI index is taken as the same cell across sessions; tuning curves of the same index agree above a shuffled null only for one pair, so a failure here may reflect the ROI mapping." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-context-decorrelation", "statement": "Interneuron tuning curves decorrelated on exposure to a novel belt, more than with the passage of time, and context could be decoded from population activity.", "source": "Figure 5B, 5C, 5D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "All three sessions are random foraging; no novel-belt session is included, and the files do not name the belt.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-novel-context-decrease", "statement": "PVBC, SomC, BiC and AAC decreased their activity in the first laps on a novel belt; CCKC were not modulated.", "source": "Figure 5F, 5H", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As for fig5-context-decorrelation.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-reward-somc-bic", "statement": "In goal-oriented learning, SomC and BiC had higher reward modulation indices than other subtypes.", "source": "Figure 6D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No goal-oriented learning session and no lick record are included.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-old-zone", "statement": "After the reward zone moved, SomC and BiC activity increased at the old zone above chance, and this decreased over the session.", "source": "Figure 6G, 6H", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As for fig6-reward-somc-bic.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-vip-subtypes-immobility", "statement": "VIP+/CCK+ and VIP+/M2R+ cells were negatively correlated with velocity, and all ISI subtypes positively.", "source": "Figure 7C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "These cells come from VIP-Cre mice and strategy 3 VGAT-Cre mice; the dandiset's mouse tg19 is a strategy 1 mouse, without VIP, CR or M2R staining.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-isi-correlations", "statement": "VIP+/CR- cells and type III ISIs were less correlated with SomC and BiC than with PV+ cells.", "source": "Figure 7H, 7I", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As for fig7-vip-subtypes-immobility.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The imaging rate is stated as 5.7981 Hz for all three sessions. For sessions 21324 and 21322 that makes imaging 680 s long against 900 s and 879 s of behaviour, and the population activity does not follow running (r = 0.16 and 0.09). Rates of 4.395 and 4.385 Hz give r = 0.72 and 0.87, decode running at 0.94 and 0.89 balanced accuracy, and make all three sessions about 898 s long. Session 21333's stated rate fits." }, { "kind": "metadata_error", "statement": "The unit of the dF/F series is given as lumens; the values are dF/F fractions." }, { "kind": "data_missing", "statement": "The Fluorescence series is the same HDF5 object as the DfOverF series, so the raw fluorescence the description lists is not in the files." }, { "kind": "metadata_error", "statement": "The description of the subtype column reads \"Recording location in Middle Earth\", and the subtype table has 232 rows for 231 ROIs (id 231 has no ROI)." }, { "kind": "metadata_insufficient", "statement": "The labels NOTHING and UNIDENTIFIED, the label \"AAC (RIGHT CELL)\", and the reward and water intervals have no description." }, { "kind": "identifier_missing", "statement": "Nothing states that a ROI index refers to the same cell in every session. The data are consistent with it (velocity correlations of the same index agree across sessions above a shuffled null) but tuning curves agree above the null for only one pair of sessions." }, { "kind": "data_missing", "statement": "The files hold no depth or position of the ROIs in the imaged volume, which several of the paper's analyses use, and no lick record." }, { "kind": "metadata_error", "statement": "All three sessions are described as \"session 1 of 4\", and the experiment description names four random-foraging sessions; only three are in the dandiset. The session ids (21322, 21324, 21333) and the start times (21333 two days before the other two) give different orders, and nothing else in the files dates the sessions." }, { "kind": "metadata_insufficient", "statement": "The pixel masks lie on a strip of the 231 cropped frames side by side (x from 0 to 10625), the imaging plane's origin_coords (0, 0) and grid_spacing (50, 50 um) are placeholders, and there are no reference images, so a ROI has no position in the field of view or in depth." }, { "kind": "selection_undocumented", "statement": "The dandiset holds one of the paper's 16 mice and only its random-foraging sessions, without saying which part of the paper it covers." }, { "kind": "metadata_error", "statement": "The emission wavelength is given as 920 nm, equal to the excitation, and the subject's age is P60D in sessions two days apart, where the paper gives 3 to 5 months." }, { "kind": "metadata_insufficient", "statement": "The description lists raw images of individual cropped ROIs, but each file holds a single cropped series (33 x 46 or 25 x 46 pixels) without saying which ROI it shows." }, { "kind": "other", "statement": "With the paper's place-field rule, which requires a peak above 100% dF/F, 1.0% of ROIs qualify, as only 1.1% of tuning curves reach 1.0 dF/F. The dF/F in the files may be scaled or smoothed differently from the paper's." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module, the claims file and the paper's full text (PMC7736348). The verifier checked the archive's version and asset metadata through the DANDI REST API, and ran synthetic checks of place_fields, run_events, sparsity_index, velocity_correlation, decode_position and lap_tuning.", "agreed": 26, "of": 26, "disagreements": [] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook after the first revision, with the conclusion cells and the summary, the helper module, the claims file, the README, the attempt record and the paper's full text (PMC7736348).", "agreed": 26, "of": 26, "disagreements": [] } ] }, { "id": "000691-scherrer-2023-01", "dandiset": "000691", "dandiset_version": "0.260827.1358", "paper": "10.1038/s41592-023-01806-1", "paper_title": "An optical design enabling lightweight and large field-of-view head-mounted microscopes", "date": "2026-10-17", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000691-scherrer-2023", "entry_title": "Imaging thousands of neurons in a freely moving mouse with a large-FOV head-mounted microscope (Scherrer et al. 2023)", "description": "Tests the findings of Scherrer, Lynch, Zhang and Fee (2023) that can be tested on dandiset 000691, which holds one session of one mouse imaged with the large-FOV head-mounted microscope while it explores a looped maze, with 2948 EXTRACT footprints and a behaviour video. It counts the footprints, tracks the mouse from the video, decodes its position and direction from the activity, maps local decoding across the field of view, looks for footprints with localized activity and for the spread of coactive populations, and tests the illumination profiles of Extended Data Fig. 2 on images in the paper's code repository. The other mice, the birds and the optical tests are not in the dandiset.", "notebooks": [ { "path": "reproduce_scherrer_2023.ipynb", "title": "Reproducing Scherrer et al. (2023) from dandiset 000691", "executed": "notebooks/000691-scherrer-2023/reproduce_scherrer_2023.html" } ], "outcomes": [ { "claim": "abstract-thousands-of-neurons", "statement": "The large-FOV microscope images thousands of neurons at once in a freely behaving mouse.", "source": "Abstract; Extended Data Fig. 6a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "All 2948 footprints have a trace above zero at some time; no two have traces correlated above 0.77, so near-duplicate merging leaves 2948. The mouse visits all four arms and runs 48.5 loop lengths during the 1081 s of imaging that overlap the tracked video. Tracking has 2 steps above 40 px between video frames (one glitch at 1064.8 s) and 55 frames with a blob under 50 px; leaving them out changes the arm of 0.05% of imaging frames and the octant of 0.06%.", "deviations": [ "The count is of EXTRACT footprints before the paper's curation (2382 kept); the dandiset does not mark the curated set." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6a-curated-footprints", "statement": "In the mouse with the 4 mm cranial window shown in the main figure, 2382 footprints remain after curation.", "source": "Extended Data Fig. 6a", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The dandiset holds 2948 footprints, the number the preprint gives for the extraction before curation, and its plane segmentation has no column that marks the 2382 kept. The selection is in the paper's Academic Torrents deposit (supporting_data/2021-07-26_isgood.mat and extract_curated.mat, infohash aa2a3d2f5ff0b3974871db47db57bc3dabf3c192); no peer connected in two attempts of 2.5 and 4 minutes from this environment, so it could not be fetched.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6bcd-other-mice", "statement": "Three other mice (3 mm and 4 mm windows) gave 1029, 401 and 112 footprints.", "source": "Extended Data Fig. 6b to 6d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds one mouse (4mm-mouse-1). The Academic Torrents deposit the paper names lists files of the same session only (2021-07-26), and no other dandiset of this paper was found.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed5-songbirds", "statement": "The weight-optimized microscope images hundreds of neurons in juvenile songbirds (46, 177 and 225 curated footprints in three birds).", "source": "Abstract; Extended Data Fig. 5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No bird data in the dandiset or in the Academic Torrents deposit, whose file list holds only the mouse session.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "abstract-kiloscope-fov", "statement": "The microscope optimized for field of view has a field of view of about 4 mm.", "source": "Abstract", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The NWB file gives no pixel size (no grid spacing in the imaging plane). Frames are 808 x 608 pixels; at the 5.94 um per pixel of the paper's code they would be 4.80 x 3.61 mm, and the footprint centroids span 3.09 x 3.31 mm. The pixel size comes from the code, so this does not test the claim on the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "abstract-weights", "statement": "The two microscopes weigh 1.4 g (large FOV) and 1.0 g (weight-optimized, 1.0 mm FOV).", "source": "Abstract", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Weights are hardware measurements; no data on them are in the dandiset or the paper's deposits.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1-ed4-resolution", "statement": "Images of a USAF 1951 target resolve elements of 2.19 um line width with the Featherscope and 4.38 um with the Kiloscope, and 2.2 um with Kiloscope optics on a sensor with 1.4 um pixels.", "source": "Extended Data Fig. 1b, 1e and 4b", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The USAF target images are not in the dandiset, the Academic Torrents deposit or the code repository (which holds bead images for a point spread function analysis whose numbers are in the main text, not available here).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3-adc", "statement": "The onboard analog-to-digital converter records test tones with a root-mean-square residual of 0.2% of full scale.", "source": "Extended Data Fig. 3", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The test recordings of the analog-to-digital converter are not in the dandiset or the paper's deposits.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed8-coactive-distributed", "statement": "The footprints that take part in a large correlated event of each NMF component are spread across the field of view.", "source": "Extended Data Fig. 8", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "For all 8 components the event has 196 to 320 active footprints, more than half of the component's members, with a spread of 0.945 to 1.055 times that of all footprints (0.98 mm) and a 90th percentile of pairwise distance of 2.05 to 2.29 mm. Active thresholds of 0.3 and 0.7 also give 8 of 8. The best of 4 NMF replicates was kept (errors 97.55 to 97.58). Two events (80.4 and 122.9 s) fall in the opening 153 s the behaviour analysis leaves out; with event times from 153 s on, 8 of 8 pass (spread ratios 0.94 to 1.05). The test is weak. In 100 random 50 s windows, the median fraction of members active is 0.399 to 0.519, and the event's fraction (0.568 to 0.851) is above the 95th percentile of random windows for 6 of 8 components. Random sets of footprints of the same size have spread ratios of 0.951 to 1.042 (5th to 95th percentiles), so any set this large passes the criterion's half. The event's spread ratio lies within its own component's random range for 3 of 8 components, below it for 2 (0.945 and 0.956, against 5th percentiles of 0.962) and above it for 3 (1.042, 1.055 and 1.050, against 95th percentiles of 1.037, 1.042 and 1.036).", "deviations": [ "All 2948 footprints in place of the 2382 curated ones.", "Event times are each component's largest temporal weight; the code sets them by hand.", "Distances use the code's 5.94 um per pixel, which the dandiset does not state; the outcome uses ratios and does not depend on it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-quadrant-direction-decoding", "statement": "The mouse's position in the maze (quadrant) together with its direction of movement can be decoded from the activity of the imaged population.", "source": "Figure 2 (legend not available); Extended Data Fig. 9a (\"in this case, direction is not coded\") and Fig. 10a; quadrant_direction_decoding.m", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "Median class accuracy 0.415 over 50 decoders (0.304 to 0.604), chance 0.125, 95th percentile of 50 shifted-label decoders 0.145; all 50 exceed it. 3.32 times chance; the preprint's text says at least four times chance, a number not used here as the version of record's text was not available. Six of eight classes reach 0.443 to 0.594, two only 0.236 and 0.239. On all frames, without the running selection, 0.348 against a null 95th percentile of 0.127. The SGD solver stops far from the optimum of its objective (2.04 to 3.21 on six splits, against 0.086 to 0.118 for an exact solver at its limit of 10,000 iterations). On the same splits the exact solver gives 0.262 to 0.318 for three real decoders and 0.131 to 0.164 for three with shifted labels, so the claim also holds with it.", "deviations": [ "Position tracked here from the video (the paper's tracking output is not in the dandiset), in the unrotated frame, with the loop's sides at the 2nd and 98th percentiles of position.", "All 2948 footprints in place of the 2382 curated ones.", "scikit-learn's SGD classifier (hinge loss, ridge alpha equal to the code's lambda, 10 passes) in place of MATLAB's fitcecoc with templateLinear, whose default for more than 100 predictors is 10 passes of dual SGD; 50 decoders in place of 200.", "The legend of Figure 2 was not available, so the claim is stated from the Extended Data legends and the code." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9b-octant-decoding", "statement": "Position within the maze can be decoded with octant resolution from the activity.", "source": "Extended Data Fig. 9a and 9b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "Median class accuracy 0.313 over 50 decoders (0.211 to 0.416), chance 0.125, null 95th percentile 0.144; all 50 exceed it, and each octant's mean accuracy (0.236 to 0.499) is above chance. On six splits fit by both solvers, SGD stops at objectives of 3.89 to 6.18 and the exact solver at 0.071 to 0.094 (at its limit of 10,000 iterations in all six); the exact solver gives 0.220 to 0.292 for three real decoders and 0.092 to 0.145 for three with shifted labels, so the claim also holds with it.", "deviations": [ "As for fig2-quadrant-direction-decoding." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9c-local-decoding-map", "statement": "Decoders that use the 32 footprints closest to a point, within 270 um, decode octant position significantly (Benjamini-Hochberg false discovery rate 5%) in parts of the field of view, and accuracy differs across the field of view.", "source": "Extended Data Fig. 9c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "With 32 footprints within 270 um (45 px), 150 grid points qualify and 18 (12%) are significant at Benjamini-Hochberg 5%, with scores of 0.112 to 0.187 (range 0.075, where the criterion asks for 0.05). Scores over all points 0.068 to 0.187, median 0.125, against null means of 0.065 to 0.123. The outcome depends on the solver. With 10 passes of SGD, as in round 1, on the same points and seeds, 1 point is significant and the criterion is not met; at four points SGD stops at objectives of 19.8 to 68.9 where the exact solver reaches 1.976 to 2.000, close to the 2.0 of predicting every class absent, so the scores rest on weak classifiers. liblinear reached its limit of 10,000 iterations in 2268 of 3000 fits. Null standard deviations per point 0.018 to 0.046 (5th to 95th percentile) from 10 shifted decoders; a point alone needs z above 3.40, and the smallest z among the significant points is 2.53. A Welch t-test of the 10 real against the 10 shifted decoders marks 80 points significant (range 0.079), and 5 with SGD (range 0.052). With the code's 64 footprints within 50 px, on a 60 px grid, 22 of 34 points are significant (scores 0.141 to 0.211, range 0.070), and 32 with the t-test. The exact fits stop at an iteration limit, so the counts can differ slightly between machines.", "deviations": [ "The legend says 32 footprints within 270 um; the code uses 64 within 50 pixels. The legend is followed for the outcome and the code's choice is shown as a variant.", "The paper does not describe its significance test. Here, 10 decoders and 10 shifted-label decoders per point and a one-sided z-test, chosen before the analysis.", "Local decoders are fit by liblinear (LinearSVC) on the same objective, as MATLAB's default for 100 or fewer predictors is BFGS run to convergence; liblinear also penalizes the intercept, weakly. Round 1 used 10 passes of SGD here, which is shown as a variant.", "A 30 pixel grid where the code uses 5 pixels; all 2948 footprints in place of 2382; position as for fig2-quadrant-direction-decoding.", "The code's variant is run on a 60 pixel grid where the criterion says 40; on the 40 pixel grid the notebook took 32 minutes on four cores, over the 30 minute limit." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed10-localized-activity", "statement": "Some footprints have activity localized to subregions of the maze.", "source": "Extended Data Fig. 10", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "100 of 2948 footprints (3.4%) have an entropy over linear position below all 100 shifted values, against 29 expected (binomial p = 4.5e-25); 448 against 175 at a looser threshold. For the 100, the entropy is 0.20 to 0.90 bits below the shifted mean (5th to 95th percentile), out of a maximum of 6.64 bits. The binomial test treats footprints as independent, but the same 100 shifts serve every footprint; treating each shifted copy in turn as the observed data gives counts with a median of 28, a 95th percentile of 54 and a maximum of 62, and none of the 100 copies reaches 100.", "deviations": [ "The paper selected its examples by eye and shows two-dimensional maps; here a test over all footprints on linear position, with the entropy measure of place_cells.m.", "All 2948 footprints in place of 2382; position as for fig2-quadrant-direction-decoding." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed2b-featherscope-flat-illumination", "statement": "For the Featherscope, the axicon correction optics give a flat signal intensity profile across the field of view, where total vignetting (optical vignetting with Gaussian illumination) makes the signal fall toward the edges.", "source": "Extended Data Fig. 2b", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "At 0.4 mm the corrected profile is 0.742, total vignetting 0.342 and optical vignetting 0.628; the corrected profile is higher, but falls below 0.8 (minimum 0.742 over 0 to 0.4 mm). The minimum is 0.785 out to 0.38 mm and 0.698 out to 0.42 mm; with the centre moved by 100 um it is 0.626 to 0.867, and 0.766 about the image centre.", "deviations": [ "The radius of 0.4 mm and the level of 0.8 that define \"flat\" were chosen here; the legend gives no number." ], "disagreed": false, "data": "elsewhere", "where": "GitHub FeeLab/Feescope-Paper-Code at commit d596646b16a505907203828d8026feb7736ca69c, folder sf3/feather (images of a thin layer of fluorescent dye)", "proposed": null }, { "claim": "ed2c-kiloscope-flat-illumination", "statement": "For the Kiloscope, the axicon correction optics give a flat signal intensity profile across the field of view, where total vignetting makes the signal fall toward the edges.", "source": "Extended Data Fig. 2c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_scherrer_2023.ipynb", "notes": "At 1.5 mm the corrected profile is 0.797, total vignetting 0.253 and optical vignetting 0.389. The corrected profile is higher, and its minimum over 0 to 1.5 mm, 0.797, is 0.003 below the criterion's 0.8; at 1.125 mm it is 0.922. The minimum is 0.846 out to 1.425 mm and 0.742 out to 1.575 mm; with the centre moved by 100 um it is 0.765 to 0.831 (above 0.8 for one of four moves), and 0.695 about the image centre.", "deviations": [ "The radius of 1.5 mm and the level of 0.8 were chosen here; the result sits at the level." ], "disagreed": false, "data": "elsewhere", "where": "GitHub FeeLab/Feescope-Paper-Code at commit d596646b16a505907203828d8026feb7736ca69c, folder sf3/widefield", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds one of the paper's four mice and none of the songbird recordings or optical test data. The Academic Torrents deposit the paper names for its imaging data holds files of the same mouse session only, so the other mice and the birds are not public." }, { "kind": "metadata_error", "statement": "The device description reads \"Head-mounted microscope (Kiloscope) optimized for weight (1.0 mm FOV; 1.0 g)\", and the dandiset description says the data come from the microscope optimized for weight. The data are from the large-FOV microscope (1.4 g, about 4 mm FOV) that the paper calls the Kiloscope; a 4 mm window, 2948 footprints and 808 x 608 pixel frames." }, { "kind": "metadata_error", "statement": "The imaging is stored as a TwoPhotonSeries and the dandiset lists two-photon microscopy among its techniques, but the microscope is a one-photon head-mounted epifluorescence microscope." }, { "kind": "metadata_error", "statement": "The behaviour video is described as about 30 fps and its AVI header says 30 frames/s, but its 15521 timestamps run at a median 12.5 frames/s over 1234 s; at 30 frames/s it would cover only 517 s of the 1234 s of imaging." }, { "kind": "metadata_insufficient", "statement": "The imaging plane gives no pixel size, and its indicator and location are \"unknown\" with no excitation wavelength, although general/virus says GCaMP7f. Distances in the paper's figures cannot be computed from the dandiset alone." }, { "kind": "selection_undocumented", "statement": "The 2948 footprints are the EXTRACT output before curation; the paper analyses the 2382 it kept (Extended Data Fig. 6a). Nothing in the dandiset marks the curated set or says that the footprints are uncurated." }, { "kind": "data_missing", "statement": "The mouse's position, which the paper's decoding and place analyses use, is not in the dandiset; it must be tracked from the behaviour video. The first 64 s of the video (by its nominal rate), which the paper's code drops because the experimenter is in view, are not marked." }, { "kind": "code_mismatch", "statement": "The Extended Data Fig. 9c legend describes decoders on the 32 closest footprints within 270 um; the code (subregion_map_octant.m) uses 64 footprints within 50 pixels, which at the code's own 5.94 um per pixel (sf3/widefield/analysis.m) is 297 um." }, { "kind": "paper_inconsistency", "statement": "The title of Extended Data Fig. 8 refers to the Kiloscope data \"shown in Figure 3\", and its legend takes the ridgeline plot from Fig. 2d, while the version of record has two figures, and Supplementary Video 1 and Extended Data Fig. 10 place the bird data in Fig. 2a-d and the mouse data in Fig. 2e-h." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's abstract and Extended Data legends from the publisher page. The verifier read the archive's asset list and metadata, read the paper's code at d596646, and tested the decoder and tracking helpers on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; all 15 agree with the record as it then stood. The revision changed the outcome of ed9c-local-decoding-map, which round 2 reviews.", "agreed": 15, "of": 15, "disagreements": [] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the first revision, the helper module, the claims file, the README and the attempt record; no paper text was downloaded this round, and the verifier worked from its round-1 reading. It agreed with all 15 outcomes. It quoted sentences the printed numbers contradict. Most of them (18 significant points, 2268 fits at the limit, NMF errors 97.55 to 97.58, 634 s) are the numbers of a run on four cores, while the executed copy it read came from another run (19, 2264, 97.79 to 97.8, 358 s, 13.7 min); the exact fits stop at an iteration limit and the NMF uses float32, so these numbers differ slightly between machines. The entry was re-run on four cores, which again gives 18, 2268, 97.55 to 97.58 and about 640 s, and the text now matches that run. The run takes about 25 minutes, so the README and entry say about 25. The verifier also found two sentences no output showed. The AVI's byte size matching the Academic Torrents listing (cell 15) is removed, and the draft holding the same blobs (cell 0) is now printed in the data check (same assets, sizes and blob ids).", "agreed": 15, "of": 15, "disagreements": [] } ] }, { "id": "000718-zaki-2024-01", "dandiset": "000718", "dandiset_version": "0.260825.1902", "paper": "10.1038/s41586-024-08168-4", "paper_title": "Offline ensemble co-reactivation links memories across days", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000718-zaki-2024", "entry_title": "Offline ensemble co-reactivation in the EEG/EMG experiment (Zaki et al. 2024)", "description": "Tests the findings of Zaki et al. (2024) that can be tested on dandiset 000718, which holds two of the nine mice of the paper's calcium imaging and EEG/EMG experiment (one high-shock, one low-shock) with their encoding and recall sessions, the first offline recording after encoding, and cell registration for the high-shock mouse. It checks the deposited freezing against the paper's per-mouse values, compares freezing between the two mice, tests offline population bursts and their skew against shuffled activity and against movement, and compares overlap-neutral with overlap-aversive co-bursting in wake. The one-hour offline, behaviour-only, inhibitory tagging and no-shock experiments are not in the dandiset.", "notebooks": [ { "path": "reproduce_zaki_2024.ipynb", "title": "Reproducing Zaki et al. (2024) from dandiset 000718", "executed": "notebooks/000718-zaki-2024/reproduce_zaki_2024.html" } ], "outcomes": [ { "claim": "source-data-link", "statement": "The two deposited mice are the mice of the same names in the paper's per-mouse source data, with the same shock group, and the freezing computed from the dandiset's freezing intervals agrees with the per-mouse freezing the paper reports for them.", "source": "Extended Data Figure 9b and 9c; source-data repository denisecailab/RetrospectiveMemoryLinkingData_2024", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zaki_2024.ipynb", "notes": "Both mice are matched by name (subject_id Ca_EEG2-1 and Ca_EEG3-4, the Mouse column of the source data), with the same shock amplitude in the files as the source data's group (1.5 and 0.25 mA). All four freezing values are within 10% under both readings; reading (a), given as measured, gives 64.09, 8.82, 17.40 and 15.06% against 63.87, 8.46, 16.90 and 14.60%, and reading (b) gives 63.45, 8.46, 16.91 and 14.61%. The recall session descriptions name the contexts (Recall1 shock, Recall2 novel, Recall3 neutral), as the source data assign them for Ca_EEG3-4. On which side a difference comes from, the dandiset's freezing intervals give the paper's per-mouse values to within 5% (reading a) and 1% (reading b), so the dandiset agrees with what the paper reports for these mice.", "deviations": [ "Only four per-mouse values can be compared, as the dandiset lacks the neutral and novel recall sessions of Ca_EEG2-1 and the other seven mice." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "ed9b-aversive-freezing-high-vs-low", "statement": "In the calcium imaging and EEG/EMG experiment, high-shock mice froze more during aversive recall than low-shock mice (t7 = 8.99, p = 0.020).", "source": "Extended Data Figure 9b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zaki_2024.ipynb", "notes": "Recall1 freezing is 64.09% for the high-shock mouse and 8.82% for the low-shock mouse (difference 55.27 percentage points). The 30 s bins differ by Mann-Whitney (U = 100, p = 0.00018); 15 s and 60 s bins give p = 8.9e-07 and 0.0079. The paper's t-test (t7 = 8.99, p = 0.020) over 5 and 4 mice cannot be run with one mouse per group, so its statistic is not tested. The bins are consecutive parts of one session per mouse and not independent, so the p-values overstate the evidence.", "deviations": [ "One mouse per group (the paper has 5 high-shock and 4 low-shock mice); the test is within sessions, over 30 s bins, chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "offline-bursts-above-shuffle", "statement": "During offline periods, hippocampal population bursts occur more often than expected from shuffled neuronal activity, so CA1 neurons fire in a more coordinated way than chance.", "source": "Results, section \"Neutral ensemble recruited into population bursts\"; Extended Data Figure 3l and 3m", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_zaki_2024.ipynb", "notes": "The analysis ran. Under the criterion's procedure (surrogates z-scored and thresholded at z = 2 as the data) the true burst rate is below the surrogate mean in all three offline recordings (5.30, 6.40 and 8.71 per min against 8.48 to 10.94; true over surrogate mean 0.63 to 0.80), which would be not reproduced. The paper's chance level for this test (source data for Extended Data Figure 3m, another cohort) is 3.38 to 4.39 surrogate bursts per min against 4.51 to 4.92 true, surrogate over true 0.72 to 0.96; this procedure gives 1.26 to 1.60, far from it, so the procedures differ and the claim is blocked as the protocol requires. The Methods do not say how bursts are counted in a surrogate. Variants disagree; merging events closer than 1 s leaves the true rate below the surrogates (4.40 to 7.31 against 6.56 to 8.52 per min), and thresholding surrogates at the true trace's own mean + 2 SD puts the true rate far above them (5.30 to 8.71 against at most 0.50 per min). At z = 2.5 the true rate is above the surrogate mean in 2 of 3 recordings and above the 95th percentile in none. On synthetic data with 6 coordinated events per minute, the criterion's test gives 5.6 true bursts per min against a surrogate mean of 34.98, and with independent cells 34.8 against 37.36, so it cannot detect coordination; the fixed-threshold variant separates the two (5.6 against 0.00, 34.8 against 38.37), but its chance level in the data (surrogate means at most 0.10 per min) is far below the paper's.", "deviations": [ "Run on the three 10 min offline recordings of the EEG/EMG experiment at 15 Hz; the paper shows the test for the one-hour recordings at 30 Hz of the single-experience cohort (Extended Data Figure 3), which is not deposited.", "Burst events taken as maximal runs of frames above threshold, as the Methods do not define an event further." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "offline-skew-above-shuffle", "statement": "The mean population activity during offline periods is more right-skewed than in shuffled data, showing brief burst-like activations that need coordinated activity of groups of neurons.", "source": "Extended Data Figure 3n and 3o", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zaki_2024.ipynb", "notes": "The population trace's skewness is 1.65, 1.34 and 1.72 in the three offline recordings, above all 1000 circular-shift surrogates in each (surrogate means 0.60, 0.40 and 0.37, 95th percentiles 0.72, 0.51 and 0.48). Both arms are lower than in the paper's source data for Extended Data Figure 3o (another cohort, 1 h at 30 Hz); the true skews are below the paper's lowest (1.76 to 3.65) and two of three surrogate means are below its lowest shuffled value (0.47 to 1.91), so the chance level is not shown to match the paper's. The outcome rests on the true skew exceeding every surrogate. On synthetic data the test separates coordinated activity (skew 8.54 against a surrogate 95th percentile of 0.94) from independent cells (0.98 against 1.09).", "deviations": [ "Run on the EEG/EMG experiment's three 10 min offline recordings; the paper shows the test for another cohort (Extended Data Figure 3o), which is not deposited." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "burst-locomotion-pause", "statement": "Offline population bursts coincide with the mouse briefly slowing down about 1 s before the burst and resuming its movement about 1 to 2 s later.", "source": "Figure 2d and 2e; Extended Data Figure 6e; Results, section \"Co-reactivation occurs more during wake\"", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_zaki_2024.ipynb", "notes": "Telemetry movement in the second before a burst is not lower than 3 to 5 s before it in any of the three recordings under either reading of time zero (peak, one-sided Wilcoxon p = 0.76, 0.89, 0.39; onset, p = 0.88, 0.94, 0.41); 30 to 60% of bursts have lower movement before them. Movement 1 to 2 s after the peak is lower than in the second before it in two of three recordings (0.155 against 0.225, and 0.129 against 0.257). The telemetry activity signal is a coarse proxy whose relation to calcium activity is weak (movement decoded at r = 0.06 to 0.24 at zero shift; Spearman r with the population trace 0.07 to 0.32 in 1 s bins). The files describe it as motion of the probe relative to the receiver and a proxy for locomotion; its mean magnitude is 4 to 15 times higher in wake than in quiet wake epochs. The test is not calibrated, giving p = 0.016 at 300 random times in Ca_EEG2-1 (0.9999 and 0.92 in the others). The outcome says this proxy does not show the pause, and is weak evidence that the pause is absent.", "deviations": [ "Movement is the magnitude of the HD-X02 telemetry activity signal; the paper tracked locomotion with a webcam, whose video is not deposited.", "Tested on the EEG/EMG experiment's offline recordings; the paper shows the effect for the single-experience cohort (Figure 2d and 2e) and the inhibitory tagging cohort (Extended Data Figure 6e)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-wake-overlap-neutral-coburst", "statement": "After a strong (high-shock) aversive experience, during wake in the offline period the overlap ensemble co-bursts more with the neutral ensemble than with the aversive ensemble (t4 = 4.94, P = 0.016).", "source": "Figure 5c (left); Methods, \"Ensemble co-participation analysis\"", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_zaki_2024.ipynb", "notes": "In Ca_EEG2-1's first offline recording after aversive encoding, under reading (a), wake and quiet wake together (all 87 bursts), OxN is below OxA (26.4 against 35.6% inclusive, 8.0 against 17.2% exclusive; 7 against 15 discordant bursts, McNemar p = 0.13). Reading (a) is the one the Methods imply. Their scoring (6 s epochs, two-state Gaussian mixture on EMG) applied to this mouse's log EMG RMS over the 12 h offline period puts 94.1% of quiet-wake frames and 98.5% of wake frames in wake (97.9% of quiet wake when fitted on the first 6 h), and all 87 bursts in wake. Under reading (b), wake alone, OxN exceeds OxA (32.0 against 28.0% of 25 bursts; 8.0 against 4.0%) on 2 against 1 discordant bursts (McNemar p = 1.0). Under the Methods' wake the order holds at thresholds 1.5 (34.9 against 41.1%) and 2.5 (21.7 against 30.0%), and no difference reaches p < 0.05. Outside bursts both are at most 1.02% of 0.5 s windows. The neutral, aversive and overlap ensembles each have more of their cells in bursts than the remaining cells (median differences 0.005 to 0.010, Wilcoxon p = 0.041 to 0.0003). The paper's statistic (t4 = 4.94, P = 0.016, across five mice) cannot be tested. The evidence against the paper is weak; one 10 min recording of 24 for one mouse of five, with ensemble traces z-scored within it, so levels are not comparable with the paper's source data for this mouse over all 24 recordings (10.37% OxN against 8.39% OxA in wake). Counted inclusively, co-participation here (26 to 36%) is 2.5 to 4 times those values; with the third ensemble excluded (8.0 and 17.2%) it is on their scale, with OxN the lower.", "deviations": [ "One high-shock mouse of five, and its first offline recording of 24 (10 min of 4 h).", "The Methods z-score the ensemble traces over all 24 offline recordings concatenated; here only one is deposited, so they are z-scored within it.", "The criterion fixed four readings (quiet wake in or out of wake; co-participation with or without the third ensemble) and would count the claim under any of them. After the first verification the outcome is judged on wake including quiet wake, as the Methods' own EMG scoring puts quiet wake in wake; under wake alone OxN exceeds OxA without a significant difference, which the criterion would have called partially reproduced.", "The EMG feature of the Methods' scoring (log RMS per 6 s epoch) is chosen here, after the data were seen; the Methods do not name one. Without the log the mixture does not separate sleep from wake.", "Bursts are assigned the sleep state of their peak frame, a choice made here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1bc-retrospective-not-prospective", "statement": "Fear spreads from an aversive context to a neutral context experienced 2 days before (retrospective linking) but not to one experienced 2 days after (prospective), with no difference in aversive recall between the groups.", "source": "Figure 1a to 1c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Behaviour-only experiment; its mice are not in the dandiset. The paper's source-data repository holds the per-mouse freezing plotted in Figure 1, but not the recordings they come from; these claims were not tested on figure values.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1ef-high-shock-drives-linking", "statement": "High-shock mice froze more than low-shock mice in the aversive context, and froze more in the neutral than in the novel context, while low-shock mice did not.", "source": "Figure 1d to 1f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The one-hour imaging cohort of Figure 1d to 1f is not in the dandiset. Its EEG-cohort counterpart is tested in ed9b-aversive-freezing-high-vs-low.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-aversive-freezing-predicts-linking", "statement": "In high-shock mice, aversive recall freezing correlates with the strength of retrospective memory linking (R2 = 0.45, P = 0.016), but not in low-shock mice.", "source": "Figure 1g", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the one-hour imaging cohort's freezing in three contexts; not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1n-offline-hippocampus-needed", "statement": "Chemogenetic inhibition of the hippocampus in the 12 h after aversive encoding prevents retrospective memory linking and leaves the aversive memory intact.", "source": "Extended Data Figure 1l to 1p", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The chemogenetic inhibition experiment is behaviour only and not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed2-cocaine-retrospective-linking", "statement": "A cocaine experience also drives retrospective memory linking to a neutral context experienced 2 days before.", "source": "Extended Data Figure 2", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The cocaine experiment is behaviour only and not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3-aversive-ensemble-reactivated", "statement": "Cells active during aversive encoding are reactivated offline and preferentially during aversive recall.", "source": "Extended Data Figure 3e to 3k", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The single-experience imaging cohort is not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed4f-neutral-ensemble-reactivated-high-shock", "statement": "During offline 2 the neutral ensemble is less active than the aversive and overlap ensembles in low-shock mice but no differently active in high-shock mice.", "source": "Extended Data Figure 4f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The one-hour offline cohort is not in the dandiset. The deposited high-shock offline recording gives one mouse of the EEG cohort, for which the paper does not report this analysis.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-offline1-neutral-participation", "statement": "During offline 1 a greater percentage of the neutral ensemble participates in bursts than of the remaining ensemble, in both shock groups.", "source": "Figure 3c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "One-hour offline cohort not deposited. In the EEG cohort, the offline-day-1 recording of Ca_EEG3-4 is deposited without registration, and Ca_EEG2-1 has none.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-neutral-recruited-high-shock", "statement": "During offline 2 the neutral ensemble preferentially participates in bursts relative to the remaining ensemble in high-shock mice (t7 = 4.88) but not in low-shock mice.", "source": "Figure 3d to 3f", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "One-hour offline cohort not deposited. The notebook shows, as context only, that in Ca_EEG2-1's offline recording the neutral ensemble has more of its cells in bursts than the remaining cells (median difference 0.005, p = 0.041).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-overlap-independent-participation", "statement": "During burst periods the overlap ensemble participates independently in more bursts than the aversive and neutral ensembles, with no difference between shock groups.", "source": "Figure 4b and 4c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "One-hour offline cohort not deposited.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-overlap-neutral-coburst", "statement": "In the one-hour offline experiment, high-shock mice show more overlap-neutral than overlap-aversive co-bursting during bursts (t7 = 4.95), low-shock mice do not, and there is no such difference outside bursts.", "source": "Figure 4e and 4f; Extended Data Figure 4k to 4o", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "One-hour offline cohort not deposited. The same analysis on the EEG cohort is tested in fig5c-wake-overlap-neutral-coburst.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6-overlap-inhibitory", "statement": "The overlap ensemble is enriched in putative inhibitory neurons identified by chemotagging.", "source": "Extended Data Figures 5 and 6", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The inhibitory tagging (Gad2-cre, CNO) experiment is not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed8-no-shock-no-coburst", "statement": "Without a shock, overlap-neutral co-bursting does not exceed overlap-aversive co-bursting and no memory linking occurs.", "source": "Extended Data Figure 8", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The no-shock cohort is not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7-contexts-discriminable", "statement": "Neural activity during neutral and aversive encoding is highly discriminable, with no difference between low- and high-shock mice.", "source": "Extended Data Figure 7", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The one-hour offline cohort of Extended Data Figure 7 is not in the dandiset. Ca_EEG2-1's neutral and aversive encoding are registered, but the paper does not report this analysis for the EEG cohort.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9c-eeg-cohort-linking", "statement": "In the calcium imaging and EEG/EMG experiment, high-shock mice froze more in the neutral than in the novel context (t4 = 4.02, p = 0.03), while low-shock mice did not.", "source": "Extended Data Figure 9c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The neutral and novel recall sessions of the only deposited high-shock mouse (Ca_EEG2-1) are not in the dandiset, and the paper's paired test needs several mice per group. The low-shock mouse's values (neutral 17.40%, novel 15.06%) are shown under source-data-link.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-sleep-no-coburst-difference", "statement": "During NREM and REM sleep, overlap-neutral and overlap-aversive co-bursting do not differ in either shock group.", "source": "Figure 5c (middle and right)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The three deposited offline recordings are each the first of 24 and hold only wake and quiet wake (no sws or rem interval); the later recordings, where sleep occurs, are not deposited.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-low-shock-wake-no-difference", "statement": "In low-shock mice, overlap-neutral and overlap-aversive co-bursting during wake do not differ (t3 = 1.20, P = 0.32).", "source": "Figure 5c (left)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The only deposited low-shock mouse (Ca_EEG3-4) has no cell registration in the dandiset, so its ensembles cannot be formed. With one mouse the paper's paired t-test could not be run either.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9-ed10-sleep-unchanged", "statement": "Mice wearing a Miniscope sleep normally, the intermittent recording scheme captures the time spent in each state, and sleep structure is not changed by neutral or aversive encoding.", "source": "Extended Data Figure 9d to 9g and Extended Data Figure 10", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs continuous EEG/EMG and sleep scores for nine mice and a control group. Only Ca_EEG2-1 has week telemetry, without sleep scores; the other mice and the scores are not deposited.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6a-overlap-reactivated-neutral-recall", "statement": "The overlap ensemble is reactivated more during neutral recall than during novel-context exposure in high-shock mice compared with low-shock mice (t12 = 3.2, P = 0.007).", "source": "Figure 6a; Extended Data Figure 4q to 4s", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "One-hour offline cohort not deposited; in the EEG cohort Ca_EEG2-1 lacks neutral and novel recall and Ca_EEG3-4 lacks registration.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6b-neutral-representation-changed", "statement": "In high-shock mice the neutral encoding-to-recall population correlation is lower than in low-shock mice and lower than the aversive encoding-to-recall correlation.", "source": "Figure 6b", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As fig6a-overlap-reactivated-neutral-recall; the neutral recall session needed is missing for the registered mouse.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds two of the nine mice of the calcium imaging and EEG/EMG experiment (Ca_EEG2-1, high shock; Ca_EEG3-4, low shock) and, of each offline period, only the first 10 min recording of the 24 the Methods describe. Ca_EEG2-1 has no offline-day-1 recording and no neutral or novel recall session. The mice of the one-hour imaging and offline experiments (Figures 1d to 1g, 2 to 4 and 6, Extended Data Figures 3, 4 and 7), the behaviour-only experiments, and the inhibitory tagging and no-shock experiments are not deposited. Twenty of the 26 claims cannot be tested for this reason." }, { "kind": "data_missing", "statement": "Ca_EEG3-4 has no cell registration in the dandiset, so its ensembles cannot be formed. The Week file of Ca_EEG2-1 holds 19 registration tables for offline-day-2 recordings, of which only the first recording is deposited, and none for offline day 1." }, { "kind": "selection_undocumented", "statement": "The dandiset does not say why these two mice, and only the first offline recording of each period, were deposited, nor that the paper analysed more." }, { "kind": "metadata_error", "statement": "The session start times of the Ca_EEG2-1 behaviour sessions (NeutralExposure, FC, Recall1), and the Week epochs built from them, are about 1 h later than the telemetry and Miniscope clock. As deposited, OfflineDay2Session1 starts 47 min before the FC session it follows. The telemetry is absent (mouse out of its home cage) in windows that contain each of these epochs moved 1 h earlier, and the offline file's EEG sits exactly at its own epoch in the week recording." }, { "kind": "format_error", "statement": "The OnePhotonSeries timestamps of three files (Ca_EEG2-1 NeutralExposure, Ca_EEG3-4 OfflineDay1Session1, Ca_EEG3-4 Recall2) run at 16.7 ms and end at half the recording's length, while their frame counts fit 30 Hz over the full length given by the deconvolved timestamps." }, { "kind": "metadata_insufficient", "statement": "The sleep states include `quiet wake`, which the paper neither uses nor maps to its wake, NREM and REM states, so it is not known which state the paper assigned these epochs to. The Methods' scoring, applied to the EMG of Ca_EEG2-1, puts 94% of them in wake. The three offline recordings hold no NREM (`sws`) or REM epochs." }, { "kind": "other", "statement": "The telemetry (EEG, EMG, activity) is sampled at 500 Hz in the offline files and the Week file; the Methods say the HD-X02 implants recorded at 100 Hz." }, { "kind": "metadata_error", "statement": "The session description of the offline recordings says that mouse behaviour and calcium were recorded for an hour with a webcam above the home cage. The deposited offline recordings last 10 min, hold telemetry and no video, and the Methods describe this experiment's offline recordings as 10 min in the telemetry home cage." }, { "kind": "metadata_insufficient", "statement": "The fluorescence series carry placeholder descriptions (\"description of deconvolved traces\") and unit \"n.a.\", the FC session descriptions give the shock amplitude without a unit, and the Week file has an empty session description." }, { "kind": "methods_unavailable", "statement": "The analysis code repository the paper names (github.com/denisecailab/RetrospectiveMemoryLinkingAnalysis_2024) returns 404, so how bursts are counted, in the data and in shuffled surrogates, could not be checked; the surrogate burst rates here differ from the paper's chance level." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. The attempt record was not among its materials, so it took its counts from the claims file and the notebook.", "agreed": 25, "of": 26, "disagreements": [ { "claim": "offline-bursts-above-shuffle", "outcome": "not_reproduced", "reason": "Not reproduced as the criterion is written, as the true burst rate is below the shuffled mean in all 3 recordings at z = 2. It did not count this as evidence against the paper, because z-scoring each surrogate again makes the test unable to detect coordination (in its synthetic data, 5.9 per min true against a null mean of 31.7 with planted coordination); the fixed-threshold variant behaves correctly but neither variant matches the paper's chance level. The criterion needs revising, or the claim should be treated as blocked with methods_underspecified. It asked for a positive control in the notebook." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the revised run, with its conclusions and summary, the helper module, the claims file, the README and the attempt record. It read the paper from Europe PMC (PMC11666460) and did not re-run the notebook. Other points it raised, not tied to one claim, were corrected in the text; cell 10 now gives the random-pair centroid distances as 169 to 196 px.", "agreed": 26, "of": 26, "disagreements": [] } ] }, { "id": "000727-brezovec-2022-01", "dandiset": "000727", "dandiset_version": "0.240106.0043", "paper": "10.1101/2022.03.20.485047", "paper_title": "Mapping the Neural Dynamics of Locomotion across the Drosophila Brain", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000727-brezovec-2022", "entry_title": "Brain-wide neural correlates of walking in Drosophila (Brezovec et al. 2022)", "description": "Tests the findings of Brezovec, Berger, Druckmann and Clandinin (2022) on dandiset 000727, which holds whole-brain two-photon imaging and ball tracking of nine walking flies. It streams 12 planes of the authors' processed volumes in the Functional Drosophila Atlas for all flies, and tests the voxel correlations with forward and turning velocity, their symmetry, the principal components and the models that predict velocity from them, the demixing of velocity components, and the timing of neural activity relative to behaviour. Region-level results cannot be tested, as the dandiset has no neuropil labels.", "notebooks": [ { "path": "reproduce_brezovec_2022.ipynb", "title": "Reproducing Brezovec et al. (2022) from dandiset 000727", "executed": "notebooks/000727-brezovec-2022/reproduce_brezovec_2022.html" } ], "outcomes": [ { "claim": "dataset-structure", "statement": "Nine flies were imaged for 30 minutes each at a volume rate of about 1.8 Hz, with 256 x 128 x 49 voxels of 2.6 x 2.6 x 5 um (about 1.6 million voxels per volume), giving 30,456 volumes in all, while the ball was tracked at 50 Hz.", "source": "Results, first section; Figure 1A legend; STAR Methods, Two-Photon Imaging and Behavior Tracking", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Nine flies, one session each, 3384 volumes per fly (30,456 in all) at 1.8797 Hz, 1,605,632 voxels of 2.61 x 2.61 x 5 um per raw volume, 30.0 minutes per session, FicTrac 90,000 frames at 50 Hz. The subject ids match the nine flies of the paper's code.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-fraction-correlated", "statement": "About 39% of the brain volume correlates with at least one of forward velocity, left and right angular velocity.", "source": "Results, Neural encoding of velocity space is widespread; Figure 2C; Figure S2", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Reading (a), single voxels at p < 1e-4, gives 31.1% of the 191,119 in-brain voxels of the 12 planes, below 35.1 to 42.9% and above 19.5%. Reading (b), 6 x 6 blocks at p < 1e-8, gives 53.5% of the same in-brain voxels, above the band. With each fly's behaviour rolled in time, 0.0% pass under either reading. With behaviour sampled at the start of each volume in place of its midpoint, reading (a) gives 39.2%, so the value depends on the neural times, which the dandiset does not hold. The fraction is 0.0 to 7.5% in the outermost planes and 21.0 to 39.1% in the others. Within single flies 2.4 to 19.7% of voxels pass the threshold for 3384 points. Almost no voxel is negatively correlated (at most 0.01% per component).", "deviations": [ "Processed volumes in the Functional Drosophila Atlas, not the paper's mean brain; 12 of 91 planes.", "Behaviour sampled at the midpoint of each volume, as the dandiset has no per-plane times; the paper used each plane's acquisition time.", "Blocks of 6 x 6 voxels in place of the paper's Ward supervoxels for reading (b).", "In-brain voxels are those inside the brain in all nine flies; with voxels inside in any fly the fraction is 20.3%." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-venn-categories", "statement": "Of the brain volume, about 15% correlates only with forward velocity, 20% with forward velocity and turning, and 4% only with turning; only about 10% of correlated voxels correlate with all three components, so 90% show a tuning preference.", "source": "Results, Neural encoding of velocity space is widespread; Figure 2C", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Under reading (a), VF only 11.9% (expected 15), VF and turning 15.9% (20), turning only 3.2% (4), and 11.5% of correlated voxels correlated with all three (10). None is within its tolerance; the ranking holds and fewer than 20% of correlated voxels correlate with all three, so most show a tuning preference, as the statement says. Under reading (b) VF and turning is 39.4% and all three 32.2%. With behaviour at the start of each volume, reading (a) gives 11.6, 24.1, 3.5 and 25.7%.", "deviations": [ "As for fig2c-fraction-correlated." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-symmetry", "statement": "Forward velocity correlations are mirror-symmetric across the midline, while left and right turning correlations are anti-symmetric, with more correlated voxels in the hemisphere ipsilateral to the turn.", "source": "Results, Neural encoding of velocity space is widespread; Figure 2D, E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "The VF map correlates with its mirror image at r = 0.823. The VL map correlates with the mirrored VR map at 0.672 and with its own mirror at 0.449. Voxels significant for VL are 2.38 times as many in image half A (x < 157) as in half B, and voxels significant for VR 3.2 times as many in half B. Per fly, the VF mirror correlation is 0.166 to 0.580, summed VL correlation is larger in half A in 8 of 9 flies, summed VR correlation larger in half B in 7 of 9, and both in 6 of 9; fly_098 and fly_105 have VR on the same side as VL and fly_099 has VL on the other side. Against the pooled maps of the other eight flies, no fly matches better mirrored for both VL and VR, as a left-right flip would give; 7 of 9 match better unflipped for both. fly_099's VL map matches the mirrored map slightly better (0.158 against 0.190), its VR map clearly does not (0.439 against 0.199). For fly_105 the check does not decide (VL 0.274 against 0.234, VR 0.212 against 0.214), so a flip of that fly is not excluded; it would lower the pooled asymmetry. The ipsilateral part of the statement is not tested; it holds if half A is the fly's left, which the dandiset does not state.", "deviations": [ "Mirror about the centre of the FDA's left-right axis (156.5), chosen from the symmetry of the brain mask; the 0.7 threshold for symmetry is a choice of this attempt, made after the prototype run had shown r = 0.82." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-region-fractions", "statement": "Behaviour-correlated voxels occupy most neuropils with non-uniform velocity preferences, strongly in the central complex, posterior slopes, vest, superior medial and lateral protocerebrum, higher visual, olfactory and auditory areas and the mushroom body; IPS, AOTU and VES hold turning-only voxels, MB and LAL forward-and-turning, SMP and SIP forward-only.", "source": "Results, two paragraphs from \"We next wondered\"; Figure 2E-I", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the neuropil of each voxel. The dandiset holds no neuropil labels, atlas or mean brain for the FDA space of its processed volumes, nor the paper's own mean brain and its registered atlas. The FDA and its labels come from a later paper (BIFROST, Dryad doi:10.5061/dryad.8pk0p2nx1) that the preprint does not use, so they cannot be brought in under the protocol. Dryad holds no deposit of this paper's data.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-topographic-maps", "statement": "Within neuropils, voxels of different velocity tuning are spatially organized, for example a forward and ipsilateral-turning column in PLP, left and right compartments in IPS, bands in LO, a dorsal-ventral split in LH, layers in FB, alternating turning in PB, glomeruli in NO and medial and lateral compartments in LAL.", "source": "Results, Distinct topographic maps; Figure 3; Figure S3", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs neuropil boundaries; see fig2e-region-fractions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4bcd-pc-structure", "statement": "The first principal components of brain-wide activity are structured by behaviour; PC1 is low when the fly is stopped and high otherwise, PC2 increases with forward velocity and not with angular velocity, and PC3 carries the sign of angular velocity.", "source": "Results, Neural activity in the central brain is highly predictive; Figure 4B-D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "All three parts hold under both readings of the threshold. Reading (a); PC1's below-threshold correlation with VF is 0.202 against 0.065 (PC2) and -0.045 (PC3); above the threshold PC2 has the largest correlation with VF (0.272, PC1 0.162, PC3 0.086) and 0.091 and 0.087 with VL and VR; PC3's above-threshold correlations are 0.114 with VL and -0.259 with VR (p = 3.5e-14 and 5.6e-72). Within each fly over all time points, PC1 correlates positively with VF (0.22 to 0.57) and PC3 more with VL than VR, in 9 of 9 flies. PC1 explains 2.22% of block variance.", "deviations": [ "PCA of 5363 blocks from 12 planes, not of 98,000 supervoxels from 49 planes." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4fg-ridge-r2", "statement": "Linear models on the principal components predict forward, left and right velocity on held-out data with average R2 of about 0.3 using 100 PCs, performance improving over the first 100 PCs before declining.", "source": "Results, Neural activity in the central brain is highly predictive; Figure 4F, G", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "With 100 superfly PCs the median R2 over flies is 0.155 (VF), 0.196 (VL) and 0.212 (VR); the means are 0.038, 0.155 and 0.178. None is within 0.27 to 0.33; all medians are at least 0.15. Mean R2 rises to 100 PCs and declines after for each component, as stated. Three flies have negative VF R2 (-0.307, -0.306, -0.503). Variants; interleaved folds give medians 0.318, 0.252 and 0.271; alpha chosen within the training folds 0.134, 0.180, 0.212; each fly's own PCs 0.151, 0.210, 0.217. With behaviour rolled in time R2 is at most -0.002. With interleaved folds two of the three medians fall in the band (VF 0.318, VR 0.271; VL 0.252), so the folds, which the paper does not state, account for much of the gap; the outcome would stay partial.", "deviations": [ "Five contiguous folds within each fly, a choice; the code does not show its folds.", "Alpha is chosen by the best held-out score, as the code does, which selects on the test folds.", "The 1000 and 2000 PC models were not run (at most 500 PCs).", "PCs of 5363 blocks from 12 planes." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-r2-vs-movement", "statement": "Flies that moved less along a velocity component were poorly predicted (R2 near 0), while flies that explored it more were well predicted, with R2 up to 0.6.", "source": "Results, Neural activity in the central brain is highly predictive; Figure 4H", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "The Spearman correlation of a fly's mean amount of a component with its R2 is positive for all three components (VF 0.017, VL 0.383, VR 0.683, p = 0.042 for VR only); the pooled within-component rank correlation is 0.361 with p = 0.064. The largest R2 is 0.534 (fly_094, VF), just below 0.54 to 0.66, and the smallest -0.503. Partially reproduced under the clause that the correlation is positive for at least two components.", "deviations": [ "Rests on the R2 of fig4fg-ridge-r2, with its contiguous folds." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4i-weights-stereotyped", "statement": "The model weights given to each PC are stereotyped across flies; PC1 is used for all components, PC2 mainly for forward velocity, and PC3 for left and right turning with opposite signs.", "source": "Results, Neural activity in the central brain is highly predictive; Figure 4I", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Median correlation of the weights on PCs 1 to 20 between pairs of flies is 0.646 (VF), 0.732 (VL) and 0.761 (VR). PC3's weight is positive for VL and negative for VR in 9 of 9 flies, PC2's weight is largest for VF in 7 of 9, and PC1's weights have one sign for all three components in 9 of 9. With each fly's behaviour rolled in time (20 rolls), the median pair correlation is at most 0.151, PC3 has opposite signs in 3 to 8 of 9 flies and PC1 one sign in 0 to 6 of 9. Part (iv) follows in part from PC1's orientation, signed to correlate positively with VF, with which it also correlates positively with VL and VR (0.222 and 0.188).", "deviations": [ "Weights from a ridge fit to all of each fly's time points at the alpha chosen in fig4fg-ridge-r2, with each component scaled to unit s.d." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-unique-variance", "statement": "Demixing with linear models shows that forward velocity is uniquely encoded by a spatially organized subset of voxels, while locomotor state (walking or stopped) is not uniquely encoded anywhere, although the single-variable maps of forward velocity and locomotor state are very similar.", "source": "Results, Demixing the unique contribution; Figure 5A", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "At the 0.01 threshold, 5 blocks (0.09%) encode walking state uniquely and 40 (0.75%) encode VF uniquely, 8 times as many, but fewer than the 5% the criterion requires. Unique contributions are small everywhere (largest 0.032 for VF, 0.012 for walking state) and the full model's median held-out R2 is 0.0019. The single-variable maps of VF and walking state correlate at 0.882 over blocks, as the statement says. At a threshold of 0.005 walking state is unique in 1.88% of blocks and VF in 2.24%; with the walking state the code intended, in 0.97% and 0.91%, so the VF advantage depends on the 0.01 threshold, which lies far above the median full-model R2, and on the definition of walking state. Within single flies walking state is unique in up to 8.35% of blocks (fly_094).", "deviations": [ "Ridge alpha 1 on behaviour scaled to unit s.d., folds as fifths of every fly, and the 0.01 threshold are choices; the Methods give none of them.", "Walking state as the code computes it, which uses forward velocity alone.", "Blocks in place of supervoxels." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-global-below-threshold", "statement": "The functional regions defined by the unique contributions of forward, left and right velocity are all correlated with velocity when the fly is below the movement threshold, a widespread increase in activity at the initiation of movement, while above the threshold each region correlates most with its own velocity component.", "source": "Results, Demixing the unique contribution; Figure 5B, C; Figure S5B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Under reading (b) of the threshold all nine below-threshold correlations of the forward, left and right regions (40, 4 and 8 blocks) with the three components are positive with p < 0.05 (0.013 to 0.221), and above the threshold each region correlates most with its own component (0.377, 0.170, 0.266). Under reading (a) the left region with VR is -0.008 (p = 0.2), so only reading (b) satisfies the criterion. The Pearson p-values treat time points as independent; against 200 rolls of each fly's behaviour in time, which keep the autocorrelation, all nine are above chance under reading (b), the weakest (left region with VR, r = 0.013) with p = 0.025 against a null 95th percentile of 0.010. The left region holds only 4 blocks.", "deviations": [ "Regions are the few blocks with a unique contribution of at least 0.01 in fig5a-unique-variance.", "The threshold readings are two interpretations of the 0.75 s.d. of Figure 4E." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-ipsi-contra", "statement": "When the fly turns, neural activity increases in specific regions of the ipsilateral hemisphere and decreases in the same regions of the contralateral hemisphere.", "source": "Results, Demixing the unique contribution; Figure 5F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Turning raises activity mostly on one side, opposite for the two directions (82% of the top 10% of blocks in half A for left turns, 25% for right turns), but the mirror blocks rise as well; their median change against slow walking is +0.0064 for left turns and +0.0022 for right turns, and 36% and 42% of them fall. The same holds with turning thresholds of 50 and 150 deg/s, and in 8 of 9 flies for left turns and 9 of 9 for right turns. With the change predicted by the demixing model of fig5a-unique-variance, as the paper derives Figure 5F, the mirror blocks rise as well (medians 0.0254 and 0.0111; 6.5% and 18.8% fall), as do the model's VL and VR coefficients of the mirror blocks (median 0.0064). The ipsilateral increase holds; the contralateral decrease does not.", "deviations": [ "The bounds for slow walking (1 to 3 mm/s, below 30 deg/s) and turning (beyond 100 deg/s) are choices; the paper does not state its own.", "Neural activity and behaviour at the same volume time, without a lag.", "The main test compares mean activity in turns and slow walking; the paper uses the demixing model, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-peak-time-range", "statement": "The time of peak cross-correlation between supervoxel activity and forward velocity ranges from about 300 ms before the change in behaviour, the earliest, to more than 1 s after it.", "source": "Results, The temporal relationship between neural activity and behavior; Figure 6A-E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Reading (b); the 99th percentile of VF lead over the 2145 top blocks is 0.32 s, within 0.27 to 0.33 s, and the 1st percentile a lag of 1.23 s. Reading (a) gives an earliest lead of 0.44 s (outside tolerance) and a latest lag of 1.44 s. VL and VR give 99th percentiles of 0.30 and 0.22 s and 1st percentiles of lags of 1.24 and 1.22 s. With volume-start times the VF 99th percentile is 0.58 s. The median VF lead changes steadily with FDA plane from 0.36 s (plane 17) to -0.30 s (plane 80), a spread of 0.66 s against a volume period of 0.532 s, the pattern unknown plane acquisition times would produce; the dandiset gives neither the times nor the order of the planes. With each plane's median removed the 99th percentile is 0.50 s and the 1st -1.02 s, so the match within 0.03 s is not robust to the neural times; the lag of more than 1 s holds in both (1st percentile at least 0.84 s of lag in every plane from 38 to 80, more than 1 s in planes 59 to 73). Only the lag of more than 1 s is robust; the earliest lead cannot be tested with the timing the dandiset gives, and the outcome follows the criterion fixed in advance. Fitted per fly, the 99th percentile is 0.36 to 4.55 s.", "deviations": [ "Neural times at the volume midpoint, an error of up to 0.27 s per block.", "Notch filter Q = 2 is a choice; the code's notch coefficients are not in the repository.", "Top 40% by peak value of the deconvolved filter." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6h-peak-vs-width", "statement": "Supervoxels whose peak correlation lags behaviour have broader temporal kernels, while those that anticipate behaviour have narrow kernels.", "source": "Results, The temporal relationship between neural activity and behavior; Figure 6H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "Over the 2145 top VF blocks, lag and FWHM correlate at r = 0.672 (p = 2.2e-281, Spearman 0.703); mean FWHM is 1.38 s for blocks leading by up to 0.5 s and 2.62 s for blocks lagging by more than 1 s. VL and VR give r = 0.442 and 0.449; volume-start times 0.673. The plane means of lag and FWHM correlate at 0.979 over 10 planes, so plane accounts for part of the relation; with plane means removed r = 0.623 (p = 6.3e-231), and within single planes r is positive in all 10 planes with at least 10 blocks (0.222 to 0.751), with p < 0.05 in 8.", "deviations": [ "As for fig6-peak-time-range; FWHM measured from 0, around the peak." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6fg-ipsi-leads-contra", "statement": "Across nearly all brain regions, the peak correlation with angular velocity comes first in the hemisphere ipsilateral to the turn, then in the contralateral one.", "source": "Results, The temporal relationship, paragraph on angular velocity; Figure 6F, G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_brezovec_2022.ipynb", "notes": "For VL, over 868 mirror pairs, the block in half A leads its partner by a median 0.16 s and is earlier in 67% of pairs; for VR, over 849 pairs, the block in half B leads by 0.14 s and is earlier in 72%; both Wilcoxon p-values print as 0. The median difference is 0.26 to 0.33 s in planes 17 to 38 for VL and 0.19 to 0.29 s in planes 17 to 59 for VR, and -0.03 to 0.03 s in planes 73 and 80. Both blocks of a pair lie in one FDA plane; whether the two halves of a plane were acquired at the same time is not known.", "deviations": [ "The ipsilateral half is the image half with more significant correlations for that turn, from fig2-symmetry, since the dandiset does not say which half is left." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6eg-region-sequence", "statement": "Peak correlations follow a sequence across regions; for forward velocity the antennal lobe and lateral horn first, then mushroom body, GNG and saddle, the central complex spanning onset, and the optic lobes lagging by up to more than a second; for angular velocity IPS, GOR and VES lead and the central complex and optic lobes lag.", "source": "Results, The temporal relationship between neural activity and behavior; Figure 6E-G", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs the neuropil of each supervoxel; see fig2e-region-fractions. The timing would also need the per-plane acquisition times and the paper's z-depth maps, which are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-within-region-gradients", "statement": "Within brain regions, peak correlation times form spatial gradients, for example a dorsal before ventral order in LH for forward velocity and ipsilateral before contralateral order in LAL, MB-ML and PLP for angular velocity.", "source": "Results, Individual brain regions display spatiotemporally structured patterns; Figure 7; Figure S7", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "Needs neuropil boundaries (see fig2e-region-fractions) and per-plane acquisition times, neither of which is in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2-tdtomato-control", "statement": "Correlations computed from the tdTomato structural channel show no behaviour-related signal, so motion artefacts are undetectably small.", "source": "Figure S2E, H legend", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds the tdTomato channel only raw, without motion correction or registration. Repeating the paper's per-volume ANTs SyN motion correction for 30,456 volumes, and the warps to a common space, is also out of reach here (not_runnable). A check on the raw, uncorrected channels (raw planes 18 and 30, high-pass filtered as the code does, within each fly) does not decide the outcome; the median share of voxels correlated with VF, VL or VR at p < 1e-4 is 0.23% for tdTomato and 0.60% for GCaMP6f, tdTomato exceeds GCaMP6f in 5 of 18 fly-planes, and it reaches 3.53% in fly_089, against 0.83% for GCaMP6f.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4a-supervoxel-number", "statement": "Behaviour prediction peaks at 2000 supervoxels per plane, among 1 to 10,000.", "source": "STAR Methods, Agglomerative Clustering Supervoxel Creation; Figure S4A", "outcome": "blocked", "blocked_by": "too_large", "notebook": null, "notes": "Needs Ward clustering of every plane of the nine flies pooled at seven cluster numbers, so every voxel of all 91 planes. The 12 planes streamed here are 22.1 GB compressed and took 306 s in the latest run (214 s in the run before), including about 40 s for metadata; all 91 planes are several times that, which leaves no room within the 30 minute limit for the clustering itself. The files total 610 GB. A partial sweep on the 12 streamed planes was not attempted. It would need each plane's voxel time series held in memory (about 27,000 in-brain voxels x 30,456 points, some 3 GB per plane) for Ward clustering at seven sizes, followed by the PCA and ridge models at each size, while the streaming here keeps only block means and per-voxel sums.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The processed volumes are registered into the Functional Drosophila Atlas, but the dandiset holds no neuropil labels, atlas or template for that space, nor the paper's own mean brain and registered atlas. None of the paper's region-level results (Figures 2E to I, 3, 6E to G, 7) can be tested." }, { "kind": "other", "statement": "The processed series is in the Functional Drosophila Atlas, a space from a later paper of the lab, while the preprint analyses its data in its own mean brain. The dandiset does not say how the FDA series relates to the preprint's analysis space or which preprocessing it shares." }, { "kind": "data_missing", "statement": "The per-plane acquisition times of the Bruker recordings are not in the files, which give only a volume rate. The paper aligns behaviour to each plane's time. Sampling behaviour at the start in place of the middle of each volume changes the correlated share of the brain from 31.1% to 39.2% and the 99th percentile of forward-velocity lead from 0.32 to 0.58 s." }, { "kind": "data_missing", "statement": "The supervoxel labels, the z-depth maps used to give each supervoxel its acquisition time, and the motion-corrected tdTomato channel used as the paper's motion control are not deposited." }, { "kind": "metadata_insufficient", "statement": "The processed series has grid spacing 1, 1, 1 in unit \"unknown\", so its voxel size is not given, and nothing states which half of the volume is the fly's left." }, { "kind": "metadata_insufficient", "statement": "Imaging and FicTrac both start at 0 s; the conversion code set FicTrac timestamps to a uniform 50 Hz from 0 because synchronisation data were missing, and the dandiset does not say so. The data are consistent with a shared start (brain-wide activity follows walking speed by 0.4 to 0.8 s in every fly), to within a few hundred milliseconds." }, { "kind": "metadata_error", "statement": "Every FicTrac SpatialSeries has unit \"meters\" and conversion 0.0045 (the ball radius), while most hold angles in radians, as their descriptions say (heading, orientations, positions in radians, speed in radians per frame). SpatialSeriesRotationDeltaError, described as an error in radians, has medians of 6067 to 10,435." }, { "kind": "code_mismatch", "statement": "The paper's code computes the walking state with np.sqrt(a, b), where b is taken as the output array, so the state reduces to absolute forward velocity over its s.d. above 0.2; the line was written to combine forward and rotational velocity. The two versions mark 47.2% and 57.3% of time points as walking." }, { "kind": "paper_inconsistency", "statement": "The Methods cite Figure 3F and 3G for the PCA model sweep and the per-fly PCs, which are in Figure 4F and 4G. The Results describe Figure 3G as the Nodulus, while the Figure 3 legend calls panel G the Ellipsoid Body." }, { "kind": "other", "statement": "The preprint says the microscopy and behavioural data were deposited at Dryad and the code at GitHub, with DOIs in a key resources table that the preprint does not include. No Dryad record of these data was found, and the dandiset links neither the analysis code nor Dryad. The analysis code was found as ClandininLab/brezovec_volition_2023, whose README gives a different title." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. It also checked the blocked claims against the archive's asset list and metadata.", "agreed": 19, "of": 20, "disagreements": [ { "claim": "fig5c-global-below-threshold", "outcome": "partially_reproduced", "reason": "The own-component part holds under both readings. The below-threshold part fails under (a): left region vs VR r = -0.008, p = 0.2. Under (b) it passes only on r = 0.013, p = 0.031, and that p-value treats 27,054 autocorrelated samples as independent and would not survive any effective-sample-size correction; the left region is only 4 blocks. It asked for a circular-shift null for the below-threshold correlations." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the revised entry (after round 1), with its conclusion cells and summary, the helper module, the claims file and this record.", "agreed": 20, "of": 20, "disagreements": [] } ] }, { "id": "000947-schwab-2020-01", "dandiset": "000947", "dandiset_version": "0.240510.2211", "paper": "10.1371/journal.pbio.3000829", "paper_title": "Neural activity during a simple reaching task in macaques is counter to gating and rebound in basal ganglia-thalamic communication", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000947-schwab-2020", "entry_title": "GPi and VLa activity during reaching in macaques (Schwab et al. 2020)", "description": "Tests the findings of Schwab, Kase, Zimnik, Rosenbaum, Codianni, Rubin and Turner (2020) on the pre-MPTP recordings of dandiset 000947, single units from the internal globus pallidus and the ventrolateral anterior thalamus of two monkeys performing a reaching task. It compares rates, spike widths, peri-movement responses and their latencies, spike and rate correlations of simultaneously recorded pairs, and the effect of GPi bursts and pauses on VLa activity, and links the dandiset's units to the paper's own unit list.", "notebooks": [ { "path": "reproduce_schwab_2020.ipynb", "title": "Reproducing Schwab et al. (2020) from dandiset 000947", "executed": "notebooks/000947-schwab-2020/reproduce_schwab_2020.html" } ], "outcomes": [ { "claim": "unit-link", "statement": "The units the paper analysed can be found in the dandiset, and the dandiset's spike times and trials reproduce the per-unit peri-movement activity the paper's code stored.", "source": "Data Availability; Dryad doi:10.5061/dryad.0cfxpnvxm, Gaia_Analy.mat and Isis_Analy.mat", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "Records are matched by file, channel id and sort letter. 364 of the 394 records the paper's code keeps (92.4%) are found in every file they span (Isis GPi 104 of 104, Gaia GPi 95 of 105, Gaia VLa 60 of 66, Isis VLa 105 of 119). For 724 matched unit-directions the SDF from the dandiset correlates with the stored SDF at a median r of 0.9992, above 0.9 for 94.6%. Valid trial counts equal the paper's for 62.6%. Detection agrees on the presence of an increase for 90.9% and of a decrease for 80.7% of unit-directions. 25 matched units the paper calls VLa are labelled \"Thalamus\" in the dandiset, and 97 records span 2 to 5 files. On the side of the outside data, the paper's list gives 209 GPi and 185 VLa units, as Table 1 does.", "deviations": [ "Trial exclusion follows the Methods (6 median absolute differences from the mean); the paper's stored trial counts differ for 37% of unit-directions, by a median of 0." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "table1-unit-counts", "statement": "209 single units met the criteria to be included as GPi neurons (105 in NHP G, 104 in NHP I) and 185 as VLa neurons (66 and 119).", "source": "Results, first section; Table 1", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "The dandiset rule gives 268 GPi units (Gaia 137, Isis 131) and 279 VLa units (78 and 201), against 209 and 185 (218 in the text). Counting the same channel and sort letter on one day once gives 132 and 186; the paper's records found in the dandiset are 199 and 165. That merge joins some units the paper kept apart (47 of the 117 merged units spanning several files hold more than one of the paper's records). 518 of the 547 units are in files the paper used. Taking the rate over the length of the raw recording instead of the span of the spike train would leave out 2 more GPi units. The dandiset holds more units than the paper analysed and does not say which were kept or which units in consecutive files are one neuron.", "deviations": [ "Units are selected by the dandiset's location labels and the Methods' rate and trial criteria; the paper's anatomical criteria (within 0.5 mm of an M1-responsive site, the VLa border) cannot be applied from the files.", "Each file's unit is counted once; the paper pools a neuron recorded over consecutive files." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "table1-rest-rate", "statement": "The resting firing rate of GPi neurons (mean 70.1 spikes/s) is significantly higher than that of VLa neurons (13.5 spikes/s), and the rates are consistent between the two animals.", "source": "Results, first section; Table 1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "Mean rest rate over unit-directions 75.65 spikes/s in GPi (531) and 12.78 in VLa (552), GPi higher with rank sum p = 1.2e-171. The animals differ slightly in GPi (73.17 and 78.25, p = 0.041), where the paper reports no difference; not in VLa (p = 0.53). With one record per presumed neuron the animals do not differ in GPi (74.23 and 74.21, p = 0.69). With the paper's records 64.26 and 13.53, with one record per presumed neuron 74.22 and 12.77.", "deviations": [ "Unit selection by the dandiset rule (see table1-unit-counts)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "table1-ap-width", "statement": "Action potentials of GPi neurons are shorter than those of VLa neurons (trough to peak 0.24 against 0.50 ms; rank sum p = 1e-33).", "source": "Results, first section; Table 1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "Mean trough-to-peak width 0.247 ms in GPi and 0.509 ms in VLa, 532 of 547 units measured, rank sum p = 2.9e-37. One width is 0 and 9 reach the end of the 1.2 ms window; without them the means are 0.249 and 0.499 ms (p = 1.9e-35). No file gives one channel id to two electrodes, so each unit's channel names one electrode.", "deviations": [ "Widths come from the dandiset's 200 Hz high-pass filtered traces (the paper filtered at 300 Hz) and from the spikes in one stored chunk (about 3.2 s, median 273 spikes) per file and series." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "hold-period-ramps", "statement": "The firing rate of most units ramps during the start-position hold period (97% of GPi and 98% of VLa units with a significant linear trend); slopes are distributed symmetrically around zero, without a difference between GPi and VLa (rank sum p = 0.29).", "source": "Results, first section; Fig 2A", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "98.5% of GPi and 98.6% of VLa units have a significant control-period slope (97.0% and 97.5% at alpha 0.01), and 49.9% of significant slopes are positive. GPi and VLa slopes differ (mean -0.598 against 0.233 spikes/s2, rank sum p = 0.042), where the paper finds no difference (p = 0.29); they also differ with one record per presumed neuron (p = 0.013) and with one mean slope per presumed neuron (p = 0.033). With the paper's records the fractions are 99.5% and 98.8% and the slopes do not differ (p = 0.187), which would meet the criterion, so the outcome depends on the selection of units. With every trial aligned to a random time, the same slope test finds a significant slope in 98.4% of GPi and 99.0% of VLa units, so the fractions do not show ramps beyond what noise in a smoothed function gives; the paper's code uses the same test.", "deviations": [ "The criterion did not define a partial outcome; the outcome is partial because the first part (ramps are common) holds and the second (no difference between areas) does not." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "mvt-responsive-fraction", "statement": "Nearly all units change their discharge around movement for at least one direction (GPi 99%, 206 of 209; VLa 88.1%, 163 of 185 in Table 1, 94% in the text).", "source": "Results, second section; Table 1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "264 of 268 GPi (98.5%) and 272 of 279 VLa units (97.5%) respond in at least one direction. VLa matches the text's 94% but not Table 1's 88.1%; the criterion accepts either reading. With alpha 0.0001 the fractions with an increase alone are 81.0% and 77.4%. With every trial aligned to a random time 62.3% of GPi and 70.8% of VLa units are responsive, so the data are well above chance; with one record per presumed neuron the fractions are 100.0% and 98.4%.", "deviations": [ "The paper gives 88.1% (Table 1) and 94% (text) for VLa; both readings were listed and only the text's matches." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "increases-most-common", "statement": "Monophasic increases are the most common form of response in both GPi and VLa (48.7% and 65.3% of responses), and increases make up most detected changes (61.5% and 68.8%, biphasic responses counted twice), more than decreases (chi-squared p = 1.2e-17).", "source": "Results, second section; Table 1; Fig 2B", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "Monophasic increase is the most common form in GPi (46.9%) and VLa (50.9%), and increases are 58.8% and 60.2% of changes (746 of 1254 overall, binomial p = 1.9e-11). The GPi values are within tolerance; the VLa values are below 65.3% and 68.8% by more than 10%, also with the paper's records (54.1% and 61.4%), with one record per presumed neuron (50.1% and 60.3%) and at alpha 0.0001 (51.9% and 60.1%). With random alignment the detector finds a decrease in 25.2% (GPi) and 33.7% (VLa) of unit-directions and an increase in 14.8% and 16.2%, so chance detections add mostly decreases.", "deviations": [ "Detrending of the control period and the ISI function are implemented here from the Methods; the paper's own implementation of these steps is not in its deposit." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "monophasic-more-in-vla", "statement": "Monophasic changes are more common in VLa than in GPi (88.9% against 66.7% of responses; chi-squared p = 2.8e-12), and polyphasic responses more common in GPi.", "source": "Results, second section; Table 1", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "Monophasic responses are 71.0% in GPi and 76.7% in VLa, chi-squared p = 0.051, and VLa is outside tolerance. With the paper's records 69.0% and 81.2% (p = 0.00036), both within tolerance, so the outcome depends on the selection of units. With one record per presumed neuron 62.6% and 74.5% (p = 0.0023), VLa outside tolerance.", "deviations": [ "Unit selection by the dandiset rule (see table1-unit-counts)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "integrated-change-positive", "statement": "The mean integrated change in firing over the peri-movement epoch is positive in both GPi and VLa (3.89 and 1.75 spikes), significantly different from zero.", "source": "Results, second section; Table 1", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "The mean integrated change is positive in GPi (3.07 spikes, signed rank p = 1.1e-10) and VLa (1.50 spikes, p = 3.7e-18), both more than 10% below 3.89 and 1.75. With the paper's records 3.42 and 1.97, with one record per presumed neuron 2.13 and 1.34.", "deviations": [ "Table 1 gives the unit as spikes x 10^3; the code's computation gives spikes, the reading used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-vla-leads-gpi", "statement": "Peri-movement changes begin later in GPi than in VLa (median onsets -47 and -90 ms; rank sum p = 2.4e-5).", "source": "Results, third section; Fig 3A", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "Median onsets of all changes are -48 ms in GPi (641) and -67 ms in VLa (613); GPi is later by 19 ms without significance (rank sum p = 0.079, one-sided p = 0.04), and the VLa median is outside tolerance. In Gaia the medians are equal (-48.5 and -48 ms). With one record per presumed neuron -73 and -72 ms (p = 0.95), with one value per presumed neuron -47 and -53 ms (p = 0.44). With the paper's records -49 and -85 ms (p = 0.004), which meets the criterion, so the outcome depends on the selection of units. At alpha 0.0001 -42.5 and -63 ms (p = 0.052).", "deviations": [ "Unit selection by the dandiset rule (see table1-unit-counts)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-gpi-decr-lag-vla-incr", "statement": "GPi decreases lag behind VLa increases (median onsets -27 and -88 ms; rank sum p = 4.9e-4), against the gating prediction.", "source": "Results, third section; Fig 3B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "GPi decreases begin at a median of -29.5 ms (264) and VLa increases at -84 ms (369), rank sum p = 0.00021. The GPi median is 0.2 ms inside its tolerance (-29.7 to -24.3 ms). Gaia 0 against -95 ms (p = 0.0014), Isis -44 against -81 ms (p = 0.055). The lag also holds with the paper's records (-36 against -85 ms, p = 0.00069), with one record per presumed neuron (-46.5 against -92 ms, p = 0.011), with one value per presumed neuron (-1.5 against -71.2 ms, p = 0.00074) and at alpha 0.0001 (-30 against -81.5 ms, p = 0.00054), but in all four the GPi median is outside its tolerance. With the paper's records the outcome would be partially reproduced, so it depends on the selection of units, and the match of the medians is fragile.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-vla-decr-lead-gpi-incr", "statement": "VLa decreases precede GPi increases (median onsets -108 and -62 ms; rank sum p = 0.01).", "source": "Results, third section; Fig 3C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "VLa decreases begin at a median of -19 ms (244) and GPi increases at -69 ms (377); VLa does not lead (rank sum p = 0.17). In Gaia VLa decreases come later (12.5 against -75 ms, p = 0.0028). With the paper's records VLa leads by 13 ms without significance (-86 against -73 ms, p = 0.2). The paper itself gives -62 ms for GPi increases here and -76 ms in Table 1. With one record per presumed neuron VLa decreases come later (-8 against -92 ms, p = 0.0082), and with one value per presumed neuron too (20.5 against -45 ms, p = 0.021). With random alignment the detector finds a decrease in 33.7% of VLa unit-directions (44.2% in the data), with a median onset of -8 ms, so many VLa decreases here may be chance detections, which would pull their median late. At alpha 0.0001 the medians are -21.5 (VLa) and -57.5 ms (GPi), p = 0.3, and chance still gives a decrease in 30.8% of VLa unit-directions (42.0% in the data), so the stricter threshold does not remove the chance decreases.", "deviations": [ "The ISI-based detection finds more decreases than the paper's on the same units (330 against 286 on the linked units), which weighs on this comparison." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "gating-conflict-fraction", "statement": "Comparing every GPi response with every VLa response, 96% of comparisons conflict with gating (178,846 of 187,154); only 4% have a GPi onset 0 to 50 ms before the VLa onset with the opposite sign.", "source": "Results, third section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "95.4% of 392,933 comparisons conflict with gating (95.6% with the paper's records, 95.1% with one record per presumed neuron). With onsets shuffled across unit-directions the fraction is 95.1% (95.0 to 95.2), so the number does not distinguish the data from random onsets; it follows the gating window (98.0% for 0 to 20 ms, 86.6% for 0 to 200 ms).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "directional-units", "statement": "A majority of GPi neurons (109 of 206) and some VLa neurons (56 of 179) respond significantly more strongly to one movement direction.", "source": "Results, second section; Methods", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "122 of 264 responsive GPi units (46.2%) and 66 of 272 VLa units (24.3%) are directional, chi-squared p = 1.7e-07; both fractions are more than 10% below 52.9% and 31.3%. With the paper's records 48.2% and 26.8%, with one record per presumed neuron 53.8% and 21.9% (p = 9.8e-09).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-ccf-rare", "statement": "Short-time-scale spike-to-spike correlations between simultaneously recorded GPi and VLa units are rare (3.5% of 427 pairs over whole recordings, 2.2% of 183 at rest, 5.2% of 172 during movement) and their peaks are not larger than those of jittered controls (p = 0.975, 0.675 and 0.998).", "source": "Results, fourth section; Fig 4A-F; Table 2", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "By the KS permutation test the peak CCFs exceed those of jittered controls over whole recordings (338 pairs, p = 0.003) and during movement (306 pairs, p = 0.045), not at rest (298 pairs, p = 0.705). Significant pairs are 5.6%, 3.4% and 6.5%, none above 5% by a binomial test, and mostly positive (15 of 19 whole, 15 of 20 movement). The shift is small (median peak 0.042 against a control median of 0.038). The part of the statement that correlations are rare holds; the part that peaks are not larger than controls does not. Keeping only pairs with an approximate c0 of at most 0.3 leaves 332, 121 and 172 pairs (paper 427, 183 and 172) with KS p = 0.003, 0.333 and 0.025; one file per pair of presumed neurons gives 0.003, 0.627 and 0.037. The significant peaks fall at lags spread over 0 to 10 ms, and GPi and VLa spikes share a sample as often as independent trains would (11,376 against 11,435 expected), so shared artefacts do not explain the excess. Spike times are at the sample resolution (24414.0625 Hz) in every file. With the paper's records, paired when a GPi and a VLa record share a file (329, 298 and 301 pairs), the peaks exceed the controls over whole recordings (p = 0.005) and at rest (p = 0.033), not during movement (p = 0.203), so the outcome would be the same. Neither pair set matches the paper's 427 whole-recording pairs (338 on the dandiset rule, 329 on the paper's records); this attempt did not find out how the paper counted its pairs.", "deviations": [ "The paper's exclusion of pairs with a minimum detectable correlation c0 above 0.3 is not applied in the main test, which the criterion fixed before the analysis; the paper's simulation is not in its deposit. It is shown as a variant, with c0 approximated by a simulation on the CCF counts (independent Poisson counts at the pair's expected count, plus an injected peak).", "Only VLa spikes are jittered; the Methods do not say which train." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-noise-corr-rare", "statement": "Trial-to-trial noise correlations between GPi and VLa are rare (5.4% of 332 pairs at rest, 7.2% of 372 during movement), not different from shuffled controls (p = 0.07 and 0.388), and equally often positive and negative.", "source": "Results, fourth section; Fig 4G-H; Table 2", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "Absolute noise correlations exceed trial-shuffled controls at rest and during movement (KS permutation p < 0.001 in both). 10.1% and 10.8% of pair-targets (17.5% and 18.6% of pairs) are significant against 5.4% and 7.2% in the paper. Signs are balanced (38 and 29 at rest, p = 0.33; 39 and 33 during movement, p = 0.56), as the paper reports. Spike counts drift with trial time in many units (VLa 36.1% and 38.3% of pair-targets, Spearman p < 0.05), but with counts linearly detrended the excess remains (9.3% and 9.7% significant, KS p < 0.001), and so it does against each pair-target's own shuffles (10.8% and 14.2%), with one file per pair of presumed neurons (KS p < 0.001) and with the paper's records (9.1% and 7.4% significant, KS p < 0.001 in both).", "deviations": [ "The paper's test statistic for noise correlations is not printed in its code; the KS permutation test on absolute correlations was fixed in the criterion before the analysis.", "Significance uses the 2.5 to 97.5 percentiles of the shuffles pooled over pairs, as the paper's code does per time point." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-vla-decrease-after-gpi-bursts", "statement": "At rest, GPi burst onsets, burst offsets and pause onsets are each followed by a small, slow decrease of the population VLa firing rate.", "source": "Results, fifth section; Fig 5A-C; Table 2", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "The population VLa rate does not fall below the control band within 300 ms of GPi burst onsets (150 pairs, lowest point 2.5% below baseline), burst offsets (150, 1.9%) or pause onsets (110, 1.9%). Bursts here last 67.1 ms on average and pauses 145.3 ms, against 24 and 195 ms in the paper, and 50.7% of pairs show a change after burst onsets against 11.6% in the paper. The same per-pair test on the shifted controls gives 47.5%, 47.8% and 47.0%, so the test as the Methods describe it is at chance here, and the paper's per-pair test must differ. Computed as Fig5_S14.m does (each pair in percent of its baseline, band shifted over 0 to 800 ms), the population rate does not fall below the band either (lowest 98.1%, 98.4% and 96.9%). The Methods' rule on noisy baselines leaves out more than half of the pairs with at least 5 events (157 of 307 for burst onsets and offsets, 143 of 253 for pause onsets). With the paper's records (131, 132 and 86 pairs kept) the rate does not fall below the band either. Because the burst detector and the per-pair test differ from the paper's, this outcome says little about the paper's finding.", "deviations": [ "Burst and pause detection is a reimplementation of the Legendy and Salcman surprise method; the paper's implementation is not in its deposit (Fig5_S14.m plots stored averages and builds the control band; it holds no burst detector and no per-pair test).", "A first run used log10 in the surprise and gave bursts far longer than the paper's; the natural log, as in the Methods' formula in the paper's MATLAB, was then used. The notebook shows the durations with log10 (bursts 254.0 ms, pauses 237.0 ms) as a variant.", "The control shifts all events of a pair by one random offset of 2 to 20 s and uses VLa rate in rest samples only; the paper does not describe its control for Fig 5." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "behavior-rt-mt", "statement": "Reaction times do not differ between the animals or reach directions; movement durations are longer for reaches to the right target, and NHP G moves more slowly than NHP I.", "source": "Results, Task performance; S2 Fig", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_schwab_2020.ipynb", "notes": "In the 165 files that hold the units analysed, reaction times differ neither between the animals (F = 0.02, p = 0.89) nor between directions (F = 0.69, p = 0.41), and movement durations are longer to the right target (Gaia 0.273 against 0.216 s, Isis 0.195 against 0.174 s; p = 5.8e-38) and longer in Gaia (p = 7.3e-56). Over all 250 pre-MPTP files with trials reaction times differ between the animals (F = 15.19, p = 0.00011); over the files of the paper's records they do not (F = 3.79, p = 0.053). The paper also reports a significant animal by direction interaction for reaction times (p = 0.002), which is not part of the claim; here p = 0.12.", "deviations": [ "The first version used all 250 pre-MPTP files with trials, including files with motor cortex, SMA or VLp units only, and gave a reaction-time difference between the animals. After round 1 the test was restricted to the 165 files with units of the dandiset rule, the files of the paper's data as the dandiset identifies them; the outcome changed from partially reproduced to reproduced. All files and the files of the paper's records are shown as variants.", "Movement durations exist for 20 of the 91 Gaia files used.", "The observations are file and direction medians (330 for RT); the paper's ANOVA has 452 error degrees of freedom and does not say what its observations are. No file set here gives 452 (326 on the files with units, 496 on all files, 320 on the files of the paper's records), and the reaction-time animal effect depends on the files used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs3-emg-onset", "statement": "Agonist EMG activity begins well before movement onset, at similar times in both animals (-123 and -135 ms).", "source": "Results, Task performance; S3 Fig", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The EMG is not in the dandiset; it is in the paper's Dryad deposit (S3_EMGdata files). The Methods do not say how the onset of the EMG change was determined, and FigS3.m only plots the trial-averaged EMG with reaction times, so the onsets cannot be recomputed by the paper's method.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Dryad doi:10.5061/dryad.0cfxpnvxm (S3_EMGdata_NHP_G.mat, S3_EMGdata_NHP_I.mat), mirrored on Zenodo record 4000719", "proposed": null }, { "claim": "fig1-vla-localization", "statement": "Thalamic neurons inhibited by GPi stimulation lie dorsal and anterior to neurons excited by SCP stimulation, with a narrow border between VLa and VLp.", "source": "Results, first section; Fig 1; S1 Fig", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The stimulation mapping (responses to GPi, SCP and motor cortex stimulation along electrode tracks) is not in the dandiset, which holds task recordings only, nor in the Dryad deposit. The files give electrode coordinates and location labels, which do not test the claim. As a proxy the notebook compares electrodes labelled VLa and VLp. VLa electrodes lie anterior of VLp ones in both animals (p = 6.4e-10 and 5.5e-58) and, by the coordinates as described (ventral positive), ventral of them (p = 1.8e-11 and 2e-27), where the claim places VLa dorsal. The files do not say how the labels were assigned.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-simulation", "statement": "In a model thalamocortical cell with N converging GPi inputs, post-spike inhibition grows with GPi synchrony c and shrinks with convergence N, approximately as ((N - 1)/N)c + 1/N.", "source": "Results, sixth section; Fig 6", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "A simulation that uses no recorded data. The Dryad deposit holds its output (Data_Fig6.mat) and a plotting script, but not the model thalamocortical cell or the generator of correlated GPi spike trains; reimplementing the model of the paper's reference 103 in XPPAUT was not attempted.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Dryad doi:10.5061/dryad.0cfxpnvxm (Data_Fig6.mat, simulation output), mirrored on Zenodo record 4000719", "proposed": null } ], "findings": [ { "kind": "selection_undocumented", "statement": "The dandiset holds more GPi and VLa units than the paper analysed (268 GPi and 279 VLa units under its own labels and the Methods' rate criteria, against 209 and 185) and does not say which units the paper kept. The paper's unit list is only in its Dryad deposit." }, { "kind": "identifier_missing", "statement": "No identifier links a neuron recorded over consecutive files. 97 of the paper's 394 units span 2 to 5 files, and the dandiset stores them as separate units." }, { "kind": "metadata_error", "statement": "Location labels are inconsistent. GPi and VLa are written GPI and VLA in some files, 54 Gaia thalamic units are labelled only \"Thalamus\" (25 of them are VLa units in the paper), and 33 Isis units have an empty location and no channel id." }, { "kind": "data_missing", "statement": "30 of the 394 units the paper analysed are not among the curated units. 21 of 254 pre-MPTP files have no curated units. 13 of them hold sorted clusters in processing/ecephys/units (124 in all, 16 in G-140813-2), whose only columns are spike times, unit name and location, so there is no channel or sort letter to match them; 8 have no such table." }, { "kind": "metadata_error", "statement": "In all 254 pre-MPTP files the session_start_time is two days after the date in the session_id." }, { "kind": "metadata_insufficient", "statement": "Sort labels are letters in some files and numbers in others, and the unit quality column is missing from some files and holds free text (for example \"B -> C\") in others, without a description of its values." }, { "kind": "other", "statement": "Error trials are flagged only in files with an error_onset_time column (127 of 253 files with trials), and movement ends are missing from 87 files, all of them Gaia (32 of 119 Gaia files have them), so the Methods' trial exclusion can be applied only in part." }, { "kind": "format_error", "statement": "One pre-MPTP file (I-160616-4) has no trials table, though it has 5 curated units and raw data, and one spike train is stored twice in I-170518-2, as two M1-S units on channels 40 and 43." }, { "kind": "other", "statement": "The pre-MPTP NWB files name the paper only by its bioRxiv preprint (doi:10.1101/546598); the dandiset metadata names the published paper." }, { "kind": "data_missing", "statement": "The EMG of S3 Fig and the stimulation mapping of Fig 1 are not in the dandiset; the EMG is in the paper's Dryad deposit and the mapping is not public." }, { "kind": "metadata_insufficient", "statement": "The electrode table's coordinates relative to the anterior commissure (acx_y, acx_z) put the electrodes labelled VLa ventral of those labelled VLp, if z is ventral positive as the column description says, where the paper places VLa dorsal of VLp. The files do not say how the VLa and VLp labels were assigned, so it cannot be told whether the description of the z axis or the labels differ from the paper." }, { "kind": "paper_inconsistency", "statement": "The Results give 218 VLa units and 94% responsive VLa units where Table 1 gives 185 and 88.1%; the text gives median onsets of -62 ms for GPi increases and -108 ms for VLa decreases (Fig 3C) where Table 1 gives -76 and -95.5 ms." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier queried the archive metadata and the Zenodo deposit and tested helper functions on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; all 21 agree with the record as reviewed. Cell numbers in the reasons are those of the round-1 notebook.", "agreed": 21, "of": 21, "disagreements": [] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full re-executed notebook after the round-1 revision, with its conclusions and summary, the README, the helper module, the claims file and this record, with the paper and the paper's Fig5_S14.m. The verifier saved the paper's text under paper/. It agrees with all 21 outcomes. Cell numbers in the reasons are those of the notebook it reviewed.", "agreed": 21, "of": 21, "disagreements": [] } ] }, { "id": "000971-seiler-2022-01", "dandiset": "000971", "dandiset_version": "0.261013.1707", "paper": "10.1016/j.cub.2022.01.055", "paper_title": "Dopamine signaling in the dorsomedial striatum promotes compulsive behavior", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "000971-seiler-2022", "entry_title": "Dorsomedial striatal dopamine and compulsive reward seeking (Seiler et al. 2022)", "description": "Tests the findings of Seiler, Cosme, Sherathiya, Schaid, Bianco, Bridgemohan and Lerner (2022) on dandiset 000971, which holds the operant behavior of a fiber photometry cohort and three optogenetic cohorts, dual-site photometry from DMS and DLS dopamine axons during RI60 and RR20 training, and western blot images. It tests the shock probe phenotypes and their behavior, the DMS and DLS rewarded-unrewarded peak scores, and the effects of DMS and DLS terminal manipulations. RI30 and shock probe photometry, fear conditioning, open field and histology are not in the dandiset.", "notebooks": [ { "path": "reproduce_seiler_2022.ipynb", "title": "Reproducing Seiler et al. (2022) from dandiset 000971", "executed": "notebooks/000971-seiler-2022/reproduce_seiler_2022.html" } ], "outcomes": [ { "claim": "fig1d-ri60-vs-rr20-shocks", "statement": "Mice trained on RI60 accept more shocks in the shock probes than mice trained on RR20 (main effect of schedule, F1,43 = 6.37, p < 0.05; schedule by time interaction, F1,43 = 4.54, p < 0.05), and RI60 mice accept more shocks on the late probe than on the early one (p < 0.01).", "source": "Results, first section; Figure 1D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "In the 32 RI60 and 5 RR20 mice with both probes, RI60 mice accept more shocks (early 11.38, late 16.31, against 4.80 and 6.60), but the schedule effect has p = 0.071 (F1,35 = 3.46) and the interaction p = 0.59. The RI60 rise has paired p = 0.032, 0.063 after Bonferroni correction, where the claim needs p < 0.01. Summing a probe day's files gives the same picture. The dandiset holds 6 RR20 mice (5 with both probes) against 9 in Figure 1D, so the test has little power on the RR20 side.", "deviations": [ "5 RR20 mice with both probes where the paper has 9, and 32 RI60 mice where it has 36 (4 lack a probe in the dandiset).", "The test is a two-way mixed ANOVA on complete cases, in Python; the paper used Prism." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-omission-ri60-longer", "statement": "RI60-trained mice take longer to complete the omission probe than RR20-trained mice (unpaired t-test, p < 0.05; n = 20 and 7).", "source": "Results, first section; Figure 1E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "RI60 mice take 33.97 min (n = 19) and RR20 mice 17.72 min (n = 4); unpaired t-test p = 0.070, Welch p = 0.0005. The direction holds without significance by the paper's test. The RR20 variance is 251 times smaller than the RI60 one, so the Student and Welch tests disagree.", "deviations": [ "4 RR20 omission probes in the dandiset against 7 in the paper, and 19 RI60 against 20.", "Completion time is the time of the 50th reward, or 60 min when fewer were earned; the Methods give the 50 reward and 60 min limits but not how incomplete sessions were scored." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-omission-shock-no-correlation", "statement": "Among RI60 mice, shocks received on the late probe and omission completion time are not significantly correlated (r = 0.42, ns).", "source": "Results, first section; Figure 1F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Late probe shocks and omission time, r = 0.335, p = 0.175, n = 18 (paper r = 0.42, ns). With the early probe r = 0.592, p = 0.0076.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-phenotype-rule", "statement": "RI60 mice are split by their shock probe counts into 9 punishment resistant (PR), 9 delayed punishment resistant (DPR) and 18 punishment sensitive (PS) mice, by the rule in the Methods (DPR when the count rises by more than 85%; otherwise PR when the early count exceeds 13).", "source": "Figure 2A; STAR Methods, Behavioral Analysis", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "The stored labels give 9 PR, 9 DPR and 18 PS, which match by construction; only the rule check is informative. The Methods rule agrees with the stored label for 31 of 32 mice with both probes; 048.392 (13 early, 18 late) is stored as PR but the rule's \"more than 13\" makes it PS. With 13 or more, 32 of 32 agree. The 85% cut is near the top quartile of change (87.7%), but the median early count is 9.0, so 13 is not the median of these mice. Summing a day's files gives 30 of 32.", "deviations": [ "Four RI60 mice have one probe in the dandiset and cannot be checked against the rule." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-only-dpr-increase", "statement": "There is an interaction of phenotype and probe on shocks received (p < 0.0001), and only DPR mice receive significantly more shocks on the late probe than the early one.", "source": "Results, second section; Figure 2B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Phenotype by probe interaction F2,29 = 26.37, p = 3e-07. DPR mice rise from 11.56 to 32.11 shocks (Bonferroni p = 0.00041); PR (23.50 to 20.50) and PS (7.00 to 6.47) do not change.", "deviations": [ "32 mice with both probes against 36; F2,29 where the paper gives F3,40." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-nosepoke-rate", "statement": "During RI60 training PR and DPR mice nosepoke at higher rates than PS mice (main effect of phenotype, p < 0.0001).", "source": "Results, second section; Figure 2C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Active nosepokes per minute over RI60 training, PR 14.20, DPR 12.79, PS 5.27; ANOVA p = 4.9e-06; Tukey PR > PS p below 0.0001, DPR > PS p = 0.0003; mixed model over 492 sessions p = 2.3e-06. With the empty files kept p = 4.3e-06, with one file per mouse-day p = 7.3e-06. Sex and phenotype are confounded (17 of 18 PS mice female, 8 of 9 PR male).", "deviations": [ "The main test is a one-way ANOVA on per-mouse means; the paper used a mixed-effects analysis over days, shown as a variant.", "Training files with no active nosepoke and no reward are left out (one PS file of 170 s here, which holds inactive nosepokes and port entries)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-omission-pr-vs-ps", "statement": "PR mice take longer than PS mice to complete the omission probe (PR 51.50 +- 17, PS 27.92 +- 13.65; one-way ANOVA F2,18 = 4.36, p < 0.05; Tukey PR vs PS p < 0.05).", "source": "Results, second section; Figure 2D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "PR 51.65 min (n = 4), PS 28.06 min (n = 10), DPR 31.67 (n = 5); ANOVA F2,16 = 3.85, p = 0.043; Tukey PR vs PS p = 0.037. Three of four PR mice reach 60 min.", "deviations": [ "The Results print the values in seconds; they are read as minutes (the Methods' median split is at 29 minutes).", "10 PS mice where the paper has 11." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2k-ps-wait-longer", "statement": "After a reward PS mice wait longer before nosepoking again (38 +- 15 s) than PR (21 +- 5 s) and DPR (22 +- 4 s) mice (one-way ANOVA p < 0.01; Tukey p < 0.01 for each).", "source": "Results, second section; Figure 2K", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "PS mice wait longest (53.94 s, SD 44.67, maximum 171 s), PR 21.05 s, DPR 21.86 s. PR and DPR are within tolerance, the PS mean is above it (23 to 53 s); with each mouse's median session PS is 32.2 s. The two highest PS mice (139.298 at 171.0 s, 348.393 at 168.7 s) each have one session with a mean wait over 1000 s. ANOVA p = 0.017; Tukey PS > PR p = 0.045, PS > DPR p = 0.051.", "deviations": [ "The rewarded port entry (first port entry after a reward) and the wait (to the next active nosepoke) are defined here from the Results; the code for them is not published." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2l-extra-nosepokes", "statement": "PS mice make fewer extra nosepokes between a rewarded nosepoke and the rewarded port entry than PR mice (PS 1.28 +- 0.85, PR 3.23 +- 1.65, DPR 2.1 +- 2.63; Tukey PS vs PR p < 0.05).", "source": "Results, second section; Figure 2L", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "PS 1.61, PR 3.33, DPR 2.28 extra nosepokes per reward, all within the stated SDs; PS < PR but Tukey p = 0.117 (ANOVA p = 0.139).", "deviations": [ "Extra nosepokes are defined here from the Results (active nosepokes after a reward and before the rewarded port entry)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2m-inter-reward-interval", "statement": "PS mice have longer inter-reward intervals (79.77 +- 26.54 s) than PR (71.2 +- 32.3 s) and DPR (69.58 +- 35.18 s) mice (Kolmogorov-Smirnov, p < 0.0001 for each).", "source": "Results, second section; Figure 2M", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Pooled RI60 intervals average PS 81.75 s, PR 71.96 s, DPR 69.57 s; KS PS vs PR p = 5e-30, PS vs DPR p = 3.3e-33. Per-mouse means give ANOVA p = 0.033.", "deviations": [ "The Methods define the interval from rewarded nosepoke to rewarded nosepoke and cite Figure 2L for it; reward times are used, which coincide with rewarded nosepokes in these files." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2n-rewards-per-session", "statement": "Averaged over RI60 training, PS mice earn fewer rewards per session (39.91 +- 7.39) than DPR mice (46.56 +- 4.49; PR 45.33 +- 4.33); one-way ANOVA p < 0.05, Tukey PS vs DPR p < 0.05.", "source": "Results, second section; Figure 2N", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Rewards per RI60 session, PS 39.12, DPR 44.98, PR 44.66, all within tolerance; ANOVA F = 4.02, p = 0.028; Tukey PS vs DPR p = 0.059, so the pairwise test fails. The result sits at the threshold. With the false start of 140.306 kept as a session of 0 rewards Tukey p is 0.048 (the first version of this attempt), and with one file per mouse-day (PS 39.98, DPR 46.16, PR 44.66) it is 0.044. The rule used (no active nosepoke and no reward) was set after round 1 and is the only one of the three that gives p above 0.05; other kept short files of 1 to 4 rewards fit the same false-start reason. The claim is borderline.", "deviations": [ "Training files with no active nosepoke and no reward are left out (one PS file of 170 s); other files count as sessions, also when a mouse has two or three on one day." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2o-escalation-timing", "statement": "PR mice escalate their nosepoking as soon as they enter RI30, while DPR mice escalate later, during RI60.", "source": "Results, second section; Figure 2O", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "RI30 rate PR 4.85 per minute, DPR 3.03 (Mann-Whitney p = 0.114), PS 2.22 (p = 0.0063), so part (i) fails on DPR. Median RI60 slope DPR 0.809, PR 0.494 nosepokes/min per day, so part (ii) holds (p = 0.289).", "deviations": [ "The paper shows this with a segmental linear regression in Prism; the measures here (RI30 rate and RI60 slope per mouse) were chosen before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1i-ri60-more-rewards", "statement": "RI60-trained mice earn more rewards per training session than RR20-trained mice (unpaired t-test, p < 0.0001).", "source": "Results, first section; Figure S1I (legend not available)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "RI60 41.97 against RR20 22.63 rewards per session, t-test p = 5.4e-07, not below the 0.0001 stated. With the 21 empty files kept as sessions of 0 rewards (the 20 RR20 files that hold port entries only and the RI60 false start), RR20 15.38, RI60 41.89 and p = 1.4e-11.", "deviations": [ "6 RR20 mice where the paper has 9 (or 7 in the Methods).", "20 RR20 files of four mice hold port entries only and are left out, with one RI60 false start." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2b-males-more-shocks", "statement": "Male mice accept more shocks than female mice in the shock probes (main effect of sex, F1,35 = 26.19, p < 0.0001).", "source": "Results, second section; Figure S2B (legend not available)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Males early 16.58 and late 23.25, females 8.25 and 12.15; sex effect F1,30 = 9.81, p = 0.0039. The paper's p < 0.0001 does not hold. Sex is confounded with phenotype (PR 8 males of 9, PS 17 females of 18).", "deviations": [ "The supplementary legend was not available; the test is a two-way mixed ANOVA of sex and probe." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-ri30-dms-peaks", "statement": "Peaks in DMS dopamine axon activity at rewarded nosepokes emerge during RI30 in PR mice, and more slowly across RI60 in DPR mice.", "source": "Results, third section; Figure 3E", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds photometry for 53 RI60 sessions, 9 RR20 sessions and one session described as a probe test, and none for RI30, so the emergence of peaks during RI30 cannot be tested.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-dms-score-phenotype", "statement": "The DMS rewarded-unrewarded peak score differs by phenotype (F2,33 = 8.16, p < 0.01) and changes across training (p < 0.001).", "source": "Results, third section; Figure 3F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Mean DMS score PR 2.35, DPR 1.66, PS 1.05 z, the paper's order, but the phenotype effect has likelihood ratio p = 0.100 and neither stage alone is significant (p = 0.124 early, 0.270 late). The score rises from early to late (paired p = 0.046, 17 mice; model stage p = 0.088). Without the dropout step the phenotype p is 0.389. 51 scores from 34 mice. The mice with a score differ from Figure 3E (late PR 4, DPR 7, PS 10 against 5, 6, 13), so the comparison with F2,33 is not like for like.", "deviations": [ "Early and late RI60 only; the paper's test also includes RI30, which is not in the dandiset.", "Channel dropouts are left out (samples below half the channel median, with 1 s around them), a step the authors' code does not have; it was added after seeing that dropouts made some session z-scores near zero, and after the per-session scores had been seen. The authors' processing without it is shown and gives p = 0.389.", "One DLS recording with dropouts over 10% of samples is excluded, and one session without rewarded nosepokes (mixed clocks) has no score.", "A linear mixed model with a random intercept per mouse replaces Prism's mixed-effects analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-dms-score-shock-correlation", "statement": "The DMS rewarded-unrewarded peak score correlates with the shocks a mouse receives in the shock probes (r = 0.53, p < 0.0001).", "source": "Results, third section; Figure 3G", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Reading (a), pooled early and late pairs, r = 0.170, p = 0.24, n = 49 (given as measured); (b) late pairs r = 0.014, p = 0.95; (c) early pairs r = 0.375, p = 0.045, n = 29. Only (c) is positive and significant, and it is below the tolerance around 0.53. The support is weak. Corrected for the three readings (c) has p = 0.13, and without the dropout step (c) gives r = 0.362, p = 0.053 and the pooled r is 0.100. The step leaves out more than 1% of samples in one DMS session of 51, but changes some scores a lot where it leaves out less (88.239 from 0.09 to 1.92, 048.392 from 0.02 to 1.81, 346.394 from 0.00 to 1.10).", "deviations": [ "The paper does not say which scores and probes form the pairs; three readings were listed before the analysis, none of which matches.", "RI30 scores, which may be among the paper's points, are not in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-dms-score-omission-no-correlation", "statement": "The DMS rewarded-unrewarded peak score does not correlate with omission completion time (r = 0.1, ns).", "source": "Results, third section; Figure 3H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Late DMS score against omission time, r = 0.014, p = 0.96, n = 12 (95% interval -0.56 to 0.58); pooled r = -0.050, p = 0.80. With 12 mice the test has little power.", "deviations": [ "12 mice with a late score and an omission probe." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-dls-score-no-phenotype", "statement": "The DLS rewarded-unrewarded peak score has no significant effect of phenotype.", "source": "Results, fourth section; Figure 4F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Phenotype likelihood ratio p = 0.48 (per stage p = 0.61 and 0.47); stage p = 0.034, as the paper also finds a training effect in DLS.", "deviations": [ "No RI30 stage; dropout step as for fig3f-dms-score-phenotype (without it p = 0.68)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4g-dls-score-shock-no-correlation", "statement": "The DLS rewarded-unrewarded peak score does not correlate with shocks received (r = -0.01, ns).", "source": "Results, fourth section; Figure 4G", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Pooled DLS score against shocks, r = 0.326, p = 0.024, n = 48, where the paper finds r = -0.01. Late pairs r = 0.374, p = 0.10; early pairs r = 0.103, p = 0.60. Without the dropout step r = 0.113, p = 0.45 (late 0.033, early 0.182), so the outcome depends on the artifact handling, a step chosen here and in neither the Methods nor the authors' code. The DLS labels are consistent with the data (the DLS response has the larger 2 to 10 s area, as the paper describes for DLS).", "deviations": [ "The pairing of scores and probes follows reading (a) of fig3g-dms-score-shock-correlation; the paper does not state it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-dls-score-omission-no-correlation", "statement": "The DLS rewarded-unrewarded peak score does not correlate with omission completion time (r = -0.21, ns).", "source": "Results, fourth section; Figure 4H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Late DLS score against omission time, r = 0.311, p = 0.32, n = 12 (paper r = -0.21, ns); 95% interval -0.32 to 0.75, so the test has little power.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-dms-chr2-escalation", "statement": "Mice receiving DMS dopamine terminal stimulation on rewarded nosepokes (ChR2) escalate their nosepoking faster than EYFP and ChR2 Scrambled controls during FR1 and RI30.", "source": "Results, fifth section; Figure 5F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "In the pooled fit no ChR2 slope differs from a control (FR1 interaction p = 0.63 and 0.98, RI30 p = 0.82 and 0.49), and the pooled FR1 ChR2 slope (0.011) is not above the controls (0.051 and 0.005). Per-mouse slopes, a variant, put ChR2 above EYFP (p = 0.015) and Scrambled (p = 0.021) in FR1 but not in RI30. ChR2 mice nosepoke more in RI30 (7.75 against 4.01 and 4.21 per minute). The pooled fit mixes mice with 1 to 13 FR1 sessions, which the per-mouse slopes avoid. A mixed model with a random intercept and slope per mouse puts the FR1 ChR2 slope above ChR2 Scrambled (p = 0.034) and EYFP (p = 0.0075) but not in RI30 (p = 0.68 and 0.70); under that model the rule would give partially_reproduced. That FR1 fit converged only after a retry with lbfgs, warns that the MLE may be on the boundary and has a random intercept variance near zero, and a model with a random intercept only puts ChR2 above neither control (p = 0.46 and 0.33). The criterion fixed the pooled fit before the analysis, so the outcome stays.", "deviations": [ "The paper fits a segmental linear regression in Prism; the pooled least squares fit with a group by session interaction was chosen before the analysis.", "33 DMS excitatory mice in the dandiset where the paper has 39." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5g-dms-chr2-more-shocks-early", "statement": "On the first shock probe ChR2 mice accept more shocks than EYFP mice (interaction of time and manipulation, F2,35 = 3.65, p < 0.05; Tukey p < 0.05); the difference fades by the second probe.", "source": "Results, fifth section; Figure 5G", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "First probe ChR2 28.69, EYFP 21.86, Scrambled 20.67 shocks, the paper's order; Tukey ChR2 vs EYFP p = 0.51; group by probe interaction F2,29 = 1.95, p = 0.16 (paper F2,35 = 3.65).", "deviations": [ "32 mice with both probes (13 ChR2, 12 Scrambled, 7 EYFP) where the paper's degrees of freedom imply 38." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5h-dms-chr2-mostly-pr", "statement": "ChR2 mice are very likely to be classified PR, while EYFP and ChR2 Scrambled mice are distributed across phenotypes as expected.", "source": "Results, fifth section; Figure 5H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "PR in 12 of 13 ChR2 (92%), 5 of 7 EYFP (71%), 6 of 12 Scrambled (50%); Fisher ChR2 against both controls p = 0.0497. The control PR fractions are higher than in the fiber photometry cohort (19%).", "deviations": [ "Phenotypes are computed with the Methods rule, as the dandiset stores none for optogenetic mice." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5f-chr2-pr-by-sex", "statement": "Under DMS ChR2 stimulation 100% of male mice and about 71% of female mice are PR.", "source": "Results, fifth section; Figure S5F (legend not available)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "7 of 7 male ChR2 mice are PR; 5 of 6 female ChR2 mice (83.3%), outside 71 +- 7.1%.", "deviations": [ "One female ChR2 mouse (126.286) has a single session in the dandiset and no probes." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5i-dms-stim-no-omission-effect", "statement": "DMS dopamine terminal stimulation does not change omission probe performance.", "source": "Results, fifth section; Figure 5I", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "ChR2 25.79, Scrambled 35.53, EYFP 37.29 min; ANOVA p = 0.17, Kruskal-Wallis p = 0.14.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-nphr-learning-dropout", "statement": "DMS dopamine terminal inhibition impairs initial learning; 25% of NpHR and 22% of NpHR Scrambled mice in group 1 failed FR1, and 29% of NpHR mice in group 2 failed RI30, and were dropped.", "source": "Results, sixth section; Figure 6F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_seiler_2022.ipynb", "notes": "The dandiset holds 13 NpHR, 13 NpHR Scrambled and 16 EYFP mice, where Figure 6F counts 16, 15 and 16. The shortfall (3, 2, 0) equals the mice the paper drops (about 4 NpHR, 2 NpHR Scrambled) less the one NpHR mouse deposited and flagged as not learning (270.476, no RI60). So the dropped mice are, but for that one, not in the dandiset. The 'Did Not Learn' flag also marks an EYFP mouse that reached RI60 (244.465), so it is not the paper's dropout criterion, and no file says which group (1 or 2) a mouse is in. Blocked under the criterion, as the dandiset does not say which mice were dropped.", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6g-nphr-fewer-shocks-late", "statement": "DMS dopamine terminal inhibition on rewarded nosepokes delays punishment resistance; NpHR mice accept fewer shocks than EYFP mice on the second probe (Tukey p < 0.01).", "source": "Results, sixth section; Figure 6G", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Second probe NpHR 9.33 against EYFP 23.47 shocks (34 mice with both probes), Tukey p = 0.069. With all 35 mice that have a second probe p = 0.043. Mixed ANOVA group p = 0.056.", "deviations": [ "34 DMS inhibitory mice with both probes; the paper's degrees of freedom (F2,36) imply 39." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6h-nphr-more-ps", "statement": "The NpHR group has more PS mice, and the NpHR Scrambled group more PR mice, than the EYFP group.", "source": "Results, sixth section; Figure 6H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "PS in 8 of 9 NpHR (89%) against 5 of 15 EYFP (33%), Fisher p = 0.013; PR in 6 of 10 NpHR Scrambled (60%) against 6 of 15 EYFP (40%), p = 0.43. The NpHR effect is in both sexes here (3 of 4 females and 5 of 5 males PS).", "deviations": [ "Phenotypes computed with the Methods rule." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6i-nphr-no-omission-effect", "statement": "DMS dopamine terminal inhibition does not change omission completion time.", "source": "Results, sixth section; Figure 6I", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "EYFP 28.74, NpHR 21.47, NpHR Scrambled 27.82 min; ANOVA p = 0.21.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7f-dls-escalation-similar", "statement": "Mice receiving DLS dopamine terminal stimulation (ChR2, EYFP, ChR2 Scrambled) escalate their nosepoking at the same rates.", "source": "Results, seventh section; Figure 7F", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "In FR1 the Scrambled slope (0.087) is below the EYFP slope (0.224), interaction p = 0.013 (F test of all group terms p = 0.034). ChR2 differs from neither control (p = 0.12 and 0.98); in RI30 no pair differs (p = 0.09 to 0.92). The difference is between the two control groups, not a ChR2 effect. A mixed model with a random intercept and slope per mouse finds no difference in slope (p = 0.43 to 0.96, FR1 EYFP vs Scrambled p = 0.76), but its FR1 fit has a singular random effects covariance, so those p values are weak evidence. A model with a random intercept only fits without warnings and finds no FR1 difference either (EYFP vs Scrambled p = 0.23). The FR1 difference rests on the pooled fit the criterion fixed.", "deviations": [ "The paper gives no test; the fit of fig5f-dms-chr2-escalation was used, judged on all three pairs." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7g-dls-stim-no-shock-effect", "statement": "DLS dopamine terminal stimulation does not change the number of shocks received.", "source": "Results, seventh section; Figure 7G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Group p = 0.055, group by probe p = 0.068, 31 mice with both probes. EYFP mice rise most (19.11 to 32.89).", "deviations": [ "4 DLS mice lack a late probe in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7h-dls-similar-phenotypes", "statement": "DLS ChR2, EYFP and ChR2 Scrambled mice have similar distributions of PR, DPR and PS.", "source": "Results, seventh section; Figure 7H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "Chi-square p = 0.12 on a 3 x 3 table with smallest expected count 1.5; ChR2 mice include no DPR.", "deviations": [ "The paper gives no test; a chi-square test was chosen before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7i-dls-no-omission-effect", "statement": "DLS dopamine terminal stimulation does not change omission completion time.", "source": "Results, seventh section; Figure 7I", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "ChR2 28.44, Scrambled 33.51, EYFP 36.08 min; ANOVA p = 0.53.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs3ab-dat-protein-not-reduced", "statement": "Heterozygous DAT-IRES-cre mice do not have reduced DAT protein in DMS or DLS compared with wild-type mice.", "source": "Results, third section; Figure S3A-B (legend not available)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_seiler_2022.ipynb", "notes": "DAT/actin of het samples is 131.3% of the WT mean in DMS (t-test p = 0.41) and 74.7% in DLS (p = 0.20). The table holds females only, 3 WT and 4 het samples per region, named as lanes of one WT mouse (410) and one het mouse (484); the male samples of Figure S3A are not in it.", "deviations": [ "Females only; the paper's test is in a legend that was not available, so an unpaired t-test was used." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.11266654 (Densitometry.xlsx)", "proposed": null }, { "claim": "figs1a-shock-aversive", "statement": "The 0.2 mA shock is aversive in a fear conditioning test, in males and females.", "source": "Results, first section; Figure S1A", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No fear conditioning session or freezing score is in the dandiset; every subject belongs to the photometry cohort, an optogenetic cohort or the western blot. The paper says data are available on request and names no archive.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs3cd-open-field", "statement": "Heterozygous DAT-IRES-cre mice are not hyperactive in a novel open field.", "source": "Results, third section; Figure S3C-D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No open field tracking is in the dandiset or in another public archive the paper or the dandiset names.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-gcamp-in-dopamine-neurons", "statement": "GCaMP7b is expressed in TH-positive dopamine neurons of medial SNc (n = 572 cells) and of medial and lateral SNc (89.56% of GCaMP neurons TH-positive).", "source": "Figures 3C and 4C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No histology images or cell counts are in the dandiset or in another public archive the paper or the dandiset names.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The Methods say photometry was recorded during RI30 and on both shock probes, but the dandiset holds photometry only for RI60 and RR20 training (62 sessions) and one session described as a probe test. The RI30 stage of Figures 3E-F and 4E-F cannot be tested." }, { "kind": "data_missing", "statement": "Mice are missing against the paper. 6 RR20 mice against 9 in Figure 1D (7 in the Methods), 33 DMS excitatory mice against 39, 42 DMS inhibitory mice against 47 in Figure 6F, and 35 DLS excitatory mice against 36. Of the photometry RI60 mice, 028.392 and 62.207 have no late probe and 89.247 and 78.214 no early one; several optogenetic mice lack a late probe." }, { "kind": "data_missing", "statement": "The fear conditioning (Figure S1A), open field (Figure S3C-D) and histology (Figures 3C, 4C and the probe placements) are not in the dandiset, and the paper says data are available on request." }, { "kind": "metadata_insufficient", "statement": "Optogenetic mice have no stored phenotype (the notes read 'Punishment Group nan'), and the DMS inhibitory files do not say whether a mouse belongs to group 1 (light from FR1) or group 2 (light from RI30). Only two mice carry a 'Did Not Learn' flag, one of them an EYFP control, while the paper drops NpHR and NpHR Scrambled mice." }, { "kind": "other", "statement": "The 137 files of the group 'Opto-DLS-Excitatory-Unknown' repeat sessions of mice that are also deposited under a named arm; 135 share subject and start time with a named file, and those loaded here have identical events. They count the same sessions twice if taken at face value." }, { "kind": "metadata_error", "statement": "Mouse 290.407 is filed under two experiments, 24 files as DMS excitatory ChR2 Scrambled and 2 (plus 2 'Unknown') as DLS excitatory ChR2." }, { "kind": "format_error", "statement": "In shock probes on the left nosepoke, the reward series is named right_reward_times while its times are left nosepokes (151 files)." }, { "kind": "format_error", "statement": "In the stitched photometry session of 332.393 on 2020-07-28, the reward times are MedPC times that coincide with no nosepoke time, while the nosepokes and port entries are TDT times, so rewarded nosepokes cannot be identified." }, { "kind": "other", "statement": "Several photometry recordings hold dropouts where a raw channel falls near zero (6 sessions reach |z| above 50 after the authors' processing, up to 1758), and in one (141.308, 2019-08-09) the DLS channels drop out through most of the recording. The dandiset does not mark these or say which recordings the paper excluded for artifacts." }, { "kind": "metadata_error", "statement": "The fiber photometry table stores the fiber coordinates without the signs the Methods give (DV 2.8 for -2.8 and DLS AP 0.1 for -0.1)." }, { "kind": "code_mismatch", "statement": "The authors' MATLAB code comments call Dv1A the control and Dv2A the GCaMP signal, while the conversion and the files take Dv1A as the DMS 465 nm signal. The data side with the files (a larger rewarded response as labelled than swapped in 46 of 61 DMS sessions)." }, { "kind": "selection_undocumented", "statement": "Mouse 048.392 is stored as PR with 13 shocks on its early probe, where the Methods classify as PR mice with more than 13, and the Methods call 13 a median split while the median early count of the RI60 mice is 9. How the stored labels were assigned is not documented." }, { "kind": "paper_inconsistency", "statement": "The Results give omission completion times in seconds (PR 51.50, PS 27.92), but sessions last at most 60 minutes and the Methods split omission times at 29 minutes; the data fit minutes. The Methods give 26 DMS inhibitory mice and 7 RR20 mice, Figure 6F counts 47 and Figure 1D 9." }, { "kind": "other", "statement": "The Zenodo densitometry table the dandiset names holds female samples only, labelled as three lanes of one wild-type mouse and four of one heterozygous mouse, while the dandiset's blot images include males." }, { "kind": "data_missing", "statement": "20 RR20 training files (mice 96.259, 97.257, 99.257 and 100.258, 2019-04-29 to 2019-05-03) hold port entries only, with no nosepoke or reward series, so those sessions' nosepokes and rewards are not in the dandiset." }, { "kind": "other", "statement": "Several fiber photometry mice have two or three RI60 files on one day (11 mouse-days), most a short file of 0 to 7 rewards beside a full session, some not (81.236 on 2019-02-06 has 6, 28 and 42 rewards). The dandiset does not say which file is the day's training session." }, { "kind": "data_missing", "statement": "Figure 6F counts 16 NpHR, 15 NpHR Scrambled and 16 EYFP mice; the dandiset holds 13, 13 and 16. The mice missing are about the number the paper dropped for not learning, so the dropped mice are mostly not deposited, and the 'Did Not Learn' flag marks one NpHR mouse and one EYFP mouse that reached RI60." }, { "kind": "other", "statement": "In 45 of 64 RR20 training files with rewards, the reward times coincide with no nosepoke time, unlike RI60 and FR1 files; the relation of RR20 rewards to nosepokes is not described." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier checked the archive's asset list and metadata for the blocked claims and tested helper functions on synthetic inputs. It agreed with 37 of the 38 outcomes and would make fig6-nphr-learning-dropout blocked. Its other points and the responses not tied to one claim are as follows. B10 (events outside a recording dropped silently) - the notebook now prints the events kept, 2336 of 2337 rewarded and 10892 of 10916 unrewarded. C (Figure S1 to S7 legends not in the PMC text) - not resolved; the supplementary legends could not be obtained here either.", "agreed": 37, "of": 38, "disagreements": [ { "claim": "fig6-nphr-learning-dropout", "outcome": "blocked", "reason": "Per arm the dandiset has NpHR 13, Scrambled 13 and EYFP 16 mice against 16, 15 and 16 in Figure 6F. The shortfall equals the paper's dropouts minus one deposited and flagged NpHR mouse, so most dropped mice were never deposited. The 'Did Not Learn' flag also marks an EYFP mouse that reached RI60, so it is not the paper's dropout criterion, and no file says which mouse is in group 1 or 2. This makes the claim blocked, not testable (B4)." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file and the attempt record. The verifier did not re-download the paper. It agreed with all 38 outcomes, and found that all round-1 points but the supplementary legends are resolved or disclosed. Its general point that the runtime of about 25 minutes matches the output needs no reply; the last runs took 883 and 892 s, and the README now says 15 to 25 minutes.", "agreed": 38, "of": 38, "disagreements": [] } ] }, { "id": "001038-azcorra-2023-01", "dandiset": "001038", "dandiset_version": "0.241111.1719", "paper": "10.1038/s41593-023-01401-9", "paper_title": "Unique functional responses differentially map onto genetic subtypes of dopamine neurons", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001038-azcorra-2023", "entry_title": "Functional responses of genetic subtypes of dopamine neurons (Azcorra, Gaertner et al. 2023)", "description": "Tests the fiber photometry findings of Azcorra, Gaertner et al. (2023) on dandiset 001038, which holds the recordings from striatal axons and SNc somas of Vglut2, Calb1, Anxa1, Aldh1a1 and DAT mice running on a treadmill and receiving rewards and air puffs. It covers locomotion signaling (Figures 2, 3 and 5), reward and air puff responses (Figure 4), clustering (Figure 6), soma and axon correlation (Figure 7) and Extended Data Figures 1 and 6 to 9. Two snRNA-seq claims of Figure 1 are tested on the paper's GEO matrices.", "notebooks": [ { "path": "reproduce_azcorra_2023.ipynb", "title": "Reproducing Azcorra, Gaertner et al. (2023) from dandiset 001038", "executed": "notebooks/001038-azcorra-2023/reproduce_azcorra_2023.html" } ], "outcomes": [ { "claim": "recording-counts-locomotion", "statement": "The striatal recordings that pass the locomotion criteria number 42 from 12 Vglut2 mice, 22 from 6 Calb1 mice, 47 from 10 Anxa1 mice, 74 from 14 DAT mice and 75 from 14 Aldh1a1 mice.", "source": "Figure 2f legend; Extended Data Figure 6c legend; Methods, Analysis of signaling during locomotion", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "With the Methods' and code's criteria (SNR above 10, stored 405 nm peak cross-correlation below 0.1, more than 100 s running and at most 5% artifact samples, both recomputed), 50, 28, 82, 89 and 85 striatal recordings pass for Vglut2, Calb1, Anxa1, DAT and Aldh1a1, against 42, 22, 47, 74 and 75; none within 10%. Mice are 14, 7, 9, 14 and 15 (legend 12, 6, 10, 14, 14; Methods 12, 6, 9, 14, 14). A 405 nm threshold of 0.05 gives 39, 24, 73, 68 and 73. The paper gives no counts by location, fiber setup or session type, so where the excess lies cannot be measured (every Anxa1 recording is from a dual-fiber file and every Calb1 recording is labelled DS). One recording per mouse, date and depth gives 47, 28, 57, 89 and 78, and recordings made before the paper's submission 50, 27, 75, 89 and 85. The stimulus counts match exactly from the same files, including 16 air puff recordings made after submission, so the recordings are present; which entered Figure 2 is not recoverable.", "deviations": [ "Running time and artifact flags are recomputed with the code's procedure, as the files do not hold them; running after rewards that were not consumed cannot be excluded, as those rewards are not in the Events table." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "recording-counts-stimuli", "statement": "The striatal recordings in the reward analysis number 28 (Vglut2), 17 (Calb1), 51 (Anxa1) and 63 (DAT), and in the air puff analysis 29, 17, 57 and 69.", "source": "Figure 4d and 4f legends; Methods, Criteria for recording inclusion", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "All eight counts and the mouse counts equal the legend's, and the recordings without consumed rewards are 1/29, 0/17 and 6/57 as in the Methods.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-xcorr-direction", "statement": "Cross-correlations between dF/F and acceleration show a trough at positive lags for Calb1 and Vglut2 axons (transients after decelerations) and a peak at positive lags for Anxa1 axons (transients after accelerations).", "source": "Figure 2d,f; Results, Genetic subtypes show different signaling patterns during locomotion", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Integral over lags 0 to 1 s, mean -0.033 for Vglut2 (94% negative), -0.036 for Calb1 (93%) and 0.014 for Anxa1 (26% negative), each p x3 below 0.0001. The 405 nm control integrals are 0.002 to 0.005. Holds in 14/14 Vglut2, 6/7 Calb1 and 7/9 Anxa1 mice. The selection has more recordings than the paper's (see recording-counts-locomotion).", "deviations": [ "Larger selection than the paper's (50, 28, 82 against 42, 22, 47 recordings)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2i-trough-lag", "statement": "Calb1 transients follow decelerations with a shorter lag than Vglut2 transients; the trough of the cross-correlation is at 0.42 s for Vglut2 and 0.17 s for Calb1 on average (P = 1e-6).", "source": "Figure 2i", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Methods timing gives Vglut2 0.416 s (within tolerance) and Calb1 0.140 s (below 0.153 to 0.187), rank-sum p x3 = 2.1e-08. The code's timing, which reports 0.02 s later, gives 0.436 and 0.160 s, both within tolerance. Mouse means 0.387 against 0.193 s, p = 0.0056.", "deviations": [ "The Methods' lag is the main result; the code adds two bins to the reported lag, shown as a variant.", "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2jk-pca-variance", "statement": "In a PCA of the cross-correlations of all Vglut2, Calb1 and Anxa1 striatal recordings, PC1 explains 64.2% and PC2 20.1% of the variance (84.3% together).", "source": "Figure 2j,k; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "PC1 58.32% and PC2 22.09% against 64.2 and 20.1; both inside tolerance by small margins (0.5 and 0.02 points). Bootstrap intervals 53.9 to 63.0% and 18.5 to 26.3%. 160 recordings against the paper's 111.", "deviations": [ "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2l-pc-angles", "statement": "The PC1/PC2 angles of the cross-correlations separate the subtypes, with mean angles of 141 degrees for Vglut2, 208 for Calb1 and 239 for Anxa1 (P = 2e-7 V-C, 4e-11 V-A, 2e-4 C-A).", "source": "Figure 2l; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Mean angles 140.1, 208.8 and 233.3 degrees against 141, 208, 239; rank-sum p x3 7.9e-09 (V-C), 7.7e-13 (V-A), 1.3e-05 (C-A). Three of nine Anxa1 mice have mean angles below 160 degrees. The arithmetic mean on 0 to 360 degrees follows the code; the circular means are 136.4, 223.0 and 301.3, so the Anxa1 mean depends on where the circle is cut.", "deviations": [ "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2g-event-counts", "statement": "Triggered averages on large accelerations and decelerations average 135 +/- 77 accelerations and 138 +/- 101 decelerations per recording (mean +/- s.d.).", "source": "Methods, Analysis of signaling during locomotion (Figure 2g)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "131.4 +/- 75.1 accelerations and 129.2 +/- 95.0 decelerations per recording over 334 recordings, against 135 +/- 77 and 138 +/- 101.", "deviations": [ "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7f-prob-transient-after-event", "statement": "The probability that a dF/F increase follows an acceleration is 57.5% for Anxa1, and that one follows a deceleration is 62.4% for Vglut2 and 62.3% for Calb1.", "source": "Extended Data Figure 7f; Methods", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "61.8% (Vglut2 decelerations), 63.9% (Calb1) and 55.8% (Anxa1 accelerations), each above 50% with p below 3e-06; the opposite event types give 38.7 to 43.6%.", "deviations": [ "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6f-dec-peak-timing", "statement": "In averages triggered on decelerations, the dF/F peak comes later for Vglut2 (0.35 s) than for Calb1 (0.23 s), P = 0.01.", "source": "Extended Data Figure 6f", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Vglut2 peaks later than Calb1 (0.476 against 0.320 s, p = 0.001), but both means are about 0.1 s above the paper's 0.35 and 0.23 s and outside tolerance; the code's timing adds 0.01 s. Vglut2 is later as a whole (median 0.5 s, peak of the mean 0.44 s, 31 of 50 recordings above 0.385 s). Calb1 peaks are skewed to the right (skewness 1.48); the median 0.25 s is within tolerance and the peak of the mean is 0.27 s, so its gap in the mean comes from a tail of late peaks (13 of 28 above 0.253 s). The cause of the Vglut2 difference is not found.", "deviations": [ "The Methods' time is the main result; the code adds one bin, shown as a variant.", "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5ab-transient-scaling", "statement": "Transient amplitude grows with the size of the deceleration (Vglut2 214%, Calb1 243%) or acceleration (Anxa1 206%) from the smallest to the largest quintile (P = 0.01, 0.002, 0.002).", "source": "Figure 5a,b; Results", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "With the recomputed onsets that are also stored (which carry the code's exclusion after every reward), ratios 241% (Vglut2), 246% (Calb1) and 232% (Anxa1), p x3 = 0.002, below 0.001 and 0.001. Calb1 is within tolerance; Vglut2 is above 235.4% and Anxa1 above 226.6%. With every recomputed onset (only consumed rewards excluded), 239, 266 and 222%. The ratio over recordings with both quintiles is the same.", "deviations": [ "The code reselects onsets and excludes 5 s after every reward; the Events table lists consumed rewards only, so the recomputed onsets are kept where the stored onsets, which carry that exclusion, agree. All recomputed onsets are shown as a variant.", "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4g-reward-response", "statement": "Vglut2 and Calb1 axons respond to unexpected rewards (means 7.9 and 12.4 normalized dF/F s), as do DAT recordings (5.9).", "source": "Figure 4d,g; Results", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "With the Methods' windows, Vglut2 8.77, Calb1 13.73 and DAT 6.69, all p x4 below 0.001, each just above tolerance (8.69, 13.64, 6.49). With the code's windows 7.90, 12.40 and 5.88, equal to the paper's values to the decimal, which suggests the paper's reward means come from the code's windows; for air puffs this holds except for DAT.", "deviations": [ "Methods' windows (+0.05 to +0.55 s minus -0.5 to 0 s) as the main result; the code's (0 to 0.5 s minus -0.55 to -0.05 s) as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4g-anxa1-no-reward", "statement": "Reward responses are almost entirely absent from Anxa1 axons (mean -0.5, P = 0.1, not significant).", "source": "Figure 4d,g; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Mean -0.42, p x4 = 0.12 (code windows -0.39, p x4 = 0.14), against -0.5 and P = 0.1. 37% of 51 recordings are above 0 and 4 above 5.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4g-airpuff-response", "statement": "Air puffs evoke increases in Vglut2 (15.8), Calb1 (5.3) and DAT (5.3) axons and a decrease in Anxa1 axons (-3.7).", "source": "Figure 4f,g; Results", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Vglut2 16.77, Calb1 5.41, Anxa1 -3.66 and DAT 2.69, all p x4 below 0.01 in the stated direction. The DAT mean is half the paper's 5.3 under either window (code 2.46), with the paper's 69 recordings; the others are within tolerance. DAT mouse means (code windows) run from -3.83 to 6.03, with 3 of 11 mice at or below 0; the cause of the difference is not found.", "deviations": [ "Methods' windows as the main result; the code's as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-reward-vs-airpuff", "statement": "Vglut2 axons respond more to air puffs than to rewards, and Calb1 axons more to rewards than to air puffs.", "source": "Figure 4h; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Vglut2 air puff minus reward 8.03 (86% of 28 recordings, p x4 = 9.1e-06); Calb1 -8.32 (18% favour air puffs, p x4 = 0.0034).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4i-reward-size", "statement": "Calb1 axons respond more to large than to small rewards (mean difference 3.9, P = 9e-3), as do DAT recordings (1.9, P = 8e-5), while Vglut2 (0.9, P = 0.6) and Anxa1 (0.04, P = 1) do not.", "source": "Figure 4i; Results", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Calb1 4.43 (p x4 = 0.0049) and DAT 2.33 (p x4 = 3.7e-06) larger for large rewards; Vglut2 1.23 (p x4 = 0.22) and Anxa1 0.22 (p x4 = 1) not, so the significance pattern holds. The Calb1 and DAT differences are above tolerance with the Methods' windows and within it with the code's (3.93, 1.83). n is 25, 14, 37 and 50 against 25, 14, 42 and 55; requiring 1 or 2 rewards of each size gives Anxa1 and DAT 47 and 58, or 40 and 53, with the same differences and p-values.", "deviations": [ "Methods' windows as the main result; the code's as a variant.", "A recording needs 3 small and 3 large rewards; the paper's Anxa1 and DAT counts are higher, so its rule for this panel differs." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed8f-rest-reward-same", "statement": "Reward responses of Vglut2 and Calb1 axons are the same for rewards delivered at rest as for the others (P = 1 for both), so the reward signal is not a movement response.", "source": "Extended Data Figure 8e,f; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "At rest minus not at rest, Vglut2 0.45 (p x4 = 1, n = 8) and Calb1 -0.15 (p x4 = 1, n = 8), against not-at-rest means 9.38 and 15.35. Anxa1 and DAT p x4 = 0.43 and 0.4. Counts differ from the legend's for Calb1 (8 against 10), Anxa1 (36 against 42) and DAT (33 against 42), and the mice for Vglut2 (3 against 6), Calb1 (4 against 6) and DAT (6 against 10); the cause is not found. The rest rows are the reward rows 0.01 s later with the same durations, and the 2647 onsets left after removing them equal the rewards minus the rest rewards in every file.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-kmeans", "statement": "Unsupervised k-means clustering on locomotion (PC1, PC2 scores), reward and air puff responses assigns recordings to clusters that match the genetic subtypes with 91% accuracy (14/16 Vglut2, 10/11 Calb1, 15/16 Anxa1).", "source": "Figure 6c; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Median accuracy over 100 seeds 92.6% (Vglut2 89.5, Calb1 92.9, Anxa1 94.3; single starts 41 to 93%), chance 33%; the code's windows give the same. 19, 14 and 35 recordings against 16, 11 and 16. A one-to-one mapping of clusters to subtypes also gives 92.6%; the code's median-label mapping sends two subtypes to one cluster in 5 of 100 seeds.", "deviations": [ "scikit-learn k-means summarized over 100 seeds, as MATLAB's seed cannot be repeated.", "Larger locomotion selection than the paper's, so more recordings are clustered." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7f-soma-axon-correlation", "statement": "Within genetic subtypes, simultaneously recorded SNc somas and striatal axons are highly correlated (mean peak cross-correlation 0.65 Vglut2, 0.67 Calb1, 0.58 Anxa1), more than in DAT recordings (0.37); P = 3e-4, 3e-3, 3e-4.", "source": "Figure 7e,f; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Mean peaks 0.650, 0.672, 0.530 and 0.377; each subtype above DAT with rank-sum p x3 = 0.0003, 0.0003 and 0.0017. 405 nm control peaks -0.011 to 0.017. 11, 5, 40 and 33 pairs against 11, 5, 43 and 35.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9c-snc-stimulus-responses", "statement": "Like their axons, Vglut2 and Calb1 somas in SNc respond to rewards and air puffs, while reward responses are largely undetectable in Anxa1 somas.", "source": "Extended Data Figure 9a-c; Results, Axons track somatic signaling within subtypes", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "SNc Vglut2 reward 10.20 and air puff 14.72, Calb1 12.34 and 4.68, all p x4 below 0.01; Anxa1 reward 0.52, p x4 = 1. Counts match the legend except Anxa1 rewards (22 against 23).", "deviations": [ "Methods' windows as the main result; the code's as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9k-snc-variance-explained", "statement": "The striatal PCs explain most of the variance of the SNc cross-correlations, 77.6% (PC1 52.4%, PC2 25.2%).", "source": "Extended Data Figure 9k legend; Methods, Analysis of signaling during locomotion", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Striatal PCs explain 75.05% of 62 SNc cross-correlations (PC1 48.09%, PC2 26.96%), within 10% of the legend's 77.6, 52.4 and 25.2. Under the Methods' 53.2 and 24.3, PC2 is outside. The SNc selection has 26 Vglut2 and 30 Anxa1 recordings against 28 and 34. The 160 striatal components capture 100.00% of the SNc total variance, so the code's denominator equals it.", "deviations": [ "The legend and the Methods give different components; the legend's reading matches.", "The striatal PCs come from the larger striatal selection." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1h-aldh1a1-depth", "statement": "Aldh1a1 axons are heterogeneous; dorsal recordings are acceleration-correlated (Type 1) and more ventral ones deceleration-correlated (Type 2).", "source": "Extended Data Figure 1h; Results", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Spearman rho = -0.569 (p = 1.3e-08) over 85 recordings, integrals positive above 2.5 mm (mean 0.024, 85% positive), but the 5 recordings below 3 mm average 0.0001, not below 0. The trend holds within 8 of 9 mice with 4 or more recordings. Depth follows the DV coordinate (Spearman rho 0.92, a median 0.83 mm above it), as a depth from the brain surface would. With the deep band from 2.75 or 2.9 mm (19 and 18 recordings) the mean integral is negative (-0.0043, -0.0036).", "deviations": [ "The paper gives no test; the Spearman correlation and the depth bands were chosen here before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1i-aldh1a1-reward-locomotion", "statement": "In Aldh1a1 recordings, larger reward responses go with deceleration-correlated signaling, and small or negative reward responses with acceleration-correlated signaling.", "source": "Extended Data Figure 1i; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Spearman rho = -0.509, p = 0.011 over 24 recordings; mean reward response 9.59 with a negative integral and 1.90 with a positive one.", "deviations": [ "The paper gives no test; the Spearman correlation was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-overlap-locomotion", "statement": "Where Calb1 and Anxa1 axons overlap in striatum, Calb1 recordings remain deceleration-correlated and Anxa1 recordings acceleration-correlated (Calb1 4 mice, 5 recordings; Anxa1 5 mice, 16 recordings).", "source": "Figure 3a; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Calb1 mean integral -0.027 (16 of 17 negative), Anxa1 0.009, rank-sum p = 0.00012. 17 Calb1 recordings from 4 mice and 20 Anxa1 from 6, against 5 from 4 mice and 16 from 5 mice.", "deviations": [ "The region is the code's two circles converted to mm with the code's own scale and offsets.", "The paper gives no test; the sign and rank-sum test were chosen here.", "Larger selection than the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4l-overlap-stimuli", "statement": "Where Calb1 and Anxa1 axons overlap, Calb1 recordings respond to rewards and Anxa1 recordings do not, and Anxa1 recordings decrease to air puffs (Calb1 4 mice, 9 recordings; Anxa1 5 mice, 13 for rewards, 17 for air puffs).", "source": "Figure 4l; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Calb1 reward mean 14.35 against Anxa1 0.94 (rank-sum p = 0.00052), Anxa1 air puff -2.06. Counts equal the paper's (Calb1 9 from 4 mice, Anxa1 13 and 17 from 5 mice).", "deviations": [ "The paper gives no test; the rank-sum test and signs were chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "snrna-nuclei-qc", "statement": "Single-nucleus RNA-seq of dopamine neurons from five DAT-Cre, Sun1-GFP mice yields 12,065 nuclei after quality control, with a mean of 3,435 UMIs and 1,683 genes per nucleus.", "source": "Methods, Analysis of snRNA-seq data; Figure 1a,b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "12,065 nuclei with 500 or more genes, mean UMI 3,436 and mean genes 1,684, from the GEO matrices.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GEO GSE222558 (samples GSM6926026 and GSM6926027)", "proposed": null }, { "claim": "snrna-anxa1-within-aldh1a1", "statement": "Anxa1 expression is limited to a subset of Aldh1a1-expressing dopamine neurons.", "source": "Figure 1c; Extended Data Figure 2b; Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_azcorra_2023.ipynb", "notes": "Aldh1a1 detected in 76.9% of Anxa1-detected nuclei (30.9% overall), odds ratio 8.22, p = 1.6e-107; Anxa1 detected in 10.6% of Aldh1a1-detected nuclei.", "deviations": [ "Tested on raw detection without the paper's clustering." ], "disagreed": false, "data": "elsewhere", "where": "GEO GSE222558 (samples GSM6926026 and GSM6926027)", "proposed": null }, { "claim": "snrna-clusters", "statement": "Clustering of the snRNA-seq nuclei gives 15 clusters; cluster 4 is enriched for Anxa1 (FDR-adjusted P = 9.4e-118) within the Aldh1a1 clusters, and clusters 9 and 11 are the Vglut2 and Calb1 subtypes.", "source": "Figure 1b-d; Extended Data Figures 3 and 4; Results", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "The paper's pipeline is Seurat 4 (SCTransform v2 integration, FindClusters at resolution 0.5, FindAllMarkers) in R, which cannot be installed in the entry's Python lock file, and a Python reimplementation would not give the same clusters. The count matrices themselves are public (GEO GSE222558) and used by the two snRNA-seq claims above.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GEO GSE222558 (samples GSM6926026 and GSM6926027)", "proposed": null }, { "claim": "scrna-meta-integration", "statement": "Integrating four published single-cell datasets gives eight clusters, one of them defined by co-expression of Aldh1a1 and Anxa1.", "source": "Extended Data Figure 2; Results", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "Needs four public datasets and Seurat 3.2 and LIGER 2.0 in R, which cannot be installed in the entry's Python lock file.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GEO GSE116138 and GSE115070, dropviz.org (Saunders et al.), Bioconductor scRNAseq LaMannoBrainData", "proposed": null }, { "claim": "histology-anxa1-cre", "statement": "The Anxa1-iCre line labels a ventral subset of Aldh1a1 neurons; about 90% of the GCaMP6f-labelled cells stain for Aldh1a1, and Anxa1 axons project to dorsolateral striatum.", "source": "Figure 1e-g; Extended Data Figure 5; Methods", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The raw images are on Zenodo (doi 10.5281/zenodo.7909331), but the claim rests on manual cell counting on them, and no counts or annotations are deposited.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.7909331", "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The `coordinates` column of the fiber table is described as (AP, ML, DV) but holds (ML, AP, DV); the second value takes only the reference-slice AP positions and is negative in the tail of the striatum, and the paper's code builds the vector as [ML, AP, DV]." }, { "kind": "metadata_error", "statement": "The column `cross_correlation_with_acceleration` is described as the cross-correlation between dF/F and acceleration but holds the peak cross-correlation of the 405 nm control with acceleration (the code's Acc405, used for exclusion), and is missing where running was under 100 s." }, { "kind": "metadata_insufficient", "statement": "The dF/F series are normalized so that the largest transient is 1, which the files do not state (unit n.a., described as DF/F); the normalization factor is in the column `normalized_fluorescence`, which in 123 files holds two values per row." }, { "kind": "selection_undocumented", "statement": "The files carry the signal-to-noise ratio and 405 nm cross-correlation but not the other exclusion flags (running time, 405 nm artifacts) or which recordings each figure uses. Recomputed with the paper's code, the stimulus analyses give the paper's counts exactly, but the locomotion criteria select more striatal recordings than Figure 2 reports (Anxa1 82 against 47, Vglut2 50 against 42)." }, { "kind": "data_missing", "statement": "The Events table lists consumed rewards only; rewards the mouse did not lick for are only in the raw 4 kHz Reward trace. The code excludes 5 s after every reward, so 911 acceleration and 767 deceleration onsets recomputed from the processed data are not in the stored WheelEvents." }, { "kind": "metadata_error", "statement": "Three subject ids (Anxa-I765L, Anxa-I767L, Calb-2246L) are recordings from the left hemisphere of mice that also have ids without the L, so the archive's 105 subjects are 102 mice. The age is a range (P8W/P16W) in every file." }, { "kind": "metadata_error", "statement": "In the published version the related resource link to the paper is malformed (https://doi.org/https://doi.org/...), fixed in the draft; the asset summary lists measurementTechnique \"analytical technique\" and variableMeasured \"ProcessingModule\" only." }, { "kind": "metadata_insufficient", "statement": "785 of 790 SNc fibers and 1281 of 2137 fibers overall have no coordinates." }, { "kind": "code_mismatch", "statement": "The Methods integrate responses from +0.05 to +0.55 s minus -0.5 to 0 s; the code integrates 0 to +0.5 s minus -0.55 to -0.05 s. The paper's reward means equal those of the code's windows to the decimal (Vglut2 7.90, Calb1 12.40, DAT 5.88), as do its Vglut2, Calb1 and Anxa1 air puff means within tolerance; its DAT air puff mean (5.3) does not (2.46). The Methods' windows give about 10% more." }, { "kind": "code_mismatch", "statement": "The code reports the trough of the cross-correlation 0.02 s, and the peak of triggered averages 0.01 s, later than the times the Methods define, and prints uncorrected p-values for Figures 2i and 7f, whose legends state Bonferroni correction." }, { "kind": "code_mismatch", "statement": "The 405 nm artifact detection marks everything from the last noisy section to the end of a recording and from the start to the first, which the Methods do not describe." }, { "kind": "paper_inconsistency", "statement": "The Results give reward P = 2e-5 for Calb1 and 0.001 for Vglut2; the Figure 4g legend gives them the other way round. The Figure 2f legend gives 10 Anxa1 mice, the Methods 9. Extended Data Figure 9k gives striatal PCs explaining 52.4% and 25.2% of SNc variance, the Methods 53.2% and 24.3%." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper (PMC10545540). The verifier queried the archive's asset list and tested the helper functions on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; all 29 outcomes agree with the record, and for the three blocked claims it gave other reasons.", "agreed": 29, "of": 29, "disagreements": [] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full re-executed notebook after the round-1 revision, with its conclusions and summary, the README, the helper module, the claims file and this record. The verifier did not re-download the paper. It agrees with all 29 outcomes. Cell numbers in the reasons are those of the notebook it reviewed. Two points are not tied to a claim. The README and cell 0 say \"about three minutes\" while cell 94 reports 2.1 min; both now say the run takes a few minutes, and the run time is printed at the end. The 123 files with two normalized_fluorescence values, the malformed DOI link, the asset-summary fields and the paper_inconsistency items appear in no output; cell 13 now prints the value counts of normalized_fluorescence and the related resources and asset summary of the published and draft versions, cells 46 and 73 print the paper's conflicting P-values and percentages (checked against the paper's text, saved under paper/), and the Figure 2f legend and Methods mouse counts were already printed in cell 16.", "agreed": 29, "of": 29, "disagreements": [] } ] }, { "id": "001075-randi-2023-01", "dandiset": "001075", "dandiset_version": "0.240930.1859", "paper": "10.1038/s41586-023-06683-4", "paper_title": "Neural signal propagation atlas of Caenorhabditis elegans", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001075-randi-2023", "entry_title": "Neural signal propagation atlas of C. elegans (Randi et al. 2023)", "description": "Tests the findings of Randi, Sharma, Dvali and Leifer (2023) on dandiset 001075, which holds the 113 wild-type-background recordings of whole-brain calcium imaging during single-neuron optogenetic stimulation, 110 of them with extracted traces. It checks the recordings, the number of measured neuron pairs, three example connections of Figure 1, the spatial specificity of the stimulation, the responses to RID stimulation in WT and, from the paper's OSF export, in unc-31 animals, and how the per-pair measurements and recordings link to the paper's Source Data and OSF export. The q values, the spontaneous recordings and the kernel analyses are not testable.", "notebooks": [ { "path": "reproduce_randi_2023.ipynb", "title": "Reproducing Randi et al. (2023) from dandiset 001075", "executed": "notebooks/001075-randi-2023/reproduce_randi_2023.html" } ], "outcomes": [ { "claim": "recordings-protocol", "statement": "Activity was recorded from 113 WT-background animals, each for up to 40 min, while a neuron was stimulated once every 30 s with a 0.5 s train of light pulses.", "source": "Results, \"Population imaging and single-cell activation\"; Methods, \"Stimulus delivery and pulsed laser\"", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "The dandiset has 113 subjects, one session each, but only 110 have the segmentation file with traces and the stimulation table; subjects 20, 23 and 33 have only the raw imaging file. The median interval between stimulations is 30.81 s, and 107 of 110 recordings last no more than 44 min (13 are longer than 40 min, the longest 48.7 min). Every stimulation is stored as 0.5 s and 1.2 mW; the conversion writes both as constants.", "deviations": [ "The stimulus duration cannot be checked against the data, as it is a constant in the files." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pairs-measured", "statement": "Responses to stimulation were imaged for 23,433 pairs of neurons (66% of all possible pairs in the head), from 186 of the 188 head neurons, and some pairs were observed as many as 59 times.", "source": "Results, \"Signal propagation map\"; Extended Data Fig. 4a", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Under reading (a), with i = j and the autoresponse required, 20,587 head pairs are observed (expected 23,433 with tolerance 2,343), from 184 head neurons (186, tolerance 18.6), with at most 50 observations of a pair (59, tolerance 5.9); only the neuron count is within tolerance. Reading (b) gives 20,422 pairs. Reading (c), without the autoresponse requirement, gives 23,813 pairs and 184 neurons, within tolerance, but at most 86 observations. 107 animals contribute; 172 head neurons are stimulated with an autoresponse (the Source Data list 168). With the stimulated ROI from the paper's export, reading (a) gives 20,351 pairs, 183 neurons and at most 55 observations.", "deviations": [ "The stimulated ROI is found from the target position for stimulations without a manually located ROI; the paper maps the nearest neuron through tracking matches that are not in the dandiset. The two agree for 66% of such stimulations.", "The paper's exclusion of some stimulations (950 marked -2 in its export) and its matchless traces for dim neurons are not in the dandiset, so all stimulations and only the regular traces are used.", "The paper's text does not say whether the 23,433 pairs include i = j; the Source Data count does. Three readings are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-avjr-avdr", "statement": "Stimulation of the interneuron AVJR evoked activity in AVDR.", "source": "Fig. 1e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Over 27 AVJR stimulations with an autoresponse in 17 animals, the mean dF/F0 of AVDR is 0.236 (Source Data 0.246), Wilcoxon p = 5.5e-05 against 0, with 12 detected AVDR responses; 16 of 17 animals have a positive mean. The code's decaying correction gives 0.197.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-aver-avar", "statement": "Activation of the premotor interneuron AVER evoked activity transients in AVAR.", "source": "Fig. 1f", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Over 7 AVER stimulations with an autoresponse in 5 animals, the mean dF/F0 of AVAR is 0.159 (Source Data 0.204), with 4 detected AVAR responses. The trials do not differ from 0 by a Wilcoxon test (p = 0.22) and 3 of 5 animals have a positive mean, so the evidence is thin. The code's decaying correction gives 0.163.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-saadl-ollr", "statement": "Activation of SAADL inhibited the activity of the sensory neuron OLLR.", "source": "Fig. 1g", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Over 5 SAADL stimulations with an autoresponse in 4 animals, the mean dF/F0 of OLLR is -0.059 (Source Data -0.040), with 2 detected OLLR responses. The trials do not differ from 0 (p = 0.44), 3 of 4 animals have a negative mean, and the code's decaying correction gives +0.014, so the sign is not robust.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "edfig2ij-spatial-specificity", "statement": "Stimulation does not elicit responses in most close neighbours of the targeted neuron; at 75% of the cumulative distribution, neighbours' responses are below a dF/F0 of 0.1.", "source": "Extended Data Fig. 2i,j and legend; Methods, \"Characterization of the size of the two-photon excitation spot\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Under reading (a), 74.1% of the neighbours 4 to 16 um from the target have dF/F0 below 0.1 (expected 0.75, tolerance 0.075; the Source Data give 0.749). The bands give 60.4% (4 to 10 um) and 81.7% (10 to 16 um), against 61.6% and 82.3% in the Source Data. The targeted ROI's median, 0.376, is 6.2 times the 4 to 10 um median (0.061). Per animal the pooled fraction ranges from 0.50 to 0.97. Leaving out rows with F0 <= 0 gives the same fractions (0.741 pooled).", "deviations": [ "The legend does not say which neighbours its 75% refers to; readings (a) and (c) are within tolerance, (b) is not.", "Distances use 0.42 um per pixel from the paper's code and the median plane step of the imaging file's depth per frame (1.22 um)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "sourcedata-link", "statement": "The per-pair measurements computed from the dandiset agree with the paper's published per-pair values, the number of observations (Extended Data Fig. 4a) and the mean response _t (Extended Data Fig. 3a).", "source": "Source Data of Extended Data Figs. 3a and 4a", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Pairs are matched by neuron names. 81.7% of the paper's 23,433 observed pairs are observed here, the Spearman correlation of observation counts is 0.768 and the Pearson correlation of mean dF/F0 is 0.551 (criterion for reproduced 90%, 0.9 and 0.7; for partial 70%, 0.7 and 0.5). Counts are equal for 27.4% of pairs (median difference 0), and the sign of the mean agrees for 65.2%. With the code's decaying correction the correlation of means is 0.617. With the stimulated ROI from the paper's export the values are 83.3%, 0.820 and 0.676, and with its labels as well 84.5%, 0.834 and 0.684, so part of the difference comes from the identification and most of it does not. Keeping only rows with F0 > 0 (Pearson 0.552) or traces corrected for photobleaching (0.551), or leaving out the nine recordings with negative traces (0.534), the 950 stimulations the export excludes (0.601) or the nine recordings with agreement below 0.6 (0.544), keeps the result in the partial band; all these filters together give 76.8%, 0.765 and 0.569.", "deviations": [ "Main reading follows the Methods' dF/F0; the code's decaying correction and the mean over detected responses only are shown as variants." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "osf-link", "statement": "The dandiset's recordings can be linked to the recordings the paper exported to its OSF repository, and the stimulated neuron found here from the target position agrees with the one the paper's pipeline assigned.", "source": "Data availability (OSF doi 10.17605/OSF.IO/E2SYT, raw_extracted_data)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "All 110 recordings with traces match one exported recording by session date and time, with the same number of stimulations, and 109 with the same number of ROIs; the 3 unmatched exported recordings are the 3 subjects with only imaging files. Of 4,479 stimulations both assign to an ROI, 3,913 (87.4%) agree, which meets the criterion's 80% as worded. All 2,812 manual targets agree by construction, as the file's target_pumpprobe_id is the pipeline's own assignment; of the 1,667 found from the target position, which is what the claim states, 1,101 (66.0%) agree, inside the 60 to 80% band of a partial result, and the outcome is judged on this figure (changed from reproduced after the first verification round). Agreement is below 0.6 in nine recordings (position-found agreement 0.10 to 0.36). Three recordings have a fitted z slope of exactly 0 (median position-found agreement 0.579, against 0.739 for the other 107), and agreement rises with the absolute slope (Spearman 0.478). The export marks 950 stimulations as excluded. ROI labels agree with the export in every recording except six. In subject 11 the export has no labels (41 distinct names here, 161 ROIs here against 200 exported); in subjects 64 and 76 the dandiset has 4 and 0 distinct names against 70 and 102 exported, and in 77 it has 15; in 86 and 91 most names are shared (35 of 69 and 59 of 81) but sit on other ROIs.", "deviations": [ "The criterion pools manual and position-found targets; the claim's statement concerns the position-found ones, and the outcome follows the statement." ], "disagreed": true, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2d-inhibitory-fraction", "statement": "11% of the functional connections at q < 0.05 are inhibitory.", "source": "Results, \"Signal propagation map\"; Fig. 2d", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Of the 1,310 Source Data pairs with q < 0.05, 1,161 are observed here and 15.1% of them have a negative mean dF/F0 (reading a; 17.4% without i = j), outside 0.11 with tolerance 0.011. The Source Data's own means give 11.5% for the same pairs, and the signs here agree with them for 89.1% of observed pairs, so the difference comes from the response amplitudes computed from the dandiset, not from the outside selection. With the code's decaying correction the fraction is 9.6%; it is 7.3% at q < 0.01 and 21.2% at q < 0.1. Inhibitory pairs are a minority under every variant. The excess is not explained by a non-positive F0 or by failed photobleaching fits (15.1% with F0 > 0 only or with corrected traces only), nor by the nine recordings with negative traces (15.3% without them), the export's excluded stimulations (15.2%) or the nine poorly linked recordings (15.6%); all these filters together give 15.8%. With the stimulated ROI from the export, which applies its exclusions, it is 14.0%, and 13.4% with the export's labels as well.", "deviations": [ "The q values come from the paper's Source Data, as the control recordings needed to compute them are not public.", "The deviations of pairs-measured apply." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig2c-1310-connected", "statement": "1,310 of the 23,433 measured neuron pairs (6%) are functionally connected at q < 0.05.", "source": "Results, \"Signal propagation map\"; Fig. 2c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The q values compare each pair's responses with a null distribution from unstimulated control recordings. These are not in the dandiset, not in the paper's OSF repository, and the code reads them from private paths (/projects/LEIFER/Sophie/Lists/No_stim_list.txt).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-bilateral", "statement": "Bilaterally symmetric neurons are eight times more likely to be functionally connected than pairs chosen at random.", "source": "Fig. 2c", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the q values, which need the unstimulated control recordings (see fig2c-1310-connected).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2efg-path-length", "statement": "The probability of a functional connection decreases with the minimal anatomical path length, functionally connected pairs are on average 2.1 hops apart, and pairs with long paths are more often functionally non-connected.", "source": "Fig. 2e-g", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the q and q_eq values, which need the unstimulated control recordings (see fig2c-1310-connected). The connectome files the paper uses are public in its code repository.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-anatomy-predictions", "statement": "Signal propagation differs from predictions of a connectome-constrained model; pairs predicted to respond strongly respond more, but agreement over all pairs is poor (R2 < 0), improves when weights and signs are fitted, and is better in unc-31 animals.", "source": "Fig. 3b-d", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The anatomy-derived predictions per pair come from a biophysical model whose outputs the paper's scripts read from private paths (/projects/LEIFER/francesco/simulations/); the model code is not in the linked repositories, and the Source Data give the predictions without pair names. Panels c and d also need the q values and the unc-31 recordings.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "edfig6-kernel-stereotypy", "statement": "Kernels of one neuron pair are more similar to each other than to kernels of other pairs, and kernel rise times characterize the speed of signal propagation.", "source": "Extended Data Fig. 6b-f", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "Kernels are fitted with the paper's pumpprobe package (convolutions of exponentials in C++ extensions). A notebook cell now builds it and the packages it imports at fixed commits, with the kernel's Python 3.13 and numpy 2.5.4. As published, pumpprobe 1dbc5e0 does not build, as the compiler does not find the numpy headers. With the headers added by hand it builds but cannot be imported, since mistofrutta 11ac8c3 fails on its version string, wormbrain d94f7a1 needs the Eigen library and wormdatamodel 2ab9561 uses numpy C API names removed in numpy 2. The paper's setup.sh also points the compiler at libraries under /projects/LEIFER. The data needed are in the dandiset. The fits were not reimplemented without the package.", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "edfig7b-unc31-fewer", "statement": "unc-31 mutants have a smaller proportion of functionally connected pairs than WT animals.", "source": "Extended Data Fig. 7b", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The unc-31 recordings are not in the dandiset; exported traces of 18 unc-31 animals are on OSF, but the q values also need unc-31 control recordings, which are not public anywhere.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-rid-wt", "statement": "URX, ADL and AWB, predicted from anatomy to have no response, respond strongly to RID stimulation in WT animals.", "source": "Fig. 4a-d; Extended Data Fig. 7c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Changed from blocked after the first verification round, which asked for a check of RID labels. The dandiset labels 11 ROIs RID in 11 recordings, and 8 stimulations in 5 animals target such an ROI (5 manually located, 3 nearest-centroid). The criterion was written after seeing these counts and before computing any response. Under both readings only AWB meets it. AWB, left and right pooled, has a mean dF/F0 of 0.076 over 12 trials in 5 animals with 3 detected responses (82nd percentile of the head-pair means); AWBR has 0.094 over 7 trials with 2 detected. URX is observed once (URXR, 0.032, not detected) and ADL is never observed with a side label (one trace labelled ADL without a side, 0.011). With the export's assignment (11 stimulations) AWB has a mean of 0.100 with 5 detected responses. \"Strongly\" holds for AWB only in the sense of the percentile given.", "deviations": [ "Only RID stimulations whose target is an ROI labelled RID are found; the paper also includes manually targeted RID stimulations in which RID was not segmented.", "The paper substitutes matchless traces for neurons such as ADL in the RID analysis; they are not in the dandiset, so only regular traces are used.", "As in the Methods for Fig. 4, no autoresponse is required and values beyond 2 in absolute value are excluded (none of URX, ADL or AWB was)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-rid-unc31", "statement": "The responses of URXL, ADLR and AWBR to RID stimulation are reduced or absent in unc-31 mutants.", "source": "Fig. 4b-d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_randi_2023.ipynb", "notes": "Changed from blocked after the first verification round. The earlier notes were wrong; the unc-31 export labels RID, and 28 stimulations in 8 of its 18 recordings target an ROI labelled RID. In unc-31, URX (left and right) has a mean dF/F0 of 0.031 over 25 trials, ADL 0.061 over 14 and AWB 0.067 over 50 (URXL 0.018, ADLR 0.033, AWBR 0.048). The neurons observed in both strains are URX and AWB under reading (a) and AWBR under reading (b), and each is lower in unc-31 than in the WT dandiset (URX 0.031 against 0.032 from one WT trial, AWB 0.067 against 0.076, AWBR 0.048 against 0.094), so the criterion holds under both readings. The evidence is thin. The differences are small, one-sided Mann-Whitney tests do not find them (p = 0.54, 0.44 and 0.31), and AWB responses are still detected in 17 of 50 unc-31 trials, so the responses are reduced in mean, not absent. Against the WT export (7 recordings), URX and AWB are also lower in unc-31, while ADL, observed once in WT (-0.062), is higher.", "deviations": [ "The unc-31 data are the paper's exported traces, processed with the dandiset pipeline (missing values interpolated linearly here, the exported stimulation volumes used); the WT side is the dandiset, whose traces differ from the export, and the WT export is shown as a variant.", "The deviations of fig4-rid-wt apply." ], "disagreed": true, "data": "elsewhere", "where": "OSF doi 10.17605/OSF.IO/E2SYT (exported_data_full.tar.gz and exported_data_unc31.tar.gz)", "proposed": null }, { "claim": "fig5-extrasynaptic-screen", "statement": "Fifty-three pairs are functionally connected in WT (q < 0.05) and functionally non-connected in unc-31 (q_eq < 0.05), with timescales similar to all functional connections.", "source": "Results, \"Extrasynaptic-dependent signal propagation screen\"; Fig. 5a; Extended Data Fig. 9", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs q in WT and q_eq in unc-31, hence the control recordings of both strains, which are not public, and the unc-31 recordings, which are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-spontaneous", "statement": "Correlations derived from the measured kernels predict spontaneous activity correlations better than anatomical weights or the connectome-constrained model.", "source": "Fig. 6", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "The spontaneous recordings are on OSF (spont_data_fig6.zip), but the kernel-based prediction needs the kernel fits of edfig6-kernel-stereotypy, which is blocked as not runnable, so this claim is blocked for the same reason (the dependency is now in the claims file). It also needs q values (control recordings not public) and the anatomy-model predictions, which are not public.", "deviations": [], "disagreed": true, "data": "elsewhere", "where": "OSF doi 10.17605/OSF.IO/E2SYT (spont_data_fig6.zip)", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "Three of the 113 subjects (20, 23, 33) have only the raw imaging file, without the segmentation file that holds the traces and the stimulation table." }, { "kind": "data_missing", "statement": "The unc-31 recordings, the spontaneous recordings of Fig. 6 and the unstimulated control recordings are not in the dandiset. The control recordings, which every q value in the paper needs, are not public on OSF either, so the paper's central statistics cannot be recomputed." }, { "kind": "identifier_missing", "statement": "For about half of the stimulations the files do not say which ROI was stimulated; they give only a target position. The paper's assignment uses tracking matches that are not in the dandiset; from the position, 66% of these stimulations get the paper's ROI. RID stimulations can be recognised only where RID was segmented and labelled (8 stimulations in 5 animals)." }, { "kind": "selection_undocumented", "statement": "The paper's export marks 950 stimulations as excluded (-2); the dandiset keeps all stimulations and does not say which were excluded or why." }, { "kind": "metadata_error", "statement": "In five recordings the labels reached through `neuropal_ids` and the NeuroPAL table differ from the paper's export for every named ROI. In subjects 64, 76 and 77 the dandiset has almost no labels (4, 0 and 15 distinct names against 70, 102 and 87 exported). In subjects 86 and 91 most names are shared with the export but sit on other ROIs. In subject 11 the number of ROIs (161) differs from the export (200), and the export has no labels for it." }, { "kind": "format_error", "statement": "The column `neuropal_ids`, documented as a NeuroPAL ROI id or blank, holds the text \"merge\" in 63 recordings and \"check\", \"I4\" or \"RIAR\" in others." }, { "kind": "metadata_error", "statement": "The target column `depth_in_um` holds values from -0.875 to 0.875, which cannot be micrometres in a volume imaged from 2.5 to 37.5 um; the unit is not stated. 122 stimulations have the target position (0, 0), meaning no stored position." }, { "kind": "metadata_error", "statement": "Every stimulation is stored as 0.5 s at 1.2 mW, constants from the paper written by the conversion; the 0.1 to 0.5 s pulses the Methods describe for AFD stimulations are not represented." }, { "kind": "metadata_error", "statement": "The red optical channel is described with the indicator GCaMP6s, but it images tagRFP-T. Two subjects (24, 25) have strain \"none\". The age is P1D for every animal, L4 or young adult. One label confidence is 11, outside the 0 to 1 range." }, { "kind": "other", "statement": "Of the 14,039 traces, 897 cannot be corrected for photobleaching with the paper's fit, 729 of them because values are missing even in the interpolated copy. 3,173 of 433,216 observation rows have a baseline F0 at or below zero, so their dF/F0 has no meaning; the variants without them change no outcome." }, { "kind": "metadata_insufficient", "statement": "The traces have unit \"n.a.\" and are described only as average baseline fluorescence, without saying what processing they have had; while preparing (not run in the notebook) they were seen to differ from the paper's exported traces. Nine recordings (subjects 2, 3, 4, 34, 35, 36, 38, 39, 40) hold values far below zero, down to -196,646." }, { "kind": "other", "statement": "Some ROIs carry the NeuroPAL label \"target\" (49 ROIs in 21 recordings), and labels such as RIG or SAAD name no single neuron." }, { "kind": "metadata_error", "statement": "Thirteen recordings last longer than the \"up to 40 min\" of the paper (up to 48.7 min), and three have gaps in their timestamps of up to 8.4 s." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier opened one imaging file of the archive and sampled asset metadata, and tested helper functions on synthetic inputs; it did not stream any segmentation file. Its report had no attempt record and gave its own outcome for each of the 19 claims.", "agreed": 15, "of": 19, "disagreements": [ { "claim": "osf-link", "outcome": "partially_reproduced", "reason": "110 of 110 recordings match by key and stimulation count and 109 by ROI count, and overall same-ROI agreement is 0.874, which meets the criterion as worded. But all 2,812 manual targets agree by construction, as target_pumpprobe_id is the pipeline's own assignment. Targets found from position, which is what the claim states, agree 1,101 of 1,667 = 0.660, inside the 60 to 80% partial band. Nine recordings fall below 0.6 and stay in every main analysis (B3). Six recordings have 0% label agreement, which suggests an ROI-order mismatch (B5)." }, { "claim": "edfig6-kernel-stereotypy", "outcome": "blocked", "reason": "Blocked, other. \"Not runnable\" is not an allowed category; the WT traces needed for kernel fits are in the archive and the Methods and code describe the fit, so this is testable in principle. It was not attempted." }, { "claim": "fig4-rid-unc31", "outcome": "blocked", "reason": "Blocked, data_missing. unc-31 is absent from the archive (the claims file lists the data under OSF); \"metadata insufficient\" is the wrong category." }, { "claim": "fig6-spontaneous", "outcome": "blocked", "reason": "Blocked, data_missing. The spontaneous recordings are not in the archive (OSF only), and \"not runnable\" is not an allowed reason." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the first revision, with its conclusions and summary, the attempt record, the README, the helper module and the claims file, with the paper. The verifier checked every conclusion sentence against the printed outputs and said which of its round-1 points were resolved.", "agreed": 19, "of": 19, "disagreements": [] } ] }, { "id": "001084-vu-2024-01", "dandiset": "001084", "dandiset_version": "0.241023.2011", "paper": "10.1016/j.neuron.2023.12.011", "paper_title": "Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001084-vu-2024", "entry_title": "Striatal dopamine release patterns and targeted stimulation through micro-fiber arrays (Vu et al. 2024)", "description": "Tests the findings of Vu, Brown, Wen et al. (2024) on dandiset 001084, which holds multi-fiber photometry from mice with arrays of 30 to 103 fibers across the striatum. It re-runs the paper's GLM of dopamine release to light and tone in 280 fibers of 7 mice (amplitude maps, latencies and their spatial gradients), the isosbestic controls, the D1 calcium correlations, the chronic reward responses, and the spread of release evoked by single-fiber stimulation with its controls. The freely moving, histology and jaw movement data of Figures 3, 7 and S1 are not in the dandiset.", "notebooks": [ { "path": "reproduce_vu_2024.ipynb", "title": "Reproducing Vu et al. (2024) from dandiset 001084", "executed": "notebooks/001084-vu-2024/reproduce_vu_2024.html" } ], "outcomes": [ { "claim": "fig1c-isosbestic-control", "statement": "In a D1-cre mouse expressing GCaMP7f in D1 spiny projection neurons, fluorescence under 470 nm excitation shows Ca2+ transients across fibers that are absent under 405 nm (isosbestic) excitation.", "source": "Figure 1C; Results, second section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Mouse 842, session 2022-11-23, 61 included fibers. The SD of DF/F under 470 nm exceeds that under 405 nm in 61 of 61 fibers (median ratio 3.01, range 1.56 to 19.41). Frames above 5 times the median 405 nm SD make up a median 6.7% of each 470 nm trace (range 0.13% to 35.9%) and a median 0.0% of each 405 nm trace (at most 1.2%; 11 of 61 have none). The session of 2022-11-18 gives a median ratio of 2.84.", "deviations": [ "The paper shows example traces; the SD ratio and its thresholds were chosen here before the analysis.", "Figure 1C describes a 93-fiber array; the mouse its code reads (842) has 82 fibers per channel, 61 included." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2d-correlation-distance", "statement": "Pairwise correlations of D1 SPN Ca2+ signals are generally low but variable, and drop off significantly with the distance between fiber tips.", "source": "Results, second section; Figure S2D; code SuppFig02/DEF/surface_brain_dist.m", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Over 1830 pairs of the 61 included fibers (470 nm, 2022-11-23), the median pairwise correlation is 0.163 (IQR -0.025 to 0.361, range -0.678 to 0.904), and correlations fall with tip distance (r = -0.190, p = 2.8e-16; mean 0.293 in the closest quarter of pairs against 0.133 in the farthest). The session of 2022-11-18 gives r = -0.238. The p-value treats pairs as independent, as the paper's code does.", "deviations": [ "The code's set of fibers (goodROIs.mat) is not published; the included fibers are used.", "The threshold of 0.3 for \"generally low\" was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2ef-no-bundle-crosstalk", "statement": "After accounting for distance in the brain, signal correlations do not depend on the distance between fibers on the bundle surface, so nearby fibers in the bundle do not cross-talk.", "source": "Results, second section; Figure S2E-F; code SuppFig02/DEF/surface_brain_dist.m", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "In the code's linear model of pairwise correlation on Euclidean, AP, ML and DV tip distances and bundle-surface distance (ROI centroids), the surface coefficient is -3.4e-05 per pixel (95% CI -2.7e-04 to 2.0e-04, p = 0.77), while Euclidean tip distance has -0.278 (p < 1e-5). The other session gives p = 0.41. Pairs adjacent on the bundle correlate at 0.222 against 0.156 for others, which the model attributes to their tips also being closer (tip and surface distances correlate at r = 0.437).", "deviations": [ "Surface distance is in pixels of the bundle image; the code converts it to mm, which does not change the p-value." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-chronic-reward-stability", "statement": "Dopamine release to unpredicted water reward is reliable and of comparable amplitude over at least 12 weeks after implantation (median over 44 fibers, normalized to week 5).", "source": "Figure 1D; Results, second section; code Fig01/D", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "In the 17 sessions with rewards and 25 rewards or fewer (2021-08-19 to 2021-09-13), the median over the 44 fibers of the weekly peak reward response, relative to week 5, is 0.903, 0.932 and 1.196 in weeks 6 to 8, within the band of 0.7 to 1.3. These sessions end at week 8; from 2021-09-10 the sessions have 44 to 70 rewards, of which the paper keeps only those of one task phase, which the files do not record, so weeks 9 to 12 cannot be tested. With all rewards of all sessions the median falls to 0.767 in week 8, 0.609 in week 10 and 0.392 in week 13, as expected if predicted rewards are included; this variant does not test the claim.", "deviations": [ "Weeks are counted from the first session, labelled week 5, because the files give no implantation date; the paper's code puts the first session on day 35, which gives the same weeks.", "Only weeks 5 to 8 can be tested." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-link-published-results", "statement": "The dandiset's DF/F traces, fibers and stimulus times are those behind the paper's salient-stimulus analysis, so that its per-fiber responses can be linked to the paper's.", "source": "Figure 4E-F; the paper's intermediate file glm_spline_results.mat (Zenodo, Fig04)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Fibers matched by order within each mouse. The raw triggered averages from the dandiset equal the published cue1_roi_mu for light in all 7 mice and cue2_roi_mu for tone in the 6 mice other than DL18 (largest difference 0.0). The GLM spline estimates correlate with the published ones at r = 0.9957 for light and 0.9922 for tone over all fibers, and significance agrees for 93.6% of fiber and stimulus pairs (lowest DL18 tone 0.684, where 44 tones are used in place of 14; DL29 light 0.822). DL18's 14 published tone trials match 14 distinct tones of the file (r at least 0.952, best competitor at most 0.693), whose raw average equals the published one. Refitted with these 14 tones, DL18's tone spline estimates correlate with the published ones at r = 0.9977 and significance agrees for 0.947 of its fibers; with them, agreement over all pairs is 94.5% and the pooled tone r is 0.9974. Per mouse, r is below 0.99 for DL29 light (0.979) and DL27 and DL29 tone (0.989, 0.986).", "deviations": [ "The GLM is a re-implementation in Python; filtering and lag selection differ in detail (see the salient-stimulus claims), which explains the significance disagreements." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig4e-light-increases-widespread", "statement": "The light evokes transient increases in dopamine release across many striatal locations.", "source": "Figure 4B, 4E; Results, fourth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "240 of 280 fibers (86%) have a significant increase to light and 38 a significant decrease; by the signed largest value 237 are increases and 11 decreases. Each mouse has increases in most fibers (34 of 51 in DL21 to 50 of 53 in DL20). The chance rate of a significant increase per fiber, from 200 null refits per mouse, is 0.024 (about 7 of 280 fibers), and 0.043 for an increase or a decrease.", "deviations": [ "The paper gives p < 1e-6 for its test (3 consecutive frames outside the 99% band), which is 0.01 cubed and assumes independent frames. With the same test, three given consecutive frames are all outside the band at a rate of 0.0037 in the null refits, and the per-fiber chance rate is 0.024. The protocol blocks a claim when the chance rate of a selection is far from the paper's, as a sign that the procedures differ; here the procedure is shown to be the paper's (raw averages identical, significance agreeing with the published calls for 93.6 to 94.5% of pairs, fig4-link-published-results), so the gap is in how the paper states the rate, and the outcome is kept. 240 increases against about 7 expected by chance.", "The low-pass filter of overall velocity is a zero-phase Butterworth filter in place of MATLAB's lowpass; locomotion lags come from a cross-correlation that shifts negative lags, where the paper's code does not (its version correlates at r = 0.997 with the light values used).", "DL18's tone regressors include all 44 tones (the files do not give tone frequency)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4e-light-anterior-posterior-gradient", "statement": "Light-evoked dopamine increases follow an amplitude gradient from the anterior striatum into the posterior tail, where increases are less prevalent and smaller.", "source": "Figure 4E; Figure S4A; Results, fourth section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "The light value is larger anteriorly (Spearman rho(AP, value) = 0.168, p = 0.0047) and smaller in the tail (median 0.0055 against 0.0117 DF/F, p = 0.0013), but increases are as prevalent there (83% of 35 tail fibers against 86% elsewhere, p = 0.38). The result is the same with the tail at -0.8 or -1.3 mm and with the code's lags (rho = 0.162). Per mouse the gradient is positive in DL18, DL20 and DL27 (rho 0.45 to 0.69) and negative in DL23 (-0.43), DL29 and DL30. With AP and the light value ranked within each mouse and a permutation test within mice, so that differences between mice cannot drive it, the correlation is r = 0.152 (p = 0.013); (a) holds this way too.", "deviations": [ "The tail boundary (AP at most -1.0 mm) was fixed here; the paper gives none." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-tone-tail-increase-anterior-decrease", "statement": "The tone evokes the strongest dopamine increases at sites in the posterior tail, while anterior to the tail it evokes primarily decreases.", "source": "Figure 4D, 4F; Figure S4C; Results, fourth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Tail fibers have larger tone values than anterior fibers (median 0.0092 against -0.0026 DF/F, p = 5.5e-13), all 10 of the largest values are in the tail, and 32 of 35 tail fibers have a significant increase (none a decrease). Anterior to the tail 103 significant responses are decreases and 60 increases (binomial p = 0.00047). The amplitude comparison and the anterior excess of decreases hold at every tail boundary, with the code's lags, and with DL18 restricted to its 14 tones of 12 kHz identified from the paper's results (108 against 60). At the -1.3 mm boundary only 5 of the 10 largest values are in the tail, so part (a) of the criterion, which needs 6, fails at that variant boundary. The anterior decrease dominates in DL21 (36 against 3) and DL23 (17 against 6) but not in DL18, DL20, DL27 or DL30.", "deviations": [ "DL18 uses all 44 tones in the main analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-decreases-lateral-ventral", "statement": "Tone-evoked decreases are slightly more prevalent in the anterior lateral and ventral striatum, with many sites showing both increases to the light and decreases to the tone.", "source": "Figure 4F; Results, fourth section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Of 245 anterior fibers, the 103 with a significant tone decrease are more ventral than the others (median DV 3.66 against 3.30 mm, p = 0.0031) but not more lateral (median ML 2.07 against 1.97 mm, p = 0.43); the same at the other tail boundaries. They are also more anterior (p = 1e-06). 79 anterior fibers (32%) have both a significant light increase and a significant tone decrease, so \"many sites\" holds by the 20% reading.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4ac-patterns-consistent-across-mice", "statement": "The modality-specific release patterns are consistent within and across mice.", "source": "Results, fourth section (Figure S4A, C)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "The tone correlation with AP is negative in all 7 mice (rho -0.44 to -0.70, each p < 0.03). The light correlation is positive in 4 of 7 mice (significant in DL18, DL20 and DL27) and negative in DL23 (rho -0.43, p = 0.026), DL29 and DL30, below the 5 required.", "deviations": [ "The supplementary legend of Figure S4 was not available; the test per mouse was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4eh-patterns-not-movement", "statement": "Locomotor changes to the stimuli are variable and bi-directional, while the dopamine release patterns to light and tone are consistent, so the patterns are stimulus and not movement driven.", "source": "Results, fourth section (Figure S4); Methods; code SuppFig04/EFGH/sal_stim_bubbles_loco.m", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Locomotion after the stimuli varies between mice and presentations (acceleration and deceleration splits from 0 and 21 in DL29 light to 21 and 23 in DL18 tone; mean velocity change of either sign for both stimuli). The fiber maps of the two splits correlate (light r = 0.873 over 235 fibers, tone r = 0.784 over 229). The tone pattern holds after acceleration (tail median 0.0073, anterior -0.0031 DF/F) but not after deceleration, where the anterior median is positive (0.0042; tail 0.0098). The test uses raw DF/F, as the paper's code for Figure S4E-H (sal_stim_bubbles_loco.m) does, with no baseline and without the GLM's locomotion regressors. With each split's mean over the 1 s before onset subtracted (a variant, which does not decide the outcome), the maps correlate at r = 0.755 (light) and 0.823 (tone) and the tone pattern holds in both splits (anterior median -0.0043 after acceleration and -0.0024 after deceleration, tail 0.0069 and 0.0101), so the failure under the code's measure follows from the level before onset in the deceleration trials.", "deviations": [ "The supplementary legend was not available; the correlation threshold and the tone-pattern test were chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5-isosbestic-no-pattern", "statement": "With isosbestic (415 nm) excitation, large fluorescence changes and spatial patterns to light and tone are not observed, ruling out a hemodynamic origin of the release patterns.", "source": "Results, fourth section (Figure S5E-H); code SuppFig05/EFGH", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "In DL31 and DL32 (96 fibers), 2 fibers respond significantly to light and 1 to tone at 415 nm, against 45 and 18 at 470 nm, and the AP correlations of the tone values at 470 nm (-0.49, -0.43) are absent at 415 nm (-0.19, 0.16). The median absolute value at 415 nm is 0.49 of that at 470 nm for light but 0.68 for tone, above the criterion's half; for tone most 470 nm fibers are not significant either, and both medians (0.0027 and 0.0018 DF/F) are near the noise level. With random onsets the median absolute value is 0.0025 at 470 nm and 0.0019 at 415 nm, so the tone median at 470 nm is only 0.0002 above this floor and the ratio cannot fall to half; for light the 470 nm median is 0.0017 above the floor and the 415 nm one 0.0001. With 13 spline functions (the Methods' number for the main GLM) in place of the code's 9 at 18 Hz, the ratios are 0.55 (light) and 0.70 (tone), with 36 and 15 significant fibers at 470 nm against 1 and 0 at 415 nm.", "deviations": [ "The spline basis has 9 functions at 18 Hz, as the paper's code (run_sal_stim_glm_470_415.m, knots every 3 frames) has; the Methods give 13 for the GLM at 30 Hz. The 13-function basis is shown as a variant.", "Events are placed by behaviour sample index for both channels, because the stored regular frame rate drifts from the frame timestamps by up to half a second; the clock check for these two sessions is weak (decoding 0.90 and 0.80 with true onsets against 0.40 to 0.65 with shifted ones, 20 presentations each).", "The 470 and 405 nm sessions of Figure S5A-D are not in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5ab-response-latencies", "statement": "Latencies to half-maximum are shorter for dopamine increases to light than to tone, and shorter for increases than decreases to tone (light increase 221.6 ms, SD 42.5; tone increase 305.4 ms, SD 100.0; tone decrease 428.3 ms, SD 197.1).", "source": "Figure 5A-B; Results, fifth section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Counted from the onset frame as the Methods define latency, the means are 187.5 ms (240 light increases), 271.7 ms (94 tone increases) and 393.2 ms (108 tone decreases); the order holds and the tone decrease is within tolerance, the other two are below it. Counted as the paper's code counts (its 1-based index divided by the frame rate, one frame later), they are 220.8, 305.0 and 426.5 ms, within 2 ms of the paper's values, with SDs of 38.1, 98.7 and 196.5 ms against 42.5, 100.0 and 197.1. One tone increase has no half-maximum crossing before its peak.", "deviations": [ "Latency follows the Methods (from the onset frame); the code's count, one frame later, is shown as a variant and matches the paper.", "Tone onsets are shifted by 11 frames, the speaker delay in the paper's code, which the Methods do not mention." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5g-light-latency-gradient", "statement": "Dopamine release latencies to light follow an anterior-posterior gradient, with faster increases in the anterior striatum, consistent with wave-like dynamics.", "source": "Figure 5C, E, G; Results, fifth section; code Fig05/general_functions", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Over 240 fibers with a light latency (median 18 presentations each), relative latency is shorter anteriorly (Spearman rho(AP, latency) = -0.285, p = 7e-06); it also increases laterally (rho = 0.263, p = 3.8e-05) and not with depth (p = 0.93). Ranked within each mouse and tested by permuting within mice, which removes differences between mice and the dependence of relative latency on the number of fibers in a mouse, the gradient remains (r = -0.223, p = 0.0014).", "deviations": [ "Relative latencies do not depend on the code's one-frame offset, which cancels in the difference." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5h-tone-latency-gradient", "statement": "Dopamine release latencies to tone follow a different gradient, faster in the posterior striatum than in the anterior striatum.", "source": "Figure 5D, F, H; Figure S6A-B; Results, fifth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Over 196 fibers with a tone latency (earlier of increase and decrease), relative latency is shorter posteriorly (rho(AP, latency) = 0.254, p = 0.00033; tail median 308 ms against 368 ms anterior). Increases alone (rho = -0.07, p = 0.5) and decreases alone (rho = -0.21, p = 0.028) do not show it, so the gradient comes from the tail's fast increases and the slower anterior decreases, as the paper says of Figure S6A-B. Ranked within each mouse and tested by permuting within mice, the gradient remains (r = 0.214, p = 0.003).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs6cd-gradients-individual-mice", "statement": "The spatial latency gradients are also present in individual mice.", "source": "Results, fifth section (Figure S6C-D)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "The tone gradient is positive in 6 of 7 mice (significant in DL20 and DL23); the light gradient is negative in 4 of 7 (significant in DL18 and DL27), zero in DL21 and positive in DL23 and DL29.", "deviations": [ "The supplementary legend was not available; the count of mice was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-inclusion-counts", "statement": "In the mouse with ChR2 in dopamine axons and rDAm3.0 in the striatum, 24 recording locations lie within or on the border of the striatum; 18 of the 24 stimulated locations evoke a significant response at another location, and 22 of the 24 recording locations respond to at least one stimulation.", "source": "Methods, \"DA release to optogenetic stimulation\"; Figure 6G legend", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "In Opto2, 22 fibers are flagged included and 20 of them respond to at least one stimulation, both within tolerance; 14 of the 19 stimulated included fibers evoke a significant response at another included fiber, below 18; as a fraction (0.74) this is close to the paper's 18 of 24 (0.75), but the denominators differ because fewer included fibers were stimulated in the files. Counting only responses to another fiber's stimulation, so that a stimulated fiber's own photoswitching does not count, still gives 20 responding locations. Adding the two fibers labelled Caudoputamen but not flagged (16 and 34) gives the paper's 24 locations and 22 responding ones, and 16 of 21 stimulated fibers with a response elsewhere; the files have 29 single-fiber sessions, of which 21 stimulate a striatal fiber, so 24 stimulated locations cannot be reached. With the code's further exclusions of fibers 8, 9 and 21 the counts are 19, 14 of 19 and 18. Session 2023-03-20f, with the laser artefact on 13 fibers, is left out.", "deviations": [ "Stimulation epochs and the stimulated fiber are found from the DF/F alone (artefact above 0.4), without the code's check against the trigger line, which the files do not hold.", "The bootstrap counts responses of either sign as significant, as the code does." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6gh-release-decays-with-distance", "statement": "Stimulating dopamine axons through one fiber evokes release at neighbouring non-stimulated sites that drops off sharply with distance in all three dimensions.", "source": "Figure 6E-H; Results, seventh section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "Over 266 pairs of 14 stimulated and 20 recording fibers (378 pairs, 18 by 21, in the paper), the fit is a = 0.0147 DF/F and b = -1.096 per mm (95% bootstrap interval over stimulation sites -1.325 to -0.890), and the response falls with absolute distance along ML, AP and DV (Spearman rho -0.30, -0.27, -0.39, all p < 1e-5). The binned mean falls from 0.0079 DF/F at 0.54 mm to 0.0013 to 0.0017 beyond 2 mm.", "deviations": [ "Fewer stimulation and recording sites than the paper, from the inclusion of fig6-inclusion-counts." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6g-dorsal-spread", "statement": "Evoked release drops off less with distance dorsal to the stimulated fiber than ventral to it, consistent with dorsally extending dopamine axon branches.", "source": "Figure 6G (D/V distance); Results, seventh section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "The decay rate is -0.971 per mm for 156 dorsal pairs and -1.403 for 109 ventral pairs, in the claimed order, but the 95% bootstrap interval of the difference (-0.094 to 0.969) includes 0.", "deviations": [ "The paper shows binned means; the comparison of fitted decay rates was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-tdtomato-control-no-response", "statement": "In control mice expressing tdTomato in place of rDAm3.0, single-fiber stimulation evokes no significant fluorescence increase at non-stimulated sites (0 of 48 sites, 26 stimulations in 2 mice), so the release is not a hemodynamic effect.", "source": "Results, seventh section; Figure 6G controls", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "No included non-stimulated fiber has a significant increase after stimulation in 304 fiber and session pairs of Opto4 (13 sessions) or 203 of Opto9 (12 sessions); median responses are -0.0002 and 0.0003 DF/F, and one Opto9 pair has a significant decrease. The same test finds increases in 142 of 619 pairs (20 distinct fibers) in Opto2. The files hold 25 tdTomato stimulations against the paper's 26.", "deviations": [ "In these mice the laser artefact spreads to many fibers, and the stimulated fiber is taken as the one with the largest artefact, which can be wrong; the true stimulated fiber is then among the fibers tested, which makes the test stricter." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs7a-photoswitch-confined", "statement": "In mice expressing rDAm3.0 without opsin, light through one fiber raises fluorescence at the stimulated site by photoswitching, but at no other site (0 of 22 non-stimulated sites for 3 stimulations).", "source": "Results, seventh section; Figure 6E, Figure S7A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_vu_2024.ipynb", "notes": "In each of UG21's 3 sessions the stimulated fiber (12, 18 and 24, the numbers of the paper's code folders) has a significant increase after the laser (0.0118 to 0.0144 DF/F), and none of the 21 other included fibers responds significantly in either direction.", "deviations": [ "The paper included these sites only if they responded to reward; UG21 has no reward events in the files, so that step is not applied.", "The files give UG21's indicator as tdTomato; it is treated as the paper's rDAm3.0 mouse without opsin from its sessions, fiber counts and stimulated fibers (see findings)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-no-tissue-damage", "statement": "Neuronal density is not reduced under 50 um fiber tips or between neighbouring fibers relative to unimplanted tissue.", "source": "Results, first section; Figure S1", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted. The histology is not in the dandiset; the paper deposited the NeuN and DAPI images and its density results on Zenodo (SuppFig01.zip, about 180 MB of TIFF images). Testing it needs the neuron detection of the paper's MATLAB code on those images.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.10272874 (SuppFig01.zip, NeuN and DAPI images and densities)", "proposed": null }, { "claim": "figs3-targeting-errors", "statement": "The magnitude and type of targeting errors (fiber tip relative to its intended target) vary across mice and fibers.", "source": "Results, third section; Figure S3", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The fiber table of every file holds the localized tips (stereotactic and Allen coordinates), the location label and the included flag, and no planned target (data check). The paper's code (SuppFig03/B/analysis_code/planned_v_actual.m) reads the planned targets from per-mouse calibration files (calibPath), which are in none of the archives of the Zenodo record; SuppFig03.zip holds the CT fiber tables (MATLAB table objects) and the code only. Changed after verification round 1 from blocked by other with the data taken to be on Zenodo.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-freely-moving-signals", "statement": "Fiber arrays imaged with a miniscope in freely moving mice show robust D1 SPN Ca2+ signals during locomotion, and dopamine transients associated with the approach to food rewards.", "source": "Figure 3; Results, fourth section", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted. The miniscope recordings in freely moving mice are not in the dandiset; Zenodo holds two videos (3.3 GB) and the example DF/F traces with scored times (Fig03.zip).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.10272874 (Fig03.zip)", "proposed": null }, { "claim": "fig7d-ventral-not-dorsal-jaw", "statement": "Stimulating D1 SPNs through a group of ventral striatum fibers, but not dorsal ones, increases jaw movement, an effect absent in a control mouse (interaction p = 7.4e-7; ventral p = 0.0002, dorsal p = 0.45).", "source": "Figure 7D; Results, eighth section", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted. None of the D1-cre mice of Figure 7 (OptoD1_6, 7, 8 and 10 in the paper's code) is in the dandiset. Their DeepLabCut outputs, DF/F and stimulation files are on Zenodo (Fig07.zip, 2.1 GB, about 24 sessions for this panel).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.10272874 (Fig07.zip, DeepLabCut outputs and stimulation files)", "proposed": null }, { "claim": "fig7ef-single-ventral-fiber", "statement": "Of the eight ventral fibers stimulated singly in each mouse, only one per mouse has a significant effect on jaw movement (3 mice), located in the posterior medial striatum.", "source": "Figure 7E-F, Figure S7B; Results, eighth section", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Not attempted, as fig7d-ventral-not-dorsal-jaw (Fig07.zip and SuppFig07.zip on Zenodo).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.10272874 (Fig07.zip and SuppFig07.zip)", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The optogenetic sessions (Opto2, Opto4, Opto9, UG21) hold no stimulation times and no record of which fiber was stimulated; the trigger line the paper's code uses is not in the files. Both can be recovered only from the laser artefact in the DF/F, which is unambiguous in Opto2 and UG21 but spreads over many fibers in the tdTomato mice." }, { "kind": "metadata_insufficient", "statement": "The event table gives tone presentations without their frequency. DL18 has 44 tones, of which the paper analysed the 14 at 12 kHz; the frequency is stored only in a MATLAB object of the behaviour file on Zenodo. The tone start times are the trigger times, 11 frames before the sound according to the paper's code, which the dandiset does not say." }, { "kind": "data_missing", "statement": "DL15's sessions from 2021-09-10 (44 to 70 rewards) were run in a ViRMEn task; the paper keeps only rewards of one task phase, but the task variables are not in the files, so unpredicted rewards cannot be separated and Figure 1D can be tested only to week 8." }, { "kind": "metadata_error", "statement": "The FiberPhotometryTable column `included` is described as \"whether this fiber has been successfully implanted\", but it marks fibers within the striatum (the paper's in_striatum); in Opto2 two fibers labelled Caudoputamen are not included, and with them the counts match the paper's \"within or on the border of the striatum\" (24 locations)." }, { "kind": "metadata_error", "statement": "UG21's indicator is given as tdTomato. Its 3 sessions, 22 included fibers and stimulated fibers 12, 18 and 24 match the paper's rDAm3.0 mouse without opsin (Figure S7A), so the indicator is consistent with being a mislabel; the files cannot show which indicator was expressed." }, { "kind": "metadata_error", "statement": "In DL31 and DL32 (18 Hz, interleaved 470 and 415 nm) the fiber photometry series store a regular rate, but the frame timestamps of the behaviour drift from it by up to 0.43 and 0.54 s over the session, so times computed from the stored rate are wrong by up to half a second." }, { "kind": "data_missing", "statement": "The data of Figures 2, 3, 7, S1 and S5A-D are not in the dandiset (the CT scans, the freely moving recordings, the D1-cre jaw experiments, histology and the 470 and 405 nm sessions of the salient-stimulus mice); they are on Zenodo. Opto9 has 12 sessions, so one of the paper's 26 tdTomato stimulations is missing." }, { "kind": "data_missing", "statement": "The planned fiber targets behind Figure S3 are neither in the dandiset, whose fiber table gives only the localized tips, nor on Zenodo, where the code reads them from calibration files that were not deposited." }, { "kind": "other", "statement": "The paper gives p < 1e-6 for its test of a significant response (3 consecutive frames outside the 99% band of the null), the value for independent frames. With the same test the chance rate of a significant increase is 0.024 per fiber and stimulus, and three given consecutive frames are all outside the band at a rate of 0.0037." }, { "kind": "code_mismatch", "statement": "The paper's latency code (sal_stim_lat_plots.m) divides the 1-based index of the half-maximum frame by the frame rate, so its latencies are one frame (33 ms) longer than the Methods' definition. With that count the dandiset gives the paper's means within 2 ms." }, { "kind": "code_mismatch", "statement": "In the paper's cross-correlation of DF/F with locomotion (sal_stim_iti_acc_cc.m), negative lags are not shifted; they correlate the two signals at zero lag over a truncated range. The Methods describe a cross-correlation over +-500 ms." }, { "kind": "code_mismatch", "statement": "The Figure 1C legend describes 23 example fibers of a 93-fiber array; the paper's code for the figure plots 33 fibers of mouse 842, whose recording has 82 fibers." }, { "kind": "metadata_insufficient", "statement": "The archive's summary gives the approach as \"cell population imaging\" and lists only NWB container types as variables measured; the files hold multi-fiber photometry, treadmill velocity and behavioural events." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper (PMC author manuscript). The verifier tested the helper functions on synthetic inputs and checked the archive's asset list for the blocked claims. Its report had no attempt record and gave its own outcome for each claim; all 26 outcomes agree with the record, and for the five blocked claims it gave data_missing as the reason.", "agreed": 26, "of": 26, "disagreements": [] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the first revision, the helper module, the claims file and the attempt record, with the paper. The verifier agreed with all 26 outcomes, found the round-1 reasons stated faithfully, and listed six sentences the outputs do not support; README line 46 said the notebook takes about 14 minutes where cell 85 printed 16.4 min. The re-run took 12.2 min, and the README now says 12 to 16 minutes.", "agreed": 26, "of": 26, "disagreements": [] } ] }, { "id": "001097-liu-2024-01", "dandiset": "001097", "dandiset_version": "0.260624.0330", "paper": "10.1038/s41586-024-07916-w", "paper_title": "Encoding of female mating dynamics by a hypothalamic line attractor", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-3" }, "tier": "agent_verified", "entry": "001097-liu-2024", "entry_title": "A hypothalamic line attractor for female mating (Liu, Nair et al. 2024)", "description": "Tests the findings of Liu, Nair et al. (2024) on dandiset 001097, which holds miniscope imaging of VMHvl alpha-cells in female mice during mating, with annotations of male and female behaviour. It tests the behavioural dynamics of mating, single-cell tuning, GLM fits and persistence, and, with the authors' deposited rSLDS weights for two mice, how the receptive-day integration dimension and its cells behave across the oestrus cycle. Claims that need new rSLDS fits are blocked, as the model cannot be built or fit within the registry's environment and time limit.", "notebooks": [ { "path": "reproduce_liu_2024.ipynb", "title": "Reproducing Liu, Nair et al. (2024) from dandiset 001097", "executed": "notebooks/001097-liu-2024/reproduce_liu_2024.html" } ], "outcomes": [ { "claim": "fig1b-accepting-escalates", "statement": "During mating the probability of accepting behaviours (lordosis, wiggle) increases gradually over the interaction, while resistance behaviours (dart, top up, kick, turn) first increase and then slowly decrease.", "source": "Figure 1b, Extended Data Figure 1a, Results \"Dynamics of female behaviours in mating\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "Over the first 600 s after male entry the mean probability of accepting behaviour rises (Spearman 0.74, p = 3e-6, 69 annotated trials; 0.59, p = 6e-4, 58 receptive trials), from 0.11 in the first third of the 20-s bins to 0.19 in the last. Resistance peaks in the third bin (0.14) and falls to 0.07 in the last third. Later bins hold fewer trials (69 down to 11); with the same 63 trials in each of the first 15 bins the rise remains (Spearman 0.63, p = 0.012, 0.080 to 0.151). Within single mice the accepting correlation is positive in 12 of 23, and within single trials in 33 of 58 (median 0.01, sign test p = 0.36), so the rise is a property of the pooled trials.", "deviations": [ "69 distinct annotated trials from 23 mice, where the paper has 74 from 28; the paper's trials are not identified.", "Time is counted from male entry and the curves are cut at 600 s; the paper's figure does not state either." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-responsive-dominates", "statement": "Females spend 83.9% of their mating behaviour time in male-responsive behaviours (accepting, resistance, staying) and 16.1% in self-initiated ones (approach, sniff, check genital area).", "source": "Figure 1c, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "Male-responsive behaviours take 84.1% of female mating time on average over the 69 annotated trials (83.5% pooled; 82.9% over receptive trials), against 83.9%. Per mouse the receptive-trial average runs from 65% to 94%.", "deviations": [ "69 distinct annotated trials from 23 mice, where the paper has 74 from 28." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-male-drives-mating", "statement": "Males spend 11.3 times more time in self-initiated mating behaviours (sniff, mount, intromission) than females do in theirs (approach, sniff, check genital area).", "source": "Figure 1d, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "The mean per-trial ratio of male to female self-initiated time is 11.75 over the 69 annotated trials, within the tolerance of 11.3. Only this one of the six readings matches; the ratio of summed times is 7.5 (7.1 on receptive trials), the median per-trial ratio 9.2 (8.2), and the mean ratio over receptive trials 9.3. Every reading is well above 1.", "deviations": [ "69 distinct annotated trials from 23 mice, where the paper has 74 from 28.", "The paper does not say how the ratio is averaged; six readings were set out before the analysis and the match rests on one of them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-interbout-interval", "statement": "Male copulation (mounting and intromission) comes in bouts separated by interbout intervals with a mean of 13.7 s (1,685 bouts and 1,611 intervals in 74 trials).", "source": "Figure 1e, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "Merging mount and intromission annotations less than 0.1 s apart, the mean interbout interval is 14.0 s over the 69 annotated trials (1,540 bouts, 1,471 intervals), 14.9 s over receptive trials and 14.6 s over all 88 distinct sessions, against 13.7 s. Merging gaps up to 1 s gives 15.5 to 16.3 s and not merging gives 9.8 to 10.8 s.", "deviations": [ "The rule for joining annotations into bouts is not stated; three were set out before the analysis.", "69 distinct annotated trials from 23 mice, where the paper has 74 from 28." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-social-in-bouts-and-intervals", "statement": "Females show social behaviours (accepting, resistance and appetitive) for 62% of the duration of each male copulation bout and continue them for 23% of each interbout interval.", "source": "Figure 1g, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "Over the 69 annotated trials females show social behaviour for 63.3% of each copulation bout and 21.8% of each interbout interval on average, against 62% and 23%. This is the only one of the four readings that matches; over receptive trials the interval value is 17.4%, outside the tolerance, and pooled over time the values are 74% and 11%. Leaving out m930's oestrogen days 3 and 4, the two closest to its receptive session, gives 21.7% to 21.9% for the interval value, still within tolerance.", "deviations": [ "69 distinct annotated trials from 23 mice, where the paper has 74 from 28.", "Social behaviour follows the Methods' grouping, which leaves out staying." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-few-tuned-cells", "statement": "Only a small percentage of VMHvl alpha-cells (approximately 2 to 13%) are tuned to any one mating behaviour by choice probability; most show mixed selectivity.", "source": "Figure 2c, Extended Data Figure 2a,b, Methods \"Choice probability\"", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "In the 15 receptive sessions (1,335 cells), 6.9% (approach) to 37.4% (dart) of cells are tuned to a behaviour, median 22.0% over the 11 behaviours with enough bins, against about 2 to 13%. Eight of the 11 exceed 15%. The shuffle test alone passes 21% to 75% of cells. Comparing pairs of behaviours, as the Methods describe, tunes 15.4% to 57.6% over 20 pairs (median 39.3%), with none within 1 to 15%.", "deviations": [ "Each behaviour is compared with every other 1-s bin of the interaction. The Methods compare two behaviours without saying which pairs Figure 2c uses, and only this comparison was set out before the analysis. Pairs of behaviours are shown as a variant, added after the first round of verification.", "A bin belongs to a behaviour when the behaviour covers at least half of it; the shuffle permutes bin labels. Neither is stated in the paper." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-glm-behaviour-explains-little", "statement": "A linear model of each neuron's activity from behaviour explains little of its variance, with mean cross-validated R2 of 0.08 from female behaviours, 0.14 from male behaviours and 0.15 from both.", "source": "Figure 2e, Extended Data Figure 2c,d, Methods \"GLM\"", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "The outcome is the one both verification rounds agreed with. After the second round the author proposed partially_reproduced, from a penalty selection added then; that change has not been verified (protocol pilot-4, \"Hand over for verification\"). With tenfold contiguous cross-validation and the ridge penalty chosen per cell by fivefold cross-validation within each training set, the mean cvR2 over 1,335 cells is -0.041 from female behaviours, -0.005 from male behaviours and -0.004 from both (mouse means -0.026, 0.014 and 0.016), against 0.08, 0.14 and 0.15. The ordering holds, both against male by a margin of 0.0003 over cells and 0.0014 over mouse means, and all three are below 0.25, so the partial rule is met by a thin margin. With the penalty chosen on the last fifth of each training set, the design used in the first two rounds, the means are -0.077, -0.013 and -0.057 (mouse means -0.050, 0.008 and -0.017) and both scores below male, so the ordering failure that gave not_reproduced came from that selection. A model with only an intercept scores -0.086 under the same folds, so the negative values come from the fold design; with the cross-validated penalty the gain over it is 0.045, 0.081 and 0.082 (mouse means 0.054, 0.095 and 0.096), below the paper's values. With the last-fifth penalty, R2 within single folds is dominated by the same offsets (medians -0.61 to -0.71, intercept -0.70). With frames assigned to folds at random, a variant not named in the criterion, the means are 0.229, 0.207 and 0.322, with neighbouring frames in both training and test sets; the value from both behaviours is then above 0.25. The test is weak, since no design here separates behaviour from the slow drift of the traces.", "deviations": [ "Lags in 1-s steps over 0 to 10 s, not every frame, to keep the run short.", "Contiguous folds, the ridge penalty chosen per cell by fivefold contiguous cross-validation within each training set, and R2 on pooled held-out predictions; the Methods state none of these. The cross-validated penalty selection was added after the second round of verification; the outcome would change with it, and that change is proposed, not verified.", "Fit over the interaction (male entry to end of annotation) on z-scored, unsmoothed traces." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": { "outcome": "partially_reproduced", "reason": "With the ridge penalty chosen by fivefold cross-validation within each training set, a selection added after the second round, the ordering of the criterion holds (both above male by 0.0003 over cells) and all three values are below 0.25, which meets the partial rule." } }, { "claim": "fig2f-glm-coupling", "statement": "Adding the activity of the other simultaneously imaged neurons as regressors raises the mean cross-validated R2 to 0.46.", "source": "Figure 2f, Methods \"GLM\"", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "Adding the instantaneous activity of the other cells gives a mean cvR2 of 0.477 over cells (0.458 over mouse means) with the cross-validated penalty, and 0.450 (0.434) with the last-fifth penalty, against 0.46. With the last-fifth penalty 73 of 1,335 cells remain below zero and the gain over the intercept-only baseline is 0.536 (0.563 with the cross-validated penalty). With random folds it is 0.814. It shares the fold design questioned for fig2e-glm-behaviour-explains-little.", "deviations": [ "As for fig2e-glm-behaviour-explains-little. Coupling uses the other cells at the same time point; the Methods do not say whether coupling filters had lags." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2i-persistent-cells", "statement": "About 30% of cells have an autocorrelation half-width (ACHW) longer than 25 s, and the mean ACHW is 20 s, longer than the mean interbout interval.", "source": "Figure 2i, Results, Methods \"Calculation of ACHW\"", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "Over the whole recording, smoothed as in the authors' code, 20.0% of 1,335 cells have an ACHW above 25 s and the mean is 15.5 s, against 30% and 20 s. The first-crossing rule gives the same, and the other readings give 10 to 17% and 9.9 to 13.1 s. Per mouse the fraction runs from 0 to 0.48, and four mice reach 0.28 or more; the lower panel of Figure 2i has n = 4 mice, which are not identified. Ending the window at the last annotation, a variant that drops the unannotated imaging at the end of 7 sessions, gives 15.5 to 19.7% and 12.7 to 15.0 s. The mean ACHW is still longer than the mean interbout interval (14.0 s), as the paper says.", "deviations": [ "The ACHW follows the authors' code (the lag closest to 0.5, up to 50 s), where the Methods say the lag where the function reaches 0.5; both are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3b-pencil-cup", "statement": "The ACHW of the same cells is shorter when the male is behind a perforated pencil cup (14.3 s) than during free interaction (19.6 s), 470 neurons from 5 mice.", "source": "Extended Data Figure 3a-c, Results", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "No annotation marks the pencil-cup period. In 17 sessions imaging continues for up to 7 minutes after the last annotation, which may be that period, but the files do not say so. An exploratory look, not judged, at the 7 receptive sessions with at least 3 minutes of it (544 cells, where the paper has 470 from 5 mice) finds a shorter mean ACHW in the tail than over the interaction (4.0 to 11.5 s against 7.3 to 17.9 s), but against a stretch of the interaction of the same length the tail is longer in 5 of 7 sessions, so the difference comes from the window length.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-rslds-fit", "statement": "An rSLDS fit to each receptive mating trial explains 64.08% (SD 6.8) of the variance of the neural trajectories, n = 15 mice.", "source": "Figure 3a, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Needs rSLDS fits. The ssm package is a Cython extension installed from GitHub that does not build in the registry's locked environment (it needs numpy at build time), and with the authors' settings one 10,000-frame session takes about 7.5 minutes to fit (10 of 150 iterations took 30 s in a separate environment), so the fits the blocked claims need would take hours against the 30-minute limit. A single linear dynamical system was tried as a stand-in and fitted rotations with two equal time constants in 14 of 15 receptive sessions, so it cannot separate an integration dimension and was not used. The Methods also leave the forward simulation interval open, and the authors' code computes this variance explained differently (a full free-running simulation). Neither timing nor stand-in is run in the notebook, so they cannot be checked from its outputs; the build failure alone blocks the fits here.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-integration-dimension", "statement": "The rSLDS reveals one integration dimension with a long time constant (110.7 +- 13.6 s) compared with the next (24.5 +- 5.1 s), forming an approximate line attractor; n = 15 mice, P = 6.5e-5.", "source": "Figure 3b,c,e, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Needs rSLDS fits to the 15 receptive sessions, which are in the dandiset; see fig3a-rslds-fit for why they cannot be run here. The Methods also find the integration dimension by partial least squares onto a ramp (Extended Data Figure 3d,e). That gives a direction but no time constants, so it cannot test this claim, and using it for the ramp and persistence claims would assume the ramp they test; it is not used.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3s-integrator-model", "statement": "A single-state linear dynamical system driven by male sniff, mount and intromission predicts activity in the integration dimension with cvR2 of 0.88 +- 0.02 and an intrinsic time constant above 200 s.", "source": "Extended Data Figure 3r-u, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Needs the integration dimension from rSLDS fits; see fig3a-rslds-fit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed4b-single-cell-ramps", "statement": "Of neurons contributing to the integration dimension, 56% correlate with an ideal ramp with r2 above 0.5, but they peak at different times.", "source": "Extended Data Figure 4a-d, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Needs the integration dimension from rSLDS fits; see fig3a-rslds-fit. The Methods do not define the ideal ramp either. An exploratory look, not judged, in the two natural-cycle mice with deposited weights, with a ramp chosen here (0 before male entry, rising linearly to the end of the annotation), finds r2 above 0.5 in 0 of 44 weighted cells in m541 and 1 of 14 in mouse 543, against 56%; these are not the paper's 15 receptive sessions.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3k-perturbation-relaxation", "statement": "Transient optogenetic inhibition of VMHvl pushes population activity off the line attractor, after which it relaxes back to the attractor, as the flow field fit to unperturbed data predicts; n = 3 mice.", "source": "Figure 3h-k, Extended Data Figure 5c-j, Results", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The sessions with 10-s optogenetic inhibition of VMHvl are not in the dandiset; no label marks such an inhibition. The eight male-inhibition sessions have one or two inhibition epochs of 106 to 351 s, the male manipulation of Figure 4c,d. The authors' code repository carries one such session (sub-M1188) as example data, outside the archive.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-persistence-during-intervals", "statement": "Activity in the integration dimension during copulation interbout intervals is as high as in the preceding bout, so a decoder cannot tell bouts from intervals (0.52 against a shuffle of 0.49, n = 4 mice, P = 0.2).", "source": "Figure 4a,b, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Needs the integration dimension from rSLDS fits; see fig3a-rslds-fit. The four mice of the figure are not identified.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-persistence-male-inhibition", "statement": "When male mating is stopped for minutes by optogenetic activation of the male's VMH, activity in the female's integration dimension stays elevated; n = 4 mice.", "source": "Figure 4c,d, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The male-inhibition sessions are in the dandiset (8 mice, where the figure has 4), but the claim needs the integration dimension from rSLDS fits; see fig3a-rslds-fit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-peak-before-ejaculation", "statement": "Activity in the integration dimension peaks just before ejaculation and drops immediately after; n = 4 mice.", "source": "Figure 4g,h, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Twelve sessions annotate an ejaculation, but the claim needs the integration dimension from rSLDS fits; see fig3a-rslds-fit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-attractor-receptive-days", "statement": "Over the natural oestrus cycle, rSLDS models fit on receptive days have a line attractor and those fit on unreceptive days do not (line-attractor score 1.9 +- 0.2 against 0.05 +- 0.02, n = 4 mice, P = 0.02).", "source": "Figure 5b-f, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Needs rSLDS fits on each day; see fig3a-rslds-fit. The files also do not say which day of a natural-cycle series was receptive, and the female's behaviour is not annotated on those days; the receptive day can be found only by matching a day to the mouse's separately deposited receptive session. The matching rule (same count of male annotations, offsets within 0.5 s) finds it for 4 of the 7 mice (543, m541, m542, m551); m438 day 1 has the same frame count and interaction length as m438's receptive session but different male annotations (60 against 76), and m610 and m764 have no receptive session.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed6e-projection-unreceptive-days", "statement": "Projected onto the integration dimension found on the receptive day, activity on unreceptive days does not ramp and stays low during male mounting (normalised value 0.09 on unreceptive against 0.69 on receptive days, n = 4 mice).", "source": "Figure 5g,h, Extended Data Figure 6c-f, Results", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "With the authors' weights, the normalised integration value during mounting in m541 is 0.61 on the receptive day against 0.23 and 0.19 on the unreceptive days (paper 0.69 against 0.09; the unreceptive values here are about twice the paper's). In mouse 543 it is 0.61 against 0.64 and 0.63, not higher. The ramp part of the claim holds in both mice; the projection rises by 2.5 and 2.1 receptive-day SDs on the receptive day and by -0.4 to 0.5 on unreceptive days. The outcome depends on which factor is taken as the integration factor. On the other factor the receptive day is higher in both mice (m541 factor 1, 0.62 against 0.48 and 0.49; 543 factor 2, 0.66 against 0.54 and 0.51), which would meet the criterion in both, though on 543's factor 2 the unreceptive days also ramp (1.07 and 1.03 SDs).", "deviations": [ "Two mice, where the paper has four; the weights of only two are deposited, and the file labelled m542 holds mouse 543's cells.", "The authors' weights are applied to the stored traces of each day; the paper's projection procedure and normalisation are not described, and min-max over the three days is used. The cell order was checked after the first round of verification; 171 of 176 cells (m541) and 71 of 72 (543) best match the session cell of the same index. The per-mouse files' own traces were processed differently (same-index median correlation 0.86 and 0.80), but the projections from them and from the stored traces correlate at 0.94 to 0.96.", "The integration factor is not labelled in the files; it is chosen by the longer ACHW of its receptive-day projection. Both factors reach the code's 50-s cap in m541, so the tie was broken with lags up to 300 s, a step not set out in the criterion. The outcome changes with the factor chosen.", "The receptive day is the one matching the mouse's deposited receptive session." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed7-achw-across-cycle", "statement": "Cells weighted on the integration dimension have shorter ACHW on unreceptive than on receptive days (16.1 +- 0.8 s against 25.2 +- 1.5 s, P < 0.001), while cells that do not contribute to it do not change.", "source": "Extended Data Figure 7a-h, Results", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "In both mice weighted cells have longer ACHWs on the receptive day, 28.4 against 17.2 s in m541 (44 cells, KS p = 2e-5) and 26.7 against 9.1 s in 543 (14 cells, KS p = 2e-4), against 25.2 and 16.1 s in the paper. Other cells do not differ in m541 (KS p = 0.23) but do in 543 (12.8 against 10.8 s, KS p = 0.005). The top 25% of weights give the same pattern; with the top 10% the 8 weighted cells of 543 no longer differ (p = 0.13). The change is not specific to the integration factor; in m541 the 44 cells above one SD on the other factor, 23 of them shared, lengthen as much (30.8 against 17.5 s, KS p = 7e-6). In 543 the 20 cells of the other factor, 7 shared, do not differ at p 0.05 (21.0 against 12.9 s, p = 0.07).", "deviations": [ "Two mice where the paper has four, with the factor and receptive day chosen as for ed6e-projection-unreceptive-days." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9j-ovx-hormone-priming", "statement": "Attractor dynamics disappear after ovariectomy and return after hormone priming.", "source": "Extended Data Figure 9j-n, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The ovariectomy series of three mice is in the dandiset, but the claim needs rSLDS fits on each day; see fig3a-rslds-fit. The deposited weights of m541 cover 176 cells, its ovariectomy days 184, so they cannot be applied.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5k-receptivity-correlation", "statement": "In oestrogen-injected females, the area under the curve of the integration dimension correlates with the percentage of time spent in accepting behaviours (r2 = 0.62, P < 0.0001, n = 50 trials), and not with resistance or appetitive behaviours.", "source": "Figure 5i-l, Extended Data Figure 10b, Results", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The oestrogen-injected cohort is in the dandiset (42 trials where the paper has 50), but the claim needs an rSLDS fit per trial; see fig3a-rslds-fit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed10c-population-mean-uncorrelated", "statement": "In the same trials, the area under the curve of the population mean of all neurons does not correlate with the percentage of time spent in accepting behaviours.", "source": "Extended Data Figure 10c,d, Results", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_liu_2024.ipynb", "notes": "Over 42 trials from 6 mice the area under the population mean does not correlate with the percentage of time in accepting behaviour under any of three readings (r2 0.015, 0.003 and 0.027; p 0.45, 0.73 and 0.30). Within mice the Spearman correlations run from -0.67 to 0.52. Without the two sessions that fail the clock check (m928 day 2, m940 day 7), r2 is 0.011, 0.005 and 0.025 over 40 trials.", "deviations": [ "42 trials where the paper has 50.", "The window of the area under the curve is not stated; three readings were set out before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "No rSLDS fits or latent factors are deposited apart from the per-cell weights of two mice, though the dandiset's description says it contains low-dimensional latent factors from dynamical models. The per-mouse files hold under analysis only a table of two weight columns, and under processing one trace series and the annotations; there are no latent time series or dynamics matrices. The paper's central line-attractor results can only be checked by refitting." }, { "kind": "data_missing", "statement": "The sessions with optogenetic inhibition of VMHvl during imaging (Figure 3h-k, Extended Data Figure 5) are not in the dandiset." }, { "kind": "metadata_error", "statement": "The per-mouse file sub-m542/sub-m542_behavior.nwb is labelled m542 but its neural data are those of mouse 543 (72 cells and 10,527 frames, matching 543's receptive day cell by cell with a median correlation of 0.80); m542's own sessions have 129 cells." }, { "kind": "identifier_missing", "statement": "One mouse is labelled 543 in its natural-cycle files and m543 in its receptive session." }, { "kind": "metadata_error", "statement": "The same recording is filed under two experiments five times. m764's natural-cycle day 1 has the same traces and annotations as its primed ovariectomy session; m776's primed session has the same traces as its male-inhibition session, with different annotations; and day 3 of the ovariectomy series of m438, m541 and m551 has the same traces as the mouse's primed session, with annotations that differ in m541 and m551 and an interaction of 290.7 against 274.6 s in m438." }, { "kind": "other", "statement": "The traces in the two per-mouse files, which carry the rSLDS weights, were processed differently from the session files of the same recordings (same-index median correlation 0.86 and 0.80, rising with smoothing of the session traces), and the files do not say how. The cell order matches the session files." }, { "kind": "other", "statement": "Which natural-cycle days were receptive is not recorded, and the female's behaviour is not annotated on most of those days, so the paper's definition of a receptive day cannot be applied. The receptive session of each mouse is deposited separately, without a link to the day it repeats." }, { "kind": "selection_undocumented", "statement": "The dandiset holds more animals or fewer trials than several analyses use, without saying which were used; 7 natural-cycle mice where Figure 5c has 4, 8 male-inhibition mice where Figure 4d has 4, 42 oestrogen-injected trials where Figure 5k has 50, and 69 annotated trials from 23 mice where Figure 1 has 74 from 28." }, { "kind": "other", "statement": "In 17 sessions imaging continues for up to 7 minutes after the last annotation, which may be the pencil-cup period of the Methods, but nothing marks it. The labels other and eat, and the two names for the male-inhibition epoch (laser_on and mating_inhibition), are not described." }, { "kind": "metadata_error", "statement": "Every session file describes a two-photon microscope with 920-nm excitation, where the paper used a one-photon miniscope; the raw traces are labelled lumens but are arbitrary units with negative values; the traces described as z-scored are not z-scored per file (per-cell means -1.6 to 2.4); experimenter, lab, institution and session start time are placeholders; image masks are 1 by 1 pixel; and the file names say ecephys for imaging data. The per-mouse files describe their session as a resident-intruder assay." }, { "kind": "methods_unavailable", "statement": "The linked code holds demonstration notebooks, not the code for the paper's figures, so the GLM, choice-probability, decoder and projection procedures cannot be checked against it." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module, the claims file and the paper's full text (PMC11499253). For the blocked claims the verifier checked the archive's asset list and metadata through the DANDI REST API. It did not run the notebook or stream any file.", "agreed": 24, "of": 24, "disagreements": [] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full re-executed notebook after the first round (79 cells) with its conclusions and summary, the README, the attempt record, the helper module, the claims file and the paper's full text (PMC11499253, re-downloaded from Europe PMC). It did not run the notebook or stream any file.", "agreed": 24, "of": 24, "disagreements": [] } ] }, { "id": "001170-ling-2023-01", "dandiset": "001170", "dandiset_version": "0.260528.1016", "paper": "10.1101/2023.04.24.538157", "paper_title": "Conserved neural dynamics and computations across species in olfaction", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001170-ling-2023", "entry_title": "ON and OFF odor responses in the mouse olfactory bulb and locust antennal lobe (Ling et al. 2023)", "description": "Tests the findings of Ling, Moss, Smith, Deng, Kroeger, Reimer, Raman and Arenkiel (bioRxiv 2023, v2 2024) on dandiset 001170, which holds two-photon imaging of olfactory bulb glomeruli in awake mice, seven sessions from four mice under the paper's block protocol and five random-order sessions. It compares glomerular ON and OFF responses, contrast enhancement between sequential odors, and odor classification after offset, and tests the locust findings on the recordings the paper deposited on Figshare.", "notebooks": [ { "path": "reproduce_ling_2023.ipynb", "title": "Reproducing Ling et al. (2023) from dandiset 001170", "executed": "notebooks/001170-ling-2023/reproduce_ling_2023.html" } ], "outcomes": [ { "claim": "mouse-sessions", "statement": "The mouse block-protocol data (four odors, 5 s pulses, 55 s between trials, blocks of ten, 15 min between blocks) come from seven imaging sessions in four mice, with a median of 215 glomeruli per imaging session.", "source": "Results, first section; Figure 2H and 4B legends; Methods, Odor delivery to mice", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "The trials tables give seven block-protocol sessions from mice 134, 141, 148 and 149. The median ROI count over these is 210 (reading a); over all twelve sessions it is 296 (reading b). The ROI counts of sub-141 ses-8 (198), sub-149 ses-1 (219) and sub-148 ses-3 (318) equal the glomerulus counts the Methods give for Figures 2F and 4C, 6D and 7. The published version's Table 1 gives the same seven counts in four mice, but puts the 318 session with the 219 session (mouse 4), where the dandiset puts it with the 286 session (sub-148).", "deviations": [ "Sessions are matched to the paper's figures by ROI count; no identifier links them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figshare-trace-link", "statement": "The dandiset's raw fluorescence of the 198-glomerulus session is the data the paper deposited for its Figure 2D to 2F and 4C (Figshare data1_mouse_glom198.mat), up to the normalisation, with glomeruli in the same order.", "source": "Methods, Time-bin-by-time-bin correlation analysis (n = 198 glomeruli for Fig. 2F); the paper's Figshare record", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "Matched by ROI count (sub-141 ses-8, the only 198-ROI session) and ROI order. With the code's frame-counted windows the median within-trial r between the dandiset's raw F and the deposited array is 0.968 (5th percentile 0.834, 0.947 to 0.994 by block), and every deposited glomerulus correlates best with the dandiset ROI of the same index. With windows placed in seconds the median r is 0.307, as the code counts 16 frames per second in a session imaged at 15.5 Hz. The deposited values are close to F z-scored within each trial window (r = 0.927). No other claim depends on this one.", "deviations": [], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig2h-onoff-angle-mouse", "statement": "In the mouse OB the angle between glomerular ON and OFF response vectors is greater than 90 degrees for each odor (mean 121.8 +/- 2.98 SEM, 4 odors, 7 sessions), so ON and OFF responses are inverted relative to each other.", "source": "Results, first section; Figure 2G and 2H", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "With the code's procedure (median subtraction, vectors centred over the 160 frames) the median ON-OFF angle exceeds 90 degrees in all 28 session-odor pairs (101.7 to 153.9) and in each odor's mean (111.0 to 140.0), but the mean is 127.9 (SEM 3.2), outside 121.8 +/- 2.98. After centring the mean ON vector is exactly opposite the mean OFF vector (cosine -1 in every case), and without centring the mean angle is 71.8 with 2 of 28 above 90. The same centred procedure gives 101.1 between the two halves of the ON window (28 of 28 above 90), 101.6 between the halves of OFF and 129.7 between the 2 s before onset and ON, and on synthetic frames around patterns 2.4 to 13.0 degrees apart it gives 91.6 to 115.6; so the angles above 90 follow the criterion but do not show that ON and OFF are inverted. Without the median subtraction the mean is 124.2 and with per-trial z-scored traces 119.5, both within tolerance; with F z-scored on the 2 s before onset 125.8 and with frame-counted windows 126.1. By mouse the means are 136.3 (134), 136.3 (141), 116.0 (148) and 117.9 (149).", "deviations": [ "dF/F with F0 from the 2 s before onset; the paper's deposited arrays are close to per-trial z-scores. The z-scored result is shown as a variant.", "Windows placed in seconds on a 16 Hz grid; the code counts frames at a nominal 16 per second." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2f-onoff-anticorrelated-mouse", "statement": "Time-averaged glomerular ON and OFF responses to the same odor are anticorrelated; glomeruli active during the odor tend to be suppressed after it and the reverse.", "source": "Results, first and second sections; Figure 2D, 2F and 4C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "The time-averaged ON and OFF vectors are positively correlated in all 28 session-odor pairs (median r 0.481, Wilcoxon p = 7.5e-09), for every odor (0.391 to 0.535) and every mouse (0.245 to 0.596). The median subtraction does not change r, by construction. With F z-scored on the 2 s before onset the median r is 0.526 and with frame-counted windows 0.446 (0 of 28 below 0 in both). With per-trial z-scored traces the median r is 0.068 (12 of 28 below 0, p = 0.33); on synthetic glomeruli with excitation only, that normalisation gives r = -0.90 between ON and 10 to 15 s after offset, against 0.30 with the pre-onset z-score. The angles of fig2h exceed 90 degrees only after centring, which makes the mean ON and OFF vectors opposite by construction.", "deviations": [ "dF/F with F0 from the 2 s before onset, not the paper's (undocumented) normalisation." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-reference-odor-mouse", "statement": "In the mouse OB the ON response to a reference odor is closer in angle to the ON responses of the other odors than to any OFF response, including its own, and this holds for every odor of the panel.", "source": "Results, second section; Figure 4B and S4B", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "Reading (a) holds for acetophenone only (ON-ON 105.7, ON-OFF 127.5 degrees, paired p = 0.018). Methyl salicylate and eugenol show no difference (p = 0.76 and 0.83), and allyl sulfide goes the other way (ON-ON 112.1, ON-OFF 59.6, p = 0.00035). Reading (b) holds in none of the seven sessions for any reference odor. Full-dimensional vectors give the same pattern. The session-mean ON-ON angles are 85.6 to 123.1 degrees, against a median of 44.7 for the acetophenone reference in the published version (Figure 2G), so the paper's procedure probably differs from the one used here.", "deviations": [ "The mouse code for this figure is not in the Figshare record (it loads precomputed angles); the locust code's procedure (top three PCs, mean vectors) was used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-clustering-mouse", "statement": "Hierarchical clustering of glomerular responses cleanly separates ON responses from OFF responses.", "source": "Results, second section; Figure 4D", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "In 0 of 7 sessions, the 198-glomerulus session included, does the two-cluster cut put the four ON vectors apart from the four OFF vectors, with dF/F or with z-scored traces.", "deviations": [ "The paper shows one representative session without naming it; the 198-glomerulus session is taken as it, and all seven are reported." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6e-contrast-msc", "statement": "Methyl salicylate presented 1 s after another odor evokes a response less correlated with that odor's solitary response than the solitary methyl salicylate response is (history dependent contrast enhancement; one-tailed t-test p < 0.01, 3 sessions from 2 mice).", "source": "Results, third section; Figure 6D and 6E (left)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "Over 21 session-odor pairs the solitary r (0.229) and the sequential r (0.219) do not differ (difference 0.009, positive in 10 of 21, one-tailed paired p = 0.39); per session p = 0.40, per first odor p = 0.33 to 0.51. On the three sessions the published version's Table 1 names (sub-148 ses-2, sub-148 ses-3, sub-149 ses-1) the solitary r is 0.133 and the sequential r 0.064 (p = 0.082). With F z-scored on the 2 s before the pair's onset there is no difference (0.251 against 0.258, p = 0.58). With per-trial z-scored traces the solitary r is 0.289 and the sequential r 0.118 (p = 5.6e-07; 0.0025 on the three sessions), as the claim states, but that normalisation can produce negative correlations with later activity by itself (fig2f).", "deviations": [ "All seven block sessions are used, as the preprint does not identify its three sessions from two mice; the three the published version names are shown as a variant.", "dF/F with F0 from the 2 s before the pair's first onset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6e-contrast-ace", "statement": "Acetophenone presented 1 s after another odor evokes a response less correlated with that odor's solitary response than solitary acetophenone (one-tailed t-test p < 0.05, 4 sessions from 2 mice).", "source": "Figure 6E (right) and Figure S6", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No sequential pair in the dandiset ends in acetophenone; in all seven block sessions the second odor is always methyl salicylate (ace, als or eug first). The Figshare code builds only (X)msc sequences too, so the (X)ace data of Figure 6E (right) and S6 were not found in public form. The published version's Table 1 assigns this panel to the 73-, 210-, 153- and 198-glomerulus sessions, which in the dandiset hold only (X)msc pairs; in those sessions the first odor's response in the pairs correlates 0.94 to 0.99 with solitary acetophenone when the first odor is labelled acetophenone, and the second odor's response 0.76 to 0.95 with solitary methyl salicylate, consistent with the dandiset's labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7d-persistent-anticorrelation", "statement": "After odor offset the glomerular population activity stays negatively correlated with the odor-evoked ON response for several tens of seconds, although overall activity returns to baseline quickly.", "source": "Results, fourth section; Figure 7B, 7D and S7C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "The median r with the ON vector over the 28 pairs is 0.481 at 0 to 5 s after offset, 0.312 to 0.328 from 5 to 20 s and 0.094 at 45 to 50 s, above 0 in every bin (p <= 0.014), while the mean dF/F falls from 0.071 to 0.005. With F0 from before each block r is positive in every bin (0.304 to 0.600); for the first block of sub-134 and sub-141 that baseline is only 14 to 24 s. With F z-scored on the 2 s before onset r is positive in every bin (0.152 to 0.527), and with frame-counted windows too (0.152 to 0.446). With per-trial z-scored traces r is negative from 5 s on (-0.344 to -0.480, 26 to 28 of 28), as the claim states, but on synthetic glomeruli with excitation only that normalisation gives negative values of the same sign and larger size (-0.90 and -0.93). Mice 148 and 149 keep r near 0.2 to 0.4 for the whole 50 s.", "deviations": [ "Correlation of the ON vector with 5-s bins, a summary of the paper's frame-by-frame matrix.", "dF/F with F0 from the 2 s before onset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7h-iti-knn-mouse", "statement": "Glomerular activity averaged over the 50 s after each odor offset classifies the preceding odor with high accuracy (k-NN, k = 20).", "source": "Results, fourth section; Figure 7G and 7H; Methods, Classification analysis of average ITI periods", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "In sub-148 ses-3 (318 glomeruli) accuracy is 45%, above the null's 99th percentile (37.5%, null mean 16.7%) but below 50%; by odor 0.9, 0.0, 0.3 and 0.6. The code's choice (cosine on the top three PCs) gives 12.5%. Across the seven sessions accuracy is 22.5% to 47.5%, above the null's 99th percentile in three. The null mean of this leave-one-out vote (16.7% to 17.4%) is below the nominal 25%, as with k = 20 only 9 of the 39 other trials share the own odor; the paper gives no chance value for this panel. With k at or below the class size accuracy is 90.0% (k = 5) and 82.5% (k = 9) in sub-148 ses-3 and 80.0% to 100% in every session (null 99th percentiles 42.5% to 45.0%). All trials of one odor lie in one block, so neither k separates the odor from slow differences between blocks (fig7j).", "deviations": [ "k = 20 from the legend; the Methods' k = 50 exceeds the 39 other vectors.", "dF/F with F0 the session median of each ROI." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7j-iti-timebin-mouse", "statement": "A time-bin k-NN classifier identifies the preceding odor from glomerular activity throughout the 55 s inter-trial interval; accuracy stays high for its whole duration and falls to chance with shuffled labels.", "source": "Results, fourth section; Figure 7J and S8C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "In sub-148 ses-3 accuracy is 88.5% in the first 10 s after offset and 71.9% to 75.6% from 10 to 50 s, above 50% and the null's 99th percentile (32.5% to 35.9%); the other sessions give 72.2% to 99.4% in every segment. The statement's reading as odor memory is not supported by the outputs. The trial-label null does not keep the block structure, and as each odor has one block no label permutation that keeps whole blocks can serve as a null. On pseudo-trials within the 15 min after each block, where no odor is given, the same classifier names the preceding block at 69.6% to 96.9% (sub-148 ses-3 69.6% to 71.2%), nearly as high as in the ITIs (the pseudo-trial maximum is below the ITI minimum in 4 of 7 sessions), so slow differences between blocks are enough for most of this accuracy.", "deviations": [ "dF/F with F0 the session median of each ROI.", "The shuffled-label control is a permutation of whole-trial labels with the neighbours kept." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs7e-ibi-chance", "statement": "During the 15 min between blocks odor-specific information is no longer present; classification of 1-min bins of the inter-block interval by the preceding odor is near chance (34.8%).", "source": "Results, fourth section; Figure S7D and S7E, Figure 7K", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_ling_2023.ipynb", "notes": "With the Methods' k = 50 on 60 one-minute bins the rate is 0.0% to 13.3% (mean 3.8%) in the four sessions with complete IBIs, and this procedure's permutation null averages 10.8%, not the 25% chance of four odors, so the paper's 34.8% cannot come from it. With k = 20 the IBI bins are classified by the preceding block at 73.3% to 95.0% in those four sessions and 35.0% to 66.7% in the other three (permutation p <= 0.02), and with k at or below the 14 other bins of the own IBI at 69.4% to 98.3% (k = 10) and 90.0% to 98.3% (k = 5) in all seven (null means 21.8% to 25.5%, p < 0.001). These rates contradict the claim, but each odor has one IBI per session, so no validation can hold out a block, and slow drift between neighbouring minutes could give them.", "deviations": [ "The 318-glomerulus session has only three complete IBIs (54 bins), so k = 50 was run on the four sessions that have four." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs8e-random-order-decline", "statement": "When eleven odors are presented in random order (1 s pulses, 19 s apart), odor information after offset is variable across odors and on average declines to chance after several seconds.", "source": "Results, fourth section; Figure S8D and S8E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "In all five random-order sessions accuracy in the first 2 s after offset is above the null (24.4% to 56.8% against 99th percentiles of 10.6% to 12.3%, chance 9.1%), with large differences between odors. In the last 5 s it is 9.6% to 15.3%, still above the null's 95th percentile in four of five sessions (not in sub-134 ses-6). The published version's Table 1 lists random-order sessions with 175, 340, 323, 306, 286, 204, 250 and 280 glomeruli; only sub-126 ses-1 (323) and sub-134 ses-6 (306) have one of these counts. In those two early accuracy is 24.4% and 29.0%, and late accuracy is above the null's 95th percentile in sub-126 ses-1 (9.6% against 9.0%) and not in sub-134 ses-6 (9.9% against 10.0%).", "deviations": [ "The paper's random-order session (286 glomeruli, mouse 129 in the Figshare code) is not in the dandiset; five sessions with the same paradigm, four of them from mice not in the block sessions, were used.", "In three of these sessions odors have different concentration values; the first 10 presentations of each odor were used regardless." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2-pid-decay", "statement": "Photoionization detector recordings at the nostril show odor concentration rising and decaying quickly at onset and offset, for every odor.", "source": "Figure S2; Methods, Odor delivery to mice", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds no photoionization detector recordings (acquisition holds the movies, treadmill and in one file respiration). No PID file is in the Figshare record's file list.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-onoff-angle-locust", "statement": "In the locust antennal lobe the median angle between PN population ON and OFF response vectors exceeds 90 degrees for every one of 11 odors (mean 106.7 +/- 0.84 SEM).", "source": "Results, first section; Figure 1F and 1G, S1", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "All 11 odors give a median ON-OFF angle above 90 degrees (99.2 to 108.7); the mean is 104.9 (SEM 0.87), 1.8 degrees below 106.7 +/- 0.84. Without centring the mean is 58.5; with each PN's pre-odor mean subtracted and no centring it is 91.9, with 9 of 11 above 90. The centring alone gives angles above 90 degrees; the two halves of the ON window are 96.0 apart on average (11 of 11 above 90).", "deviations": [ "Data from the Figshare record of the published version; the preprint's data may differ." ], "disagreed": false, "data": "elsewhere", "where": "Figshare doi:10.6084/m9.figshare.31435543.v2 (data2_locust_PN66.mat)", "proposed": null }, { "claim": "figs4a-reference-odor-locust", "statement": "In the locust the ON response to a reference odor is closer to other odors' ON responses than to OFF responses for most reference odors, significantly for 5 of 11.", "source": "Results, second section; Figure 3B and S4A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "Four reference odors have ON angles significantly smaller than OFF angles (hex, hxa, phn, vny), and 9 of 11 have smaller ON angles on average. Ammonia differs significantly the other way (ON 107.3, OFF 52.5 degrees, p = 0.0033). The 11 ON angles include the reference's own 0 degrees, as the criterion states; without it the count is still 4, and ON is smaller on average for 8 of 11. Benzaldehyde (p = 0.052) and octanoic acid (p = 0.059) are near the threshold.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Figshare doi:10.6084/m9.figshare.31435543.v2 (data2_locust_PN66.mat)", "proposed": null }, { "claim": "fig5e-contrast-locust", "statement": "In the locust, PN responses to geraniol presented 0.5 s after another odor are less correlated with that odor's solitary response than solitary geraniol is (one-tailed t-test p < 0.05, 5 odor pairs).", "source": "Results, third section; Figure 5D and 5E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "Solitary first odors correlate with solitary geraniol at 0.486 on average and with geraniol after them at 0.227, lower for all five (one-tailed paired p = 0.0055). With hexanol as the second odor the difference is smaller (0.407 against 0.321, p = 0.13).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Figshare doi:10.6084/m9.figshare.31435543.v2 (data4_locust_PN85.mat)", "proposed": null }, { "claim": "fig7f-iti-knn-locust", "statement": "In the locust, PN activity averaged over the 20 s after odor offset classifies the preceding odor (k-NN on angular distance), so ITI activity is odor specific.", "source": "Results, fourth section; Figure 7E and 7F; Methods, Classification analysis of average ITI periods", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "The 20-s ITI averages classify all 70 trials correctly (null 99th percentile 25.7%, chance 14.3%); the code's choice (k = 4, cosine on three PCs) gives 97.1%. The published version's Table 1 gives this dataset a solitary block structure; the Figshare file holds only the 40 s around each trial, so no control for slow differences between blocks can be built, and the accuracy cannot be attributed to the odor alone.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Figshare doi:10.6084/m9.figshare.31435543.v2 (data5_locust_PN85.mat)", "proposed": null }, { "claim": "fig7i-iti-timebin-locust", "statement": "In the locust a time-bin k-NN classifier's accuracy decays across the 20 s after offset to about 40% averaged over odors, but for most odors does not fall to chance.", "source": "Results, fourth section; Figure 7I", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_ling_2023.ipynb", "notes": "Accuracy decays from 78.7% in the first 2 s after offset to 29.0% averaged over odors in the last 5 s, below 40 +/- 4; every one of the 7 odors stays above its null's 99th percentile in the last 5 s (16.0% to 54.0% against 14.0% to 27.6%). Averaged over the whole 0 to 21 s the accuracy is 39.6%, a reading of \"about 40%\" the criterion did not list. As for fig7f, the files allow no control for the block structure.", "deviations": [ "The paper's ~40% is read from its text; the last 5 s of the ITI was taken as the end." ], "disagreed": false, "data": "elsewhere", "where": "Figshare doi:10.6084/m9.figshare.31435543.v2 (data5_locust_PN85.mat)", "proposed": null } ], "findings": [ { "kind": "metadata_insufficient", "statement": "The fluorescence traces are raw F (unit \"n.a.\") with no description of how they were extracted or of the normalisation the paper applied. The paper's deposited arrays are close to F z-scored within each 57-s trial window. With that normalisation the contrast enhancement and negative correlations between the ON response and activity from 5 s after offset appear in these data, and they do not with dF/F relative to the 2 s before each odor or with F z-scored on those 2 s. The time-averaged ON and OFF vectors are not anticorrelated with any of these (median r 0.068 with the whole-window z-score, 12 of 28 below 0). On synthetic glomeruli with excitation only, the whole-window z-score gives such anticorrelations by itself." }, { "kind": "metadata_insufficient", "statement": "The trials table has one row per second of valve opening, without a description; odor presentations, blocks and sequential pairs have to be rebuilt from timing. Five block sessions fill the gaps with \"Empty\" rows and two do not. The concentration column has no unit, gives 0.0 to two odorants (2-ethylphenol, anisaldehyde) in three random-order sessions, and 0.1 to the Empty rows of sub-141 ses-5." }, { "kind": "data_missing", "statement": "In sub-134 ses-22, sub-141 ses-5 and sub-141 ses-8 the raw TwoPhotonSeries holds half the frames of the fluorescence traces (91000 against 182000 in sub-134 ses-22) at twice the frame interval; the conversion notes give 182000 frames for sub-134 ses-22." }, { "kind": "data_missing", "statement": "No sequential pair ends in acetophenone (Figure 6E right, S6) and no PID recordings are included (Figure S2). The published version's Table 1 assigns the acetophenone panel to the 73-, 210-, 153- and 198-glomerulus sessions, which in the dandiset hold only pairs ending in methyl salicylate. The random-order session of Figure S8D and S8E (286 glomeruli) is not in the dandiset, and of the eight random-order sessions that Table 1 lists (175, 340, 323, 306, 286, 204, 250 and 280 glomeruli) only two (323 and 306) match a dandiset session by ROI count." }, { "kind": "selection_undocumented", "statement": "The dandiset holds the paper's seven block-protocol sessions from four mice and five random-order sessions from five mice (four not in the block sessions) with odor-specific concentrations, apparently from a second study (the conference paper it also names, whose authors are the dandiset's contributors). Neither the metadata nor the description says which sessions belong to which paper, and the description is that of the second study." }, { "kind": "identifier_missing", "statement": "No identifier links the paper's datasets to the dandiset's sessions. They match by ROI count (198, 219, 318), but the session names in the paper's Figshare code (for example m149_3_1, m129_1_2) do not all exist in the dandiset (it has no mouse 129 and only session 1 of mouse 149)." }, { "kind": "other", "statement": "The dandiset and the published version's Table 1 disagree on which mouse one session belongs to. The dandiset puts the 318-ROI session under sub-148 with the 286-ROI session; Table 1 puts the 318-glomerulus session under mouse 4 with the 219-glomerulus session (sub-149 here). Which is right cannot be told from the data." }, { "kind": "other", "statement": "The random-order odorant names differ from the paper's; the files have 2-ethylphenol and anisaldehyde where the Methods list 2-ethylpyrizine (2ep) and isoamyl acetate (asa). Names are spelled differently across sessions (\"Anisole\" and \"anisole\"), and \"2-methypyrazine\" is misspelled." }, { "kind": "metadata_insufficient", "statement": "The genotype (Thy1-GCaMP6f) and the ages are not stated, and every session starts at 00:00, so the time of day is missing. In sub-124 ses-3 the last trial ends 8.9 s after the last imaging frame." }, { "kind": "code_mismatch", "statement": "The paper's code counts windows in frames at a nominal 16 per second, while the sessions are imaged at 13.7 to 17.8 Hz, so a nominal 57-s window of 912 frames lasts 51.2 to 66.4 s; in sub-141 ses-8 (15.5 Hz) the deposited trial windows match the dandiset only when counted in frames (r 0.968) and not in seconds (r 0.307)." }, { "kind": "paper_inconsistency", "statement": "The Methods give k = 50 for the ITI-average classifier of Figure 7H, which has 40 vectors, while the legend gives k = 20 and the code uses k = 20 on three PCs. For the IBI classifier (60 vectors, k = 50) the procedure's own null is 10.8%, not the 25% chance of four odors." }, { "kind": "code_mismatch", "statement": "The Figure 5E legend states a one-tailed t-test; Script_Fig4.m uses MATLAB's ttest, which is two-tailed (p = 0.011 against 0.0055 one-tailed here)." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier had no attempt record and took its counts from the claims file. bioRxiv refused the preprint download, so it read the v2 abstract and the published version (iScience, PMC13066794); the preprint's Fig 4B ON-ON value and Table S1 were not checked. It gave its own outcome for each claim; 18 of 19 agree with the record.", "agreed": 18, "of": 19, "disagreements": [ { "claim": "figs7e-ibi-chance", "outcome": "not_reproduced", "reason": "The k = 50 rate is 3.8%, far below 34.8 +/- 3.48 and below chance, because the k = 50 classifier is degenerate; on random data with 4 x 15 vectors it gives 10.7%, so the <= 38.3% criterion is met by construction (problem 1). The only usable classifier (k = 20) gives 73 to 95% with permutation p = 0 in the four complete sessions, which contradicts \"no longer present\", though adjacent 1-minute bins of the same IBI serve as each other's neighbours, so slow drift alone could explain it." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook with conclusions and summary, the README, the attempt record, the helper module and the claims file, with the paper. The verifier read the v2 preprint text (bioRxiv API JATS, saved in paper/), which confirms 121.8, 106.7, 34.8, n = 286 and the 11-odor list; its Fig 4B text gives no ON-ON value, and Table S1 is an image and was not checked. It agrees with 19 of 19 outcomes.", "agreed": 19, "of": 19, "disagreements": [] } ] }, { "id": "001172-lohani-2022-01", "dandiset": "001172", "dandiset_version": "0.260129.0829", "paper": "10.1038/s41593-022-01202-6", "paper_title": "Dual color mesoscopic imaging reveals spatiotemporally heterogeneous coordination of cholinergic and neocortical activity", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "runs", "entry": "001172-lohani-2022", "entry_title": "Cholinergic and calcium dynamics across behavioural states (Lohani, Moberly et al. 2022)", "description": "Tests the findings of Lohani, Moberly et al. (2022) on dandiset 001172, which holds dual-colour mesoscopic imaging of ACh3.0 and jRCaMP1b with face video, pupil and wheel data from 4 of the paper's 6 mice. It tests the regression of both signals on behaviour, transients at face movement and locomotion onsets, amplitudes in sustained states, and the state dependence of correlations between areas and between the two signals, using the Allen parcel masks of the paper's code. ECoG, pharmacology, control mice and cholinergic axon imaging are not in the dandiset.", "notebooks": [ { "path": "reproduce_lohani_2022.ipynb", "title": "Reproducing Lohani, Moberly et al. (2022) from dandiset 001172", "executed": "notebooks/001172-lohani-2022/reproduce_lohani_2022.html" } ], "outcomes": [ { "claim": "allen-parcel-link", "statement": "The paper's Allen parcel masks, from its code, can be laid on the dandiset's \u0394F/F pixels, so that the areas the paper names can be found in the data.", "source": "Methods, Preprocessing of imaging data and Post-processing analysis; parcells_updated121519.mat and brainMask.mat in the paper's code at commit c337686", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Per session (pixels non-zero in either \u0394F/F movie) the non-zero pixels equal the code's brainMask.mat rotated by 180 degrees in all 9 sessions (agreement 1.0; best other orientation 0.98). Per movie, 25 of the 26 movies of the 13 sessions (the 9 state sessions and the 4 visual stimulus sessions) agree at 1.0; the calcium movie of grabAM08 11232019 spont agrees at 0.996, as 263 pixels inside the mask, all in the right AUD parcel, are zero in every frame and none outside is non-zero. With 100% contrast gratings in one visual stimulus session per mouse (47 to 49 trials), the largest calcium response of the 46 parcels is in a left visual parcel in all 4 mice and left VISp exceeds right VISp in all 4 (0.108 to 0.216 against -0.024 to 0.065 percent \u0394F/F), but left VISp ranks 1, 1, 3 and 2, so first in 2 of 4 mice where the criterion asks 3 for reproduced. The dependent claims are tested; the partial result bears on parcel borders, not on which areas are where.", "deviations": [ "The criterion's \"pixels with non-zero \u0394F/F in the blue and green movies\" can be read per movie or per session; the per-session reading was chosen after seeing that one movie fails the 99.9% bar under the per-movie reading. Under the per-movie reading the mask part fails on that movie and the claim would be not reproduced by the letter of the criterion. The failing pixels are all in the right AUD parcel, which the left-hemisphere analyses do not use." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2a-r2-differs-across-areas", "statement": "The variance of ACh3.0 and jRCaMP1b signals explained by a ridge regression on FaceMap PCs 1 to 25, locomotion speed and pupil area differs across cortical areas (Friedman's ANOVA p < 0.001 for both, n = 6 mice).", "source": "Results, Calcium and cholinergic signals encode behavioral state; Figure 2a,b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Friedman across the 23 left parcels with 4 mice, ACh chi2 = 67.98, p = 1.4e-06, calcium chi2 = 63.51, p = 6.7e-06. Full-model R2 ranges 0.030 to 0.397 (ACh) and 0.084 to 0.387 (calcium). Spontaneous sessions alone give p = 6e-07 and 0.005. With |speed| as the wheel predictor p = 1.3e-06 and 7.7e-06. For the three mice that match rows of the paper's own R2 file (grabAM05, grabAM07, grabAM08), mean full-model R2 is 0.182, 0.126 and 0.140 (ACh) and 0.207, 0.216 and 0.227 (calcium) against the file's 0.166, 0.126 and 0.142 and 0.193, 0.229 and 0.254.", "deviations": [ "4 of 6 mice; spontaneous and air-puff sessions (9) averaged per mouse, as the Methods do not say which sessions were used.", "The ridge regression code is not public; the penalty is chosen per parcel by marginal likelihood over a grid of 91 values, as ridgeMML does by optimisation.", "The wheel predictor is the files' WheelSpeed, which is signed, as the Methods (\"a differential of distance\") and the code's wheel_changepoints.m (db1SpeedMpS) define speed. The first revision had switched to |speed|; the second revision returned to the signed series, and |speed| is a variant.", "Predictors are scaled with the training folds' statistics; the first run z-scored them over the whole session." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2b-ap-gradient-inverted", "statement": "The coupling of behaviour to fluorescence has anterior-posterior gradients that are inverted between the signals, with ACh most strongly linked to behaviour in frontal areas and calcium in posterior areas.", "source": "Results, Calcium and cholinergic signals encode behavioral state; Figure 2b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Spearman of mean R2 with anterior-posterior rank (1 = MOs) gives ACh rho = -0.761 (p = 2.5e-05) and calcium rho = 0.555 (p = 0.0059). Per mouse ACh rho -0.44 to -0.87; calcium 0.57 to 0.70 in three mice and -0.01 in grabAM05. Spontaneous sessions alone give -0.897 and 0.655. With |speed| -0.758 and 0.558.", "deviations": [ "4 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2c-face-best-predictor-ach", "statement": "For ACh3.0, facial movement (FaceMap PC1) predicts activity better than locomotion or pupil, in single-variable models (Friedman p = 0.006, face against locomotion and against pupil p = 0.031) and as unique contribution (Friedman p = 0.003).", "source": "Results, Calcium and cholinergic signals encode behavioral state; Figure 2c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Single-variable R2 averaged over left parcels, face PC1 0.081, wheel 0.026, pupil 0.009; face highest in all 4 mice, Friedman p = 0.018 (exact p = 0.0046). Unique contributions face 0.081, pupil 0.016, wheel 0.004, face largest in all 4 mice, Friedman p = 0.039 (exact p = 0.042). The same holds with |speed|. Signed-rank tests give p = 0.125, the smallest possible with 4 mice, so the paper's p = 0.031 cannot be reached.", "deviations": [ "The paper's post hoc signed-rank tests are replaced by the direction in every mouse.", "Unique contribution of face is from shuffling PC1 only; the Methods do not say which face PCs were shuffled." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig2c-face-best-predictor-calcium", "statement": "For jRCaMP1b, facial movement (FaceMap PC1) is the most robust predictor of activity (single-variable Friedman p = 0.006; face against locomotion and pupil p = 0.031).", "source": "Results, Calcium and cholinergic signals encode behavioral state; Figure 2c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Changed to reproduced in the third verification round, from the partially_reproduced of the first revision, which rested on |speed| as the wheel predictor. With the signed speed of the Methods and the code, now the main analysis, single-variable R2 is face PC1 0.112, wheel 0.084, pupil 0.010, face best in all 4 mice by 0.016 to 0.053 over wheel speed, Friedman p = 0.018 (exact p = 0.0046). Unique contributions face 0.058, pupil 0.025, wheel 0.014, face largest in all 4 mice (in grabAM05 by 0.002 over pupil), Friedman p = 0.039. With |speed| wheel speed is higher in grabAM06 (0.147 against 0.142), face is best in 3 of 4 mice and the claim would be partial. In the paper's own per-mouse values (Fig2RawData.mat) face PC1 is the best single variable in all 6 mice, and in grabAM05 (row 1, matched by full-model R2 across parcels, Spearman 0.94 to 0.98) the wheel R2 is 0.0246 for calcium against 0.0253 here with signed speed and 0.0483 with |speed|. The paper found face against pupil not significant for the unique contribution here (p = 0.063).", "deviations": [ "As for fig2c-face-best-predictor-ach.", "The regression code is not public; signed speed follows the Methods and wheel_changepoints.m." ], "disagreed": true, "data": "with_labels", "where": null, "proposed": null }, { "claim": "s7-face-onset-transients", "statement": "Facial movement onset without locomotion is associated with significant whole-cortex transients in ACh (0.64 \u00b1 0.09 \u0394F/F, p = 0.001) and calcium (0.69 \u00b1 0.15 \u0394F/F, p = 0.006).", "source": "Results, paragraph on state transitions; Figure S7", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "ACh 0.728 \u00b1 0.119 percent \u0394F/F (paper 0.55 to 0.73), calcium 0.920 \u00b1 0.131 (paper 0.54 to 0.84), positive in all 4 mice, one-sample t-test p = 0.0089 and 0.0060. 12 to 31 onsets per mouse. The ACh mean is inside tolerance by 0.002. The same peak at random times in sustained quiescence (200 draws) has per mouse means 0.049 to 0.088 (ACh) and 0.113 to 0.177 (calcium); every mouse's transient is above the null's 95th percentile. Keeping the quiescent period after the last locomotion epoch (which the code's onset function drops) gives 0.728 and 0.871.", "deviations": [ "4 of 6 mice; face onsets from the code's procedure, which the Methods describe only in part." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "s7-locomotion-onset-transients", "statement": "Locomotion onset is associated with transient increases in ACh (0.68 \u00b1 0.17 \u0394F/F, p = 0.010) and calcium (1.50 \u00b1 0.11 \u0394F/F, p < 0.001).", "source": "Results, paragraph on state transitions; Figure S7", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "ACh 0.761 \u00b1 0.272 percent \u0394F/F (paper 0.51 to 0.85, p = 0.068 here), calcium 1.985 \u00b1 0.489 (paper 1.39 to 1.61, p = 0.027), positive in all 4 mice; grabAM08 has the largest values (ACh 1.555, calcium 3.436). 17 to 39 onsets per mouse. Null peaks at random quiescent times have per mouse means 0.044 to 0.082 (ACh) and 0.111 to 0.212 (calcium); every mouse's transient is above the null's 95th percentile.", "deviations": [ "4 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "s7-ach-transients-same-across-states", "statement": "ACh transients vary across cortical areas (p < 0.001) but do not differ between locomotion and facial motion onsets (p = 0.734, two-way repeated measures ANOVA).", "source": "Results, paragraph on state transitions; Figure S7", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Two-way repeated measures ANOVA (4 mice), onset type F = 0.03, p = 0.88; area F = 9.39, p < 0.0001. Whole-cortex locomotion minus face per mouse -0.285 to 0.625 (three negative, one positive), mean 0.034 percent \u0394F/F. An absence result with 3 denominator degrees of freedom, which carries little weight.", "deviations": [ "4 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "s7-calcium-transients-largest-at-locomotion", "statement": "Calcium transients vary across cortical areas (p < 0.001) and states (p = 0.005), with locomotion onset associated with the largest signal.", "source": "Results, paragraph on state transitions; Figure S7", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Locomotion transient above face transient in all 4 mice (by 0.447 to 2.245, mean 1.065 percent \u0394F/F), onset type F = 6.94, p = 0.078; area F = 31.6, p < 0.0001.", "deviations": [ "4 of 6 mice; the ANOVA has 3 denominator degrees of freedom for onset type." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "s7-ap-gradient-transients", "statement": "Transient magnitudes show a significant anterior-posterior gradient for ACh but not for calcium.", "source": "Results, paragraph on state transitions; Figure S7", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "ACh rho = -0.605 (p = 0.0022) at face onset and -0.752 (p = 3.5e-05) at locomotion onset, larger anteriorly; calcium rho = 0.014 (p = 0.95) and 0.106 (p = 0.63).", "deviations": [ "The paper does not say which onsets the gradient refers to; both are tested." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3b-ecog-desynchronization", "statement": "Sustained facial movement and locomotion are associated with progressively increasing 30 to 100 Hz ECoG power.", "source": "Results; Figure 3b", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The files hold no ECoG; the conversion code reads the Spike2 LFP channel but does not write it. The paper offers its data on request only.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-ach-sustained-face", "statement": "Sustained facial motion elevates whole-cortex ACh (low face -0.13 \u00b1 0.04, high face 0.18 \u00b1 0.08 \u0394F/F; low against high p = 0.046, post hoc LSD), with a main effect of state (p = 0.015).", "source": "Results, paragraph on sustained states; Figure 3c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "With 3 mice (grabAM07 has no sustained high face epoch), low face -0.129 \u00b1 0.031 and high face 0.158 \u00b1 0.047 percent \u0394F/F, both inside the paper's ranges; high above low in all 3 mice (0.138 to 0.384), LSD p = 0.027; state effect F = 11.1, p = 0.023. Matched epochs per mouse 10, 2 and 13 (71.7, 14.6 and 93.7 s per state). Without grabAM06, high exceeds low in both other mice but LSD p = 0.207.", "deviations": [ "3 of the paper's 6 mice; grabAM06 contributes 2 epochs per state." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3c-ach-locomotion-no-further-increase", "statement": "Locomotion does not further increase whole-cortex ACh beyond high facial motion (locomotion 0.16 \u00b1 0.06 \u0394F/F; locomotion against high face p = 0.717).", "source": "Results, paragraph on sustained states; Figure 3c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Locomotion minus high face LSD t = 1.09, p = 0.34. The locomotion mean, 0.250 percent \u0394F/F, is above the paper's 0.10 to 0.22, and exceeds high face in all 3 mice (by 0.027 to 0.179), so the data point against the claim; the outcome rests on an absence test with 3 mice, which carries little weight.", "deviations": [ "3 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3c-calcium-sustained", "statement": "Sustained facial movement and locomotion both increase whole-cortex calcium (low face -0.02 \u00b1 0.02, high face 0.17 \u00b1 0.04, locomotion 0.63 \u00b1 0.19 \u0394F/F; low against high p = 0.020, locomotion against high p = 0.044), with a main effect of state (p = 0.005).", "source": "Results, paragraph on sustained states; Figure 3c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Low face -0.002, high face 0.164 (inside the paper's ranges), locomotion 1.106 percent \u0394F/F (paper 0.44 to 0.82). High above low in all 3 mice (0.124 to 0.222) but LSD p = 0.24; locomotion above high in all 3 (0.656 to 1.2), LSD p = 0.001; state effect F = 48.3, p = 0.0016. Without grabAM06 high minus low has p = 0.266 and locomotion minus high p = 0.019.", "deviations": [ "3 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "s7-ap-gradient-sustained", "statement": "Differences across sustained states have significant anterior-posterior gradients, for ACh comparing high and low facial movement, with larger increases in anterior areas, and for calcium comparing locomotion and high facial movement.", "source": "Results, paragraph on sustained states; Discussion; Figure S7", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "ACh high minus low face rho = -0.801, p = 4.3e-06 (larger anteriorly); calcium locomotion minus high face rho = 0.329, p = 0.125. Without grabAM06 (2 epochs per state) ACh rho = -0.874 (p = 5.3e-08) and calcium rho = 0.437 (p = 0.037), so the calcium half would be met with 2 mice; the criterion fixes the 3 mice.", "deviations": [ "3 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3d-ach-frontal-above-visual", "statement": "During high facial motion ACh3.0 amplitude is higher in frontal-motor areas than in visual areas (paired t-test, p < 0.05).", "source": "Results; Figure 3d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "High face ACh, frontal-motor 0.166 to 0.427 against visual 0.032 to 0.108 percent \u0394F/F, higher in all 3 mice, paired t = 4.34, p = 0.049. Without grabAM06 (2 epochs per state) the difference holds in both other mice but p = 0.247.", "deviations": [ "3 of 6 mice; p is just below 0.05." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig3e-scopolamine-motor-not-visual", "statement": "The muscarinic blocker scopolamine decreases cortical activity in motor but not visual areas, and the nicotinic blocker mecamylamine has no significant effect.", "source": "Results; Figure 3e", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No drug or vehicle sessions are in the dandiset (its sessions are spontaneous, air-puff and visual stimulus); the paper offers its data on request only.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4a-ach-correlations-up-with-face", "statement": "Increased facial movement is associated with significant increases in between-area correlations of ACh in anterior somatosensory and motor areas.", "source": "Results, State-dependent modulation of cortical network architecture; Figure 4a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "High minus low face, 64 of 253 pairs increase significantly (BY q = 0.01) and none decreases; 39 of 45 motor-somatosensory pairs (0.867) against 25 of 208 other pairs (0.120). Mean change in z per mouse 0.095, 0.314 and 0.362. At q = 0.05, 98 increases.", "deviations": [ "3 of 6 mice; the permutation test permutes epochs within mice, so its power comes from epochs (25 per state in all) more than mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig4a-ach-correlations-down-with-locomotion", "statement": "Locomotion is associated with a reduction in between-area correlations of ACh that is significant across the cortex.", "source": "Results, State-dependent modulation of cortical network architecture; Figure 4a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Locomotion minus high face, 243 of 253 pairs (0.960) decrease significantly, none increases, all six area groups involved; mean r 0.539 against 0.791; per mouse mean change in z -0.337 to -0.648.", "deviations": [ "3 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig4b-calcium-correlations-up-with-face", "statement": "Increased facial movement is associated with broad, significant increases in between-area calcium correlations.", "source": "Results, State-dependent modulation of cortical network architecture; Figure 4b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "High minus low face, 161 of 253 pairs (0.636) increase significantly, none decreases, all six area groups involved; per mouse mean change in z 0.227 to 0.567.", "deviations": [ "3 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig4b-calcium-correlations-down-posterior", "statement": "Locomotion occurs with modest decreases in calcium correlations that are significant primarily across posterior cortical areas.", "source": "Results, State-dependent modulation of cortical network architecture; Figure 4b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "Locomotion minus high face, 100 pairs decrease significantly and none increases; 55 of 66 posterior pairs (0.833) against 45 of 187 other pairs (0.241). Per mouse mean change in z -0.183 to -0.513.", "deviations": [ "3 of 6 mice; posterior is defined here as ranks 12 to 23 of the Methods' order." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig5-coupling-up-with-face", "statement": "Sustained facial movement is associated with a significant increase in the correlation between ACh and calcium signals broadly across the cortex.", "source": "Results; Figure 5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "ACh-calcium coupling increases in all 23 left parcels (z 0.173 to 0.737) and significantly in 10 (none decreases), short of the 12 the criterion asks; 22 have uncorrected p < 0.05 and 20 pass BY at q = 0.05. Mean r 0.573 against 0.185; per mouse mean change 0.182 to 0.694.", "deviations": [ "3 of 6 mice." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig5-coupling-down-frontal-with-locomotion", "statement": "Sustained locomotion is associated with a significant reduction in the correlation between ACh and calcium that is restricted to the frontal cortex.", "source": "Results; Figure 5", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_lohani_2022.ipynb", "notes": "No parcel decreases significantly at q = 0.01 (2 at q = 0.05). Coupling is lower with locomotion in all 23 parcels (z -0.370 to -0.037) and in each mouse (-0.138 to -0.269); the largest decreases are in PTLp and SSp-tr (p = 0.0007 and 0.0006), and MOs and MOp have p = 0.072 and 0.076. The decrease is broad here, not restricted to frontal cortex.", "deviations": [ "3 of 6 mice, with 25 matched epochs per state in all." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "s3-hemodynamic-correction", "statement": "The spatial regression on 395 nm signals removes stimulus-evoked and behaviour-related negative hemodynamic transients better than pixel-wise regression, shown in GFP and mCherry control mice and in ACh3.0 mice.", "source": "Results, first section; Methods, Validation of hemodynamics correction; Figures S3, S4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The comparisons rest on GFP, mCherry and backscatter data from control mice, which are not in the dandiset. The ACh3.0 part (visual stimulus negativity in V1 before and after correction) would need the uncorrected blue \u0394F/F, which is not in the files. It could in principle be recomputed from the raw blue and violet movies of the visual stimulus sessions (about 50 GB each), but that needs a reimplementation of the spatial regression and the atlas areas in native space, because the code's registration transforms are not in the files; this attempt did not do it. A check on one session (data check) shows the archived blue \u0394F/F shares almost no fluctuation with the violet \u0394F/F (r = 0.070) where the raw movies share much (r = 0.576), consistent with a correction having been applied.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "s2-ach-sensor-validation", "statement": "ACh3.0 specifically reports cholinergic signalling, ex vivo (carbachol, blocked by scopolamine) and in vivo (basal forebrain stimulation).", "source": "Results, first section; Figure S2", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The slice imaging with carbachol and scopolamine and the basal forebrain stimulation sessions are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "s8-cholinergic-axons", "statement": "The relationship between behavioural state and cholinergic signalling is also seen with mesoscopic imaging of GCaMP6s in cholinergic axons.", "source": "Results, paragraph on sustained states; Figure S8", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No ChAT-Cre Ai162 (GCaMP6s) mice are in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The \u0394F/F series (DFFOnePhotonSeriesBlue, Green and Violet) are given the starting time of the first LED pulse, the time of raw frame 0, but their frame 0 is raw frame 499, as the detrending drops the first frames. Their times are 49.9 s early in every session; both the raw movies and the alignment of calcium with wheel speed show it." }, { "kind": "metadata_error", "statement": "The FaceMap, pupil, eye and video timestamps are spaced 111 ms (9 Hz) where the camera pulses are 100 ms apart, span about 10% longer than the session, and end with two values equal to the first camera pulse. With these timestamps face movement and wheel speed are misaligned by 23 to 60 s; with frame i at camera pulse i, as the paper's code does, they align." }, { "kind": "metadata_error", "statement": "RoiResponseSeriesParcellated holds the calcium (green excitation) \u0394F/F averaged over its ROIs, but its segmentation is linked to the ACh imaging plane. Its image masks are transposed relative to the \u0394F/F images, and its starting time is that of the first green pulse, 64.9 s before its first frame (150 frames after the \u0394F/F's first frame)." }, { "kind": "metadata_insufficient", "statement": "The \u0394F/F descriptions mention detrending only; the blue and green \u0394F/F are also hemodynamically corrected and registered to the Allen atlas, rotated by 180 degrees, as the paper's code shows (the data are consistent with the correction, in one session checked). The Allen parcels the paper analyses are not in the files; they come from the paper's code. The parcellation in the files is a different, functional one with 89 to 107 ROIs per session and no area names." }, { "kind": "metadata_error", "statement": "In the VisualStimulus tables the columns from stimulus_size on are shifted by one; stimulus_size holds the duration (2) and the first screen coordinate holds the size (20 degrees)." }, { "kind": "data_missing", "statement": "The air-puff session grabAM07 11262019 has no Airpuff table, so its puff times are unknown." }, { "kind": "selection_undocumented", "statement": "No air puff in the Airpuff tables is followed by a locomotion onset within 5 s (29 puffs), which fits the paper's code keeping only puffs without running. The tables then hold a selection of the puffs given, which the files do not say." }, { "kind": "metadata_insufficient", "statement": "WheelSpeed and pupil_area have the unit \"unknown\"; the paper's code treats wheel speed as m/s, and its range fits that. WheelSpeed is signed (minimum -0.07 to -0.14 per session), which its description does not say." }, { "kind": "other", "statement": "In the calcium \u0394F/F of grabAM08 11232019 spont, 263 pixels inside the brain mask, all in the right AUD parcel, are zero in every frame; in the other 25 \u0394F/F movies every pixel of the mask is non-zero." }, { "kind": "metadata_insufficient", "statement": "The VisualStimulus tables give screen coordinates but not where the monitor stood relative to the mouse, so the hemisphere expected to respond cannot be read from the files." }, { "kind": "data_missing", "statement": "The dandiset holds 4 of the 6 ACh3.0 and jRCaMP1b mice of the paper's code (grabAM05 to grabAM08, not grabAM09 and grabAM10), and no ECoG, drug sessions, control mice or ChAT-GCaMP6s mice. Five of the paper's findings cannot be tested." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper (PMC10661869). The verifier had no attempt record and took its counts from the claims file. It gave its own outcome for each claim; all 26 agree with the record as it then stood.", "agreed": 26, "of": 26, "disagreements": [] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the first revision, with its conclusions and summary, the helper module, the claims file, the attempt record and the paper (PMC10661869). The verifier agreed with 25 of the 26 outcomes and did not accept the reason for fig2c-face-best-predictor-calcium. It also asked for corrections to the robustness text without grabAM06, the runtime and some minor statements.", "agreed": 25, "of": 26, "disagreements": [ { "claim": "fig2c-face-best-predictor-calcium", "outcome": "reproduced", "reason": "The arithmetic is not disputed; with |speed| wheel beats face in grabAM06 (0.147 vs 0.142), so the result is partial. The reason for switching to |speed| is disputed. The Methods define speed as \"a differential of distance\" after unwrapping, which keeps its sign; the paper's code computes it signed (wheel_changepoints.m line 50, db1SpeedMpS) and takes abs only for the threshold on mean epoch speed (line 135); the file's WheelSpeed is very likely that same series. The code repository contains Figure2Regression/Fig2RawData.mat, the paper's own per-mouse R2 (6 x 52); for calcium its single-variable face R2 is above wheel in all 6 mice; if its rows 1 to 4 are grabAM05 to grabAM08 (not established), its wheel R2 for mouse 1 is 0.0246 (calcium) and 0.0014 (ACh), against 0.0253 and 0.0017 here with signed speed and 0.0483 and 0.0031 with |speed|; the other mice are mixed. On this evidence signed speed is the better-supported reading, and under it the claim is reproduced. The outcome should either go back to reproduced with |speed| as the variant, or stay partial with a reason that matches the sources. Compare the per-mouse values with Fig2RawData.mat after confirming its row-to-mouse mapping; this would also give the first external check of the ridgeMML port." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 3. The one proposed change of outcome, fig2c-face-best-predictor-calcium from partially_reproduced to reproduced, with the notebook cells behind it (cells 15, 26, 27, 33, 36 and 38 to 43), the attempt record and the paper (PMC10661869).", "agreed": 1, "of": 1, "disagreements": [] } ] }, { "id": "001453-fouke-2025-01", "dandiset": "001453", "dandiset_version": "0.250518.1950", "paper": "10.1016/j.cub.2025.04.027", "paper_title": "Neural circuits underlying divergent visuomotor strategies of zebrafish and Danionella cerebrum", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-5" }, "tier": "agent_verified", "entry": "001453-fouke-2025", "entry_title": "Optomotor swimming of zebrafish and Danionella cerebrum (Fouke et al. 2025)", "description": "Tests the freely swimming findings of Fouke, He, Loring and Naumann (2025) on dandiset 001453, which holds the tracking data of 25 zebrafish and 12 Danionella cerebrum larvae during the optomotor protocol. It compares swimming speed, turning and angular acceleration between species and stimuli, the response to monocular stimuli, and how steady the swimming is. The imaging and head-fixed tail tracking of the paper's Figures 2 to 4 are not in the dandiset.", "notebooks": [ { "path": "reproduce_fouke_2025.ipynb", "title": "Reproducing Fouke et al. (2025) from dandiset 001453", "executed": "notebooks/001453-fouke-2025/reproduce_fouke_2025.html" } ], "outcomes": [ { "claim": "stimulus-code-link", "statement": "The dandiset's stimulus codes can be linked to the stimuli the paper names, using the paper's analysis code and the protocol file of its stimulus software, and the values computed through that link agree with those the paper's code printed.", "source": "Data and Code Availability; the paper's Fig1-S1.ipynb at GitLab commit 33a5c29", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "Codes are matched by their integer value. All 21 codes are in the dandiset, including every code the analysis uses. Through the link, 17 of 18 species and stimulus speed medians are within 10% of the values printed by Fig1-S1.ipynb (DC static is 10.52 against 11.9 mm/s), and the angular velocities differ from the printed ones by a median of 0.02 deg/s. The fish counts (25 ZF, 12 DC) match the code's lists; fish cannot be matched one by one, as no identifier links the dandiset's subjects to the code's folders. The static window is the code's (first 35 s of the code-20 block, measured from 3 s), and no fish median is exactly 0, so the code's exclusion of zero medians changes nothing. On codes 9 and 11 the ZF medians are 0.02 and 1.59 deg/s. Over 3 to 35 s DC turn more to the right for code 11 than for code 9 (median difference 5.82 deg/s, 10 of 12 fish, Wilcoxon p = 0.0093), and ZF go the same way without significance (1.66 deg/s, 16 of 25 fish, p = 0.141). If fish turn with lateral motion as they do with medial motion, code 11 is lateral right, as the protocol file has it; the data do not show that they do, so the assignment is not settled.", "deviations": [ "The code's filter on a `vel` column is not applied to DC trials, as the DC files have no such series; this is the remaining difference that may explain the one DC static value outside 10%.", "The timing of the DC stimulus labels could not be confirmed from the turning response (the contrast is 4.6 deg/s with true labels and 0.1 with shifted ones); the DC labels are taken as they are." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1d-dc-faster-all-codes", "statement": "Danionella cerebrum (DC) swim at a higher median velocity than zebrafish (ZF) across the visual stimuli.", "source": "Results, first section; Figure 1D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "Over all 21 codes, the median over fish and code values is 94.0 pixels/s for DC and 55.2 for ZF; species effect F = 78.4, p = 6.3e-18. The ANOVA treats each fish and code value as independent; with one value per fish, DC 87.4 against ZF 52.9 pixels/s, Mann-Whitney p = 0.02. With positions resampled to 30 Hz, 95.2 against 53.8 (p = 1.3e-08). DC are faster within each frame-rate group.", "deviations": [ "Tested over all stimulus codes without their names; the paper's figure uses nine whole-field stimuli.", "The comparison assumes one spatial scale for all rigs, which the files do not state." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-median-velocity", "statement": "Across the whole-field stimuli DC have a higher median velocity than ZF (9.8 against 6.4 mm/s), with a significant main effect of species in a two-way ANOVA.", "source": "Results, first section; Figure 1D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "All four readings put both values within tolerance; (a) median of stimulus medians DC 10.02 and ZF 6.39 mm/s, (b) median of fish and stimulus values 9.87 and 6.41 (given as measured), (c) median of fish medians 9.36 and 6.33, (d) median of trials 9.88 and 6.28. Species effect F = 20.8, p = 7.5e-06. With 30 Hz positions DC 9.43 to 10.15 and ZF 6.07 to 6.30 (p = 0.0011). Without the trial rejection (4487 trials in place of 4458) readings (a) to (c) are unchanged and (d) gives DC 9.85 and ZF 6.30 (p = 6.7e-06).", "deviations": [ "The paper does not say how the overall median is taken; four readings are shown, and all match.", "25 ZF, where the paper states 26.", "Speeds rely on the code's scale of 10 pixels per mm, which the dandiset does not state." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1d-zf-forward-faster-than-static", "statement": "ZF modulate their velocity with the direction of motion; forward motion increases their median velocity (static 5.0 mm/s, forward 8.8 mm/s).", "source": "Results, first section; Figure 1D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "ZF static 4.84 mm/s over 18 fish and forward 8.78 mm/s over 25 fish. Of 18 fish with both, 14 are faster to forward motion (median difference 3.67 mm/s, Wilcoxon p = 0.0077). The static value is 8.31 mm/s in the 5 fish from 167 to 171 Hz files and 4.50 in the 13 from 32 to 35 Hz files. Static is the start of the blank block after all motion trials (4 hours in the protocol, 0.2 to 787.3 min in the files), one period per fish, and 7 ZF have none.", "deviations": [ "25 ZF, where the paper states 26." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1d-dc-no-modulation", "statement": "DC lack the direction-dependent velocity modulation seen in ZF.", "source": "Results, first section; Figure 1D legend", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "By the paper's test (Tukey's HSD over the 18 species and stimulus groups) 3 of 36 DC pairs differ, all static against a motion direction (backward left, backward right, forward left; adjusted p 0.030 to 0.049). The DC static values come from 9 fish and include one at 106.5 mm/s and two near 0. Among the eight directions no DC pair differs (smallest adjusted p 0.999), DC per-stimulus medians span 8.81 to 10.52 mm/s (ratio 1.19, ZF 2.03), and a one-way ANOVA across the nine DC stimuli gives p = 0.479 (ZF p = 0.00082). With values above 100 mm/s left out, no DC pair differs. The same Tukey test finds no ZF pair over the 18 groups (smallest p 0.835). The printed output of Fig1-S1.ipynb finds the same three DC pairs significant (adjusted p 0.0236, 0.0373 and 0.0397), so the paper's own test disagrees with the claim and this result matches the paper's computation. The DC-sub-2 static value of 106.5 mm/s is one trial measured over a 14.6 s motion phase in a 100 mm dish, likely a tracking artefact. It passes the code's speed check because the check covers 0 to 35 s (21.9 mm/s from the stored `dist`, 92.5 from positions); computing the check from positions, or leaving out zero medians as the code does, gives the same 3 pairs. The outcome is a property of the paper's test on this data, not evidence that DC modulate their speed with stimulus direction.", "deviations": [ "The DC static block is the code's window, but the code's filter on DC `vel` cannot be applied (DC static 10.52 against the code's printed 11.9 mm/s)." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1d-dc-faster-oblique", "statement": "DC swim at a significantly higher velocity than ZF for oblique stimuli.", "source": "Figure 1D legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "Under reading (b), motion at 90 degrees or more, DC are significantly faster than ZF for right (p = 0.0002) and backward right (p = 0.0047), 2 of 4; under reading (a), the intercardinal directions, for 1 of 4 (backward right). Backward motion also differs (p = 0.0002).", "deviations": [ "The legend's \"oblique\" can be read two ways; the claim is reproduced under one of them (b) and not under the other (a)." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1g-follow-direction", "statement": "Both species follow the direction of optic flow, turning right (positive angular velocity) to rightward motion and left to leftward motion.", "source": "Figure 1G; Results, second section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "ZF turn with the motion; the rightward minus leftward difference is positive in 23 of 25 fish (median 29.51 deg/s, one-sided Wilcoxon p = 9.8e-07). DC do not by this test; 7 of 12 positive, median 0.88 deg/s, p = 0.151, and the DC median for left motion is +0.25 deg/s, the same sign as the paper's code printed (+0.3). DC turn right to right motion (8.67 deg/s).", "deviations": [ "The paper gives no test for following the direction; the per-fish rightward minus leftward difference and its test were chosen here before the analysis." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1h-zf-higher-angular-acceleration", "statement": "Across directional stimuli ZF have higher angular acceleration than DC, and the distributions of the two species differ for every stimulus.", "source": "Results, second section; Figure 1H (Kruskal-Wallis test with Bonferroni correction)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "With angular acceleration as the Methods define it, DC are higher than ZF for all nine stimuli (medians 143 to 191 against 55.4 to 66.4 deg/s2, Kruskal-Wallis p below 0.05/9 for each), the reverse of the claim. Per-fish medians, and the files at 128 to 171 Hz alone (ZF 84.9, DC 178.6 deg/s2, p = 6.3e-05), give the same. The quantity Fig1-S1.ipynb computes gives ZF higher with p below 0.05/9 for 7 of 9 stimuli; it divides the heading change per frame by the file's mean frame interval, which in DC files is a median 8.73 times the frame interval (ZF 1.37), as DC files hold only trial frames. Part of the DC values may be tracking noise. In the 3 s stationary phase the DC median is 205 deg/s2, higher than the 171 during motion (per fish median ratio 1.24, p = 0.016), but ZF are also higher at rest (66.9 and 60.8, ratio 1.07, p = 0.00012), so this does not separate the species. In frames where the fish is still (below 1 mm/s) DC are higher than ZF (per-fish medians 72.4 and 34.9 deg/s2, Mann-Whitney p = 0.00014), and DC are higher in every speed band (at 5 mm/s or more, 207 and 85.8). The outputs cannot say whether the higher values in moving DC are noise or turning during continuous swimming. With the heading from the unwrapped `f0_theta` DC are higher still (218 to 278 against ZF 61.8 to 77.3 deg/s2, 0 of 9). The reversal should not be read as evidence against the paper.", "deviations": [ "Follows the Methods' definition (degrees per second squared) on heading resampled to 30 Hz; the code's quantity, which disagrees with the Methods, is shown as a variant.", "Heading is taken from the cumulative sum of `f0_vtheta`, as the code does; in DC files it does not match `f0_theta`." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "figs1e-dc-respond-less-monocular", "statement": "DC generally respond less than ZF to monocular stimuli, suggesting that they need more visual motion input to drive the optomotor response.", "source": "Results, second section; Figure S1E", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "Species effect F = 23.3, p = 2.5e-06. DC turn less toward the stimulus than ZF for medial stimuli (3.26 against 13.48 deg/s, p = 0.0003) and binocular ones (2.87 against 21.87, p = 0.0002). For lateral stimuli DC are below ZF only nominally (-1.07 against -0.13 deg/s, p = 0.96); neither species turns toward lateral motion. With the protocol file's assignment of codes 9 and 11, the lateral medians change sign and DC are no longer below ZF there, which would make the claim partially reproduced. The DC turning to codes 9 and 11 leans toward the protocol file's assignment (see stimulus-code-link), so the lateral part is fragile.", "deviations": [ "Codes 9 and 11 are assigned as the figure code has them; the stimulus software's conversion has them the other way, and the data do not settle it." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1c-continuous-vs-bouts", "statement": "ZF swim in discrete bouts separated by glides, while DC swim continuously at a relatively constant velocity.", "source": "Results, first section; Figure 1C and Figure S1D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_fouke_2025.ipynb", "notes": "The median-to-mean ratio of instantaneous speed is 0.306 in ZF (25 fish, 0.244 to 0.580) and 0.908 in DC (12 fish, 11 above 0.74, one at 0.140), Mann-Whitney p = 5.4e-05. It holds in files at 128 to 171 Hz alone (0.298 against 0.898, p = 0.0028) and in forward trials alone.", "deviations": [ "The paper shows this with representative traces and a bout analysis whose bout files are not in the dandiset; the measure was chosen here before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1cef-representative-values", "statement": "In representative trials ZF bouts reach a peak velocity of 44.7 mm/s with a median of 1.8 mm/s, DC swim at a median of 13.7 mm/s to forward motion; to oblique motion ZF show a median angular velocity of 12.0 degrees/s and median peak angular acceleration of 174 degrees/s2, and DC an average peak of 103 degrees/s2 to rightward motion.", "source": "Results, first and second sections; Figure 1C, 1E and 1F", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The numbers come from single representative fish and trials. Fig1-S1.ipynb selects them by the index of a data folder and a trial number (for example DC folder 29, trial 79), and the dandiset gives no mapping from those folders to its subjects, nor the original file names.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-shared-architecture", "statement": "Both species have spatially intermixed, direction-selective neurons enriched in the pretectum and anterior hindbrain, and share the major functional response types.", "source": "Figure 2B to 2F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The two-photon imaging data are not in the dandiset, which holds only freely swimming tracking. The GitLab repository the paper names for \"all behavioral and imaging data\" holds notebooks only, and no other dandiset of this lab or paper was found on the archive.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2g-dsi-similar", "statement": "The average direction selectivity index is similar in ZF and DC (0.62 against 0.66, p > 0.05, Student's t-test, 5 fish each).", "source": "Figure 2G", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Imaging data not in the dandiset, nor found elsewhere (see fig2d-shared-architecture).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2h-fewer-motion-responsive", "statement": "ZF tend to have a higher proportion of motion-responsive neurons than DC (0.13 against 0.06, p = 0.059).", "source": "Figure 2H", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Imaging data not in the dandiset, nor found elsewhere (see fig2d-shared-architecture).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2k-more-monocular", "statement": "DC have a higher proportion of purely monocular neurons than ZF (0.37 against 0.16, p < 0.05).", "source": "Figure 2K", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Imaging data not in the dandiset, nor found elsewhere (see fig2d-shared-architecture).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2l-bi-ratio", "statement": "The binocularity index ratio is higher in ZF than in DC (0.72 against 0.24, p = 0.010).", "source": "Figure 2L", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Imaging data not in the dandiset, nor found elsewhere (see fig2d-shared-architecture).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-longer-swims", "statement": "Head-fixed DC perform longer swims than ZF (median 0.75 s against 0.29 s, p < 0.0001).", "source": "Figure 3E and 3F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The head-fixed tail tracking recorded during imaging is not in the dandiset, nor in the paper's GitLab repository.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3cd-zf-turn-more", "statement": "Head-fixed ZF show larger directional tail angles than DC to turn-inducing stimuli, and shorten their swims for oblique stimuli while DC do not.", "source": "Figure 3C and 3D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The head-fixed tail tracking is not in the dandiset, nor in the paper's GitLab repository.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4f-longer-on-duration", "statement": "Swim-onset-associated neurons in DC have a longer active (ON) phase than in ZF, while non-motor-associated neurons have similar ON durations.", "source": "Figure 4E and 4F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the imaging and the head-fixed tail tracking, neither of which is in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4hi-vspn-lateralized", "statement": "Motor-associated neurons in the putative ventromedial spinal projection neurons of both species encode turn direction in a lateralized way, correlating more with ipsilateral turns.", "source": "Figure 4H and 4I", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the imaging, the tail tracking and the registration to the mapzebrain atlas, none of which is in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds only the freely swimming tracking of Figure 1 and Figure S1. The two-photon imaging and the head-fixed tail tracking behind Figures 2 to 4 are not in it, and the GitLab repository the paper names for all behavioural and imaging data holds analysis notebooks only. Nine of the paper's main findings cannot be tested." }, { "kind": "metadata_insufficient", "statement": "The stimulus codes 0 to 20 have no names or description in the files or the dandiset metadata. They can be named only from the paper's analysis notebook and the protocol file of its stimulus software." }, { "kind": "code_mismatch", "statement": "The paper's analysis notebook labels code 9 as lateral right and 11 as lateral left, while its conversion of the stimulus software's names gives the reverse (it carries a remap that swaps them). The data do not settle which is right; zebrafish barely turn to either, and Danionella turn more to the right for code 11, which fits the stimulus software's assignment only if the fish turn with lateral motion." }, { "kind": "metadata_error", "statement": "Subject ids 0 to 11 are each used for one zebrafish and one Danionella cerebrum, so subject_id does not identify an animal. The archive's summary counts 25 subjects and lists only Danio rerio; the files hold 37 fish of two species." }, { "kind": "metadata_error", "statement": "f0_vtheta is stated in radians/s but holds the heading change per frame in radians, and f0_vx and f0_vy are stated in pixels/s but are per frame. In most Danionella files the sum of f0_vtheta over a trial does not match the change of f0_theta (median ratios 0.09 to 0.89)." }, { "kind": "other", "statement": "18 of 25 zebrafish files and 1 of 12 Danionella files are sampled at 32 to 35 Hz, where the Methods state tracking at more than 150 Hz. Their timestamp intervals are regular (28.8 to 30.8 ms) and their trials last the protocol's 35 s, so these are the acquisition rates. Some measures differ with frame rate, such as the zebrafish static speed (8.31 against 4.50 mm/s)." }, { "kind": "metadata_insufficient", "statement": "No spatial scale is given; positions are in pixels. They are consistent with the 10 pixels per mm in the paper's code, except one Danionella file (sub-5) whose positions reach 1490 pixels against about 1120 in the others." }, { "kind": "other", "statement": "Zebrafish and Danionella files were exported differently. Zebrafish files keep untracked frames and frames between trials; Danionella files hold only tracked trial frames and add a `dist` series. The paper's code filters Danionella frames on a `vel` column that is not in the files." }, { "kind": "code_mismatch", "statement": "The paper's code computes the angular acceleration of Figure 1H as the heading change per frame divided by the file's mean frame interval, an angular velocity. In Danionella files the mean interval includes the gaps between trials (a median 8.73 times the frame interval), which scales their values down. With the Methods' definition Danionella have the higher angular acceleration." }, { "kind": "code_mismatch", "statement": "Figure 1H and its legend state a Kruskal-Wallis test with Bonferroni correction; the code runs two-sample Kolmogorov-Smirnov tests, and its loop selects the stimulus with a variable left from an earlier loop, so the nine tests compare the same stimulus." }, { "kind": "code_mismatch", "statement": "The Results state that Danionella lack the direction-dependent speed modulation of zebrafish, but the Tukey test printed by Fig1-S1.ipynb for Figure 1D finds three Danionella pairs significant (static against backward left, backward right and forward left, adjusted p 0.024 to 0.040), as this attempt does." }, { "kind": "other", "statement": "The `dist` series of the Danionella files does not agree with the positions; over the first 35 s of a trial its sum is a median 1.11 times the path length of the smoothed positions, with a 5th to 95th percentile of 0.31 to 3.79. The paper's speed check uses it, though computing the check from positions passes the same trials." }, { "kind": "code_mismatch", "statement": "The Figure 1D legend gives 26 zebrafish; the paper's code lists 25, its ANOVA degrees of freedom fit 25, and the dandiset holds 25." }, { "kind": "selection_undocumented", "statement": "The dandiset holds the 25 zebrafish and 12 Danionella the code keeps after exclusion (its comments give 28 and 40 recorded). The dandiset does not say that the excluded fish were left out or why." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's accepted manuscript (PMC12218792). The verifier listed the version's assets through the DANDI API and ran synthetic checks of angular_acceleration, trial_measures and the steadiness measure.", "agreed": 20, "of": 20, "disagreements": [] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The second executed notebook in full, with the conclusion cells and the summary, the helper module, the claims file and the attempt record. The verifier did not download the paper again.", "agreed": 20, "of": 20, "disagreements": [] } ] }, { "id": "001528-hadjas-2025-01", "dandiset": "001528", "dandiset_version": "draft", "paper": "10.1101/2025.06.03.657460", "paper_title": "Parkinson\u2019s Disease-vulnerable and -resilient dopamine neurons display opposite responses to excitatory input", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001528-hadjas-2025", "entry_title": "Responses of SNr GABA and SNc dopamine neuron subtypes to STN and PPN input (Hadjas et al. 2025)", "description": "Tests the mouse fiber photometry findings of Hadjas et al. (2025) on dandiset 001528, which holds recordings from 120 mice during optogenetic stimulation of STN or PPN inputs to the substantia nigra. It compares responses of SNr GABA neurons, SNc pan-DA neurons, striatal dopamine release in TS and DLS, DA terminals, and Vglut2+ and Anxa1+ DA neurons across train durations and frequencies, using the lab's dF/F stored in the files. The human tissue counts of Figure 1 are not in the dandiset.", "notebooks": [ { "path": "reproduce_hadjas_2025.ipynb", "title": "Reproducing Hadjas et al. (2025) from dandiset 001528", "executed": "notebooks/001528-hadjas-2025/reproduce_hadjas_2025.html" } ], "outcomes": [ { "claim": "cohort-sizes", "statement": "The number of mice per experimental group is as given in the figure legends; SNr GABA neurons STN 7 and PPN 8 (Figure 2); SNc pan-DA neurons STN 11 and PPN 9 (Figure 3); GRAB-DA in TS and DLS, STN 6 and 7, PPN 9 and 9 (Figure 4); DA terminals in TS and DLS with STN stimulation, 9 and 9 (Figure S3); Vglut2+ DA neurons STN 10 and PPN 10, Anxa1+ terminals in DLS STN 8 and PPN 10 (Figure 5); Anxa1+ cell bodies in SNc STN 5 and PPN 4 (Figure S4).", "source": "Legends of Figures 2 to 5, S3 and S4", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "10 of 16 counts match. SNr GABA, pan-DA and GRAB-DA groups match exactly, as do DA terminals in TS and Vglut2 with PPN. DA terminals in DLS have 8 mice (paper 9) and Vglut2 with STN 9 (paper 10). The Anxa1 groups have DLS recordings for 5 (STN) and 4 (PPN) mice against the paper's 8 and 10, and SNc recordings for 8 and 10 against 5 and 4. All four Anxa1 counts would match if the nine recordings without a site suffix were DLS recordings; their signals resemble the SNc recordings, and the paper's cell-body statistics are matched by the dual mice's SNc recordings alone, so the DLS recordings of those nine mice appear to be missing. For Vglut2 STN the paper's own Wilcoxon statistics fit 9 mice (W = 41, 43, -5 give exact p = 0.0117, 0.0078, 0.82 with n = 9, the paper's values, and 0.037, 0.027, 0.85 with n = 10), so the legend's 10 is likely an error; counted that way 11 of 16 match, still below 12.", "deviations": [ "Counted from the durations protocol; the frequencies protocol gives the same counts." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-gaba-excited", "statement": "Optogenetic stimulation of STN or PPN inputs increases SNr GABA neuron activity (paired t-test on the 1 s train, STN t = 3.8, p = 0.008; PPN t = 9.2, p < 0.0001).", "source": "Results, second section; Figure 2B and 2E with insets", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "1 s 40 Hz trains, mean during the train against the 1 s before onset. STN mean 18.89 % dF/F, paired t = 3.86, p = 0.0083, n = 7 (paper t = 3.8, p = 0.008); PPN 6.45 %, t = 9.19, p = 3.7e-05, n = 8 (paper t = 9.2). The 0.25 and 4 s trains also give significant increases (p 1.4e-05 to 0.0066).", "deviations": [ "The response window (mean during the train) and pre-stimulus window (same length, before onset) are choices; the paper does not state them.", "All seven STN mice have 10 trials per condition, where the Methods state 5." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-gaba-frequency", "statement": "The SNr GABA response scales with stimulation frequency from 5 to 40 Hz (Friedman test on 1 s trains, STN F = 21.0, p = 0.0001; PPN F = 18.2, p = 0.0004).", "source": "Results, second section; Figure 2C and 2F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "1 s trains of the frequencies protocol. STN means rise from 4.07 to 32.66 % between 5 and 40 Hz, Friedman 21.00, p = 0.00011, 7 of 7 mice higher at 40 than 5 Hz; PPN 1.57 to 6.10 %, Friedman 18.15, p = 0.00041, 8 of 8 (paper 21.0 and 18.2). A repeated-measures ANOVA variant gives p = 0.014 and 0.0001.", "deviations": [ "The conversion code names the STN 1 s block of these mice as 10 mW, while the files and the Methods give 5 mW; the analysis takes the files as they are." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-da-stn-250ms-peak", "statement": "A 250 ms 40 Hz train of STN inputs elicits a net increase in SNc pan-DA neuron activity that peaks after stimulus offset (latency to peak 0.50 +/- 0.03 s, mean +/- SEM).", "source": "Results, third section; Figure 3B", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "With the window fixed in the criterion (peak from onset to 2.25 s) the mean latency is 0.786 s, SEM 0.204, n = 11, outside 0.50 +/- 0.03 s, because two mice peak at 2.03 and 2.24 s. Ten of 11 mice peak after offset and the net response over 0 to 1.25 s is positive (2.89 %, t = 3.28, p = 0.0083). With a window ending at 1.25 s, a variant, the mean latency is 0.492 s, SEM 0.033, the paper's value. The two late-peaking mice (C4217, B8612) have small responses, an early local maximum at 0.41 and 0.62 s, and a slow rise that continues past the window (maximum over 0 to 5 s at 2.97 and 2.78 s), which looks like a late rebound or drift.", "deviations": [ "The paper does not give the window in which the peak is sought; the criterion fixed 0 to 2.25 s, and the variant 0 to 1.25 s matches the paper." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-da-stn-duration", "statement": "For SNc pan-DA neurons the STN-evoked response varies with train duration; with 1 and 4 s trains an initial increase is followed by inhibition (Friedman test, F = 13.0, p = 0.005).", "source": "Results, third section; Figure 3B and 3C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "Means during 0.25, 1 and 4 s trains are 0.52, 0.97 and -3.13 %, n = 11. Reading (a), Friedman over three durations, 13.64, p = 0.0011; reading (b), with the pre-stimulus window as a fourth group, 12.93, p = 0.0048, matching the paper's F = 13.0, p = 0.005; reading (c), area under the curve, p = 0.06. In 4 s trains the first 0.5 s (0.71 %) is above the last 1 s (-5.05 %) in all 11 mice, paired t = 4.81, p = 0.00071.", "deviations": [ "The paper's F and p fit four groups while three durations were tested; readings (a) and (b) match, and (b) gives the paper's value." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-da-stn-frequency-ns", "statement": "The amplitude of the SNc pan-DA response during STN stimulation does not scale with frequency (Friedman test, F = 4.2, p = 0.24).", "source": "Results, third section; Figure 3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "1 s trains, Friedman 4.20, p = 0.24, n = 11 (paper F = 4.2, p = 0.24); 40 minus 5 Hz 0.21 % dF/F. Variants with 0.25 s (p = 0.31) and 4 s trains (p = 0.18, 5 mice with all four frequencies) also find no effect.", "deviations": [ "The paper does not say which train duration Figure 3D shows; the 1 s train was fixed in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-da-ppn-duration", "statement": "PPN stimulation also evokes SNc pan-DA responses that vary with train duration (Friedman test, F = 11.5, p = 0.009).", "source": "Results, third section; Figure 3F and 3G", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "Means during 0.25, 1 and 4 s PPN trains are -0.60, 1.03 and 0.70 %, n = 9. Friedman p = 0.26, 0.25 and 0.46 under readings (a) to (c), where the paper reports F = 11.5, p = 0.009. Without the three PPN recordings whose clock could not be shown from the response (C3164, C5007, C5008), n = 6, readings (a) and (b) give p = 0.11 and 0.14.", "deviations": [ "The paper's measure for this comparison is not stated; the mean during the train (and the area under the curve) were used, as for the STN comparison, which matches the paper there." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-da-ppn-frequency-ns", "statement": "The SNc pan-DA response to PPN stimulation does not vary with frequency (repeated-measures one-way ANOVA, F2,15 = 1.35, p = 0.28).", "source": "Results, third section; Figure 3H", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "1 s trains, repeated-measures ANOVA F = 1.35 on Greenhouse-Geisser corrected df 1.85 and 14.8, p = 0.29, n = 9 (paper F2,15 = 1.35, p = 0.28); 40 minus 5 Hz 1.30 %. Variants with 0.25 and 4 s trains give p = 0.83 and 0.32.", "deviations": [ "The 1 s train was fixed in the criterion, as the paper does not name the duration." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4cf-ts-dls-opposite", "statement": "STN or PPN stimulation evokes opposite DA release in TS (increase) and DLS (decrease) (two-way ANOVA, striatal site, STN F1,11 = 40.9, PPN F1,16 = 36.4, p < 0.0001; site by time interaction of the same size).", "source": "Results, fourth section; Figure 4C and 4F", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "GRAB-DA, 1 s 40 Hz trains. STN, TS 12.45 % (6 of 6 above 0), DLS -8.91 % (7 of 7 below 0), site by time interaction F(1, 11) = 40.9, p = 5.1e-05; PPN, TS 11.39 % (9 of 9), DLS -5.75 % (9 of 9), F(1, 16) = 36.4, p = 1.7e-05, the paper's values. The 0.25 and 4 s trains give the same pattern.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4dg-ts-frequency", "statement": "In TS, the DA increase evoked by either input scales with frequency, for all train durations (STN, repeated-measures ANOVA, 0.25 s F2,8 = 7.5, 1 s F2,7 = 13.6, 4 s F2,9 = 16.9; PPN, Friedman, F = 20.0, 24.0, 23.2).", "source": "Results, fourth section; Figure 4D and 4G; Figure S3C, S3D, S3I and S3J", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "All six tests hold, with the 40 Hz mean above the 5 Hz mean. STN repeated-measures ANOVA F = 7.62, 13.76, 17.31 for 0.25, 1 and 4 s (p = 0.019, 0.0044, 0.0011; paper 7.5, 13.6, 16.9); PPN Friedman 19.80, 24.33, 23.27 (p at most 0.0002; paper 20.0, 24.0, 23.2).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4eh-dls-frequency", "statement": "In DLS, the DA inhibition scales with frequency and is most prominent at higher frequencies (STN, repeated-measures ANOVA, 0.25 s F = 7.5, 1 s F = 12.8, 4 s F = 46.8; PPN, 0.25 s Friedman F = 12.3, 1 s and 4 s repeated-measures ANOVA F = 12.8 and 10.2).", "source": "Results, fourth section; Figure 4E and 4H; Figure S3E, S3F, S3K and S3L", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "All six tests hold, with the 40 Hz mean below the 5 Hz mean (p below 0.0001 to 0.013). STN 0.25 and 4 s F = 7.89 and 47.23 (paper 7.5, 46.8); PPN 0.25 s Friedman 11.53 (paper 12.3), PPN 1 and 4 s F = 12.98 and 15.92 (paper 12.8, 10.2). STN 1 s gives F = 26.17 where the paper gives F1,11 = 12.8, p = 0.0005, the same F and df it gives for PPN 1 s.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4eh-dls-5hz-increase", "statement": "Low-frequency (5 Hz) stimulation of either STN or PPN increases DLS dopamine.", "source": "Results, fourth section; Figure 4E and 4H; Figure S3F and S3L", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "1 s trains at 5 Hz (Figure 4E and 4H), mean GRAB-DA in DLS during the train, STN 1.51 % (4 of 7 above 0, p = 0.22), PPN 1.40 % (6 of 9, p = 0.13). The sentence also cites Figure S3F and S3L, the 4 s DLS panels; for 4 s trains, a variant, STN 5.41 % (7 of 7, p = 0.00062) and PPN 2.01 % (6 of 9, p = 0.07), one input of two, which would be partially reproduced under that reading. The 1 s after offset is positive in all six conditions (0.96 to 6.76 %).", "deviations": [ "The paper does not state the window or test for this observation; the mean during 1 s trains (Figure 4E and 4H) against 0 was fixed in the criterion. The sentence cites both the 1 s panels and the 4 s panels (Figure S3F and S3L), and its account of summation over pulses fits longer trains; under the 4 s reading the effect holds for STN only." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4cf-dls-rebound", "statement": "In DLS the DA inhibition is followed by a post-stimulus rebound above baseline.", "source": "Results, fourth section; Figure 4C and 4F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "After 1 s 40 Hz trains, PPN 4.53 % (8 of 9 above 0, p = 0.017), STN 0.87 % (5 of 7, p = 0.29). After 0.25 and 4 s trains the rebound is significant for both inputs (p 0.0039 to 0.015).", "deviations": [ "The rebound window (1 s after offset) and test are choices; the paper gives no statistic." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs3-terminals-opposite", "statement": "Calcium in DA terminals in TS and DLS shows opposite responses to STN stimulation, as the GRAB-DA recordings do.", "source": "Results, fourth section; Figure S3N and S3O", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "DA terminal GCaMP, 1 s trains, TS 8.96 % (9 of 9 above 0), DLS -4.41 % (7 of 8 below 0), site by time interaction F(1, 15) = 26.2, p = 0.00013. The DLS terminals rebound after offset (6.73 %, 8 of 8 above 0).", "deviations": [ "8 DLS mice, where the paper has 9." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-vglut2-excited", "statement": "Stimulation of STN or PPN inputs increases the activity of Vglut2+ DA neurons in SNc (STN, Wilcoxon, 0.25 s W = 41, p = 0.012, 1 s W = 43, p = 0.008, 4 s W = -5, p = 0.82; PPN, paired t-test, 0.25 s t = 2.9, p = 0.02, 1 s t = 3.4, p = 0.008, 4 s t = 3.0, p = 0.01).", "source": "Results, fifth section; Figure 5B, 5C, 5G and 5H; Figure S4A and S4D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "STN Wilcoxon W = 43 and 43 for 0.25 and 1 s (p = 0.0078 each, n = 9; paper 41 and 43); PPN paired t = 2.89 and 3.42 (p = 0.018 and 0.0076, n = 10; paper 2.9 and 3.4). For 4 s trains STN W = -5, p = 0.82 as in the paper, and PPN t = 2.56, p = 0.031 (paper 3.0, p = 0.01).", "deviations": [ "9 STN mice, where the legend gives 10; the paper's W and p values are the exact values for 9 mice." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-vglut2-frequency", "statement": "The Vglut2+ DA neuron increase scales with frequency for short STN trains and for all PPN durations (Friedman, STN 0.25 s F = 15.5, p = 0.001, 1 s F = 5.9, p = 0.11, 4 s F = 7.0, p = 0.07; PPN F = 18.8, 24.8, 20.2, p <= 0.0003).", "source": "Results, fifth section; Figure 5D, 5E, 5I and 5J", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "STN 0.25 s Friedman 13.53, p = 0.0036; PPN 0.25, 1 and 4 s 11.23, 17.91, 16.20 (p = 0.011, 0.0005, 0.0010), all with the 40 Hz mean above the 5 Hz mean. STN 1 and 4 s are not significant (p = 0.43 and 0.16), as in the paper (0.11 and 0.07).", "deviations": [ "The PPN tests use the 7 of 10 mice that have all four frequencies; C3412, C3798 and C4707 have no 5 Hz trains in the dandiset. The paper's PPN 1 s Friedman statistic of 24.8 needs at least 9 mice (the maximum is 3n), so the paper had 5 Hz trains that are not deposited." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-anxa1-dls-inhibited", "statement": "In DLS terminals of SNc Anxa1+ neurons, STN and PPN stimulation produce inhibition (STN, 0.25 s t = 6.4, p = 0.0004, 1 s W = -36, p = 0.005, 4 s W = -36, p = 0.008; PPN, 0.25 s t = 3.9, p = 0.004, 1 s W = -55, p = 0.002, 4 s t = 3.8, p = 0.004).", "source": "Results, fifth section; Figure 5L, 5M, 5Q and 5R; Figure S4B and S4E", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_hadjas_2025.ipynb", "notes": "The dandiset holds Anxa1 DLS recordings for 5 (STN) and 4 (PPN) mice where the paper has 8 and 10. At these numbers the Wilcoxon tests the paper uses for three of the six conditions cannot reach p < 0.05 (smallest p 0.0625 and 0.125), so reproduced (6 of 6) cannot be reached with the deposited mice. The three t-tests can reach it, so partially reproduced (3 to 5 of 6) was reachable and was not reached; 2 of 6 tests are significant (STN 0.25 s t = -6.14, p = 0.0036; PPN 0.25 s t = -3.46, p = 0.041; PPN 4 s p = 0.13). No STN mouse goes up in any condition, and one PPN mouse in 4 s trains. With the nine recordings without a site suffix added to DLS, a variant, all 6 tests are significant. Its STN 4 s W = -36 (p = 0.0078) is the paper's, but the other two W (-34 and -51 against -36 and -55) and the t values (2.65, 2.47, 2.98 against 6.4, 3.9, 3.8) differ, while the cell-body statistics match closely with the dual mice (p to two digits, t within 0.08). The paper's statistics fix its n; W = -36 and -55 equal -n(n+1)/2 for n = 8 and 10, and t = 6.4 with p = 0.0004 needs 7 df (4 df give p = 0.0031). The DLS recordings of nine of the paper's mice are not in the dandiset.", "deviations": [], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-anxa1-dls-frequency", "statement": "The Anxa1+ terminal inhibition scales with frequency (STN, 0.25 s F = 18.0, 1 s F = 15.5, 4 s F = 15.3; PPN, 0.25 s F = 11.5, 1 s F2,15 = 11.0, 4 s F2,18 = 7.2).", "source": "Results, fifth section; Figure 5N, 5O, 5S and 5T", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "With the dandiset's DLS recordings (5 STN, 4 PPN mice) 5 of 6 tests hold (p 0.0043 to 0.026, 40 Hz below 5 Hz); PPN 4 s does not (F = 1.95, p = 0.24). With the unsuffixed recordings added, 3 of 6 hold. The paper's F2,15 and F2,18 for PPN 1 and 4 s imply about 8.5 and 10 mice (6.8 to 13.3 with the dfs rounded), against 4 here, so the samples are smaller than the paper's for the reason given under fig5-anxa1-dls-inhibited.", "deviations": [ "5 and 4 mice, where the paper has 8 and 10 (see fig5-anxa1-dls-inhibited)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-anxa1-dls-rebound", "statement": "Anxa1+ terminals in DLS show a transient increase in activity at stimulus offset, for both inputs.", "source": "Results, fifth section; Figure 5L and 5Q", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "After 1 s trains, STN 1.02 % (5 of 5 above 0, p = 0.0044), PPN 0.57 % (3 of 4, p = 0.14). The 0.25 and 4 s trains give the same picture (STN p = 0.036 and 0.026, PPN p = 0.20 and 0.11).", "deviations": [ "5 and 4 mice, where the paper has 8 and 10.", "The rebound window (1 s after offset) and test are choices; the paper gives no statistic." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4-anxa1-soma-inhibited", "statement": "Anxa1+ SNc cell bodies show stimulation-induced inhibition (paired t-test, STN 0.25 s t = 3.1, 1 s t = 4.0, 4 s t = 7.2, n = 5; PPN t = 4.8, 8.4, 3.3, n = 4) followed by post-stimulus rebound activation.", "source": "Results, fifth section; Figure S4C and S4F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "With all SNc-labelled recordings (8 STN, 10 PPN mice) 5 of 6 tests show a significant decrease (p 0.0003 to 0.014); STN 0.25 s does not (t = -1.56, p = 0.16). Restricted to the mice with both a DLS and an SNc file (5 and 4, the paper's n), a variant, all 6 are significant with the paper's statistics (t = 3.13, 3.98, 7.26, 4.72, 8.35, 3.33 against 3.1, 4.0, 7.2, 4.8, 8.4, 3.3). The statement's post-stimulus rebound is not seen in the cell bodies after 1 s trains (STN -0.08 %, PPN 0.03 %, p = 0.65 and 0.80; dual mice p = 0.53 and 0.16).", "deviations": [ "The dandiset labels 8 and 10 mice as SNc where the paper analysed 5 and 4; the outcome uses the dandiset's labels as fixed in the criterion." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-opposite-subtypes", "statement": "Excitatory inputs from STN and PPN activate PD-resilient Vglut2+ DA neurons but inhibit PD-vulnerable Anxa1+ DA neurons.", "source": "Title; Abstract; Results, fifth section; Figure 5", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hadjas_2025.ipynb", "notes": "1 s 40 Hz trains. STN, Vglut2 6.54 % against Anxa1 DLS -1.73 % (Welch t = 3.56, p = 0.0066); PPN 9.35 % against -1.48 % (t = 3.90, p = 0.0032). It holds with the unsuffixed Anxa1 recordings added to DLS (p = 0.0097 and 0.005) and against the Anxa1 SNc recordings (p = 0.017 and 0.0065).", "deviations": [ "Anxa1 DLS recordings of 5 and 4 mice, where the paper has 8 and 10." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1de-th-anxa1-reduced", "statement": "In human SNc, TH+ neurons (Mann-Whitney U = 2.0, p = 0.002) and TH+/ANXA1+ neurons (U = 1.0, p < 0.0001) are fewer in PD cases (n = 7) than in controls (n = 12).", "source": "Results, first section; Figure 1D and 1E", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The human RNAscope counts are not in the dandiset, which holds mouse photometry only. The preprint has no data availability statement, and the dandiset metadata and the conversion repository link no other deposit.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-anxa1-de-enriched", "statement": "Among remaining DA neurons in PD, ANXA1+ neurons are de-enriched to 10 +/- 7% of control, ALDH1A1+ to 41 +/- 12%, while CALB1+ neurons trend toward enrichment (301 +/- 103%).", "source": "Results, first section; Figure 1F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Human tissue counts are not in the dandiset nor in any deposit the paper or the dandiset names (see fig1de-th-anxa1-reduced).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-calb1-aldh1a1-counts", "statement": "TH+/CALB1+ neuron counts are not significantly changed in PD (U = 19.5, p = 0.08) while TH+/ALDH1A1+ counts are reduced (U = 1.0, p < 0.0001).", "source": "Results, first section; Figure S1B to S1F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Human tissue counts are not in the dandiset nor in any deposit the paper or the dandiset names (see fig1de-th-anxa1-reduced).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-if-aldh1a1", "statement": "Immunofluorescence confirms fewer TH+ and TH+/ALDH1A1+ neurons and a lower fraction of TH+ neurons expressing ALDH1A1 in PD (n = 11) than in controls (n = 15), and counts agree with RNAscope in four cases processed both ways.", "source": "Results, first section; Figure S1G to S1J", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Human immunofluorescence counts are not in the dandiset nor in any deposit the paper or the dandiset names (see fig1de-th-anxa1-reduced).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "For the Anxa1 mice the dandiset holds DLS terminal recordings for 5 (STN) and 4 (PPN) mice where the paper analyses 8 and 10. Nine mice (C5903, C5906, C5992, C6900, C6902, C7244, C7245, C7248, C7249) have only recordings labelled SNc, without a site suffix in the file name. Their signals resemble SNc recordings, and the paper's cell-body statistics are reproduced closely by the other nine mice's SNc recordings (p to two digits, t within 0.08), so the DLS recordings of these nine mice appear not to be deposited, and the nine SNc recordings were not used in the paper." }, { "kind": "selection_undocumented", "statement": "The dandiset includes Anxa1 SNc recordings from nine mice that the paper's cell-body analysis (n = 5 and 4) leaves out, and it does not say which recordings the paper used." }, { "kind": "data_missing", "statement": "The human RNAscope and immunofluorescence counts of Figure 1 and Figure S1 and the histology of Figure S2 are not in the dandiset, and the preprint has no data availability statement." }, { "kind": "data_missing", "statement": "DA terminals in DLS have 8 mice where Figure S3 gives 9." }, { "kind": "paper_inconsistency", "statement": "The Figure 5 legend gives 10 mice for Vglut2+ neurons with STN stimulation, while the paper's Wilcoxon statistics (W = 41, 43, -5 with p = 0.012, 0.008, 0.82) are the exact values for 9 mice; the dandiset holds 9." }, { "kind": "data_missing", "statement": "Three Vglut2 PPN mice (C3412, C3798, C4707) have no 5 Hz trains in their frequencies sessions, while the paper's Friedman statistic for PPN 1 s (24.8) needs at least 9 mice with all four frequencies." }, { "kind": "data_missing", "statement": "Subject C4608 (SNr GABA, PPN) has no 4 s trains in its frequencies session; the conversion notes say they were recorded in a separate session, which is not in the dandiset." }, { "kind": "metadata_error", "statement": "The dF/F series are stated in a.u. but hold percent (100 times (Gc - fit) / fit); a recomputation from the stored signals agrees with a median correlation of 0.9999 (durations) and 0.9988 (frequencies)." }, { "kind": "metadata_error", "statement": "Every session start time carries the offset -00:01, the local mean time of London that pytz gives when a time zone is attached with replace; the true offset is lost." }, { "kind": "metadata_error", "statement": "The session description of the frequencies protocol gives an interval of 10 s between trains; the epochs and the Methods give 20 s." }, { "kind": "other", "statement": "Thirteen mice (SNr GABA and pan-DA, ids starting with B) have 10 trials per condition where the Methods state 5, and 30 mice have 16 s trains that the paper does not mention." }, { "kind": "code_mismatch", "statement": "The conversion code names the 1 s block of the STN to SNr GABA frequencies sessions s1s10mW, suggesting 10 mW, while the epoch tables and the Methods give 5 mW." }, { "kind": "code_mismatch", "statement": "The conversion repository's Python re-implementation of the dF/F forces the robust fit through the origin, saying the MATLAB version does so, while its own description of the MATLAB scripts includes an intercept." }, { "kind": "metadata_error", "statement": "The files describe the modulation inconsistently. The excitation source descriptions give 465 nm modulated at 210 Hz and 405 nm at 330 Hz, as the Methods do, while the processed series descriptions give the calcium signal as demodulated at 330 Hz and the isosbestic signal at 210 Hz, as the conversion repository's description of the MATLAB scripts does. This attempt did not check which is right against the raw signal." }, { "kind": "metadata_insufficient", "statement": "The file names and session ids of nine Anxa1 mice carry no recording site, and every Anxa1 file lists both an SNc and a DLS fiber in its fiber photometry table, so the site rests on the name of the dF/F series alone." }, { "kind": "other", "statement": "Eight subject ids are written in lower case (c3015, c3016, c4379, c4708, c4709, c4977, c4978, c5113) while the others are upper case." }, { "kind": "paper_inconsistency", "statement": "The Results give F1,11 = 12.8 for the DLS frequency effect with 1 s trains for both STN (p = 0.0005) and PPN (p = 0.002); F(1, 11) = 12.8 gives p = 0.0043, and the data give F = 26.2 for STN. Two Friedman entries for Anxa1 terminals also do not fit their p-values (F = 11.5 with p = 0.0002, F = 15.5 with p = 0.015; with 3 df these give 0.0093 and 0.0014). F1,11 is also not possible for a one-way repeated-measures ANOVA in 7 or 9 mice. The Figure 5 legend says the Anxa1 STN frequency panels (N, O) show no significant effect of frequency, while the Results report significant effects for all three STN durations." }, { "kind": "methods_unavailable", "statement": "The lab's MATLAB analysis scripts are not public; the preprint names custom MATLAB code and has no code availability statement. The conversion repository describes them." }, { "kind": "other", "statement": "The dandiset has no published version; this attempt used the draft as modified on 2026-09-01T15:27:47Z." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier queried the archive's asset list and metadata and tested the helper functions on synthetic inputs. It gave its own outcome for each claim; 24 of 25 agree with the record. It would give not_reproduced for fig5-anxa1-dls-inhibited, which the record has as blocked.", "agreed": 24, "of": 25, "disagreements": [ { "claim": "fig5-anxa1-dls-inhibited", "outcome": "not_reproduced", "reason": "2 of 6 significant with the DLS labels, n 5 and 4. Every mouse decreases except one in PPN 4 s, so the failure comes from sample size. With n = 5 the smallest two-sided Wilcoxon p is 0.0625 and with n = 4 it is 0.125, so three of the six tests cannot pass whatever the data show. The paper's W = -36 and -55 equal -n(n+1)/2 for n = 8 and 10, and t 6.4 with p 0.0004 needs df 7, so the paper analysed 8 and 10 DLS mice. The unsuffixed-recordings variant does not reproduce these statistics, so those recordings are not the paper's DLS data. The outcome reflects data missing from the archive, which the notebook never states as such." } ] }, { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, the helper module, the claims file and the attempt record, with the paper. The verifier checked every conclusion, the Summary, the README and the record's notes and findings against the printed outputs, and gave its own outcome for each claim; it agrees with all 25. It found wording to correct in cell 70, cell 0, the README run time, and the word exactly for the cell-body match. In reply the README now gives about seven minutes (6.9 min in the round-2 run); the other changes are under the claims below.", "agreed": 25, "of": 25, "disagreements": [] } ] }, { "id": "001538-zhai-2025-01", "dandiset": "001538", "dandiset_version": "0.260527.1302", "paper": "10.1126/sciadv.adv8224", "paper_title": "State-dependent modulation of spiny projection neurons controls levodopa-induced dyskinesia in a mouse model of Parkinson\u2019s disease", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001538-zhai-2025", "entry_title": "State-dependent modulation of spiny projection neurons in levodopa-induced dyskinesia (Zhai et al. 2025)", "description": "Tests the findings of Zhai, Cui, Wokosin, Sun, Tkatch, Crittenden, Graybiel and Surmeier (2025) on dandiset 001538. It measures somatic excitability (rheobase and spike counts) and the dendritic excitability index of dSPNs and iSPNs in the LID off- and on-states and under D1R, D2R and M1R antagonists, CDGI deletion and M1R deletion, and evoked ACh release with GRAB-ACh3.0. It links the recordings to the paper's per-cell tables on Zenodo. The Sr2+-oEPSC, ACh and AIM data hold too few cells or mice for most of the paper's tests, and the spine data are raw stacks only.", "notebooks": [ { "path": "reproduce_zhai_2025.ipynb", "title": "Reproducing Zhai et al. (2025) from dandiset 001538", "executed": "notebooks/001538-zhai-2025/reproduce_zhai_2025.html" } ], "outcomes": [ { "claim": "link-somatic-cells", "statement": "The dandiset's somatic current-step recordings are those behind the paper's somatic excitability figures, and the spike counts computed from them agree with the paper's per-cell tables.", "source": "Figures 1E, 3C, 6C, 7C and 9D; the paper's tables at Zenodo doi:10.5281/zenodo.17307059", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Groups are matched by name and every group the dandiset holds has the paper's n (12 of 12 groups, 123 cells). 90 of 123 cells (73.2%) match a row of the paper's table exactly over 20 to 300 pA and 105 (85.4%) within 3 spikes, below the 80% and 95% of the criterion; 108 have the same rheobase as their best match. dSPN on has the fewest exact matches (6 of 15). The best matches are not one-to-one (9 paper rows are the best match of two or three cells); with each row used once, 89 cells (72.4%) match exactly and 103 (83.7%) within 3 spikes. The best-match rows follow the dandiset's order by date and cell number, every cell at its own rank in 8 of 12 groups and 10 of 15, 11 of 15, 11 of 12 and 10 of 11 cells in the others. Of the 14 cells with a repeated step, keeping the last sweep in place of the first gives the same best-match difference in 13 and a closer one in 1.", "deviations": [ "The paper's spike counts come from its script run on Prairie View exports; the differences of 1 to 24 spikes may come from the export or from cells whose steps are missing or repeated in the files (18 cells miss a step, 14 repeat one)." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "link-dendritic-cells", "statement": "The dandiset's dendritic line scans are those behind the paper's dendritic excitability index figures, and the index computed from them agrees with the paper's per-cell values.", "source": "Figures 1I, 3F, 6D and 7F; the paper's tables at Zenodo doi:10.5281/zenodo.17307059", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Three site series hold six trials, two sites under one name; split, they give their cells 0.293, 0.146 and 0.327 against the paper's 0.299, 0.146 and 0.309. With the split, 91 of 92 cells have an index (iSPN on+sul 20190508 cell 3 has only a distal site). Counts of cells with an index equal the paper's n in 9 of 10 groups, and counts of cells with dendritic sites in 10 of 10, so every group is matched, by order or (Figure 6D) by date and letter. Over 91 matched cells the index differs from the paper's by a median of 2.9% (78 within 10%, Spearman 0.938). Two cells differ by more than the paper's value, dSPN on+SCH 20190411 cell 1 (0.584 against 0.228; only its second pair of sites is in the dandiset) and iSPN off 20160524 cell 2 (1.062 against 0.527; its first proximal site has one trial, and without it the cell gives 0.553). The best-match rows of the somatic link follow the dandiset's order (link-somatic-cells), which supports matching by order. With the sites as labelled, 89 of 92 cells have an index.", "deviations": [ "Outside Figure 6D the paper's table has no cell identifiers, so cells are matched by order, an assumption supported by the somatic link.", "The background constants of the paper's script (55 red, 161 green) are used for every session, as the files carry no per-session background.", "Three six-trial series are split into their first and last three trials, the half with the smaller area taken as distal, a choice made here from the data; the sites as labelled are a variant." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "link-sr-cells", "statement": "The dandiset's Sr2+-oEPSC recordings are cells of the paper's Figures 2 and 4, and their events agree with the paper's per-cell values.", "source": "Figures 2G to 2I and 4F to 4H; the paper's tables at Zenodo doi:10.5281/zenodo.17307059", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "All 14 dandiset cells match a paper identifier (date and session letter); the paper has 33 cells (17 off, 16 on), so the dandiset holds one cell per mouse. In every cell the detector here finds fewer events (2 to 85, against 29 to 127 in the paper's tables) and a higher mean amplitude than the paper's events; 2 of 14 cells are within 25% on both, and also 2 of 14 when the paper's amplitude is read as its per-cell value (0.70 to 0.96 times the mean of its histogram events). In 20230405b (2 events against 73) the detection window opens on the slow decay of a large synchronous current, and the small events on it stay below the threshold (figure in the notebook). The paper's frequency equals its event count over 3.6 s. With the paper's per-cell amplitudes, on-state dSPNs are all above off-state ones and on-state iSPNs all below (Mann-Whitney P = 0.057 each).", "deviations": [ "Events are found with a threshold detector written here (low-pass 1 kHz, five robust SD, local baseline); the paper used TaroTools with visual verification, which cannot be repeated." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "link-grab-rois", "statement": "The dandiset's GRAB-ACh recordings are regions of the paper's Figure 5F, and the normalised areas computed from them agree with the paper's per-region values.", "source": "Figure 5F; the paper's tables at Zenodo doi:10.5281/zenodo.17307059", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "The dandiset holds one region per mouse, 11 of the paper's 34 (3 of 13 unlesioned, 3 of 10 6-OHDA, 5 of 11 off-state). The paper's regions have no identifier linking them to mice; by the nearest vector of single-pulse areas only 5 of 11 mice have a paper region within 0.05 on every treatment (the 20240402 mouse within 0.007), so the regions cannot be identified. One paper region is the best match of two off-state mice; with each region used once, 5 of 11 are still within 0.05.", "deviations": [ "The stimulus time is taken from the trial table (3 s after the trial start in six files), where the paper's script fixes 10 s." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "link-aim-mice", "statement": "The dandiset's AIM score tables are mice of the paper's Figures 8 and 10, with genotypes and scores that agree with the paper's tables.", "source": "Figures 8B, 8C and 10B; the paper's tables at Zenodo doi:10.5281/zenodo.17307059", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "7 of 9 dandiset mice are in the paper's tables (4124 and 5871 are not). The two Figure 10 mice (5844 control, 5846 M1R deletion) have totals equal to the paper's in all 10 sessions; the five Figure 8 mice (1945, 2519, 2828 and 6572 KO, 2587 wild type) agree in 5 of 25 sessions (for 1945, session 1, 33.5 against 27.0). The dandiset's own genotype labels for the CDGI mice contradict each other, so the paper's labels were used. The paper's tables give session totals only; for the Figure 8 mice they equal neither the dandiset's sums over 20 to 80 min nor, outside those 5 sessions, the sums over all time points (1945 session 1 has four time points summing to 33.5), so the scores differ, not only the time points summed.", "deviations": [ "The paper's session total is taken to be the sum over the session's time points; the Figure 8 mice have 4 time points in some dandiset sessions and 6 in others." ], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1f-dspn-rheobase-on-lower", "statement": "In dSPNs the rheobase is lower in the LID on-state than in the off-state.", "source": "Figure 1F; Results, first section (P < 0.0001, Mann-Whitney)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Rheobase on-state 140 pA against off-state 220 pA (15 cells each from 10 and 8 mice), Mann-Whitney P = 8.86e-06, effect r = -0.95. With one value per mouse P = 0.000425 and complete separation.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-dspn-fi-on-higher", "statement": "In on-state dSPNs suprathreshold current steps evoke more spikes than in off-state dSPNs across a range of intensities.", "source": "Figure 1E; Results, first section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Summed spikes 20 to 300 pA, median 88 on against 36 off, P = 8.8e-05 (0.00015 for the 22 cells with every step). The on-state median is higher at every step from 120 to 300 pA (per-step P at most 0.012).", "deviations": [ "The paper shows F-I curves without a test; the summed count and its test were chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-dspn-sch-no-change", "statement": "Bath application of the D1R antagonist SCH 23390 does not reverse the lower rheobase of on-state dSPNs.", "source": "Figure 1F; Results, first section (P = 0.589, Mann-Whitney)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Rheobase on-state 140 pA (15 cells) against on-state with SCH 140 pA (10 cells), P = 1.0, effect r = 0.007. In the 5 cells recorded in both conditions the median paired difference is 0 pA (Wilcoxon P = 1.0). Five cells are in both groups, so the unpaired test's samples are not independent; the criterion follows the paper's test.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1i-dspn-dendritic-on-higher", "statement": "The dendritic excitability index of dSPNs is higher in the on-state than in the off-state.", "source": "Figure 1I; Results, first section (P = 0.0115, Mann-Whitney)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Index on-state 0.476 against off-state 0.330 (10 cells each), P = 0.0058 (exact 0.0039), effect r = 0.74; without background P = 0.0046; with a basal-ratio rule of 0.8 to 1.25 (8 cells each) P = 0.0070; with the sites as labelled P = 0.0091.", "deviations": [ "Background constants from the paper's script; basal-ratio rule (0.5 to 2) chosen here, dropping no pair; one six-trial series split into two sites." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1i-dspn-dendritic-sch-lower", "statement": "SCH 23390 reverses the higher dendritic excitability of on-state dSPNs.", "source": "Figure 1I; Results, first section (P = 0.0133, Mann-Whitney)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "The criterion (P < 0.05 with the SCH median lower) is not met, though the difference has the stated direction. On-state with SCH 0.419 (9 cells) against on-state 0.476 (10 cells), P = 0.0662 (exact 0.0653), effect r = -0.51; with the stricter basal-ratio rule P = 0.524. The difference from the paper comes from one cell, SCH 20190411 cell 1, whose index is 0.584 here and 0.228 in the paper's table; the dandiset holds only its second pair of sites. Without that cell P = 0.0266; with the paper's value for it P = 0.016 (exact 0.0133, the paper's P). The other eight SCH cells differ from the paper's values by 2.4% to 10.9%. That the missing sites explain the difference is an inference from the recovered P, as the paper does not list each cell's sites.", "deviations": [ "Matching the SCH cells to the paper's rows by order is an assumption (link-dendritic-cells)." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2h-dspn-sr-amplitude-on-larger", "statement": "The amplitude of Sr2+-oEPSCs evoked from cortical afferents is larger in on-state than in off-state dSPNs.", "source": "Figures 2G and 2H (P = 0.0003, Mann-Whitney)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The dandiset holds one cell per mouse, 3 off-state and 4 on-state dSPNs of the paper's 10 and 8. With 3 against 4 cells the smallest attainable two-sided Mann-Whitney P is 0.057, so the paper's test cannot reach P < 0.05. The per-cell values are shown under link-sr-cells; with the detector here the on-state amplitudes are all above the off-state ones (P = 0.057).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2i-dspn-sr-frequency-unchanged", "statement": "The frequency of Sr2+-oEPSCs in dSPNs does not differ between states.", "source": "Figure 2I (P = 0.127)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Same 3 against 4 cells as fig2h; the test cannot detect a difference at P < 0.05 whatever the data, so the claim of absence cannot be judged. The frequencies are shown under link-sr-cells (P = 0.229).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2bc-dspn-spines", "statement": "dSPN spine density falls in the off-state, and mushroom spines are more common in the on-state than in the off-state.", "source": "Figures 2A to 2C", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The dandiset holds the two-photon z-stacks of dSPN dendrites (off- and on-state) but no spine counts; none of the 86 spine files has a processing module or analysis entry. The paper deconvolved them in AutoQuant X3 and counted spines semi-automatically in NeuronStudio with manual classification of mushroom spines, a procedure that cannot be repeated from its description (also not runnable here, AutoQuant being commercial software). No control or 6-OHDA stacks for dSPNs were found. The per-cell densities are in the paper's Zenodo tables.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-ispn-rheobase-on-higher", "statement": "In iSPNs the rheobase is higher in the on-state than in the off-state.", "source": "Figure 3D; Results, second section (P = 0.0013, Mann-Whitney)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Rheobase on-state 160 pA (11 cells, 8 mice) against off-state 120 pA (12 cells, 5 mice), P = 0.000829, effect r = 0.81; one value per mouse P = 0.00899.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-ispn-fi-on-lower", "statement": "The F-I relationship of iSPNs shifts to the right in the on-state.", "source": "Figure 3C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Summed spikes 65 on against 118.5 off, P = 7.2e-05 (0.000165 for complete cells); lower on-state median at every step from 120 to 300 pA (per-step P at most 0.012).", "deviations": [ "The summed count and its test were chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-ispn-sul-no-change", "statement": "Sulpiride does not alter the somatic excitability of on-state iSPNs.", "source": "Figure 3D; Results, second section (rheobase P = 0.287)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Rheobase on-state 160 pA (11) against on-state with sulpiride 120 pA (7), P = 0.143, effect r = -0.43. The two cells recorded in both conditions have a lower rheobase with sulpiride (160 to 120 and 160 to 100 pA), so the absence rests on the test's power. Those two cells are in both groups, so the unpaired samples are not independent; the criterion follows the paper's test.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-ispn-dendritic-on-lower", "statement": "The dendritic excitability index of iSPNs falls in the on-state compared with the off-state.", "source": "Figure 3F; Results, second section (P = 0.0029)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Index on-state 0.339 (10) against off-state 0.524 (10), P = 0.0073 (exact 0.0052), effect r = -0.72; without background P = 0.0073; with the sites as labelled (9 on-state cells) P = 0.0128; dropping sites with fewer than 3 trials P = 0.0091. With the stricter basal-ratio rule (0.8 to 1.25, 9 cells each) P = 0.0774, so the result depends on keeping pairs whose basal ratios differ by more than 25%. The stricter rule moves fig3f-ispn-dendritic-sul-no-change the other way (P = 0.0663, which would meet that criterion).", "deviations": [ "One on-state cell gets its index only from splitting a six-trial series into two sites.", "The Methods keep pairs with similar G0/R0 without a threshold; the 0.5 to 2 rule chosen here drops no pair." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3f-ispn-dendritic-sul-no-change", "statement": "Sulpiride does not significantly alter dendritic excitability in on-state iSPNs.", "source": "Figure 3F; Results, second section (P = 0.0545)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "The paper's test finds the difference the claim says is absent. On-state with sulpiride 0.506 (7 cells) against on-state 0.339 (10 cells), P = 0.0097, effect r = 0.74; the paper reports P = 0.0545 with 8 and 10 cells, and its own medians go the same way (0.499 and 0.345). With the sites as labelled P = 0.0164, with the stricter basal-ratio rule P = 0.0663. The sulpiride cell without an index (20190508 cell 3, only a distal site in the dandiset) has 0.217 in the paper's table; with that value P = 0.0545, the paper's P. Under the main basal-ratio rule the outcome turns on that one cell; under the stricter rule P = 0.0663 without it, which would also meet the criterion, so the outcome depends on the basal-ratio rule as well. That the missing site explains the difference is an inference from the recovered P, as the paper does not list each cell's sites.", "deviations": [ "One sulpiride cell has no index here (only a distal site)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4g-ispn-sr-amplitude-on-smaller", "statement": "The amplitude of Sr2+-oEPSCs is smaller in on-state than in off-state iSPNs.", "source": "Figures 4F and 4G (P = 0.0003)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "One cell per mouse, 3 off-state and 4 on-state iSPNs of the paper's 7 and 8; the smallest attainable P is 0.057. With the detector here the on-state amplitudes are not all below the off-state ones (P = 0.229), while the paper's own per-cell values for these cells are (P = 0.057); shown under link-sr-cells.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-ispn-sr-frequency-unchanged", "statement": "The frequency of Sr2+-oEPSCs in iSPNs does not differ between states.", "source": "Figure 4H (P = 0.23)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Same 3 against 4 cells as fig4g; the claim of absence cannot be judged by a test that cannot reach P < 0.05.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4bc-ispn-spines", "statement": "Apparent iSPN spine density (2PLSM) falls after the lesion, returns in the off-state and falls in the on-state, in total and mushroom spines.", "source": "Figures 4A to 4C", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Two-photon z-stacks of iSPN dendrites are in the dandiset (off- and on-state, CDGI KO, M1R antagonist, M1R deletion) but no counts; counting needs AutoQuant deconvolution and semi-automatic NeuronStudio reconstruction with manual checks, which the paper does not describe well enough to repeat. The control and 6-OHDA stacks the lesion part needs are not in the dandiset (data_missing); the off- and on-state part is blocked by the counting alone.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4k-confocal-spines", "statement": "Confocal spine density of iSPN proximal dendrites is higher than the 2PLSM estimate (median 2.084 against 1.243 spines per um), falls after the lesion, rises modestly in the off-state and falls in the on-state.", "source": "Figures 4I to 4K; Results, second section", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Eleven confocal files of sparsely labelled iSPN dendrites (3 control, 3 6-OHDA, 3 off and 2 on) are in the dandiset, of the paper's 87 dendrites, with no counts. Counting used Imaris 10 with trained pixel classification and manual correction, which cannot be repeated from its description (and Imaris is commercial software).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-ach-off-elevated", "statement": "Evoked ACh release (GRAB-ACh3.0) in slices from LID off-state mice is greater than in unlesioned striatum.", "source": "Figure 5F; Results, third section (P < 0.0001)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Single-pulse normalised area without drug, off-state 0.359 (5 mice) against unlesioned 0.112 (3 mice), P = 0.0357, the smallest attainable (complete separation). Burst stimulation gives the same; the unnormalised dF/F0 area does not (P = 0.25).", "deviations": [ "One region per mouse, 8 of the paper's 24 regions in these two groups.", "Stimulus time from the trial table." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-ach-off-like-6ohda", "statement": "Evoked ACh release in the off-state is similar to that after a 6-OHDA lesion.", "source": "Figure 5F; Results, third section (P = 0.4679)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "6-OHDA 0.240 (3 mice) against off-state 0.359 (5 mice), P = 0.143, effect r = 0.73; burst P = 1.0. With 3 and 5 mice the test detects only complete separation, so the absence is weakly supported.", "deviations": [ "One region per mouse, 8 of the paper's 21 regions in these two groups.", "The test cannot find any difference short of complete separation, so this claim of absence passes with little power." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-ach-6ohda-elevated", "statement": "Evoked ACh release is markedly elevated in 6-OHDA-lesioned striatum compared with unlesioned striatum.", "source": "Figure 5F (P < 0.0001)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "3 unlesioned and 3 6-OHDA mice, one region each; the smallest attainable P for 3 against 3 is 0.10. The values (unlesioned 0.089 to 0.113, 6-OHDA 0.179 to 0.269) are shown under link-grab-rois.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-ach-d2-control", "statement": "In unlesioned striatum sulpiride increases and quinpirole suppresses evoked ACh release.", "source": "Figure 5F (P = 0.0005 and 0.0034)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "3 unlesioned mice; a paired Wilcoxon test on 3 pairs cannot reach P < 0.05 (smallest 0.25). In all three, quinpirole lowers and sulpiride raises the area (shown under link-grab-rois).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-ach-da-suppresses", "statement": "Dopamine (50 nM) strongly suppresses evoked ACh release in 6-OHDA-lesioned and off-state striatum, and sulpiride has no effect after the lesion.", "source": "Figure 5F (P = 0.002, 0.001; sulpiride P = 0.5566)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "3 6-OHDA and 5 off-state mice; paired tests on 3 or 5 pairs cannot reach P < 0.05 (smallest 0.25 and 0.0625). Dopamine lowers the area in all 8 mice (shown under link-grab-rois); sulpiride after the lesion raises it in two of three.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-m1r-antag-somatic-unchanged", "statement": "M1R antagonism throughout the off-state does not have a strong impact on the elevated somatic excitability of off-state iSPNs.", "source": "Figure 6C; Results, fourth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Rheobase vehicle 120 pA (8) against antagonist 140 pA (10), P = 0.681, effect r = 0.125; summed spikes P = 0.45.", "deviations": [ "The paper gives no test; its default Mann-Whitney test on rheobase was used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-m1r-antag-dendritic-lower", "statement": "M1R antagonism prevents the off-state elevation of iSPN dendritic excitability.", "source": "Figure 6D (P = 0.012)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Index vehicle 0.451 (9) against antagonist 0.269 (7), P = 0.0229, effect r = -0.68; with the stricter basal-ratio rule P = 0.0164.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6f-m1r-antag-spines", "statement": "M1R antagonism prevents the off-state elevation of apparent iSPN spine density.", "source": "Figures 6E and 6F (P = 0.0003)", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Z-stacks are in the dandiset without counts (see fig4bc-ispn-spines).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7c-cdgi-ko-somatic-oscillation", "statement": "Deletion of CDGI does not blunt the oscillation of iSPN somatic excitability between on- and off-states.", "source": "Figures 7A to 7C; Results, fourth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "KO rheobase on-state 210 pA (8) against off-state 140 pA (13), P = 0.00104, effect r = 0.87; summed spikes P = 0.00335.", "deviations": [ "The paper shows F-I curves without a test; a Mann-Whitney test of rheobase was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7f-cdgi-ko-dendritic-unchanged", "statement": "The off-state elevation of iSPN dendritic excitability is absent in CDGI KO mice (off against on not different), while it is present in wild type.", "source": "Figure 7F (KO P = 0.395; wild type P = 0.0029)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "KO index off-state 0.312 (11) against on-state 0.286 (8), P = 0.310, effect r = -0.30 (P = 0.659 with the stricter rule, 0.315 with the sites as labelled); wild type P = 0.0073.", "deviations": [ "One KO off-state cell gets its index only from splitting a six-trial series into two sites." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7h-cdgi-ko-spines", "statement": "The off-state increase in apparent iSPN spine density is absent in CDGI KO mice.", "source": "Figures 7G and 7H (P = 0.613)", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Z-stacks are in the dandiset without counts (see fig4bc-ispn-spines).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig8bc-cdgi-aims", "statement": "Axial, limb, orolingual and total AIMs are less severe in CDGI KO mice than in wild type.", "source": "Figures 8B and 8C (repeated-measures two-way ANOVA, group P < 0.001 to 0.002)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The dandiset holds AIM tables for 5 of the paper's 23 Figure 8 mice (4 KO, 1 wild type) and 2 mice not in the paper; with one wild-type mouse the paper's repeated-measures ANOVA cannot be run. The dandiset's genotype labels contradict each other, and the session totals of these mice differ from the paper's in 20 of 25 sessions (link-aim-mice, not reproduced).", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig9d-m1r-crispr-somatic-unchanged", "statement": "Deletion of M1Rs from iSPNs does not alter the elevated somatic excitability of off-state iSPNs.", "source": "Figures 9C and 9D; Results, fifth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "Rheobase control 160 pA (6) against M1R CRISPR 120 pA (8), P = 0.147, effect r = -0.48; summed spikes P = 0.245. The control group is 6 cells from 2 mice, so the absence rests on little power.", "deviations": [ "The paper gives no test; its default Mann-Whitney test on rheobase was used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig9f-m1r-crispr-spines", "statement": "Deletion of M1Rs from iSPNs blunts the off-state increase in apparent spine density.", "source": "Figures 9E and 9F (P = 0.0005)", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Z-stacks are in the dandiset without counts (see fig4bc-ispn-spines).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig10b-m1r-aims", "statement": "AIMs are attenuated by deletion of M1Rs in iSPNs.", "source": "Figure 10B (repeated-measures two-way ANOVA, group P < 0.001 to 0.0015)", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The dandiset holds AIM tables for 2 of the paper's 21 Figure 10 mice, one control (5844) and one M1R deletion (5846), whose totals equal the paper's; one mouse per group cannot be tested. Mouse 5846 has lower totals than 5844 in every session.", "deviations": [], "disagreed": false, "data": "with_labels", "where": null, "proposed": null }, { "claim": "fig1-dspn-lesion-and-off-somatic", "statement": "dSPN somatic excitability (rheobase) rises after the 6-OHDA lesion and falls in the LID off-state.", "source": "Figure 1F; Results, first section (both P < 0.0001)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's table, rheobase 120 pA after the lesion against 220 pA in controls (P = 0.000295) and 200 pA in the off-state against 120 pA (P = 9.54e-05). The paper reports P < 0.0001 for both.", "deviations": [ "Tested on the paper's per-cell table; the raw recordings in Zenodo doi:10.5281/zenodo.17260198 were not reanalysed." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (per-cell rheobase, Figure 1F sheet); raw recordings in Zenodo doi:10.5281/zenodo.17260198", "proposed": null }, { "claim": "fig1-dspn-lesion-dendritic-unchanged", "statement": "The dSPN dendritic excitability index is not changed by the 6-OHDA lesion or in the off-state.", "source": "Figure 1I; Results, first section (P = 0.824 and 0.905)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's table, P = 0.82 and 0.903 (reported 0.824 and 0.905).", "deviations": [ "Tested on the paper's table, not the raw line scans." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (Figure 1I sheet)", "proposed": null }, { "claim": "fig3-ispn-lesion-and-off-somatic", "statement": "iSPN somatic excitability is lowered by the 6-OHDA lesion and restored in the LID off-state.", "source": "Figure 3D; Results, second section (both P = 0.002)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's table, rheobase 200 pA after the lesion against 120 pA in controls (P = 0.000401) and 130 pA in the off-state (P = 0.000608); reported P = 0.002 for both.", "deviations": [ "Tested on the paper's table." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (Figure 3D sheet)", "proposed": null }, { "claim": "fig3-ispn-lesion-dendritic-up", "statement": "The iSPN dendritic excitability index rises after the lesion and stays raised in the off-state.", "source": "Figure 3F; Results, second section (P = 0.0327 and 0.0220)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's table, 0.516 after the lesion and 0.519 off-state against 0.405 in controls (P = 0.0348 and 0.0242; reported 0.0327 and 0.0220).", "deviations": [ "Tested on the paper's table." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (Figure 3F sheet)", "proposed": null }, { "claim": "fig7e-oxom-cdgi", "statement": "Oxotremorine-M increases bAP invasion of iSPN dendrites in wild-type but not in CDGI KO mice.", "source": "Figure 7E (P = 0.0098 and 0.910, Wilcoxon)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's table, wild type 8 of 10 increase, Wilcoxon P = 0.009766 (reported 0.0098); KO 4 of 12 increase, P = 0.4697 (reported 0.910). Pairs are formed by the table's experiment number (printed); an unpaired Mann-Whitney test gives 0.885 for KO and 0.0539 for wild type, so neither test gives the reported 0.910.", "deviations": [ "Tested on the paper's table; the oxo-M line scans are not in the dandiset." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (Figure 7E sheet); raw line scans in Zenodo doi:10.5281/zenodo.17260198", "proposed": null }, { "claim": "fig8a-cdgi-rotations", "statement": "Levodopa induces more contralateral rotations in CDGI KO mice than in wild type at the fifth dose.", "source": "Figure 8A (P = 0.0092 in the text; the legend marks P < 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's table, KO 8.5 against wild type 4.25 rotations (10 and 12 mice), P = 0.012 (the text reports 0.0092, the legend P < 0.05).", "deviations": [ "Tested on the paper's table; the dandiset holds rotation videos for 7 CDGI-study mice without counts." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (Figure 8A sheet)", "proposed": null }, { "claim": "fig10a-m1r-rotations", "statement": "Levodopa induces more contralateral rotations in mice lacking M1Rs in iSPNs.", "source": "Figure 10A (P = 0.0056)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's table, 8.5 with M1R deletion against 6.0 in controls, P = 0.00782 (reported 0.0056).", "deviations": [ "Tested on the paper's table." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (Figure 10A sheet)", "proposed": null }, { "claim": "fig10ef-open-field", "statement": "In MCI-Park mice, a low dose of levodopa increases locomotion profoundly only when M1Rs are deleted from the striatum; M1R deletion alone does not.", "source": "Figures 10D to 10F; Results, fifth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_zhai_2025.ipynb", "notes": "On the paper's tables, MCI-Park against control distance 4.678 against 10.35 m (P = 1.05e-05), time mobile P = 6.97e-06; M1R deletion alone P = 0.628 and 0.467; levodopa with deletion against levodopa alone 28.09 against 6.52 m (P = 0.000332) and 276.4 against 127.45 s (P = 0.000567).", "deviations": [ "Tested on the paper's tables; the open-field data are not in the dandiset." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.17307059 (Figure 10E and 10F sheets); raw ANY-maze data in Zenodo doi:10.5281/zenodo.17260198", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds no patch-clamp recordings from unlesioned control or 6-OHDA-lesioned mice, which make up the control and 6-OHDA groups of Figures 1E, 1F, 1I, 3C, 3D and 3F (10, 12, 11 and 9 dSPNs; 21, 11, 14 and 9 iSPNs), nor the oxo-M line scans of Figure 7E or the open-field data of Figure 10. The paper's raw data on Zenodo (doi:10.5281/zenodo.17260198) list folders for all of these." }, { "kind": "selection_undocumented", "statement": "The Sr2+-oEPSC files hold one cell per mouse (14 of the paper's 33 cells), the GRAB-ACh files one region per mouse (11 of 34 regions) and the AIM tables 7 of the paper's 44 mice plus two mice (4124, 5871) not in the paper. The dandiset does not say that it holds a subset or how the cells, regions and mice were chosen, and with these numbers the paper's tests cannot reach P < 0.05 for most comparisons." }, { "kind": "metadata_error", "statement": "Session names state a drug (D1RaSch, D2RaSul) for files that also hold baseline on-state sweeps. 11 cells in such files have a baseline condition; 7 of them were also recorded with the drug and 4 are baseline only (dSPN 20190507 cell 1, iSPN 20190408 cell 1, 20190409 cell 1 and 20190508 cell 2). The condition of each sweep is only in the RecordingsIndexTable column condition_subfolder; grouping by session name puts baseline cells in the drug groups." }, { "kind": "metadata_error", "statement": "The genotypes of the CDGI behaviour mice contradict each other. Subject genotype is Wild-type CDGI and every session name says WT for all of them; the AIM table's genotype column says CDGI Knockout, Wild Type or unknown, changing between sessions of one animal; the video files of mice 1945, 2519, 2587, 2828 and 6572 say CDGI KO. The paper lists 2587 as wild type and the others as KO." }, { "kind": "other", "statement": "The AIM session totals of the five Figure 8 mice in the dandiset differ from the paper's table in 20 of 25 sessions (mouse 1945 session 1, 33.5 against 27.0), while the two Figure 10 mice agree in all sessions. Some dandiset sessions have 4 time points and others 6." }, { "kind": "metadata_error", "statement": "Three dendritic site series hold six trials, two sites under one name, while the cell has no series of the other compartment with that number (iSPN 20160526 cell 3 Distal1, iSPN 20160608 cell 1 Proximal1, dSPN 20170204 cell 1 Proximal1); their first and last three trials differ in baseline and area. Split, they give the paper's values for these cells. One series holds a single trial (iSPN 20160524 cell 2 Proximal1), one two and one four." }, { "kind": "data_missing", "statement": "Two dendritic cells lack the sites the paper's values need. dSPN on+SCH 20190411 cell 1 has only its second pair of sites, which gives 0.584 against the paper's 0.228; with the paper's value the SCH test gives the paper's P (0.0133), without it P = 0.066. iSPN on+sul 20190508 cell 3 has only a distal site; with the paper's 0.217 the sulpiride test gives the paper's P (0.0545), without it P = 0.0097. Under the main basal-ratio rule these two cells decide fig1i-dspn-dendritic-sch-lower and fig3f-ispn-dendritic-sul-no-change; under the stricter rule (0.8 to 1.25) the sulpiride test gives P = 0.0663 without the cell. Reading the gap as data missing is an inference from the recovered P values, as the paper does not list each cell's sites." }, { "kind": "metadata_insufficient", "statement": "The dandiset holds the raw spine image stacks and the rotation videos but no spine counts or rotation counts (none of the 86 spine files has a processing module or analysis entry), the measurements behind Figures 2B, 2C, 4B, 4C, 4K, 6F, 7H, 8A, 9F and 10A. They are only in the paper's Zenodo tables." }, { "kind": "metadata_error", "statement": "The stimulus series of every dendritic sweep (CurrentClampSeries_CellN_Dendritic_Stimulus) is all zero, though the three spikes per sweep show the 2 nA injections were delivered; and the index table gives no kymograph slice for 53 of 997 dendritic sweeps." }, { "kind": "metadata_error", "statement": "In the Sr2+-oEPSC files the light-pulse OptogeneticSeries is all zero in 69 of 140 sweeps, and the intracellular recordings table references no stimulus (its stimulus rows are empty). The pulse time (0.02 s) is only in the optogenetic epochs table." }, { "kind": "metadata_error", "statement": "The GRAB-ACh background reference images are described as taken at zero laser power, but their mean (381 to 525) is above the signal (F0 179 to 355), so they cannot be the PMT background the Methods subtract." }, { "kind": "metadata_error", "statement": "The files cite the bioRxiv preprint (related_publications) and describe the behaviour data with the preprint's figure numbers (\"Figure 7J\" for the CDGI AIM scores, \"Figure 8\" for the M1R study), which are Figures 8 and 10 in the published paper the dandiset names." }, { "kind": "identifier_missing", "statement": "Patch-clamp subjects are named by recording date (for example Subject20160523LIDOFFeGFP and SubjectRecordedAt20160523000000 for the same day), with no animal identifier, so recordings and spine stacks of one mouse cannot be linked, and the archive has 185 subject folders." }, { "kind": "paper_inconsistency", "statement": "Recomputed on the paper's own per-cell tables, some reported P values differ; the oxo-M test in CDGI KO gives P = 0.47 where the paper reports 0.910, and the rotation test of Figure 8A gives 0.012 where the text reports 0.0092. Others agree closely (0.009766 against 0.0098 for oxo-M in wild type)." }, { "kind": "other", "statement": "18 somatic cells miss one or more current steps between 20 and 300 pA and 14 repeat a step; spike counts for these cells cannot be complete." } ], "verifications": [ { "date": "2026-10-18", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file.", "agreed": 44, "of": 45, "disagreements": [ { "claim": "fig1i-dspn-dendritic-sch-lower", "outcome": "not_reproduced", "reason": "P = 0.066 (paper 0.0133). The SCH median is 0.419 against the paper's 0.338; one SCH cell differs 2.6-fold from the paper and may drive this. Replacing each of the top five SCH values in turn with value/2.559 gives P = 0.014 to 0.041, so the claim may fail because of one computed index, not the data. The stricter 0.8 to 1.25 basal-ratio variant gives P = 0.52." } ] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the revised run, with the conclusions and the summary, the helper module, the claims file and the attempt record.", "agreed": 45, "of": 45, "disagreements": [] } ] }, { "id": "001550-pagan-2025-01", "dandiset": "001550", "dandiset_version": "0.260916.0811", "paper": "10.1038/s41586-024-08433-6", "paper_title": "Individual variability of neural computations underlying flexible decisions", "date": "2026-10-18", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001550-pagan-2025", "entry_title": "Context-dependent evidence accumulation in rats (Pagan et al. 2025)", "description": "Tests the findings of Pagan, Tang, Aoi, Pillow, Mante, Sussillo and Brody (2025) on dandiset 001550, which holds the behaviour of 26 rats trained on a task that switches between accumulating location and frequency evidence. It links the dandiset to the paper's published behavioural tables, checks the session statistics and selection, fits the behavioural pulse kernels and their slope indices, tests the optogenetic inactivation, and, with the paper's neural data from GitHub, the link between behavioural and neural slope indices.", "notebooks": [ { "path": "reproduce_pagan_2025.ipynb", "title": "Reproducing Pagan et al. (2025) from dandiset 001550", "executed": "notebooks/001550-pagan-2025/reproduce_pagan_2025.html" } ], "outcomes": [ { "claim": "session-link", "statement": "The dandiset's sessions can be linked to the paper's published per-session behavioural tables, and the linked records agree on trial counts, outcomes, evidence and pulse timing.", "source": "Data availability; the paper's data/Sessions_trials at GitHub commit 0ea8fdb", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Sessions are matched by rat and session name taken from the source file names in the paper's tables. Of 15,278 paper sessions with valid trials, 15,277 (0.9999) are in the dandiset; the missing one, P189 TaskSwitch6-210516a, has 27 valid trials. In all 15,277 the number of valid trials and the fraction correct are equal, and both relative weights agree to 1e-6 in 0.898; of the 1,553 that differ, 861 agree once this attempt's values are capped at 1 as the paper's table does. Of the 692 left, 627 have a missing value on both sides, 5 in the paper's table only, and 60 differ with both values present (median difference 0.87 after capping, not explained); 3 of the 692 are in the paper's selection. In 20 seeded sessions every valid trial agrees on context, correct side, strengths, choice, outcome and position in block, and 0.99996 of 10 ms pulse bins agree. Over every matched session, 627 have an empty per-trial record in the paper's tables; in the other 14,650 the 7,447,692 valid trials agree on every per-trial field and position in block, and 0.99996 of 50 ms pulse bins agree over the 6,532,005 trials whose pulses were binned. The dandiset's Methods selection keeps all 8,843 sessions of the paper's selection plus 6 (5 P187 and P189 sessions not in the paper's tables, and P059 TaskSwitch4-170331a, whose relative weight of 1.112 the paper's table caps at 1.0). Per-rat selected trial counts equal the paper's numhits for 23 of 26 rats and exceed them by 213 (P059), 1,442 (P187) and 609 (P189).", "deviations": [ "The paper's `good` flag is not in the dandiset and is not applied; it removes no session that passes the other criteria." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "subjects", "statement": "The study used 26 male Long-Evans rats, aged between 6 and 24 months.", "source": "Methods, Subjects", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "26 subjects, all male Long Evans, one date of birth each. Ages at the 8,849 selected sessions are 3.0 to 39.1 months (median 15.4); 0.913 lie within 5.4 to 26.4 months and 0.844 within 6 to 24. Eighteen rats have selected sessions before 5.4 months and eight after 26.4. The dates of birth put 25 rats at 1.6 to 2.7 months at their first session in the dandiset; P189 is at 14.1 months, on the day P187 (born 2019-02-21) starts, and its date of birth (2018-02-21) may be a year early.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "trials-per-session", "statement": "Rats performed on average 542 trials per session.", "source": "Methods, Behaviour", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Mean valid trials per session 551.8 over the 8,849 selected sessions (reading b) and 494.2 over all 15,400 task sessions (reading d), both within 487.8 to 596.2. All trials average 817.9 and 749.7 (readings a and c), outside. The 13 unreadable sessions (1 to 3 trials) are left out of readings c and d; added, they give 749.1 and 493.8.", "deviations": [ "The Methods do not say which sessions or trials are counted; four readings are shown and two match." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "blocks-per-session", "statement": "On average, rats switched across 14.6 context blocks per session.", "source": "Methods, Behaviour", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Blocks per session average 16.98 over selected sessions and 13.90 over all task sessions; switches average 15.98 and 12.90. Blocks over all sessions (13.90) and switches over selected sessions (15.98) are within 13.14 to 16.06; the first is recorded as measured.", "deviations": [ "Whether blocks or switches are counted, and over which sessions, is not stated; two of four readings match." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "session-duration", "statement": "Behavioural sessions lasted 2 to 4 hours.", "source": "Methods, Behaviour", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Median duration 2.50 h over selected sessions and 2.57 h over all task sessions. Only 0.559 and 0.556 of sessions last 2 to 4 h (0.65 within 1.8 to 4.4); 5% to 95% of selected sessions span 1.26 to 4.41 h, and the range is 0.26 to 7.74 h.", "deviations": [ "Duration is taken from the first trial start to the last trial stop; the files hold no session end time." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "block-min-30", "statement": "Block switches occurred after a minimum of 30 trials per block, and when a local estimate of performance reached 80% correct.", "source": "Methods, Behaviour", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "All 141,359 non-final blocks of selected sessions have at least 30 trials counted over all trials (1st percentile 30, median 44); counted over valid trials 0.817 do. Over the last 30 valid trials before a switch the median fraction correct is 0.828 and 0.601 of blocks reach 0.8, so the 80% part is not shown on that window; the task's local estimate is not described.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-20-rats", "statement": "Twenty rats each contributed more than 120,000 trials after training.", "source": "Figure 1c legend; Extended Data Figure 1c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Twenty rats have more than 120,000 valid trials in selected sessions (the twentieth, P189, has 128,309; the next, P124, 115,123). The same 20 pass at 120,000 or more.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-context-selection", "statement": "After training, choices are mostly driven by location in the location context and by frequency in the frequency context.", "source": "Figure 1c; Extended Data Figure 3a,d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "In all 20 rats both relative weights exceed 0.5; location in the location context 0.770 to 0.860, frequency in the frequency context 0.724 to 0.870.", "deviations": [ "Tested by the Methods' logistic regression on generative strengths, not by the four-parameter psychometric fits that the figure shows." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1e-switch-four-trials", "statement": "Rats switch the feature they attend to within about four trials of a new context block.", "source": "Results, first section; Extended Data Figure 1e (legend panel g)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Across 26 rats, at position 4 of a new block the relevant relative weight is 0.91 of its plateau when switching to location and 0.963 when switching to frequency (Methods selection), and 0.914 and 0.961 with the code's 0.65 selection. At position 1 it is 0.502 and 0.560, against plateaus of 0.854 and 0.789. All 26 rats have a fit at positions 1 to 5 (103 to 6,096 trials), so the 30-trial minimum drops nothing. Bootstrapping rats, the position 4 value for the switch to location has a 95% interval of 0.874 to 0.946 and reaches 0.9 in 0.678 of resamples; at position 5, which the criterion also allows, the values are 0.956 and 0.977 and reach 0.9 in 0.998 and 1.000 of resamples.", "deviations": [ "The paper's code uses a 0.65 selection for this analysis; the Methods selection is the main result and the code's is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed2g-learning-2-5-months", "statement": "Most rats learned the task in two to five months.", "source": "Results, first section; Extended Data Figure 2g", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "From each rat's first session to its first session with an index of at least 0.7, 17 of 26 rats took 1.8 to 5.5 months (times 0.85 to 8.18 months). With the full selection 19 of 26; counted from the first TaskSwitch session 13 (exactly half) and 17. Within the unwidened 2 to 5 months the counts are 12, 16, 10 and 13. 24 rats start with ProAnti3Marino sessions.", "deviations": [ "The paper does not define the start of training or when a rat counts as trained; four pairings of readings are shown, three match." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-converging", "statement": "Differential behavioural kernels predominantly converge towards the end of the pulse train, that is the difference between contexts in the weight of a feature shrinks for later pulses.", "source": "Methods, Behavioural logistic regression; Figure 4; Extended Data Figure 3c,f", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "All 36 slope indices of the 18 Figure 4 rats are negative (median -0.432, range -0.774 to -0.097). With the code's fixed penalty of 200 all 36 are negative (median -0.491), and they agree with the indices from the paper's saved weights to at most 0.0177 (r = 0.99973).", "deviations": [ "The Methods' ridge penalty is read as the code's penalty on neighbouring weight differences, with its weight chosen by 3-fold cross-validation over 20, 200 and 2000 (chosen weights 20 to 2000); the code fixes it at 200.", "The differential kernel is divided by its largest absolute value before the line fit, as the code does; the Methods do not say." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-loc-frq-uncorrelated", "statement": "Across rats, the shape of the differential behavioural kernel for one feature does not predict the shape for the other feature.", "source": "Results, Linking neural and behaviour variability; Figure 4 top right", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Across 18 rats r = 0.180 (95% CI -0.313 to 0.597), p = 0.475; with the fixed penalty r = 0.092, p = 0.717; from the paper's saved weights r = 0.094, p = 0.71.", "deviations": [ "The paper gives no test; a two-sided Pearson correlation was chosen before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3g-halfsplit", "statement": "The behavioural slope index computed from the first half of a rat's trials is correlated with the index from the second half (r = 0.58, p = 0.000013).", "source": "Extended Data Figure 3g legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Over 24 rats and 48 values r = 0.552 (95% CI 0.318 to 0.723), p = 4.7e-05, within 0.522 to 0.638. With the fixed penalty r = 0.577, p = 1.8e-05. Location alone r = 0.470, frequency alone r = 0.736.", "deviations": [ "The halves use the penalty weight chosen on all of that rat's trials in that context." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed4-bilateral-fof-impairs", "statement": "Bilateral optogenetic silencing of the frontal orienting fields during the stimulus impairs performance of the task (three rats).", "source": "Results, first section; Extended Data Figure 4g", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Four rats have opto sessions (P116 47, P124 74, P127 4 and P131 88 with at least 100 valid trials). With bilateral full-trial epochs accuracy is lower than on control trials in the same sessions with p < 0.05 in 2 of the 3 rats with most sessions, P116 (0.639 against 0.733, 873 trials, p below 1e-4) and P131 (0.686 against 0.727, 1,988 trials, p = 0.0001). P124 is higher (0.712 against 0.687, p = 0.17) and P127 lower but not significantly (0.603 against 0.634, p = 0.55). Any bilateral epoch gives 2 of 3 and 2 of 4 as well. Every trial with an epoch has the laser connected; with laser-connected trials only the accuracies and p values are the same.", "deviations": [ "The paper does not say which three rats were analysed, which sessions, or its test; the readings and the Fisher test were chosen before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "neural-link", "statement": "The neurons in the paper's published neural data can be linked to the dandiset's rats and sessions; they come from 199 sessions of 7 rats.", "source": "Results, first section (n = 199 sessions, n = 7 rats); the paper's data/neural_data and data/rat_for_each_neuron.mat at GitHub commit 0ea8fdb", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "All 7 rats are in the dandiset and every cell file names one of them. Under the criterion's rule (the cell's trials equal a contiguous run of one session's valid trials) 2,371 of 3,495 cells (0.678) match one session and none matches more than one; they come from 110 sessions against 199. With gaps allowed (a variant) 3,269 cells (0.935) match exactly one session, from 112 sessions; 226 cells match none, 189 of them P100's. The neural files leave out some trials of a session, so the contiguous rule is stricter than needed, but neither rule finds 199 sessions. Searching every TaskSwitch protocol (adding P100's 13 TaskSwitch4repeat sessions) gives 2,425 contiguous matches (0.694) from 113 sessions and 3,349 with gaps (0.958) from 115; the 146 cells left share a median 0.43 of their 8-trial windows with their best session, and 61 of those 64 best sessions are already matched.", "deviations": [ "The neural files carry no session identifier; cells are matched by their trial sequence." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "units-per-rat", "statement": "The recordings yielded 3,495 putative single units, 2,047, 832, 258, 94 and 54 from five rats in FOF and 112 and 98 from two rats in mPFC.", "source": "Results, first section; Methods, Analysis of neural data", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "The cell files hold 3,495 units, FOF 2,047 (P100), 832 (P059), 258 (P055), 94 (P095) and 54 (P049), mPFC 112 (P101) and 98 (P102), and rat_for_each_neuron.mat agrees with every file. The Methods sentence that puts all 3,495 in FOF counts the 210 mPFC units as well.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GitHub Brody-Lab/flexible_decision_making_rats at commit 0ea8fdb7c56d755d99155171cc314dbbc24393ac (data/neural_data, data/rat_for_each_neuron.mat)", "proposed": null }, { "claim": "fig3h-neural-uncorrelated", "statement": "Neural slope indices vary across rats and features, with no apparent correlation between the location and frequency indices across the seven recorded rats.", "source": "Results, Pulse analyses distinguish solutions; Figure 3h", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Neural slope indices range from -0.221 to 1.728 (location) and 0.465 to 1.500 (frequency); across the 7 rats r = -0.177 (95% CI -0.821 to 0.665), p = 0.704. The Methods say differential pulse responses only showed positive (or zero) slope indices; three location indices here are negative (P049 -0.221, P101 -0.045, P095 -0.007). The criterion does not test this.", "deviations": [ "The per-neuron kernels are the paper's fitted ones from its repository; the GLM was not refitted from spikes.", "The paper gives no test; a two-sided Pearson correlation was chosen before the analysis." ], "disagreed": false, "data": "elsewhere", "where": "GitHub Brody-Lab/flexible_decision_making_rats at commit 0ea8fdb7c56d755d99155171cc314dbbc24393ac (data/combined_kernels.mat)", "proposed": null }, { "claim": "choice-axes-parallel", "statement": "Choice axes estimated separately in the two contexts are essentially parallel (average angle 1.6 degrees, not different from 0 in 6 of 7 rats).", "source": "Results, first section; Extended Data Figure 5", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "By ExtDataFigure5ag.m on the paper's per-context kernels, the angle the code plots (the two context choice axes projected on the first 3 principal components of both contexts' choice kernels, folded to at most 90 degrees) is 5.53, 7.91, 4.49, 1.82, 1.12, 4.25 and 8.00 degrees (P049, P055, P059, P095, P100, P101, P102), mean 4.73, against the reported 1.6 (tolerance 1.44 to 1.76); no rat is in the tolerance. The 3 components explain 0.85 to 0.94 of the variance. The full-space angle, which the code computes first and overwrites, averages 40.34 (29.43 folded). All units of each rat have fits in both contexts. The reported test against 0 (not different from 0 in 6 of 7 rats) is a permutation test the Methods describe, shuffling the trials' context labels and recomputing both axes; it is not in the repository's code and needs the per-neuron kernels refitted for every shuffle, so it was not run.", "deviations": [ "The criterion was corrected after the first verification round to follow the angle the code plots; it first described only the full-space angle, now a variant. Both are outside the tolerance." ], "disagreed": false, "data": "elsewhere", "where": "GitHub Brody-Lab/flexible_decision_making_rats at commit 0ea8fdb7c56d755d99155171cc314dbbc24393ac (data/combined_kernels_per_context.mat)", "proposed": null }, { "claim": "fig5d-behaviour-neural", "statement": "The behavioural slope index and the neural slope index are anti-correlated across rats and features (r = -0.73, P < 0.01), and for location (r = -0.71) and frequency (r = -0.71) alone (P < 0.1).", "source": "Results, Linking neural and behaviour variability; Figure 5d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pagan_2025.ipynb", "notes": "Behavioural slope indices from the dandiset (Methods selection, bins 14 to 26) against neural indices from the paper's kernels give r = -0.697 over 14 values (95% CI -0.896 to -0.264), p = 0.0056, within -0.803 to -0.657. Location alone r = -0.675 (p = 0.096), frequency alone r = -0.772 (p = 0.042); the paper reports -0.71 for each with P < 0.1, and both hold at that level. With the code's 0.65 and 0.6 selection and penalty 200, r = -0.765 (p = 0.0014), and the paper's saved behavioural indices give -0.768. The match of neurons to rats, which this claim needs, holds for every cell; the session-level link that fails in neural-link is not used here.", "deviations": [ "The Methods selection keeps 23,014 and 25,847 trials of P049 and P059 against 135,001 and 162,317 under the code's selection, and their location indices change sign (0.131 against -0.432, 1.292 against -0.613).", "Neural kernels are the paper's fitted ones, not refitted from spikes.", "The result is close to the tolerance and depends on P049 and P059. With those two rats from the code's selection r = -0.834, and with the code's selection and cross-validated penalty r = -0.830, both beyond the tolerance on the negative side; leaving out one rat at a time gives -0.655 to -0.895, inside the tolerance for 4 of 7. All five 14-point correlations shown are negative with p < 0.01." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig1e-choice-axis", "statement": "Choice-related population activity in FOF evolves along an essentially one-dimensional line during the stimulus (73.3% of variance; 81.3% for the two-dimensional choice subspace).", "source": "Results, first section; Figure 1e", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Figure1e.m projects the per-context choice kernels on principal components but computes neither 81.3% nor 73.3%, and the text does not say which kernels, time window or normalisation the percentages refer to. The data (combined_kernels_per_context.mat, and the mTDR fits in data/Arrays_Pagan) are public in the paper's repository.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GitHub Brody-Lab/flexible_decision_making_rats at commit 0ea8fdb7c56d755d99155171cc314dbbc24393ac (data/Arrays_Pagan, mbtdr)", "proposed": null }, { "claim": "fig1f-irrelevant-encoded", "statement": "In FOF, trajectories for different evidence strengths separate along each sensory axis whether the feature is relevant or irrelevant, so irrelevant information is not gated out before frontal cortex.", "source": "Results, first section; Figure 1f", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "Needs the mTDR fits of the MATLAB toolbox in the repository's mbtdr folder (with minFunc) on data/Arrays_Pagan. MATLAB cannot be installed in the entry's locked Python environment and the toolbox was not ported.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GitHub Brody-Lab/flexible_decision_making_rats at commit 0ea8fdb7c56d755d99155171cc314dbbc24393ac (data/Arrays_Pagan)", "proposed": null }, { "claim": "fig3a-trained-rnn-svm", "statement": "RNNs trained by backpropagation through time favour selection vector modulation.", "source": "Figure 3a", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "Needs 1,000 RNNs trained by backpropagation through time (train_model.py in flexible_decision_making_rnn at commit 13cd245) and their linearisation; the repository holds three trained models. Training them is far beyond the 30-minute limit.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GitHub Brody-Lab/flexible_decision_making_rnn at commit 13cd24544258da2e3d846115afb075443db8a8a1", "proposed": null }, { "claim": "fig5c-engineered-rnn", "statement": "In RNNs engineered across the solution space, neural and behavioural slope indices are tightly anti-correlated.", "source": "Figure 5c", "outcome": "blocked", "blocked_by": "not_runnable", "notebook": null, "notes": "The engineered RNNs and their pulse and behavioural kernels are built by MATLAB scripts (handcraft_model.m and others in flexible_decision_making_rnn at commit 13cd245), which cannot run in the entry's environment and were not ported.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "GitHub Brody-Lab/flexible_decision_making_rnn at commit 13cd24544258da2e3d846115afb075443db8a8a1", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds only the behaviour. The electrophysiology behind Figures 1d to 1f, 3h and 5d (3,495 units from 7 rats) is not in it; it is public only in the paper's GitHub repository, as one MATLAB file per unit with binned spike counts, without raw data or spike sorting output." }, { "kind": "identifier_missing", "statement": "Nothing links the paper's units to dandiset sessions. Matched by trial sequence, 3,269 of 3,495 units fall in exactly one dandiset session when gaps are allowed (2,371 without gaps), from 112 sessions, where the paper reports 199; 226 units match no session. Searching every TaskSwitch protocol gives 3,349 units from 115 sessions, and 146 unmatched." }, { "kind": "metadata_error", "statement": "Every optogenetic epoch gives a wavelength of 473 nm; Extended Data Figure 4 says 450 nm, and the conversion's documentation says the value was corrected to 450." }, { "kind": "metadata_insufficient", "statement": "Optogenetic epochs are present for four rats (P116, P124, P127, P131), where the paper reports three; nothing in the dandiset or the paper says which three were analysed." }, { "kind": "metadata_error", "statement": "The dates of birth give ages of 3.0 to 39.1 months at the sessions the paper's selection keeps (18 rats younger than 5.4 months at some), where the Methods state 6 to 24 months. Either the dates of birth or the stated ages are wrong. The dates of birth put 25 rats at 1.6 to 2.7 months at their first session; P189's (2018-02-21) puts it at 14.1 months on the day P187, born 2019-02-21, starts, and may be a year early." }, { "kind": "format_error", "statement": "Thirteen task sessions (1 to 3 trials each) lack HistorySection_result_history or a pulse column, and 95 of the other 15,400 lack HistorySection_hit_history. Where both outcome columns exist they agree on every trial." }, { "kind": "data_missing", "statement": "One session of the paper's tables with 27 valid trials, P189 TaskSwitch6-210516a, is not in the dandiset; the conversion's notes list it among aborted sessions left out." }, { "kind": "other", "statement": "Six task sessions of P187 and P189 (TaskSwitch6, 2021) are in the dandiset but not in the paper's tables; five of them pass the Methods selection, adding 1,442 and 609 trials to those rats." }, { "kind": "other", "statement": "HistorySection_gammafreq_history, a signed strength, is stored as uint8 or int16 in 570 files; in all of them its values equal the float gamma_freq, so nothing was lost." }, { "kind": "selection_undocumented", "statement": "The paper's code also requires a per-session `good` flag that the Methods do not describe and the dandiset does not hold, and caps relative weights at 1; neither changes the selection except for one P059 session." }, { "kind": "code_mismatch", "statement": "The Methods describe ridge regression with the regulariser chosen by cross-validation; the code adds a fixed penalty of 200 on squared differences of neighbouring weights. The code also uses looser selections (0.65 correct and 0.6 index) for the recorded rats in Figure 5d and for Extended Data Figure 1e than the Methods' 0.7." }, { "kind": "code_mismatch", "statement": "The paper's own code (ExtDataFigure5ag.m), applied to its own fitted per-context kernels, gives angles of 1.1 to 8.0 degrees between the context choice axes (mean 4.7), not the reported average of 1.6 degrees. The permutation test of each angle against 0 that the Methods describe is not in the code." }, { "kind": "paper_inconsistency", "statement": "The Methods say 3,495 units were recorded from 5 rats in FOF and list FOF counts that sum to 3,285; the 3,495 include the 210 mPFC units. The main text calls a converging differential behavioural kernel a slope index above 0, while the Methods and the code give converging kernels negative indices, as the data have." } ], "verifications": [ { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text. The verifier recomputed the choice-axis angles from combined_kernels_per_context.mat, read ExtDataFigure5ag.m and get_neural_slope.m, listed the version's assets, and tested bin_pulses, relative_weights, slope_index, fit_logistic and opto_trials on synthetic inputs.", "agreed": 23, "of": 23, "disagreements": [] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the first revision with its conclusions and summary, the helper module, the claims file, the README and this attempt record, with the paper's full text (paper/PMC11903320.txt).", "agreed": 23, "of": 23, "disagreements": [] } ] }, { "id": "001616-gerken-2025-01", "dandiset": "001616", "dandiset_version": "0.260702.0824", "paper": "10.7554/elife.106758.1", "paper_title": "Decoding movie content from neuronal population activity in the human medial temporal lobe", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "001616-gerken-2025", "entry_title": "Single units of the human medial temporal lobe during a full-length movie (Gerken, Darcher et al. 2025)", "description": "Tests the findings of Gerken, Darcher et al. (eLife reviewed preprint 106758, 2025) on dandiset 001616 (SUMMER), which holds 2286 units from 29 patients watching \"500 Days of Summer\" with 53 frame-wise annotations. It counts units responsive to the onsets of movie features, runs the cluster permutation test by region, and decodes characters, location and cuts with the paper's logistic regression, pooled, per patient, per region and on subsets of units. The paper's LSTM is not run.", "notebooks": [ { "path": "reproduce_gerken_2025.ipynb", "title": "Reproducing Gerken, Darcher et al. (2025) from dandiset 001616", "executed": "notebooks/001616-gerken-2025/reproduce_gerken_2025.html" }, { "path": "top_ranked_units.ipynb", "title": "Top-ranked units for decoding Summer (Figure 7)", "executed": "notebooks/001616-gerken-2025/top_ranked_units.html" }, { "path": "responsive_zeta_cuts.ipynb", "title": "Responsive units by the dataset code's ZETA test, camera and scene cuts (variant)", "executed": "notebooks/001616-gerken-2025/responsive_zeta_cuts.html" }, { "path": "responsive_zeta_labels.ipynb", "title": "Responsive units by the dataset code's ZETA test, character, person and location labels (variant)", "executed": "notebooks/001616-gerken-2025/responsive_zeta_labels.html" } ], "outcomes": [ { "claim": "dataset-composition", "statement": "The data are 2286 single and multi-units from 29 patients (17 female), 30 to 137 units per patient, in the amygdala (580), hippocampus (794), entorhinal cortex (440), parahippocampal cortex (373) and piriform cortex (99).", "source": "Results, first paragraph; Figure 1d; Patient-wise decoding performance", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "29 patients, 2286 units and 17 female patients, as stated, with 30 to 137 units per patient. With AH, MH and PH grouped as hippocampus (the dataset's code), the regions hold A 559 (paper 580), H 846 (794), EC 493 (440), PHC 293 (373) and PIC 68 (99), and 27 units lie in FF, LG and PRC. A and H are within 10%; EC, PHC and PIC are not. Every unit's region matches that of its electrode.", "deviations": [ "Regions are read from the dandiset's `brain_region` and grouped as in the dataset's code; the paper gives no mapping." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-phc-camera-cuts", "statement": "Over half of the parahippocampal neurons responded to camera cuts (193 of 373, 51.74%).", "source": "Results, Stimulus-aligned responsive neurons; Figure 2b; Table S1", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_gerken_2025.ipynb", "notes": "The Methods' test counts 222 of 293 PHC units (75.77%) responsive at alpha 0.001 and 228 (77.82%) at 0.01 (paper 193 of 373, 51.74%). The same test counts 72.35% of PHC units and 68.4% of all units responsive at random event times (69.2% in the per-label check with 884 random times), and all synthetic Poisson units at 2 Hz with 884 random events, so its false-positive rate is far from its alpha and the procedure differs from the paper's. The test compares integer counts in 100 ms bins with the baseline mean per 100 ms across hundreds of trials, which a signed-rank test finds different even without a response. The dataset code's ZETA test (responsive_zeta_cuts.ipynb, all units) is not anticonservative (none of 400 units at random times at alpha 0.001, 1.0% at 0.01) and finds 35 of 293 PHC units (11.95%) at 0.001 and 67 (22.87%) at 0.01, below the paper's fraction; neither test as run here gives the paper's count.", "deviations": [ "The responsive-unit test follows the Methods as fixed in the claims file (baseline count over -1000 to 0 ms divided by 10, 19 overlapping 100 ms bins, two-sided Wilcoxon signed-rank, Simes); the Methods do not say more.", "The ZETA variant uses 100 resamplings in place of the code's 1000, for time; for PHC units and scene cuts, 1000 resamplings change the counts by 1 and 2 units.", "The fraction is compared, as the dandiset's PHC holds 293 units against the paper's 373." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "tables1-camera-cuts-regions", "statement": "Camera cuts evoked responses in a large share of neurons in every region (amygdala 46.90%, entorhinal cortex 45.68%, hippocampus 38.92%).", "source": "Table S1; Results, Stimulus-aligned responsive neurons", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_gerken_2025.ipynb", "notes": "Depends on fig2b-phc-camera-cuts. The miscalibrated test counts A 73.70%, EC 73.63%, H 64.54% and PHC 75.77% at alpha 0.001 (paper 46.90, 45.68, 38.92, 51.74%), and 62 to 73% of each region at random times. The ZETA test of the dataset's code counts A 3.22%, EC 0.61%, H 1.30% and PHC 11.95% (responsive_zeta_cuts.ipynb).", "deviations": [ "The responsive-unit test follows the Methods as fixed in the claims file (baseline count over -1000 to 0 ms divided by 10, 19 overlapping 100 ms bins, two-sided Wilcoxon signed-rank, Simes); the Methods do not say more." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-phc-scene-cuts", "statement": "Few parahippocampal neurons responded to scene cuts (25 of 373, 6.70%), but the modulation was consistent across the responsive neurons (cluster permutation test, p = 0.018).", "source": "Results, Stimulus-aligned responsive neurons; Figure 2b; Table S1", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_gerken_2025.ipynb", "notes": "The Methods' test counts 138 of 293 PHC units (47.10%) at alpha 0.001 and 180 (61.43%) at 0.01 (paper 6.70%); with as many random times as there are scene cut onsets it counts 48.25% of all units, so it is miscalibrated. With this split the largest cluster has p = 0.055 with the Methods' z-scoring and p = 0.020 with the code's per-trial z-scoring at alpha 0.001, and there is no cluster at 0.01. The ZETA test finds 12 of 293 (4.10%) at 0.001 and 29 (9.90%) at 0.01, either side of the tolerance of 4.16 to 9.24%; with 1000 resamplings 11 and 31 (responsive_zeta_cuts.ipynb).", "deviations": [ "The responsive-unit test follows the Methods as fixed in the claims file (baseline count over -1000 to 0 ms divided by 10, 19 overlapping 100 ms bins, two-sided Wilcoxon signed-rank, Simes); the Methods do not say more.", "Cluster p is the fraction of 1000 label permutations whose largest cluster is at least the observed largest cluster; the Methods compare each cluster with the permuted histogram." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "tables1-few-semantic-responses", "statement": "Only a few neurons responded to the onset of semantic features (Summer 46, Tom 216, Persons 6 and Outdoor 4 of 2286 neurons), in contrast to camera cuts (1025).", "source": "Abstract; Results, Stimulus-aligned responsive neurons; Table S1", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_gerken_2025.ipynb", "notes": "The test counts 1013 units responsive to Summer and 1174 to Tom at alpha 0.001 (paper 46 and 216), and 9.93 to 51.36% of units for each semantic label. At random times, as many as each label's onsets, it counts about as many (Summer 44.05% against 44.31% at the real onsets, Tom 50.26% against 51.36%), so the counts are dominated by false positives. The code's onset rule (no minimum duration) changes them little (1019 and 1191). The ZETA test of the dataset's code, conservative at random times, counts 11 for Summer and 13 for Tom (responsive_zeta_labels.ipynb), and 79 for camera cuts (paper 1025).", "deviations": [ "The responsive-unit test follows the Methods as fixed in the claims file (baseline count over -1000 to 0 ms divided by 10, 19 overlapping 100 ms bins, two-sided Wilcoxon signed-rank, Simes); the Methods do not say more.", "Onsets for labels with a duration also last at least 1 s (Results); the code does not require this, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "tables1-no-indoor-response", "statement": "No neuron responded to the onset of indoor scenes.", "source": "Results, Stimulus-aligned responsive neurons; Table S1", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_gerken_2025.ipynb", "notes": "The test counts 299 units responsive to Indoor onsets at alpha 0.001 and 810 at 0.01, and 439 for McKenzie and 227 for Summer Presence at 0.001, where Table S1 has 0; with 44 random times in place of the Indoor onsets it counts 11.46% of units. An absence cannot be judged with this test. The paper's test as written is the one run here; the alpha of 0.001 is that of the Results paragraph making the claim. The ZETA test of the dataset's code, which is not the paper's test, counts 2 Indoor units at 0.001 (responsive_zeta_labels.ipynb).", "deviations": [ "The responsive-unit test follows the Methods as fixed in the claims file (baseline count over -1000 to 0 ms divided by 10, 19 overlapping 100 ms bins, two-sided Wilcoxon signed-rank, Simes); the Methods do not say more." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "results-cluster-regions", "statement": "By the cluster permutation test, parahippocampal neurons responded to the largest set of features (Summer, Persons, Camera Cuts, Scene Cuts, Outdoor), compared with the hippocampus (Tom, Camera Cuts, Outdoor), the amygdala (Camera Cuts) and the entorhinal cortex (none).", "source": "Results, Stimulus-aligned responsive neurons", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_gerken_2025.ipynb", "notes": "The responsive and non-responsive split comes from the miscalibrated test. With it, 11 of 32 cells agree with the paper at alpha 0.001 and 12 at 0.01; camera cuts give no cluster in any region (p = 1.000), and at 0.001 PHC has 6 significant labels against 7 in H.", "deviations": [ "The responsive-unit test follows the Methods as fixed in the claims file (baseline count over -1000 to 0 ms divided by 10, 19 overlapping 100 ms bins, two-sided Wilcoxon signed-rank, Simes); the Methods do not say more." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-single-neuron-threshold", "statement": "Thresholding the activity of single neurons does not reliably predict whether Summer is on screen; most neurons perform near chance, below the population decoder.", "source": "Results, Decoding from neuronal activity; Figure 3b; Methods, Single-neuron decoding performance", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "Median unit kappa for Summer 0.0076 over 2286 units; 89.8% below 0.05; best unit 0.276 (patient 7, amygdala); no unit reaches 0.31 or the pooled logistic regression (0.301).", "deviations": [ "The threshold and its direction are searched over 50 quantiles of each unit's window counts on the validation set; the Methods say only that the best threshold was chosen on the validation set." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-logreg-characters-location", "statement": "A logistic regression on spike counts decodes characters and location about as well as the LSTM; pooled over patients it reaches kappa 0.28 for Summer and 0.31 for Indoor/Outdoor.", "source": "Results, Choice of architecture and Patient-wise decoding performance; Figure 3c; Figure 4a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "Pooled logistic regression, mean over 5 folds, Summer 0.301 (SEM 0.056), Indoor/Outdoor 0.359 (SEM 0.049), both within tolerance of 0.28 and 0.31; Tom 0.218, McKenzie 0.324 and Persons 0.410 reach the LSTM values less their SEM. Test-label shuffles give p = 0.001 in every fold for Summer, McKenzie, Persons and Indoor/Outdoor; one Tom fold has kappa 0.002 (p = 0.45). Over the C grid the test kappa ranges from 0.266 to 0.311 (Summer) and from 0.349 to 0.393 (Indoor/Outdoor). With Summer labels shifted by 300 s the kappa is 0.015.", "deviations": [ "Class weights balanced in place of oversampling the minority class.", "C chosen on the validation kappa from 0.001, 0.003, 0.01 and 0.03; the Methods do not give the range.", "The fold layout is that of the dataset's code with the 1.6 s window added to the 32 s gap, which gives the paper's sample counts (30822, 7194, 7194 against 30800, 7200, 7200).", "The 0.28 for Summer is the pooled value of Figure 4; the paper does not state the Figure 3c logistic regression values in numbers." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-logreg-cuts-lower", "statement": "For scene and camera cuts the logistic regression performs below the LSTM, by 0.1 and 0.07, that is about kappa 0.10 and 0.11.", "source": "Results, Choice of architecture; Figure 3c; Table S2", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "Scene Cuts 0.0771 (SEM 0.027) and Camera Cuts 0.0961 (SEM 0.020), within tolerance of 0.10 and 0.11 (Camera Cuts by 0.001 above the lower bound of 0.095) and below the LSTM's 0.20 and 0.18. Camera Cuts are above chance in every fold (p = 0.001); one Scene Cuts fold is not (kappa -0.008, p = 0.89).", "deviations": [ "Scene cut labels are extended to 520 ms after the cut, as the Methods state for camera cuts.", "The expected values are derived from the stated drops (0.1, 0.07) and the LSTM values of Table S2." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-temporal-gap", "statement": "Without temporal gaps between training, validation and test samples, decoding of Summer is almost perfect (kappa 0.99), and it falls to 0.31 as the gap grows to 32 s.", "source": "Results, Avoiding spurious decoding performance; Figure 3e; Figure S9", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "Summer with a random split 0.948 (5 draws, 0.942 to 0.953); with gaps of 4, 8, 16 and 32 s 0.555, 0.524, 0.451 and 0.301. The LSTM values held in the dataset's code are 0.987, 0.584, 0.539, 0.429 and 0.309.", "deviations": [ "Logistic regression in place of the LSTM.", "Gaps other than 32 s use the dataset's code table of repeated parts per gap." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-patients-below-pooled", "statement": "Decoding from a single patient's neurons is lower than from the pooled population; no patient matches the pooled performance, for Summer, Scene Cuts or Indoor/Outdoor.", "source": "Results, Patient-wise decoding performance; Figure 4", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "No patient reaches the pooled kappa. Summer best patient 7 at 0.268 against 0.301 (median 0.060); Scene Cuts patient 20 at 0.043 against 0.077 (median 0.010); Indoor/Outdoor patient 2 at 0.256 against 0.359 (median 0.099). By the test-label shuffle 5, 5 and 12 patients are above chance (p = 0.001) in all five folds for the three labels.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-named-patients", "statement": "For Summer, patients 7, 10, 15 and 22 exceed kappa 0.2; for Indoor/Outdoor, patients 2, 13, 20 and 25 exceed 0.2.", "source": "Results, Patient-wise decoding performance; Figure 4b and 4d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "7 of 8 named pairs exceed 0.2; Summer patients 7 (0.268), 10 (0.227), 22 (0.241), and 15 at 0.197, each above chance in all five folds; Indoor/Outdoor patients 2 (0.256), 13 (0.210), 20 (0.217), 25 (0.201). For Scene Cuts three of the paper's patients (20, 19, 2) are among the four best here, and patient 10 is fifth.", "deviations": [ "Assumes the dandiset's subject ids are the paper's patient numbers; neither gives a mapping, and the Figure 4 legend gives no unit counts per patient to compare. The agreement of the named patients supports this." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-region-decoding", "statement": "Decoding from single regions depends on the feature; the amygdala is best and the hippocampus worst for Summer, and the parahippocampal cortex is best and the amygdala worst for Indoor/Outdoor.", "source": "Results, Parahippocampal cortex drives decoding; Amygdala drives decoding; Figure 5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "Summer A 0.291, EC 0.149, PHC 0.096, H 0.068, so A highest and H lowest hold. Indoor/Outdoor PHC 0.357, H 0.302, A 0.122, EC 0.117, so PHC highest holds; A is not lowest, though A and EC differ by less than their SEMs (0.041, 0.052). 3 of 4 orderings hold. Six region folds have test-shuffle p above 0.05 (A Indoor/Outdoor, EC Summer, EC Indoor/Outdoor and PHC Summer once each, H Summer twice).", "deviations": [ "Logistic regression in place of the LSTM.", "Regions as stored in the dandiset, which hold different units from the paper's (PHC 293 against 373)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-faces-presence", "statement": "Face labels decode slightly better than character labels (Summer 0.33, Tom 0.27), and Summer Presence (0.27) is decoded best from the amygdala (0.26).", "source": "Results, Differences in character's visual appearances; Figure 5b and 5c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_gerken_2025.ipynb", "notes": "One of three conditions holds. Summer Presence is decoded best from the amygdala (0.292; PHC 0.132, EC 0.110, H 0.103; pooled 0.234). Face labels decode worse than the character labels, Summer Faces 0.217 against Summer 0.301 and Tom Faces 0.167 against Tom 0.218 (paper LSTM 0.33 against 0.31 and 0.27 against 0.23). Every fold of the three labels is above chance (p = 0.001). The face labels keep as negatives the frames the Methods exclude, which may lower their kappa; the dandiset does not mark those frames, so this cannot be checked.", "deviations": [ "Logistic regression in place of the LSTM; the criterion was written after the first verification round, before these labels were decoded.", "Face labels keep the frames the Methods exclude (a face neither shown nor clearly absent) as negatives." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-responsive-subsets", "statement": "Responsive neurons drive decoding of camera cuts but not of Summer; without them, Summer is decoded about as well as from all neurons while camera cuts drop the most, and responsive neurons alone decode camera cuts about as well as all neurons but Summer less well.", "source": "Results, Decoding with non-responsive versus responsive neurons; Figure 6", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_gerken_2025.ipynb", "notes": "Depends on the responsive sets of the miscalibrated test (1013 units for Summer, 1616 for Camera Cuts at alpha 0.001). With them three of four conditions hold; Summer 0.294 without responsive units, 0.256 with them only (condition b needs below 0.251), 0.301 complete; Camera Cuts 0.115 with responsive units only, 0.013 without, 0.096 complete. Size-matched non-responsive sets give 0.262 to 0.300 for Summer; none can be drawn for Camera Cuts (670 non-responsive units). 548 of those 670 spike in fewer than a third of the pseudo-trials and get p = 1 untested; the 122 that spike give 0.034, a drop of 0.062, against 0.060 for the 730 active non-responsive units of Summer.", "deviations": [ "Logistic regression in place of the LSTM, over all regions together." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7b-top500-overlap", "statement": "Across the five rankings of neurons by logistic regression weights for Summer, the top 500 neurons share 78 neurons, against about 1 expected by chance.", "source": "Results, Top-ranked neurons; Figure 7b; Methods, Intersection of top-performing neurons", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "top_ranked_units.ipynb", "notes": "95 units are common to the top 500 of the five rankings, against 78 (tolerance 70.2 to 85.8) and a chance level of 1.14 by the paper's formula (1.12 simulated), 83 times chance. No unit in a top 500 was tied at zero; ties by unit index give the same 95. Chance values for 100, 350, 750 and 1000 (0.00, 0.19, 8.69, 36.6) match the paper's (0, 0, 9, 37), so the chance computation agrees; observed overlaps are 20, 65, 156 and 252.", "deviations": [ "The four sub-splits of a test fold take each of the other four folds once as validation; the Methods say only that they alternate training and validation data.", "The Methods average the absolute coefficients 'across the five splits' within a set of four models; the mean over the four models is used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7a-500-neurons", "statement": "Decoding Summer from the 500 top-ranked neurons gives the peak performance (kappa 0.38), above that of the full population.", "source": "Results, Training on pre-selections of top-ranked neurons; Figure 7a", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "top_ranked_units.ipynb", "notes": "With the logistic regression and nested averaging over the 20 sub-splits, the top 500 units give kappa 0.375 against 0.357 for all 2286 units, a difference of 0.018, less than the SEMs (0.026, 0.029). The peak is at 229 units (0.394), with 150 units at 0.389 and the top 23 at 0.341. Every fit is above chance (p = 0.001). The paper's LSTM peaks at 0.38 with 500 units.", "deviations": [ "Logistic regression in place of the LSTM; the criterion was written after the first verification round, before any fit on top-ranked units.", "Sizes of 23, 114, 150, 229, 500, 750, 1000, 1500 and 2286 units; the paper does not list its sizes besides 500 and 150." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-lstm-decoding", "statement": "An LSTM decodes every label above chance from the pooled population, with kappa 0.36 for Persons, 0.31 for Indoor/Outdoor, 0.31 for Summer, 0.32 for McKenzie, 0.23 for Tom, 0.20 for Scene Cuts and 0.18 for Camera Cuts.", "source": "Results, Decoding from neuronal activity; Figure 3c; Table S2", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The LSTM's code is not in the paper's materials, the dataset's GitHub repository (commit 59fc242) or its Zenodo archive, which hold a two-layer linear baseline; the Methods choose layers, hidden sizes, batch size, learning rate, weight decay and dropout per label without stating them. Training 700 epochs per label and fold on a CPU would also exceed the time limit; this was not tried. The logistic regression results are under fig3c-logreg-characters-location and fig3c-logreg-cuts-lower.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-temporal-shuffle", "statement": "Shuffling the order of time bins in the test data lowers the LSTM's performance, most for visual transitions.", "source": "Results, Choice of architecture; Figure 3d", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs the trained LSTM; see fig3c-lstm-decoding. The logistic regression on window sums does not see the order of the 20 bins, so it cannot stand in.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "other", "statement": "The units' `brain_region` gives A 559, hippocampus 846 (AH 418, MH 16, PH 412), EC 493, PHC 293 and PIC 68 units, and 27 in FF, LG and PRC, where the paper reports A 580, H 794, EC 440, PHC 373 and PIC 99 for the same 2286 units. Neither the dandiset nor the paper maps one assignment to the other, so the paper's region analyses cannot be repeated on the paper's regions." }, { "kind": "format_error", "statement": "Spike times in the units table are in milliseconds (its description says so), where NWB requires seconds; the watchlogs' recording times are also in milliseconds." }, { "kind": "metadata_error", "statement": "The start and stop columns of `annotations_patient_aligned` are described as seconds but hold milliseconds of the recording clock, as the table's own description says." }, { "kind": "metadata_insufficient", "statement": "The face labels (summer-faces, tom-faces and others) hold only 0 and 1. The Methods define face labels with frames excluded when a face is neither shown nor clearly absent; those frames cannot be identified." }, { "kind": "other", "statement": "Published version 0.260519.1133 holds 57 files, the 29 of the later version and 28 older copies (`ses-1_behavior+ecephys`) with the same units and spike times, one per patient except patient 3. Version 0.260702.0824 holds each recording once." }, { "kind": "code_mismatch", "statement": "The dataset's code identifies responsive units with the ZETA test (zetapy; alpha 0.01 in its notebook), where the Methods describe a bin-wise Wilcoxon signed-rank test with Simes correction. With ZETA, 79 units respond to camera cuts at alpha 0.001 (Table S1 1025), 11 to Summer (46) and 13 to Tom (216), and 11.95% of PHC units to camera cuts (51.74%)." }, { "kind": "methods_unavailable", "statement": "The responsive-unit test as the Methods describe it (spike counts in 19 bins of 100 ms against the baseline count per 100 ms, signed-rank across pseudo-trials, Simes) counts 68% of units responsive at random event times on this data with 884 events, and 10 to 55% with as many as each label's onsets, so the procedure behind Figure 2 and Table S1 cannot be recovered from the text. The ZETA test of the dataset's code does not give the paper's counts either. The paper's LSTM code and its per-label hyperparameters are not published." }, { "kind": "paper_inconsistency", "statement": "The threshold for responsive units is alpha 0.01 in the Methods and 0.001 in the Results, the Figure 2 legend and Table S1; the cluster test section splits units at p 0.01." }, { "kind": "paper_inconsistency", "statement": "The Results give the 29 patients' ages as 22 to 63; the Methods give 19 to 62 for all 46 patients recorded. The dandiset's 29 patients are 19 to 62." }, { "kind": "other", "statement": "The dandiset has 958 camera cuts in the 83-minute film, one every 5.25 s; the supplement says one every 3 s." }, { "kind": "code_mismatch", "statement": "The training code of the dataset's repository (ML_framework/nwb_loading/nwb_loading.py, get_unit_ids_for_patient_nwb) compares `brain_region` with the region group name in place of its subregions; no unit is labelled `H`, so asking for the hippocampus selects no unit." }, { "kind": "identifier_missing", "statement": "Neither the dandiset nor the paper states that subject ids are the paper's patient numbers. Taking them as such, the patients the paper names in Figure 4 are among the best here (7 of 8 above kappa 0.2)." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text. The verifier listed the version's assets, and tested wilcoxon_simes, split, kappa, ranking, threshold_unit and the L1 setting of fit_logreg on synthetic inputs.", "agreed": 18, "of": 20, "disagreements": [ { "claim": "fig5-faces-presence", "outcome": "blocked", "reason": "LSTM claim. The summer-presence, summer-faces and tom-faces labels are in the files (0/1 only), so a logistic regression stand-in for the orderings could have been tested, as was done for fig5-region-decoding. Its list of problems marks this block as affecting a conclusion." }, { "claim": "fig7a-500-neurons", "outcome": "blocked", "reason": "The Results compare the full-population value with the LSTM's 0.31, which suggests an LSTM, but the Methods describe the 20-split logistic regression. The 20 sub-split fits and rankings already exist, so a logistic regression stand-in on the top-k units was cheap to run. Its list of problems marks this block as affecting a conclusion, and it asked for kappa on the top-k units (k = 100 to 2286) with nested averaging over the 20 sub-splits." } ] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebooks of the revision (the main notebook, top_ranked_units.ipynb, responsive_zeta_cuts.ipynb and responsive_zeta_labels.ipynb) with their conclusions and summary, the helper module, the claims file, the README and this record.", "agreed": 20, "of": 20, "disagreements": [] } ] }, { "id": "001636-pasquereau-2013-01", "dandiset": "001636", "dandiset_version": "0.260518.1819", "paper": "10.3389/fnsys.2013.00098", "paper_title": "Primary motor cortex of the parkinsonian monkey: altered neuronal responses to muscle stretch", "date": "2026-10-15", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "001636-pasquereau-2013", "entry_title": "M1 responses to muscle stretch in the parkinsonian monkey (Pasquereau and Turner 2013)", "description": "Tests the findings of Pasquereau and Turner (2013) on dandiset 001636, which holds single-unit recordings from M1 of two monkeys before and after MPTP, with torque perturbations, joint angle and EMG. Only monkey V can be tested, as the monkey L files mark no perturbation. The notebook checks the cells, resting rates and antidromic latencies, detects torque responses, and compares the torque-evoked movements and triceps EMG before and after MPTP.", "notebooks": [ { "path": "reproduce_pasquereau_2013.ipynb", "title": "Reproducing Pasquereau and Turner (2013) from dandiset 001636", "executed": "notebooks/001636-pasquereau-2013/reproduce_pasquereau_2013.html" } ], "outcomes": [ { "claim": "cell-counts", "statement": "In monkey V, 112 neurons were studied before MPTP and 159 after, of which 49 and 54 were PTNs and 31 and 48 CSNs; three neurons in all were activated from both the peduncle and the putamen.", "source": "Supplementary table (monkey V); Results, Database; Table 1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Monkey V units with at least 5 perturbations of each direction number 112 before and 159 after MPTP, with 49 and 54 PTNs and 31 and 48 CSNs, exactly the supplementary table's counts. The files hold 3 units activated from both the peduncle and the putamen, all in monkey V and all among the cells studied. Dropping the two unit copies found in repeated files gives 53 post-MPTP PTNs.", "deviations": [ "The paper's location and isolation criteria cannot be applied; the units in the dandiset are taken as the selected units, which the matching counts support." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "monkey-l-perturbations", "statement": "In monkey L, 57 of 115 neurons before MPTP and 35 of 73 after responded to torque perturbations of the wrist, and the monkey L responses enter all pooled results.", "source": "Supplementary table (monkey L); Table 1", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No monkey L (Leu) file marks a torque perturbation; torque_perturbation_type is \"none\" and the onset NaN in every Leu trial. The Leu torque command is NaN in all 98 pre-MPTP files with analog data, and 15 of 51 post-MPTP Leu files have no analog data. The joint moves by more than 2 deg in the hold window in 15% (pre) and 1% (post) of Leu trials, against 66 to 86% of monkey V perturbed trials. The 35 post-MPTP Leu files with a torque command show 91 to 413 command excursions per file, starting a median 0.31 to 0.84 s after the lateral target appears, during the active movement; one of their 2048 trials has an excursion starting in the hold window. In monkey V such an excursion starts in the hold window in 1811 and 3563 trials, against 1862 and 3649 labelled perturbations. The perturbations may exist in the lab's source files; they are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "baseline-rate", "statement": "Before torque onset, the firing rate of M1 neurons was lower after MPTP, because PTN rates fell (Mann-Whitney p < 0.001) while CSN rates did not change (p = 0.5). In monkey V the rates were 12.6 and 8.9 spikes/s for all cells, 20.3 and 14.8 for PTNs, and 3.5 and 3.4 for CSNs, before and after MPTP.", "source": "Supplementary table; Table 1; Results, Database", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "All six monkey V means are within tolerance. PTN rates are lower after MPTP (Mann-Whitney p = 0.034), CSN rates do not differ (p = 0.73), and the M1 rate is lower (p = 0.0033, below the paper's 0.05/2). The statement's p < 0.001 for PTNs, from both monkeys, is not reached in monkey V alone.", "deviations": [ "Monkey V only.", "The baseline is the mean SDF over the 500 ms before onset over all perturbation trials, a reading of the Methods." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ptn-faster-than-csn", "statement": "Before MPTP, PTNs fired much faster than CSNs at rest (Mann-Whitney p < 0.001).", "source": "Results, Database; Table 1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Pre-MPTP monkey V PTNs 18.03 spikes/s (n = 49), CSNs 3.42 (n = 31), Mann-Whitney p = 1.3e-11. The paper's pooled means differ between its text (16.3 and 3.6) and Table 1 (18.3 and 3.2).", "deviations": [ "Monkey V only." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "antidromic-latency", "statement": "PTN antidromic latencies did not change after MPTP (1.9 ms, p = 0.9), while CSN latencies were longer (5.1 against 6.1 ms, p < 0.05/3).", "source": "Results, Database; Table 1", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "The four means are within tolerance and PTN latencies do not differ (p = 0.54). CSN latencies are longer after MPTP with p = 0.018, just above the paper's 0.05/3 = 0.0167, so one test fails. With every monkey L PTN and CSN unit added (their selection by perturbations cannot be made), p = 0.0071 for CSNs and 0.91 for PTNs, and the post-MPTP CSN mean (7.01 ms) is outside tolerance. 18 PTNs and CSNs studied have no antidromic latency.", "deviations": [ "Monkey V cells studied, against expected values that pool both monkeys." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "false-positive-rate", "statement": "The detection threshold, p < 0.01 divided by 5 independent comparisons, holds the chance of a false response over the 200 ms epoch near 0.01.", "source": "Methods, Data analysis", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "The analysis ran. At a pseudo onset 600 ms before the torque, a threshold crossing in the 200 ms epoch occurs in 0.22 of the 542 monkey V cell-directions with the main detection and 0.46 with the t-test variant; unperturbed trials taken at the usual torque time give 0.19 and 0.45. A response with onset in 20 to 60 ms occurs in 0.044 (pseudo onset) and 0.047 (unperturbed trials), against 0.37 at the true onset. The paper's threshold implies 0.01; the rates here are about 20 times higher, so the procedure differs from the paper's in a way the Methods do not settle (how the SDF values are compared with the baseline, and any minimum duration), and this claim and those that rest on the selection are blocked. Stationary Poisson spike trains at each cell-direction's baseline rate give 0.15 (main) and 0.49 (t-test), so most of the excess comes from the detection procedure, though about a third of the observed 0.22 is not explained by the Poisson trains, and the rate does not fall with baseline rate (0.17 to 0.27 by quartile) or number of trials (0.21 to 0.24). The pseudo-onset rate of responses is 0.12 of the true-onset rate. 14 cell-directions (10 CSN) have no baseline spike and cannot respond. A threshold calibrated to a pseudo-onset rate of 0.01 (t = 6.67 against 3.11) finds 30.4% and 32.7% of M1 cells torque-related. Whether the paper's procedure differs or its stated rate does not hold cannot be told from this analysis.", "deviations": [ "The detection compares the trial-averaged SDF with mean +/- t * SD of its baseline values, a reading of the Methods; a t-test across trials is shown as a variant.", "A response's onset is its first crossing within 20 to 60 ms; the Methods define the onset as the first crossing, so a variant takes the first crossing anywhere in 0 to 200 ms (6 of 202 responses have an earlier crossing)." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "torque-related-fractions", "statement": "In monkey V, 84 of 112 M1 neurons (75%) were torque-related before MPTP and 108 of 159 (68%) after; for PTNs 27 of 49 (55%) and 37 of 54 (68%); for CSNs 14 of 31 (45%) and 10 of 48 (21%).", "source": "Supplementary table; Table 1; Figure 3A", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is (false-positive-rate). The analysis finds 61 of 112 and 75 of 159 monkey V cells torque-related (54.5% and 47.2%, paper 75% and 68%), PTNs 71.4% and 66.7%, CSNs 16.1% and 16.7%; only the post-MPTP PTN value is within tolerance. The t-test variant gives 39.3% and 59.7% for M1, the calibrated threshold 30.4% and 32.7%, and taking the first crossing anywhere in 0 to 200 ms as the onset 52.7% and 46.5%.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "prevalence-unchanged", "statement": "MPTP did not change the fraction of torque-related neurons, in M1, in PTNs or in CSNs (chi-square, p > 0.05/3).", "source": "Results, Torque-evoked neuronal responses, pre- vs. post-MPTP; Figure 3A", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. With the main detection the paper's test finds no change in M1 (-7.3 points, p = 0.29), PTNs (-4.8 points, p = 0.76) or CSNs (+0.5 points, p = 1.0). The t-test variant finds increases in M1 (+20.5 points, p = 0.0014) and PTNs (+25.3 points, p = 0.016), both below 0.05/3.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ptn-more-responsive", "statement": "PTNs responded to torque more often than CSNs (68% against 31% over both monkeys, chi-square 32.3, p < 0.001).", "source": "Results, Torque-evoked neuronal responses, prevalence; Figure 3A", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. PTNs 71 of 103 (68.9%) against CSNs 13 of 79 (16.5%), chi-square 47.5, p = 5.6e-12; both fractions are outside tolerance (PTNs above 62.1 +/- 6.2, CSNs below 30.4 +/- 3.0). The t-test variant gives 60.2% and 32.9% (p = 0.00046).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "one-direction-half", "statement": "About half of the torque-related cells (124 of 284, 44%) responded to only one direction of rotation.", "source": "Results, Torque-evoked neuronal responses, prevalence", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. 70 of 136 torque-related cells (51.5%) respond to one direction only (59.0% pre, 45.3% post); the t-test variant gives 63.3%.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "excitatory-majority", "statement": "Most torque responses were increases in firing (86% of M1 responses before and 88% after MPTP; 70% and 75% for PTNs), and MPTP did not change the PTN balance (chi-square 0.1, p = 0.7).", "source": "Table 1; Results, Torque-evoked neuronal responses, pre- vs. post-MPTP", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Increases are 82.6% and 76.7% of M1 responses and 68.1% and 59.3% of PTN responses; the PTN balance does not change (chi-square 0.53, p = 0.47). The paper's Table 1 marks its CSN change p < 0.01, but its own counts (23 of 24 against 19 of 22) give p = 0.54 with the Yates-corrected chi-square test that reproduces its other values.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "magnitude-unchanged", "statement": "The magnitude of torque responses did not differ before and after MPTP, for M1 cells or for PTNs, by any of three measures (mean change, maximum change, area; Kolmogorov-Smirnov and Mann-Whitney, all p > 0.15).", "source": "Results, Torque-evoked neuronal responses, pre- vs. post-MPTP; Figure 4A", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. With the main detection, responses are smaller after MPTP; 11 of the 12 tests (directions pooled) have p < 0.05, for example M1 maximum change 43.7 against 32.4 spikes/s (Kolmogorov-Smirnov p = 0.0017) and PTN mean change 23.4 against 15.4 (Mann-Whitney p = 0.0001).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "venus-response-magnitudes", "statement": "In monkey V, the mean response magnitudes were 42.4 and 37.9 spikes/s for M1 flexion responses, 50.9 and 42.6 for M1 extension responses, 33.4 and 26.1 for PTN flexion and 38.8 and 29.3 for PTN extension responses, before and after MPTP.", "source": "Supplementary table", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Under reading (a), maximum change, the four pre-MPTP means are within tolerance and none of the post-MPTP ones; readings (b) and (c) match 1 and 0 of 8.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "latency-shorter", "statement": "Response latencies were shorter after MPTP for M1 cells and for PTNs, for flexion and extension (Kolmogorov-Smirnov, all p < 0.05). In monkey V the means were 39.2 and 34.6 ms (M1 flexion), 40.4 and 33.4 ms (M1 extension), 43.9 and 35.5 ms (PTN flexion) and 44.4 and 36.7 ms (PTN extension), before and after MPTP.", "source": "Results, Torque-evoked neuronal responses, pre- vs. post-MPTP; Figure 4B; supplementary table", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. With the main detection all four comparisons are shorter after MPTP (Kolmogorov-Smirnov p = 0.0086, 0.0048, 0.022, 0.0023) and all eight means are within tolerance; pooled, M1 responses 41.8 and 35.9 ms and PTN responses 45.0 and 37.8 ms (earliest per cell 40.9 and 34.7, 44.2 and 35.4). The t-test variant finds no significant shortening (p 0.27 to 0.87).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "latency-not-training", "statement": "The latency shortening was not a history effect; latencies did not correlate with the days of training (monkey V Spearman |rho| = 0.02, p = 0.85).", "source": "Results, Torque-evoked neuronal responses, pre- vs. post-MPTP", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Over both states latency correlates with the recording day (Spearman rho = -0.26, p = 0.0022, n = 136), as post-MPTP sessions come later and have shorter latencies; within each state it does not (rho = 0.11, p = 0.42; rho = -0.15, p = 0.21).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fwhm-shorter-ptn", "statement": "Torque-evoked increases in PTN firing were briefer after MPTP; the FWHM fell from 73 to 50 ms over both monkeys (Mann-Whitney, p < 0.05 for each direction). In monkey V the PTN FWHM was 97 and 52 ms for flexion and 57 and 41 ms for extension, before and after MPTP.", "source": "Results, Torque-evoked neuronal responses, pre- vs. post-MPTP; supplementary table", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. PTN increases are briefer after MPTP for flexion (p = 0.039) but not for extension (p = 0.39); over all PTN responses the means are 97.4 and 52.3 ms for flexion and 56.9 and 60.7 ms for extension.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dsi-reduced", "statement": "Directional selectivity fell after MPTP; reciprocal and unidirectional responses became less common and bidirectional and non-directional ones more common (by about 10% of torque-related M1 cells; chi-square 22.2, p < 0.001).", "source": "Results, Response directionality; Figure 6", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Reciprocal and unidirectional cells fall from 59.0% to 52.0% of torque-related cells (-7.0 points), chi-square 6.26 (3 dof), p = 0.10. For PTNs they fall from 65.7% to 50.0% (p = 0.015). With categories set from the DSI value as the paper words them, 62.3% and 50.7% (p = 0.42). There is no reciprocal cell before MPTP; the smallest expected count is 2.2.", "deviations": [ "Categories are set from which directions respond and their signs, as fixed in the claims file; the paper words them by DSI value. The DSI value reading is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "venus-dsi", "statement": "In monkey V the mean DSI of torque-related cells was 0.72 and 0.66 for M1, 0.73 and 0.75 for PTNs and 0.81 and 0.83 for CSNs, before and after MPTP.", "source": "Supplementary table", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Three of six means are within tolerance (PTN pre and both CSN values).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dsi-not-baseline", "statement": "The loss of selectivity was not due to resting rates, as pre-torque rates did not differ between directional categories (one-way ANOVA, F = 0.77, p = 0.46).", "source": "Results, Response directionality", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Baseline rates do not differ between the four categories (F = 0.58, p = 0.63) or three groups (F = 0.69, p = 0.50).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "kinematics-slower", "statement": "After MPTP, torque-induced displacements were slower and smaller; mean peak velocity fell by 16.2% and amplitude by 6.6% (ANOVA, F > 515 and F > 49).", "source": "Results, Behavioral effects of MPTP; Figure 1", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Over 294 monkey V sessions (repeated files left out), torque-induced movements are faster and larger after MPTP; session-mean peak velocity +28.8% and amplitude +15.2% (flexion +30.3% and +12.0%), MPTP F = 103 and 26, p < 0.0001. The torque command's pulse is about four times larger in most post-MPTP sessions; in the sessions with the same command size (43 pre, 12 post) the increases are +101.9% and +113.4%. The mean of the session-mean peak velocities is 58.7 deg/s, and only one response comes from a session in the paper's 130 to 200 deg/s window of matched sessions; mean displacements (3.09 deg) are smaller than its 10 deg. The angle's scale agrees with the files' own kinematic columns (active movements measured here within 2% of derived_peak_velocity and derived_movement_amplitude), so the small movements are in the data. The torque command differs between the states, so the change cannot be attributed to MPTP.", "deviations": [ "Monkey V only; the paper's ANOVA has animal as a third factor.", "The peak velocity and amplitude windows (0 to 200 and 0 to 300 ms) and the FIR length are choices; the Methods give the filter and velocity threshold only.", "Perturbations with the joint moving before onset (490 of 5413) are kept." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "kinematic-latency-unchanged", "statement": "The latency of torque-induced displacements did not change after MPTP (F < 0.2, p > 0.05).", "source": "Results, Behavioral effects of MPTP; Figure 1", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Movement onset is earlier after MPTP (session means 9.8 and 3.2 ms for flexion, 11.0 and 6.0 ms for extension; MPTP F = 1032, p < 0.0001), with an MPTP by direction interaction (F = 19.1; the paper reports F > 94). In sessions with the same command size it does not differ (7.81 and 7.73 ms, p = 0.79). The zero-phase filter can move an onset earlier, and 219 of 5413 perturbations have a latency of 0 ms. With a causal 10 ms average of the unfiltered velocity the session means are 12.6 to 18.6 ms and still shorter after MPTP (F = 781); without the trials already moving before onset F = 1037 (filtered) and 743 (causal). At the middle command size the causal variant gives p = 0.25, and 0.026 without the trials moving before onset. The difference goes with the torque command, so it cannot be attributed to MPTP.", "deviations": [ "Monkey V only.", "Zero-phase (forward and backward) filtering; the Methods do not say how the filter was applied." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "emg-m2-larger", "statement": "The long-latency (m2, 41 to 80 ms) EMG response of the stretched triceps was larger after MPTP (Kolmogorov-Smirnov, p < 0.05).", "source": "Results, Behavioral effects of MPTP; Figure 2", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "For flexion torques the m2 response is larger after MPTP in both triceps longus channels and the triceps lateralis (medians 3.0 against 164.2, 3.1 against 297.5 and 5.2 against 76.2 A/D units; Kolmogorov-Smirnov p = 1.1e-58, 1.9e-50, 4.7e-15). The increase follows the torque command; median m2 is 0.61 at the smallest command size (pre only), 40.8 (pre) and 1.81 (post) at the middle, and 17.09 (pre, n = 5) and 194.6 (post) at the largest, so within a state it does not rise simply with command size, and in the middle-size sessions m2 is not larger after MPTP (triceps longus 1 median 46.7 against 1.3, p = 0.013, with 40 and 6 sessions). The outcome is the criterion's comparison; as the torque command is about four times larger in most post-MPTP sessions, the increase cannot be attributed to MPTP.", "deviations": [ "EMG in A/D units; the paper reports microvolts." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "emg-duration-longer", "statement": "The total duration of EMG responses to torque increased after MPTP, from 57 +/- 6 to 79 +/- 3 ms (Kolmogorov-Smirnov, p < 0.001).", "source": "Results, Behavioral effects of MPTP; Figure 2", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Responses last longer after MPTP (24.5 against 50.4 ms, Kolmogorov-Smirnov p = 1.8e-39, 283 and 281 channel-sessions), but both means are outside tolerance (57 +/- 6 and 79 +/- 3); thresholds of 1.5 and 3 SD give 16.4 against 48.5 and 17.3 against 49.5 ms. At the middle command size they do not differ (28.4 and 27.9 ms, p = 0.96). Before MPTP 63.6% of the durations are 10 ms or less (median 9 ms, against 59 ms after).", "deviations": [ "The response threshold (2 SD of the baseline) and the pooling of three triceps channels are choices; the Methods cite an earlier paper for the EMG analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "emg-onset-unchanged", "statement": "The latency of the earliest EMG responses did not change after MPTP (p > 0.05).", "source": "Results, Behavioral effects of MPTP", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "EMG responses start earlier after MPTP (40.8 against 24.0 ms, Kolmogorov-Smirnov p = 5.5e-21), in the same direction at 1.5 and 3 SD. At the middle command size the onsets do not differ (28.8 and 45.6 ms, p = 0.18), the post-MPTP onset being the later one there.", "deviations": [ "The paper does not name its test here; the Kolmogorov-Smirnov test it uses for the other EMG measures is used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "emg-m1-weak", "statement": "The short-latency m1 component (15 to 40 ms) was poorly formed and generally much smaller than the m2 component.", "source": "Results, Behavioral effects of MPTP; Figure 2", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "After MPTP, m2 exceeds m1 in 96.5% of 282 channel-sessions, median m1 / m2 0.22 (0.23 over channel-sessions with m2 > 0). Before MPTP the median ratio is 0.10 (0.09 with m2 > 0) but m2 exceeds m1 in 73.5% of 310, below the criterion's 75%.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "velocity-matched-magnitude", "statement": "In sessions with equivalent torque-induced velocities (130 to 200 deg/s), MPTP did not change the magnitude of responses (Mann-Whitney, p = 0.19 for flexion and 0.46 for extension, with 24 and 33 flexion and 22 and 31 extension responses).", "source": "Results, Torque-evoked neuronal responses, pre- vs. post-MPTP; Supplementary Figure 1", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Also, only one response comes from a session whose mean peak velocity is between 130 and 200 deg/s (session means reach 145.3 deg/s), so the matched groups cannot be formed on this velocity scale.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "session-correlations", "statement": "Across sessions, the mean PTN response latency did not correlate with the peak velocity of the torque-induced movement (|rho| < 0.18) or with the m2 EMG response (|rho| < 0.26; Spearman, p > 0.05 with threshold 0.05/4).", "source": "Results, Analysis of neural-behavioral correlations", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_pasquereau_2013.ipynb", "notes": "Blocked as the selection is. Over 67 sessions mean PTN latency against mean peak velocity gives rho = -0.22, p = 0.080; against triceps longus 1 m2 (64 sessions) rho = -0.32, p = 0.011, below the paper's 0.0125. Within each state neither correlates (p 0.36 to 0.997).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "trial-correlations", "statement": "Trial by trial, PTN response latencies did not correlate with the peak velocity or the m2 EMG response (Spearman |rho| < 0.34, p > 0.05).", "source": "Results, Analysis of neural-behavioral correlations", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "The Methods define response onset on the trial-averaged SDF and give no single-trial latency, which the test needs. No analysis code is published.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The monkey L (Leu) files mark no torque perturbation; torque_perturbation_type is \"none\" in every Leu trial, the Leu torque command is NaN in every pre-MPTP file, and 15 of 51 post-MPTP Leu files have no analog data. The monkey L half of the paper (115 and 73 cells, and its EMG and kinematics) cannot be tested." }, { "kind": "format_error", "statement": "The analog streams (ElbowAngle, ElbowTorque, ElbowVelocity, EMG) are not on the clock of the trials table and spikes. The conversion lays each trial's analog samples end to end by sample count, while trials and spikes use the behavioural trial end, about 5 ms later per trial, so the stored analog clock falls behind by up to 365 ms within a session. Moving each analog segment to its trial's start puts the torque command step 4 to 7 ms after every labelled onset; on the stored clock it falls up to 108 ms before it." }, { "kind": "other", "statement": "The torque command's 50 ms pulse has three sizes (about 46, 91 and 183 units above rest). Most pre-MPTP monkey V sessions have the smallest (108 of 157) and most post-MPTP sessions the largest (129 of 141), and post-MPTP pulses are followed by an opposite swing. The paper describes one 0.1 Nm, 50 ms impulse; the command's scale is not given, so the change may be of the torque or of the command's recording. Movement and EMG results differ between command sizes." }, { "kind": "metadata_error", "statement": "The ElbowAngle reference_frame says positive is extension; active flexion movements and flexion torques raise the angle in both monkeys, so positive is flexion. The series are named Elbow for monkey L, whose task used the wrist." }, { "kind": "metadata_error", "statement": "Four monkey V files (v4527b, v4810b, v5604b, v5812) repeat a block of another file's trials. In two of them the same unit, with identical spikes in every repeated trial, is stored twice with different projection types (v4527 unit 2 not_tested and v4527b unit 2 a PTN; v5811 unit 2 a PTN and v5812 unit 2 no_response)." }, { "kind": "metadata_error", "statement": "unit_also_in_session_id uses the prefixes V and L where session ids use Venus and Leu, and 35 of its 43 references name files that are not in the dandiset. Where the file is present, it holds a different unit (another unit number, spike count and often projection type), not the same neuron." }, { "kind": "metadata_error", "statement": "The dandiset description says MPTP was given systemically, that both monkeys made elbow movements and that Leu was recorded in 1993. The files and the paper say unilateral intracarotid MPTP, monkey L used the wrist, and Leu files date from August 1992." }, { "kind": "other", "statement": "The monkey L analog streams are sampled at 100 Hz; the paper says 200 Hz. The EMG is described as sample-hold integrated over 10 ms in the files and low-pass filtered at 100 Hz in the paper, and is stored in uncalibrated A/D units." }, { "kind": "other", "statement": "The torque onset comes 1.70 to 1.73 s after center_target_appearance_time in 90% of monkey V perturbations, where the Methods put it 1 to 2 s after center capture at random. Either the column marks another event or the torque was predictable from the target's appearance." }, { "kind": "methods_unavailable", "statement": "No analysis code is published. The response detection as described gives a false-positive rate near 0.2 over the 200 ms epoch, against the 0.01 its threshold implies, and stationary Poisson spike trains give 0.15, most of it, so the paper's exact procedure cannot be recovered, and single-trial latencies are not defined." }, { "kind": "paper_inconsistency", "statement": "The pre-MPTP PTN and CSN resting rates are 16.3 and 3.6 spikes/s in the text and 18.3 and 3.2 in Table 1. Table 1 marks the CSN change in the fraction of excitatory responses p < 0.01, but its own counts (23 of 24 against 19 of 22) give p = 0.54 with the Yates-corrected chi-square test that reproduces its other chi-square values." } ], "verifications": [ { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text. The verifier streamed 7 monkey L files and ran synthetic checks of stretch.detect (stationary Poisson spike trains) and stretch.kinematics.", "agreed": 27, "of": 28, "disagreements": [ { "claim": "false-positive-rate", "outcome": "not_reproduced", "reason": "Cell 27: the any-crossing rate over 0 to 200 ms is 0.22 (main) and 0.46 (t-test variant). Unperturbed trials give 0.19, and stationary Poisson spike trains through detect give 0.13 to 0.20 (the verifier's test), so the excess comes from the threshold procedure, whose threshold is t times the SD over time of the trial-averaged SDF and is not a test of trial-to-trial variance. A single run cannot tell whether the paper's claim is wrong or its procedure differs. The Methods' literal reading, a 2-tailed t-test against the baseline, is closer to the t-test variant, which also fails (0.46). The response rate at the pseudo onset is 0.044 against 0.37 at the true onset, so about 12% of detected responses are expected to be false. It asked for example mean SDFs with their thresholds drawn, and the pseudo-onset false-positive rate split by baseline rate and by number of trials." } ] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook with conclusions and summary, the attempt record, the README, the helper module, the claims file, the round-1 report and the paper's full text from Europe PMC. It checked the paper_inconsistency finding against the paper and found it supported. Other changes in reply are the README run time (the verifier saw 1.5 min printed by cell 104; this run printed 2.4 min) and the round-1 false-positive-rate reason, which now carries two points from its round-1 problem 1 that it found left out. It did not inspect the plotted figures.", "agreed": 28, "of": 28, "disagreements": [] } ] }, { "id": "001692-bouabid-2026-01", "dandiset": "001692", "dandiset_version": "0.260303.1724", "paper": "10.64898/2026.01.20.700614", "paper_title": "An anatomical hotspot for striatal dopamine-acetylcholine interactions during reward and movement", "date": "2026-10-19", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001692-bouabid-2026", "entry_title": "Striatal dopamine-acetylcholine hotspot (Bouabid, Vu et al. 2026)", "description": "Tests the findings of Bouabid, Vu et al. (2026) on dandiset 001692, which holds multi-fiber photometry of dopamine and acetylcholine across the striatum of 17 mice. It reproduces the spontaneous cross-correlations and their anterior dorsolateral hotspot, paired transients, reward, Pavlovian cue, locomotion and optogenetic stimulation analyses, and the control mice, and tests the ex vivo slice statistics of Figure 8 on the paper's source data on Zenodo.", "notebooks": [ { "path": "reproduce_bouabid_2026.ipynb", "title": "Reproducing Bouabid, Vu et al. (2026) from dandiset 001692", "executed": "notebooks/001692-bouabid-2026/reproduce_bouabid_2026.html" } ], "outcomes": [ { "claim": "fig1e-dominant-polarity", "statement": "Across 174 sites in 5 mice, the dominant DA-ACh cross-correlation (the largest magnitude Pearson r within 1 s lags) during spontaneous behavior is negative at 132 sites, 127 of them with DA leading, and positive at 42 sites, 31 of them with ACh leading.", "source": "Results, first section; Figure 1e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Of 174 sites, 133 have a dominant negative correlation (128 with DA leading) and 41 a dominant positive one (32 with ACh leading); 6 have their extreme at lag 0. All four counts are within 10% of the paper's. Every mouse has more negative than positive sites. Correlation over concatenated sessions gives 133, 128, 41 and 30.", "deviations": [ "One UG27 reward session (240313r) lacks the artifact-removed green series and is skipped, as the code skips empty series; it is not a spontaneous session, so this claim is unaffected." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-adls-hotspot", "statement": "The dominant correlations form a significant hotspot, identified by local Moran's I, in the anterior dorsolateral striatum (aDLS), where the strongest correlations are negative.", "source": "Results, first section; Figure 1f", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The hotspot procedure finds a significant hotspot of 1.01 mm3 with mean smoothed r -0.368 (hull mean -0.185). Its centroid (AP 0.63, ML 2.02, DV -3.14 mm) is anterior and dorsal of the median site (0.10, 2.04, -3.21 mm) but 0.02 mm medial of it, which fails the lateral part of the criterion fixed beforehand. With the 99th percentile of the null the hotspot has 518 voxels and its centroid is at ML 2.09 mm, lateral of the median. 28 sites from all five mice are inside. The location test against the median site is a coarse stand-in for the paper's maps, in which the hotspot lies in aDLS; the shortfall is small. Finding a hotspot is not evidence on its own, as the procedure finds one in 67 of 100 shuffles of the values across sites; none of these is as large (at most 482 voxels) or has a mean as low.", "deviations": [ "The hotspot procedure is simplified from the paper's code (linear in place of natural-neighbor interpolation, 100 um voxels in place of 50 um, the convex hull of the sites in place of the Allen striatum mask, 200 in place of 10000 shuffles).", "The paper does not define the aDLS location in numbers; the criterion compares the centroid with the median site coordinates." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1h-in-vs-out", "statement": "Sites inside the aDLS hotspot have more negative dominant correlations than sites outside (Wilcoxon rank-sum p = 1.67e-16).", "source": "Figure 1h", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The 28 sites inside have median dominant r -0.41 against -0.14 for the 146 outside, rank-sum p = 1.9e-13 (the paper 1.67e-16). The test is partly circular, as in the paper.", "deviations": [ "The hotspot is the simplified one of fig1f-adls-hotspot." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-positive-posterior", "statement": "Dominant positive correlations lie in the posterior striatum.", "source": "Results, first section; Figure 1f", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Sites with a positive dominant r have median AP -0.40 mm (41 sites) against 0.24 mm for negative sites (133), one-sided rank-sum p = 4.3e-07. The direction holds in all five mice and is significant in UG27, UG29 and UG31.", "deviations": [ "The paper shows this on maps; the test of AP coordinates was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed2-hotspot-per-mouse", "statement": "The hotspot is consistent across mice; in each mouse, sites inside the group hotspot have more negative dominant correlations than sites outside.", "source": "Extended Data Figure 2d; Results, first section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "All five mice have lower median r inside the group hotspot; p < 0.05 in UG27, UG28, UG30 and UG31, and p = 0.084 (exact p = 0.087) in UG29, which has 2 sites inside.", "deviations": [ "The per-mouse hotspots of Extended Data Figure 2b-c are not computed." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed1-controls-no-organization", "statement": "Mice expressing non-functional sensors (a mutant ACh sensor and tdTomato, n = 3) show only sparse, weak positive red-green correlations with no anatomical organization; no hotspot is found.", "source": "Extended Data Figure 1i-k; Results, first section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "In AD4 to AD6 (ACh4.3mut and tdTomato) the hotspot procedure finds a hotspot with mean smoothed r +0.33 (551 voxels, centroid AP 0.68, ML 1.29, DV -4.14 mm), so by the paper's test the claim of no organization fails. The procedure also finds a hotspot in 73 of 100 shuffles of the control values across sites, but none of those reaches 551 voxels (31 have a mean of at least +0.33), so by the paper's own test the control correlations are organized in space. The correlations are mostly positive (68% of 124 sites, median 0.20), as stated, but not weak; the median absolute dominant r is 0.238 against 0.240 in the sensor mice, and 65% of control sites exceed 0.2 against 54%. One control site has no defined correlation (a constant red trace) and is dropped; 19 site-sessions have constant red traces. Keeping the reward periods gives median r 0.22. Two deviations could add correlated red-green signal and so bear on this outcome; the controls use the high-pass series without artifact removal (none is in their files), and only their 15 reward sessions, where the paper used all ITI data.", "deviations": [ "The 15 uncued reward sessions of the control mice are used, with 6 s after rewards and first licks left out; the paper used the ITI data of all their sessions, which the files' event tables would allow but which would take most of the time limit to stream.", "The control files hold no artifact-removed series; the high-pass series is used." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2a-directionality", "statement": "For coincident transients of opposite polarity (ACh trough with DA peak, ACh peak with DA trough) the DA transient leads; for same-polarity pairs (peak with peak, trough with trough) the ACh transient leads.", "source": "Figure 2a; Results, second section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Median directionality indices are -0.27 (ACh trough with DA peak), -0.30 (ACh peak with DA trough), +0.33 (peak with peak) and +0.12 (trough with trough) over 174 sites, each with Wilcoxon p below 1e-24, and each mouse has the same four signs.", "deviations": [ "Pairs are matched by the Methods' rule (each first transient takes its earliest partner, each partner used once), a simplification of the code's two-way matching.", "The code keeps only sites flagged as having signal in both channels (`sig`); these flags are not in the files and all 174 included sites are used, as the paper reports 174." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2-magnitude-correlations", "statement": "Magnitudes of paired transients are negatively correlated at many sites for opposite-sign pairs (121 of 174 for ACh troughs with DA peaks, 81 of 174 for ACh peaks with DA troughs) and positively for same-sign pairs (97 of 174 peak-peak, 78 of 174 trough-trough), with no site significant in the other direction.", "source": "Results, second section; Figure 2d", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Significant sites of the stated sign are 114, 69, 97 and 78 against 121, 81, 97 and 78; the second is 3.9 below its tolerance. The counts move by several sites with the random draws (the first run gave 115, 70, 90 and 76). No site is significant in the opposite direction, as stated. All sites have at least 100 pairs. The code's computation (Pearson r over all pairs, p < 0.05) finds 142 to 149 sites per type, so the paper's counts fit the Methods' bootstrap.", "deviations": [ "1000 in place of 10000 repetitions of the 100-pair bootstrap." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-magnitude-in-out", "statement": "Magnitude correlations of opposite-sign pairs, but not same-sign pairs, are stronger inside the aDLS hotspot than outside (rank-sum p < 0.05 for opposite-sign pairs, p > 0.05 for same-sign pairs).", "source": "Figure 2d; Results, second section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "ACh troughs with DA peaks are more negative inside (median -0.33 against -0.23, p = 0.0001); ACh peaks with DA troughs do not differ (-0.19 against -0.16, p = 0.11). Same-sign pairs do not differ (p = 0.11 and 0.22), as stated.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2b-pairing-overlaps-hotspot", "statement": "The frequency of paired transients is highest in aDLS, in a region overlapping the correlation hotspot, for all four pair types (volume overlap test, p < 0.01 for each).", "source": "Figure 2b-c; Results, second section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The occurrence hotspot of each pair type overlaps the correlation hotspot by 780 to 826 voxels against null medians of 88 to 111 (overlap p 0.005, 0.015, 0.005 and below 0.005; the paper 0.005, 0.005, 0.002 and below 0.001). Occurrence is higher inside than outside for each type (p < 0.001). With the chance occurrence subtracted (DA and ACh transients from different sessions of the same site, as in the Methods), every site keeps an excess for every type, the excess is higher inside (p < 0.001), and its hotspots overlap the correlation hotspot with p 0.030, 0.005, 0.015 and below 0.005.", "deviations": [ "200 random volumes in the overlap test, so p cannot fall below 0.005.", "The chance occurrence is the mean of 10 shuffles of sessions, in place of 10000." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed3e-transient-rates-in-hotspot", "statement": "DA and ACh transient rates are higher at sites inside the global correlation hotspot than outside.", "source": "Extended Data Figure 3d-e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "All four transient types are more frequent inside the hotspot (for example DA peaks 0.226 against 0.176 per second of usable data), p of 0.0013 or less. Rates are now per second of data that is not NaN and not within 6 s after a reward; the first run divided by the whole session and gave the same result.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-reward-correlation", "statement": "After unpredicted rewards, trial-by-trial DA peak magnitude correlates with ACh; dominant correlations are negative at 114 of 174 sites with DA leading (mean latency 177.9 +/- 96.7 ms) and positive at 58 of 174 with ACh leading (-41.2 +/- 218.9 ms).", "source": "Results, third section; Figure 3b", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "122 sites are dominant negative (mean latency 172.1 ms, 120 with DA leading) and 52 dominant positive (mean latency -59.8 ms, 37 with ACh leading). Three values are within tolerance; the positive count is 0.2 below its range (52.2 to 63.8). Negative sites outnumber positive ones in every mouse.", "deviations": [ "The latency tolerances are the standard errors implied by the paper's spreads.", "One UG27 reward session (240313r) is skipped for lacking the artifact-removed green series." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-reward-in-out", "statement": "Reward-evoked DA-ACh correlations are significantly more negative inside the global hotspot than outside.", "source": "Figure 3d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Median r -0.52 inside against -0.31 outside, p = 7.3e-09; same sign in all five mice, significant in three.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-reward-hotspot-overlap", "statement": "Reward anti-correlations form an aDLS hotspot that significantly overlaps the hotspot of spontaneous correlations (volume overlap test, p = 0.008).", "source": "Figure 3c, 3e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The reward hotspot has mean -0.53 (1022 voxels, centroid AP 0.54, ML 2.07, DV -3.26 mm) and shares 721 voxels with the spontaneous hotspot against a null median of 116, overlap p = 0.01 (the paper 0.008).", "deviations": [ "200 random volumes in the overlap test." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4-cue-sequence", "statement": "After Pavlovian conditioning, the conditioned light cue evokes an ACh peak, then a DA peak, then an ACh dip at a majority of sites (49 of 75).", "source": "Results, fourth section; Figure 4a", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The sequence is found at 58 of 75 sites under both readings (code percentiles 55 and 52), above the tolerance of 44.1 to 53.9. The qualitative statement holds; a majority of sites shows the sequence overall and in each mouse (12 of 17, 19 of 24, 27 of 34). The criterion counted only a shortfall as partial; a count above the range is not reproduced by its wording.", "deviations": [ "The paper does not define how the sequence is identified; significant ACh peak, DA peak and ACh dip with ordered extremes in the mean trace was chosen here.", "Learning sessions are identified from the events (every light cue rewarded); the last 3 per mouse are used, following the code's intent (see findings on the code).", "Tone trials cannot be analysed (no tone events); the paper's figure uses light trials." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-cue-correlation", "statement": "For conditioned light cues, ACh correlates with the trial-by-trial DA peak negatively at lagging times at 39 of 75 sites (ACh lagging, 202.28 +/- 128.4 ms) and positively at leading times at 26 of 75 (ACh leading, -79.1 +/- 224.0 ms).", "source": "Results, fourth section; Figure 4c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "All 75 sites have a significant cue DA peak, so the two readings agree. 41 sites are negative (mean latency 206.0 ms, 37 with ACh lagging) and 34 positive (-83.3 ms, 22 with ACh leading). The positive count is above its range (23.4 to 28.6); the paper's 39 plus 26 make 65, which fits neither reading here. The code's percentiles also give 75 sites, and the null draws from 68868 to 74196 candidate times per mouse, so neither explains the difference. The difference remains unexplained.", "deviations": [ "The denominator is ambiguous (75 sites or those with a significant DA peak); both readings are shown and agree here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-extinction-correlation", "statement": "After cue-specific extinction (light cue rewarded on 20% of trials), cue-evoked DA dips correlate negatively with lagging ACh (DA dip then ACh late peak) at 41 of 74 sites, mean lag 117.9 +/- 176.2 ms.", "source": "Results, fourth section; Figure 4g-h", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Under reading (a), 38 of 61 sites with a significant DA dip are negative with mean lag 118.4 ms (the paper 41 of 74, 117.9 ms). Over all 75 sites, 47 negative with mean lag 114.7 ms. Only 28 of the 38 have ACh lagging, and AD2's negative sites have a mean lag of -79.4 ms. The code's polarity (DA peak) gives 44 sites with mean lag 137.6 ms.", "deviations": [ "The DA trough is used, as the legend and Methods state; the code correlates the DA peak in this step, shown as a variant.", "The paper's denominator (74) and the legend's 48 sites in 5 mice do not match each other or the 75 sites in 3 mice of the files; two readings are shown." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-cue-in-out", "statement": "Conditioned-cue DA-ACh correlations are more negative at sites inside the global aDLS hotspot than outside.", "source": "Figure 4d-e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The 9 AD1 to AD3 sites inside the global hotspot have median r -0.31 against 0.02 for the 66 outside, p = 0.024 (exact p = 0.022). The cue hotspot's own overlap with the global hotspot is not significant (p = 0.175), unlike the paper's Figure 4e.", "deviations": [ "Sites of the Pavlovian cohort are placed in the global hotspot by their coordinates on the shared grid." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4j-extinction-in-out", "statement": "After extinction, DA dip to ACh correlations are more negative at sites inside the global aDLS hotspot than outside.", "source": "Figure 4i-j", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Among dip sites, median r -0.35 inside (8 sites) against -0.21 outside (53), p = 0.035 (exact p = 0.034); all sites p = 0.018. The extinction hotspot's overlap with the global one is not significant (p = 0.17).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5d-initiation-responses", "statement": "At locomotion initiations, ACh rises and then falls at 131 of 174 sites; DA dips at 119 of 174 sites, rises at 73, and both rises and dips at 32.", "source": "Results, fifth section; Figure 5d", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "DA dips at 129 sites and rises at 77 are within 10% (the paper 119 and 73); both at 46 is not (32). ACh rise then fall at 107 sites under reading (a) and a rise at 147 under reading (b), neither within 117.9 to 144.1. Code percentiles give 114 dips, 61 rises and 26 both. The code's bout of 2.2 s gives 132, 74 and 44. UG27 contributes 501 initiations against 92 to 149 for the others; its wheel velocity exceeds the threshold 49% of the time.", "deviations": [ "A zero-phase Butterworth filter replaces MATLAB's lowpass.", "1000 bootstrap samples in place of 10000.", "The Methods' bout of 2.27 s is used; the code's 2.2 s is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5-latency-order", "statement": "Initiation-related signals occur in sequence; DA dips first (median latency 111.11 ms), then ACh peaks (222.22 ms) and DA peaks (227.78 ms), then ACh dips (611.11 ms).", "source": "Results, fifth section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Medians are 111.1 ms (DA dips), 277.8 ms (ACh peaks), 277.8 ms (DA peaks) and 666.7 ms (ACh dips), in the stated order; the ACh peak and dip medians are exactly one sample later than the paper's, at the edge of the tolerance. The per-mouse order is irregular (DA peak medians from -388.9 to 527.8 ms).", "deviations": [ "The Methods do not say how latency is measured; the time of the extreme of the triggered average in -0.5 to 1 s was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5e-initiation-topography", "statement": "Initiation-related DA dips are concentrated in the aDLS and DA peaks in dorsomedial and posterior striatum; ACh dips are localized to the aDLS.", "source": "Results, fifth section; Figure 5e-g", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Dominant DA dips are more anterior than DA rises (median AP 0.36 against -0.48 mm, p < 0.0001) but more medial (ML 1.88 against 2.30 mm) and ventral; ACh-dip sites (148 of 174) are not more anterior or lateral than the 26 others (p = 0.33 and 0.25). All 28 hotspot sites have a dominant DA dip and an ACh dip. The paper describes maps; with ACh dips at 85% of sites a contrast between sites with and without dips may not capture where dips are strongest.", "deviations": [ "The paper shows the topography as smoothed maps; site-level coordinate tests were chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6a-initiation-correlation", "statement": "At sites with initiation-related DA dips (119 sites), trial-by-trial DA dip magnitudes correlate negatively with ACh with DA leading (mean latency 193.80 +/- 177.68 ms).", "source": "Results, sixth section; Figure 6a", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Of 129 sites with a DA dip (the paper 119), 98 are dominant negative (88 with ACh lagging), mean latency 188.8 ms under reading (a); 98.2 ms under reading (b). Most dip sites are negative in every mouse. The trough search now ignores NaNs; before the fix a trough within 2 samples of a NaN was missed. 2197 of 30341 site-trials have a NaN in the range searched, so at most that many were affected. Before the fix the result was 99 sites and 182.4 ms.", "deviations": [ "The latency tolerance is the standard error implied by the paper's spread." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-initiation-in-out", "statement": "Initiation DA dip to ACh correlations are concentrated in the aDLS and more negative inside the global hotspot than outside.", "source": "Figure 6b-d", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Median r -0.35 inside (28 sites) against -0.21 outside (101), p = 1.7e-05 (6.1e-08 before the fix of the trough search).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6g-invigoration-in-out", "statement": "At locomotion invigorations, GLM-estimated DA peak magnitudes correlate negatively with ACh at lagging times, and these correlations are concentrated in the aDLS, more negative inside the global hotspot (131 sites with invigoration DA peaks).", "source": "Results, sixth section; Figure 6e-h; Methods, generalized linear model", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The GLM finds invigoration DA peaks at 160 sites (the paper 131); 105 are dominant negative (97 with ACh lagging, mean lag 179.4 ms); median r -0.34 inside (28) against -0.21 outside (132), p = 4.5e-05.", "deviations": [ "Ordinary least squares in numpy in place of MATLAB fitglm (normal family, identical model)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-da-release", "statement": "Optogenetic stimulation of midbrain DA neurons evokes significant DA release at 179 of 180 sites.", "source": "Results, seventh section; Extended Data Figure 10b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "179 of 180 sites show a significant DA peak after ITI stimulation (178 with the code's percentiles); 115 ITI trains in total (20 per mouse, 15 in ADS6).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7e-ach-suppression", "statement": "DA stimulation evokes significant ACh suppression at a subset of sites (116 of 180, 64%).", "source": "Results, seventh section; Figure 7e", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "147 of 180 sites (82%) show a significant ACh dip against 116 (64%); 128 (71%) with the code's percentiles. The 33 sites without a dip are mostly in ADS19 (17 of 27) and ADS16 (9 of 37).", "deviations": [ "1000 bootstrap samples in place of 10000." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ed9-cohort-hotspot", "statement": "The stimulation cohort replicates the aDLS anti-correlation hotspot in spontaneous release outside stimulation periods; its dominant correlations are more negative inside the original hotspot, and its own hotspot overlaps the original.", "source": "Extended Data Figure 9a-d; Results, seventh section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The 9 cohort sites inside the original hotspot are more negative (median -0.42 against -0.30, p = 0.049, exact p = 0.048; OR exclusion p = 0.041). The cohort's own hotspot is negative (mean -0.44, 1536 voxels, centroid AP 0.71, ML 2.00, DV -3.45 mm) and shares 564 voxels with the original against a null median of 65, but overlap p = 0.085 with 200 random volumes. 167 of 180 cohort sites are dominant negative. The AND exclusion leaves out 6.5% of samples and the OR exclusion 32.7%. Of the samples within 3 s after a stimulation, AND keeps 42% and OR none. With OR the cohort hotspot is similar (mean -0.41, centroid AP 0.72, ML 2.08, DV -3.43 mm), with overlap p = 0.085.", "deviations": [ "The code's AND of the three exclusions is followed; OR is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7f-ach-dip-in-out", "statement": "Stimulation-evoked ACh dips are larger inside the cohort's correlation hotspot than outside, and their own hotspot overlaps it.", "source": "Figure 7d, 7f-g", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "ACh minima are deeper inside the cohort hotspot (median -0.0179 against -0.0149 dF/F, 17 against 163 sites, p = 0.0005). The AND exclusion keeps 42% of the samples within 3 s after a stimulation, so its cohort hotspot is built partly from stimulation responses; with the hotspot of the OR exclusion, which leaves them out, the result holds (19 against 161 sites, median -0.0188 against -0.0149, p = 0.0003). Against the original hotspot p = 0.094; the ACh-minimum hotspot's overlap with the cohort hotspot has p = 0.065, so the claim's second part is not supported at p < 0.05; the criterion treats it as a variant. Inside sites are lower in all six mice, significantly in ADS19.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig8b-quinpirole-region", "statement": "The D2 agonist quinpirole suppresses evoked ACh release in DLS and NAcC, more strongly in DLS; two-way ANOVA region effect F(1,40) = 105.9, region by stimulus interaction F(4,40) = 3.014, stimulus effect F(4,40) = 17.80.", "source": "Figure 8b", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Region F 105.87, interaction F 3.014 and stimulus F 17.80 match the paper; DLS mean 25.1 against NAcC 68.1. Type III sums of squares are used, as Prism computes them; Type II gives the same values here.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.18202873, file Bouabid_Vu (2026)_Source_Data_Fig8.xlsx", "proposed": null }, { "claim": "fig8e-cocaine-region", "statement": "Cocaine reduces evoked ACh release more in DLS than in NAcC; two-way ANOVA stimulus by region interaction F(4,55) = 10.75, stimulus effect F(4,55) = 36.37, region effect F(1,55) = 199.9.", "source": "Figure 8e", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "With Type III sums of squares, interaction F 10.75, stimulus F 36.37 and region F 199.86 match the paper (10.75, 36.37 and 199.9); DLS 32.8 against NAcC 74.1. The design is unbalanced (8 DLS and 5 NAcC slices). The first run used Type II sums of squares, which give stimulus F 47.68, and scored the claim partially reproduced.", "deviations": [], "disagreed": true, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.18202873, file Bouabid_Vu (2026)_Source_Data_Fig8.xlsx", "proposed": null }, { "claim": "fig8fg-d2-block", "statement": "The D2 antagonist L-741,626 attenuates the cocaine-induced suppression in both regions; D2R block effect F(1,55) = 231.9 in DLS and F(1,40) = 32.57 in NAcC.", "source": "Figure 8f-g", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_bouabid_2026.ipynb", "notes": "Block F 231.87 (DLS) and 32.57 (NAcC) match; the antagonist raises ACh in both (32.8 to 78.6, 74.1 to 107.9). With Type III sums of squares the DLS stimulus F is 34.46, as in the legend (Type II 45.04).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.18202873, file Bouabid_Vu (2026)_Source_Data_Fig8.xlsx", "proposed": null }, { "claim": "fig8c-cocaine-da-similar", "statement": "Cocaine elevates evoked DA release to a similar degree in DLS and NAcC (two-way ANOVA, cocaine by region interaction F(8,36) = 0.20, p = 0.98).", "source": "Figure 8c", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_bouabid_2026.ipynb", "notes": "The sheet Figure_8c_TP holds a voltammogram (voltage and current). Figure_8c_LP and _RP hold mean DA time courses (24 time points from 0.625 to 3.5 s) for three mice per region and two conditions. The legend's ANOVA has 8 degrees of freedom for cocaine and 36 residual, which fits neither a two-level cocaine factor nor the 24 time points, so the test cannot be repeated. Descriptively, the cocaine peak is 1.48 times the control peak on average in both regions (per mouse 1.31 to 1.77 in DLS, 1.10 to 2.09 in NAcC).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.18202873, file Bouabid_Vu (2026)_Source_Data_Fig8.xlsx", "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "Every photometry series states a sampling rate of 9 Hz (starting_time rate 8.999 to 9.0). Each series has as many samples as the behavior series, which steps at 55.6 ms (18 Hz), and the Methods and code use 18 Hz; at the stated rate the recordings would last twice as long as their timestamps." }, { "kind": "metadata_insufficient", "statement": "No field in the files states which experiment (spontaneous, unpredicted reward, Pavlovian learning or extinction, control, stimulation) a session belongs to, or which Pavlovian phase. Cohorts can be told only from subject names and indicators, and phases only by counting rewarded light cues (1.0, 0.8 or 0.2). The paper's Zenodo record has a table of this mapping outside the dandiset." }, { "kind": "data_missing", "statement": "The Pavlovian files have light cue events but no tone cue events, although each session has 30 tone cues (the 68 rewards of a learning session are 30 light, 30 tone and 8 uncued). Tone trials cannot be analysed." }, { "kind": "data_missing", "statement": "Session sub-UG27_ses-240313r lacks the high-pass, artifact-removed green series that all other UG sessions hold, so it cannot enter the analyses that use it." }, { "kind": "metadata_error", "statement": "The device description of ExcitationSource470 describes 470 nm and 405 nm (isosbestic) light alternated at 100 Hz, and that of ExcitationSource570 reads \"405 nm\"; the Methods alternate 470 and 570 nm at 36 Hz. The mutant sensor is named ACh4.3mut in the files where the Methods and Key Resources Table name ACh3.0-mut. The session description gives 9 uL rewards at 5 to 30 s, where the Methods give 5 uL at 10 to 30 s, and stores the micro sign mis-encoded." }, { "kind": "metadata_insufficient", "statement": "The code keeps only sites with signal in both channels (a `sig` flag per site) for the transient analyses; the flags are not in the files. All 174 included sites gave the paper's count, so this did not change the result here." }, { "kind": "code_mismatch", "statement": "In fig4_pav.m (commit 833fa3d) the loop over a phase's last three sessions loads exp_dirs{d} in place of task_dirs{d}, so it reads the mouse's first three recordings for every phase, and the extinction correlation is called with polarity 1 (the DA peak) although the legend and Methods describe the DA trough. The notebook follows the evident intent and the Methods." }, { "kind": "code_mismatch", "statement": "The code departs from the Methods in several parameters; triggered-average significance uses the 0.5th and 99.5th percentiles (Methods 2.5th and 97.5th), the minimum locomotion bout is 2.2 s (Methods 2.27 s), paired-transient magnitude correlations are Pearson r over all pairs (Methods a 100-pair bootstrap), and the stimulation cohort's exclusion of reward and stimulation periods combines the three conditions with AND, so a sample is dropped only when all three hold. hotspot_comparison.m places the second hotspot's random volumes with the first grid's dimensions." }, { "kind": "paper_inconsistency", "statement": "For extinction, the Results give 41 of 74 sites and the Figure 4g legend 48 sites in 5 mice, while the Methods give 3 Pavlovian mice and the files hold 75 sites in 3 mice. For learned cues the Results give 39 of 75 negative and 26 of 75 positive sites, which sum to 65." }, { "kind": "paper_inconsistency", "statement": "In the Figure 8 source data, the Figure 8b DLS group holds 6 slice labels from 4 mouse labels (slice_B_4 holds only stimulus 5) where the legend states 5 slices from 5 mice." }, { "kind": "other", "statement": "The ex vivo slice data of Figure 8 are not in the dandiset; their source data are in the paper's Zenodo record (doi:10.5281/zenodo.18202873)." } ], "verifications": [ { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. It also read the paper and the Zenodo Figure 8 source data, and queried the DANDI asset list.", "agreed": 32, "of": 33, "disagreements": [ { "claim": "fig8e-cocaine-region", "outcome": "reproduced", "reason": "Cell 81 used Type II sums of squares, giving stimulus F = 47.68. Rerun with Type III (GraphPad Prism, which the Methods name, uses Type III; the design is unbalanced at 8 against 5 slices) gives 36.374, 10.754 and 199.857, all within tolerance (B2)." } ] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the revised run (121 cells), the helper module, the claims file and the attempt record. It also read the paper, checking the Figure 8 legend statistics against it.", "agreed": 33, "of": 33, "disagreements": [] } ] }, { "id": "001699-moore-2025-01", "dandiset": "001699", "dandiset_version": "0.260917.2322", "paper": "10.1101/2025.01.09.632139", "paper_title": "Age-dependent alterations in the head-direction signal in a rat model of Fragile X Syndrome", "date": "2026-10-19", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "runs", "entry": "001699-moore-2025", "entry_title": "Head-direction coding in juvenile and adult Fmr1-/y rats (Moore et al. 2025)", "description": "Tests the findings of Moore, Duszkiewicz, Asiminas, Dudchenko, Peyrache and Wood (bioRxiv 2025) on dandiset 001699, which holds silicon-probe recordings of the postsubiculum of 24 juvenile and adult Fmr1-/y and wild-type rats during open-field exploration and sleep. It recomputes the cell selection, head-direction tuning, its stability within and between sessions, decoder drift, and tuning to the Isomap angle of waking and REM population activity, and compares genotypes in each age group.", "notebooks": [ { "path": "reproduce_moore_2025.ipynb", "title": "Reproducing Moore et al. (2025) from dandiset 001699", "executed": "notebooks/001699-moore-2025/reproduce_moore_2025.html" } ], "outcomes": [ { "claim": "unit-counts", "statement": "406 units were recorded from 7 juvenile WT rats and 372 from 5 juvenile Fmr1-/y rats; 543 units from 6 adult WT rats and 507 from 6 adult Fmr1-/y rats.", "source": "Results, paragraphs 2 and 5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "Counting all units of each recording once (reading a), juvenile WT 406 units in 7 rats, juvenile Fmr1-/y 372 in 5 and adult WT 543 in 6 match the paper exactly; adult Fmr1-/y has 440 units in 5 rats against 507 in 6, as H4825's file holds H4824's recording. Counting H4825's file as a recording of its own gives 528 units in 6 rats, within tolerance, but counts one recording twice. As putative excitatory units (reading b) no group matches (326, 249, 399, 289). With the archive's labels no group matches (juvenile WT 328 units in 5 rats, juvenile Fmr1-/y 221 in 4, adult WT 575 in 7). Version 2 of the paper gives 372 units in 6 adult Fmr1-/y rats and 406 in 6 adult WT rats, the juvenile numbers repeated.", "deviations": [ "H3026 is counted as a juvenile Fmr1-/y rat and H3029 as a juvenile WT rat, where the archive labels H3026 WT and gives H3029 a birth date that makes it an adult; this grouping is the one that matches the paper's counts, and it was chosen from those counts.", "H4825's file is left out as a copy of H4824's recording." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "units-per-recording", "statement": "Juvenile recordings held 8 to 83 putative excitatory units each, adult recordings 30 to 114.", "source": "Results, paragraphs 2 and 5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "Under reading (a), all units, juvenile recordings hold 8 to 83 units (paper 8 to 83) and adult recordings 55 to 114 (paper 30 to 114), so the juvenile pair and the adult maximum match and the adult minimum does not. Under reading (b), putative excitatory units by trough-to-peak duration, juvenile 5 to 50 and adult 30 to 81; under (c), cells of session 1, juvenile 5 to 49 and adult 30 to 80. The paper's adult minimum of 30 is the putative excitatory count of H4822, while its other three bounds are counts of all units, so the reported ranges mix two readings.", "deviations": [ "The paper calls these putative excitatory units; three of its four bounds match all units instead." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1c-juvenile-behaviour-similar", "statement": "Juvenile Fmr1-/y and WT rats do not differ in the time spent inactive, the time spent in the centre of the arena, or the speed while active.", "source": "Figure S1c (t-tests on animal averages, t(10) = 1.53, 1.07 and 1.53, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "t-tests on the means of 7 WT and 5 Fmr1-/y rats; time inactive (speed below 1 cm/s) 0.177 against 0.107, t(10) = -0.90, p = 0.39; time in the centre 0.084 against 0.180, t(10) = 1.86, p = 0.093; speed while active 4.88 against 5.74 cm/s, t(10) = 2.10, p = 0.063. With 2 cm/s thresholds and a larger centre, p = 0.25, 0.11 and 0.26. With the first day of each rat alone the active speed differs (t(10) = 2.45, p = 0.034), so the absence of a speed difference is fragile.", "deviations": [ "The paper does not define inactivity, the centre or the active period; the thresholds were fixed in the criterion and variants are shown.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2c-adult-behaviour-similar", "statement": "Adult Fmr1-/y and WT rats do not differ in the time spent inactive, the time spent in the centre of the arena, or the speed while active.", "source": "Figure S2c (t-tests on animal averages, t(10) = 1.21, 0.29 and 0.51, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "6 WT and 5 Fmr1-/y rats; time inactive p = 0.91, time in the centre p = 0.355, speed while active 7.34 against 7.59 cm/s, p = 0.70 (t(9)). The threshold variants give p = 0.80, 0.74 and 0.51.", "deviations": [ "5 Fmr1-/y rats where the paper has 6 (H4825's data are a copy of H4824's).", "The thresholds are not given in the paper; fixed in the criterion, variants shown.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-juvenile-cell-metrics-similar", "statement": "In juveniles, cluster contamination, mean and peak firing rates, and the resultant vector length of PoSub cells do not differ between genotypes.", "source": "Figure S1f-i (LME, no genotype effect, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "LME tests over 323 WT and 237 Fmr1-/y cells; contamination p = 0.71, mean rate p = 0.72, peak rate p = 0.62, vector length p = 0.11 (median 0.425 against 0.265). With H3026 left out p = 0.58, 0.94, 0.76 and 0.20. Mann-Whitney tests on cells, which ignore the rat, find differences in mean rate (p = 0.038) and vector length (p = 0.0001).", "deviations": [ "Contamination is computed here from the spike trains, as the files hold no quality metric.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2-adult-cell-metrics-similar", "statement": "In adults, cluster contamination, mean and peak firing rates, and the resultant vector length of PoSub cells do not differ between genotypes.", "source": "Figure S2f-i (LME, no genotype effect, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "LME tests over 395 WT and 282 Fmr1-/y cells; contamination p = 0.11, mean rate p = 0.34, peak rate p = 0.10, vector length p = 0.26. Mann-Whitney tests on cells find lower mean rate, peak rate and vector length in Fmr1-/y cells (p = 0.022, 0.0026 and 0.0032).", "deviations": [ "5 Fmr1-/y rats where the paper has 6.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1ef-juvenile-sharper-tuning", "statement": "PoSub cells of juvenile Fmr1-/y rats are more sharply tuned to head direction than those of WT littermates, with higher HD information and narrower tuning curves.", "source": "Figure 1e-f; Results, paragraph 3 (LME, genotype effect, P < 0.05 for both)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "HD information is higher in Fmr1-/y cells (median 0.596 against 0.189 bits/spike, LME coefficient 0.34, p = 0.030; first day alone p = 0.035). It is not significant on log values (p = 0.12), with uniform occupancy as in version 2 (p = 0.081), on rat means (t(10) = 2.11, p = 0.061), with H3026 left out (p = 0.072) or with the archive's labels (p = 0.23). The half-width does not differ (median 50 against 62 degrees, p = 0.54; 26 Fmr1-/y and 46 WT cells never fall below half their peak).", "deviations": [ "Cells re-recorded on consecutive days could not be excluded as in the paper; the first day alone is a variant.", "A linear mixed model on raw values; the paper chose linear or generalized models by the distribution.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-juvenile-halves-correlation", "statement": "In juveniles the HD information of a cell is stable between the two halves of an exploration session (WT r = 0.90, Fmr1-/y r = 0.95).", "source": "Figure 1g", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "With the sessions as the claims file defines them (tracking blocks over 30 min cut to 1300 s, the others whole), HD information of the two halves of session 1 correlates with r = 0.761 over 323 WT cells (paper 0.90, lower bound 0.81) and 0.839 over 237 Fmr1-/y cells (paper 0.95, lower bound 0.855), so neither value is within tolerance. With H3026 left out the Fmr1-/y r is 0.869, within tolerance, and WT stays at 0.761; with the first day of each rat alone WT r is 0.650. With sessions cut to their first 20 min, the definition used for the main analysis, WT r is 0.815 (0.005 above its bound) and Fmr1-/y r 0.835; that cut was adopted after the first round and departs from the claims file, and the outcome follows the claims file's definition. Spearman correlations with the 20 min sessions are 0.863 and 0.909. Version 2 reports 0.86 and 0.93.", "deviations": [ "The claims file gave no rule for values outside tolerance; the claim is taken as partially reproduced when one of its two values is within tolerance and not reproduced when neither is, as for the other correlation claims." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1h-juvenile-smaller-offset", "statement": "Within a session, the tuning curves of juvenile Fmr1-/y cells drift less relative to the room than those of WT cells; the angular offset between the two halves is smaller.", "source": "Figure 1h (LME, genotype effect, P < 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "The absolute offset between the two halves' tuning curves is smaller in Fmr1-/y cells (median 7 against 26 degrees, LME coefficient -24.1, p = 0.035). First day alone p = 0.017; cells with half-width below 120 degrees p = 0.060; rat means t(10) = -2.09, p = 0.063; H3026 left out p = 0.068; archive labels p = 0.17; with the claims file's session definition p = 0.014.", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1j-juvenile-less-drift", "statement": "Bayesian decoding shows less drift of the HD signal relative to the room in juvenile Fmr1-/y rats than in WT rats.", "source": "Figure 1i-j (t-test on animal averages, t(10) = 2.44, P < 0.05)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "Mean absolute decoder drift over rat means is 17.0 degrees in 5 Fmr1-/y rats and 35.0 in 7 WT rats, the paper's direction, but t(10) = -1.91, p = 0.085 (paper t(10) = 2.44, P < 0.05; version 2 t(10) = 3.17). With version 2's 1.5 cm/s threshold p = 0.064, for the SD of drift p = 0.12, with the first day alone p = 0.088, with the archive's labels p = 0.20, with H3026 left out p = 0.14. H3019 210618-1 is left out (5 cells). H3001 200201 is decoded on 279 bins where the others have 491 to 2480; only 330 of its 3000 second-half bins have speed above 2 cm/s, though 2914 have valid tracking. Leaving out recordings under 300 bins gives p = 0.085. With the claims file's session definition p = 0.069.", "deviations": [ "Version 1 does not describe the decoder; version 2's Methods were followed (Hampel filter, 0.8 s smoothing, tuning curves from the first half), with version 1's 2 cm/s threshold.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1j-juvenile-epochs-correlation", "statement": "In juveniles HD information is preserved between the two exploration sessions (WT r = 0.85, Fmr1-/y r = 0.85).", "source": "Figure S1j", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "HD information correlates between the two sessions with r = 0.853 over 309 WT cells (paper 0.85, within tolerance) and 0.753 over 225 Fmr1-/y cells (paper 0.85, lower bound 0.765). Spearman 0.869 and 0.810. Version 2 reports 0.87 and 0.86.", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1k-juvenile-epoch-drift-similar", "statement": "In juveniles the drift of tuning curves between the two exploration sessions does not differ between genotypes.", "source": "Figure S1k (LME, no genotype effect, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "The offset between the tuning curves of the two sessions does not differ (median 14 degrees in Fmr1-/y, 21 in WT; LME coefficient 2.3, p = 0.87; first day p = 0.72; archive labels p = 0.44; H3026 left out p = 0.60). Version 2's text says juvenile Fmr1-/y rats were more stable between sessions, while its legend for the same panel reports no genotype effect.", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-juvenile-isomap-wake-correlation", "statement": "In juveniles the HD information of tuning curves computed against the Isomap angle of the waking population activity matches that of real HD tuning curves (WT r = 0.84, Fmr1-/y r = 0.92).", "source": "Figure 2c", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "Isomap and real-HD information (200 ms bins, 6 degree bins) correlate with r = 0.815 over 323 WT cells and 0.910 over 232 Fmr1-/y cells (paper 0.84 and 0.92). The Isomap angle aligned with real HD with Rayleigh lengths of 0.21 to 0.90 over 23 recordings; H3019 210618-1 is left out (5 cells).", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-juvenile-isomap-wake-sharper", "statement": "Juvenile Fmr1-/y cells are better tuned than WT cells to the internal HD signal of the waking manifold, independently of any reference frame.", "source": "Figure 2d (LME, genotype effect, P < 0.05)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "Isomap HD information is higher in Fmr1-/y cells (median 0.416 against 0.243 bits/spike, LME coefficient 0.20) but p = 0.056. On log values p = 0.13, first day alone p = 0.15, archive labels p = 0.14, H3026 left out p = 0.075, rat means t(10) = 1.89, p = 0.089; only the Mann-Whitney test on cells (p = 0.0007) is below 0.05. The direction matches the paper. Isomap is fitted on every bin, as the criterion says; a fit on 3000 bins raises the median Isomap information of H3026 211003 from 0.435 to 0.546 bits/spike.", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2g-juvenile-isomap-rem-correlation", "statement": "In juveniles the HD information of tuning curves computed against the Isomap angle of REM sleep activity matches that of real HD tuning curves (WT r = 0.73, Fmr1-/y r = 0.90).", "source": "Figure 2e-g", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "REM Isomap information correlates with waking real-HD information with r = 0.831 over 323 WT cells (paper 0.73, above the tolerance of 0.657 to 0.803) and 0.833 over 231 Fmr1-/y cells (paper 0.90, within tolerance). REM per recording 539 to 1706 s. With the REM intervals inside exploration sessions left out, 0.831 and 0.831. Version 2 reports 0.84 and 0.93.", "deviations": [ "REM intervals are the files' sleep_stages.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2h-juvenile-isomap-rem-sharper", "statement": "Juvenile Fmr1-/y cells are better tuned than WT cells to the internally generated HD signal during REM sleep.", "source": "Figure 2h (LME, genotype effect, P < 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "REM Isomap HD information is higher in Fmr1-/y cells (median 0.401 against 0.169 bits/spike, LME coefficient 0.21, p = 0.045). The result is at the threshold; on log values p = 0.092, first day p = 0.16, archive labels p = 0.25, H3026 left out p = 0.095, rat means t(10) = 1.95, p = 0.079; with the REM inside exploration left out p = 0.045. Waking Isomap information (fig2d) has a similar coefficient (0.20) and p = 0.056. With the claims file's session definition p is unchanged (0.045), as REM Isomap does not use the sessions and session 1 holds the same cells.", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3ef-adult-tuning-similar", "statement": "In adults HD tuning does not differ between Fmr1-/y and WT rats, in HD information or tuning curve width.", "source": "Figure 3e-f (LME, no genotype effect, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "In adults HD information (median 0.193 in Fmr1-/y against 0.318 in WT, LME p = 0.55) and half-width (78 against 76 degrees, p = 0.59) do not differ. The Mann-Whitney test on cells finds lower HD information in Fmr1-/y cells (p = 0.0095).", "deviations": [ "5 Fmr1-/y rats where the paper has 6.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-adult-halves-correlation", "statement": "In adults HD information is stable between the two halves of an exploration session (WT r = 0.94, Fmr1-/y r = 0.94).", "source": "Figure 3g", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "r = 0.804 over 395 WT cells and 0.748 over 282 Fmr1-/y cells, against 0.94 for both in the paper (lower bound 0.846); neither value is within tolerance. Spearman 0.862 and 0.818. Version 2 reports 0.95 and 0.95.", "deviations": [ "The claims file gave no rule for values outside tolerance; the claim is taken as not reproduced when neither value is within tolerance.", "5 Fmr1-/y rats where the paper has 6.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-adult-larger-offset", "statement": "Within a session the tuning curves of adult Fmr1-/y cells drift more relative to the room than those of WT cells.", "source": "Figure 3h (LME, genotype effect, P < 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "The offset between halves is larger in Fmr1-/y cells (median 60 against 20 degrees, LME coefficient 32.1, p = 0.030); with the archive's labels p = 0.043; for cells with half-width below 120 degrees p = 0.017. On rat means t(9) = 2.20, p = 0.056.", "deviations": [ "5 Fmr1-/y rats where the paper has 6.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3j-adult-more-drift", "statement": "Bayesian decoding shows more drift of the HD signal relative to the room in adult Fmr1-/y rats than in WT rats.", "source": "Figure 3i-j (t-test on animal averages, t(10) = 3.33, P < 0.01)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "Decoder drift over rat means is 68.4 degrees in 5 Fmr1-/y rats and 20.1 in 6 WT rats, t(9) = 2.93, p = 0.017 (paper t(10) = 3.33, P < 0.01; version 2 t(10) = 3.55). Version 2's threshold gives p = 0.016 and the SD of drift p = 0.099. Three Fmr1-/y rats drift by 91 to 101 degrees; H4819 (32.9) and H4827 (18.3) lie within the WT range of 11.3 to 37.1.", "deviations": [ "Decoder from version 2's Methods, as for the juveniles; 5 Fmr1-/y rats where the paper has 6.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2j-adult-epochs-correlation", "statement": "In adults HD information is preserved between the two exploration sessions (WT r = 0.90, Fmr1-/y r = 0.76).", "source": "Figure S2j", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "r = 0.787 over 395 WT cells (lower bound 0.81) and 0.562 over 276 Fmr1-/y cells (lower bound 0.684), lower in Fmr1-/y as in the paper (0.90 and 0.76), with neither value within tolerance. Spearman 0.888 and 0.714; five of the ten cells farthest from the diagonal are from H4817 and gain information in session 2. Version 2 reports 0.91 and 0.75.", "deviations": [ "The claims file gave no rule for values outside tolerance; the claim is taken as not reproduced when neither value is within tolerance.", "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2k-adult-epoch-drift-larger", "statement": "In adults the tuning curves of Fmr1-/y cells drift more than those of WT cells between the two exploration sessions 90 min apart.", "source": "Figure S2k (LME, genotype effect, P < 0.05); Results, paragraph 5", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "The offset between the sessions is larger in Fmr1-/y cells (median 74 against 30 degrees, LME coefficient 37.0, p = 0.028; archive labels p = 0.022; rat means t(9) = 2.20, p = 0.055).", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-adult-isomap-wake-correlation", "statement": "In adults the HD information of Isomap tuning curves from waking activity matches that of real HD tuning curves (WT r = 0.95, Fmr1-/y r = 0.90).", "source": "Figure 4c", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "r = 0.945 over 395 WT cells (paper 0.95, within tolerance) and 0.614 over 282 Fmr1-/y cells (paper 0.90, outside). The Isomap angle aligned poorly with real HD in H4822 (0.152), H4824 (0.224) and H4817 (0.386), the three Fmr1-/y rats with the largest decoder drift; the three Fmr1-/y cells with the highest Isomap information are from H4817 and carry 0.45 to 0.67 bits/spike of real-HD information. Version 2 reports 0.99 and 0.96.", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4d-adult-isomap-wake-similar", "statement": "In adults tuning to the internal HD signal of the waking manifold does not differ between Fmr1-/y and WT rats.", "source": "Figure 4d (LME, no genotype effect, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "Isomap HD information does not differ between genotypes (median 0.279 in Fmr1-/y against 0.336 in WT; LME p = 0.79; rat means t(9) = -0.26, p = 0.80).", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4g-adult-isomap-rem-correlation", "statement": "In adults the HD information of Isomap tuning curves from REM activity matches that of real HD tuning curves (WT r = 0.82, Fmr1-/y r = 0.80).", "source": "Figure 4e-g", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "r = 0.820 over 378 WT cells (paper 0.82) and 0.651 over 280 Fmr1-/y cells (paper 0.80, lower bound 0.72); with the REM intervals inside exploration sessions left out (196 s in H4822) the Fmr1-/y r is 0.691. REM per recording 116 to 988 s; H4823 and H4830 have 116 and 133 s. Version 2 reports 0.84 and 0.83.", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4h-adult-isomap-rem-similar", "statement": "In adults tuning to the internally generated HD signal during REM sleep does not differ between Fmr1-/y and WT rats.", "source": "Figure 4h (LME, no genotype effect, P > 0.05)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_moore_2025.ipynb", "notes": "REM Isomap HD information does not differ between genotypes (median 0.413 in Fmr1-/y against 0.332 in WT; LME p = 0.27; with the REM inside exploration left out p = 0.73; rat means p = 0.27).", "deviations": [ "Sessions are cut to their first 20 min, the paper's session length, where the claims file cuts only tracking blocks over 30 min, to 1300 s; the change was made after the first round of verification, and the claims file's definition is shown as a variant in the notebook." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1d-probe-in-posub", "statement": "In every rat the probe tracts passed through PoSub, confirmed histologically.", "source": "Figure S1d, Figure S2d; Methods, Recording", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Every one of the 36 files holds RGB histology images (acquisition/histology_images, for example H3001_D2 and H3001_D3), including the four whose asset names lack +image (H3001 on both days, H4822, H4823). No image annotates the probe tract or the postsubiculum, and the electrodes table gives a location string per channel but no histological confirmation. Judging whether a tract passes through PoSub from the images needs an anatomist; it was not attempted.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The paper's unit counts (406 units in 7 juvenile WT rats, 372 in 5 juvenile Fmr1-/y rats, 543 in 6 adult WT rats) and its range of 8 to 83 units per juvenile recording are matched exactly only if H3026, labelled WT, is a juvenile Fmr1-/y rat and H3029, whose date of birth makes it 97 days old, is a juvenile WT rat. With the archive's labels the juvenile groups have 5 WT and 4 Fmr1-/y rats, and the juvenile effects weaken (HD information p = 0.23, offsets p = 0.17)." }, { "kind": "metadata_error", "statement": "The dates of birth of H3023 (2022-08-13) and H3026 (2022-09-13) are after their recordings in 2021, so the archive's asset metadata, which derive the age from the date of birth, give them negative ages (P-366D to P-344D). H3029 shares H4830's date of birth. No NWB file sets the subject's age." }, { "kind": "data_missing", "statement": "The file of H4825 holds the recording of H4824 (identical waveforms, unit and spike counts, and spike times up to 1248 s), with its spike and tracking times shifted piece by piece onto H4825's epoch table and clipped at its end, where 131373 spikes share the last spike time and 12970 tracking frames repeat a timestamp. H4825's own recording is not in the dandiset, so the adult Fmr1-/y group has 5 rats and 440 units where the paper has 6 and 507." }, { "kind": "selection_undocumented", "statement": "The units table holds all curated units with only spike times, mean waveforms, electrode group and sampling rate; no cell type, contamination or depth. The paper excluded cells recorded in the part of PoSub already recorded on the previous day, and the files give no probe depth per day, so that selection cannot be repeated." }, { "kind": "metadata_error", "statement": "The epochs and processing/tasks tables do not mark the exploration sessions reliably. In H3001 200202 task epoch 1 is called wake but lasts 94 min without tracking; in H3026 211003 epoch 1 spans 112 min of waking and sleep; in H3023 210813-1 epoch 2 runs from the end of the first session into the second; H4823 has a single epoch and no sleep task. Every file's session description mentions a cue rotation, and most files hold a third tracked session (`wake_cue_rot`), which version 1 of the paper does not describe." }, { "kind": "metadata_error", "statement": "In H3015 210417 and H4823 221108 position is stated in centimetres but spans about 300 and 700 units, so it is in pixels, and head direction runs from -pi to pi where the other files use 0 to 2 pi." }, { "kind": "format_error", "statement": "One unit of H3023 210812 has spike times out of order. 22 of the 24 juvenile files have one to three tracking frames whose timestamp does not increase." }, { "kind": "metadata_error", "statement": "The dandiset's `about` field lists \"Fmr1 protein, rat\" as an anatomy term with the MeSH identifier of Fragile X Syndrome (D005600)." }, { "kind": "methods_unavailable", "statement": "The paper's analysis code (Matlab and R, per its Methods) is not public; its Code Availability says it will be released at publication. The repository the dandiset links, woodcode (commit 61ee178), is the lab's general library and does not hold the paper's analysis. Version 1 does not describe the Bayesian decoder; version 2 does." }, { "kind": "paper_inconsistency", "statement": "The Methods exclude units with contamination scores \"below 0.5\", which would remove nearly every unit (1727 of 1761 are below). The ranges of units per recording mix counts of all units (8 to 83, maximum 114) with a count of putative excitatory units (minimum 30), while the text calls them all putative excitatory. Version 2 gives the adult counts as 372 and 406 units in 6 rats each, the juvenile numbers repeated." } ], "verifications": [ { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with version 1 of the paper. The verifier queried the archive's file list and asset metadata and tested the helper functions on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; 24 of 27 agree with the record as it then stood. Replies to the report's problems that are not tied to one claim, all in the revised notebook: frame_counts now counts each frame on its own window, with a synthetic test in the data check (problem 4); every session is cut to its first 20 min, the paper's length, and the notebook says that H3001 200202's only session follows the sleep (problem 5); Isomap is fitted on every bin, with a 3000-bin fit shown beside it for two recordings (problem 6); the decoder error is unwrapped over valid bins before interpolating across invalid ones (problem 7); the notebook prints the archive's asset ages, including the negative ages of H3023 and H3026 (problem 9); the juvenile tests gain an H3026-left-out variant (problem 1). Cells recorded on more than one day are still counted on each day (problem 2), as the files give no probe depth; the first-day variant is shown. The 22-bin recording of problem 3 has 279 bins with 20 min sessions. Each file has exactly one frame with y = 0, an offset, not missing tracking. The adult Isomap maximum of 2.476 in both genotypes does not recur with the full fit (2.639 and 2.417).", "agreed": 24, "of": 27, "disagreements": [ { "claim": "fig1g-juvenile-halves-correlation", "outcome": "not_reproduced", "reason": "Cell 36: WT r = 0.761 (needs \u2265 0.81), KO r = 0.840 (needs \u2265 0.855)." }, { "claim": "fig3g-adult-halves-correlation", "outcome": "not_reproduced", "reason": "Cell 50: WT 0.810 and KO 0.742, both needing \u2265 0.846." }, { "claim": "figs2j-adult-epochs-correlation", "outcome": "not_reproduced", "reason": "Cell 56: WT 0.786 (needs \u2265 0.81), KO 0.570 (needs \u2265 0.684). WT is still above KO, as in the paper." } ] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full re-executed notebook of the first revision, with its conclusions and summary, the helper module, the claims file and the attempt record. The verifier could not download the paper (bioRxiv rate limits), so the version-2 numbers quoted in the notes were unchecked; this revision could not get the text either (bioRxiv answered 429 again). It agreed with all 27 outcomes. Replies to the points not tied to one claim: the first finding now gives the re-executed values with the archive's labels (HD information p = 0.23, offsets p = 0.17); a new notebook section repeats the main test of every claim with the claims file's session definition (tracking blocks, only those over 30 min cut to 1300 s), which changes only fig1g, for which a change of outcome is proposed; the 20 min cut is recorded as a deviation under every claim that uses the sessions and in the Summary. Cells counted on every day (problem 2) and H3026's label (problem 1) cannot be settled from the files and stay as variants.", "agreed": 27, "of": 27, "disagreements": [] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 3. The one proposed change of outcome (fig1g-juvenile-halves-correlation) and the analysis behind it in the executed notebook after the round-2 revision (cells 43, 83 and 84), with the helper module and the claims file. Nothing else was reviewed, and the paper text was not needed. Report in transcripts/001699/verifier-3-report.md.", "agreed": 1, "of": 1, "disagreements": [] } ] }, { "id": "001712-davatolhagh-2025-01", "dandiset": "001712", "dandiset_version": "draft", "paper": "10.1101/2025.09.12.675910", "paper_title": "Altered Use of Prior Expectations and Modified Neural Dynamics in a Mouse Model of Autism", "date": "2026-10-19", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001712-davatolhagh-2025", "entry_title": "Prior use and cortical dynamics in a Nrxn1a mouse model (Davatolhagh et al. 2025)", "description": "Tests the findings of Davatolhagh et al. (2025) that can be tested on dandiset 001712, which holds one widefield imaging and behaviour session of one mouse of unstated genotype in the IBL biased choice task. It tests the psychometric curve, reaction times, the use of the block prior, adaptation after block switches, lateralized visual responses and a linear encoding model of the imaging with task and movement predictors. The comparisons between knockout and wild-type mice cannot be tested.", "notebooks": [ { "path": "reproduce_davatolhagh_2025.ipynb", "title": "Reproducing Davatolhagh et al. (2025) from dandiset 001712", "executed": "notebooks/001712-davatolhagh-2025/reproduce_davatolhagh_2025.html" }, { "path": "encoding_all_cameras.ipynb", "title": "Encoding model with the video components of all three cameras (variant)", "executed": "notebooks/001712-davatolhagh-2025/encoding_all_cameras.html" } ], "outcomes": [ { "claim": "fig1c-psychometric", "statement": "Mice of both genotypes show sigmoidal psychometric curves, with the proportion of rightward choices increasing as the stimulus contrast increases on the right.", "source": "Figure 1C; Results, first section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_davatolhagh_2025.ipynb", "notes": "P(right) rises at every step of signed contrast, from 0.112 at -100% to 1.000 at +100% (Spearman rho 1.000 over nine levels, span 0.887). The lapse-and-erf fit gives sigma 17.04% contrast (bootstrap 95% interval 13.98 to 20.47), bias -6.77% and left lapse 0.116. The claim covers both genotypes; this is one mouse of unknown genotype.", "deviations": [ "One session of one mouse, where the paper pools 10 sessions from each of 19 mice.", "The criterion (Spearman rho and span) was set here; the paper shows the curves without a test." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-psychometric-params-genotype", "statement": "Psychometric bias, slope and lapse rates do not differ between WT and KO mice (bias p = 0.94, slope p = 0.95, left lapse p = 0.16, right lapse p = 0.22).", "source": "Figure 1D; Results, first section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes. The dandiset holds one mouse (FD-28), and its genotype is not in the files or the dandiset metadata, nor in the public IBL database (openalyx subject FD_28 has an empty genotype list, from a query made by hand during the attempt and not part of the notebook). Openalyx holds other sessions of the cohort's FD and MFD mice, but is a live database without a pinned version and also has no genotypes.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1e-rt-contrast", "statement": "Reaction time (time to first movement) is longer at lower contrasts in both genotypes.", "source": "Figure 1E", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_davatolhagh_2025.ipynb", "notes": "Over 750 trials with a movement onset after the stimulus, the Spearman correlation of absolute contrast with reaction time is -0.053 (p = 0.15); the median at 0% (0.089 s) exceeds that at 100% (0.081 s), the second part of the criterion. Medians are 0.081 to 0.095 s at every contrast, and 161 trials have no movement onset after the stimulus (149 with an onset at or before it and 12 with no onset). With reaction times above 0.15 s only (226 trials) the correlation is -0.226 (p = 0.00062), so the relation appears among slower responses. Of the 899 onsets, 149 fall at or before the stimulus and 346 within 0.08 s after it, so many may mark movements begun before the stimulus could guide them. The response time (choice registration minus stimulus onset) is shorter at higher contrast over all 911 choice trials (rho -0.134, p = 5.2e-05; medians 0.326 s at 0% and 0.281 s at 100%), a variant that does not decide the outcome. The paper's text calls reaction time the time to first movement and does not say how that movement is detected or how earlier movements are treated.", "deviations": [ "One session of one mouse.", "Trials with a movement onset at or before the stimulus onset are left out; the paper does not say how it treats them." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1f-rt-genotype", "statement": "Reaction times do not differ between genotypes on correct (p = 0.234) or incorrect (p = 0.522) trials.", "source": "Figure 1F; Results, first section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1g-learning-genotype", "statement": "WT and KO mice learn the task with similar trajectories, reaching asymptotic performance after about 20 sessions.", "source": "Figure 1G and Supplementary Figure 1", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs the training sessions of both genotypes; the dandiset holds one biased-task session.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2bc-prior-shift", "statement": "Mice use the block prior; rightward choices are more frequent in right-likely blocks than in left-likely blocks, most clearly when contrast is low, shifting the psychometric curve toward the likely side (shown for WT, and present but smaller in KO).", "source": "Figure 2B and 2C; Results, second section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_davatolhagh_2025.ipynb", "notes": "At 0% contrast P(right) is 0.831 (74 of 89) in right-likely blocks and 0.507 (37 of 73) in left-likely blocks, difference 0.325, one-sided Fisher p = 9.2e-06. The difference is 0.182 to 0.458 at every signed contrast except +100% (0.000), and the psychometric bias moves by 19.41% contrast between blocks. Whether the shift is smaller in KO than in WT is not testable here.", "deviations": [ "One session of one mouse; the test (Fisher exact at 0% contrast) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2bd-ko-smaller-shift", "statement": "KO mice shift their choices less between biased blocks than WT mice, with a difference in psychometric bias and none in slope or lapses.", "source": "Figure 2B to 2D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2ef-block-adaptation", "statement": "After a block switch, mice adapt their choices toward the newly likely side, and the proportion of choices toward the block side rises from an initial value A to an asymptote B with a time constant tau.", "source": "Figure 2E to 2G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_davatolhagh_2025.ipynb", "notes": "Over 14 switches between biased blocks, choices toward the new block side are 0.543 in trials 0 to 4 and 0.827 in trials 20 to 39 (one-sided Fisher p = 2.7e-06). The fit gives A = 0.480, B = 1.000 (at its bound) and tau = 25.12 trials (SE 16.14), so tau is poorly determined. Resampling the switches gives 95% intervals of 0.279 to 0.643 for A, 0.836 to 1.000 for B and 6.41 to 38.37 trials for tau; B exceeds A in every draw and tau is 40 or more in 0.018 of them. A maximum-likelihood fit on single trials gives A = 0.479, B = 1.000, tau = 25.03. At contrasts of 12.5% or less, 0.452 against 0.820, tau 21.57.", "deviations": [ "The paper's parametric curve is not given; B - (B - A) exp(-t / tau) over trials 0 to 39, all contrasts, was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2g-ko-slower-adaptation", "statement": "KO mice adapt more slowly after a block switch (longer tau, p = 0.004) and have lower initial performance after the switch (p = 0.041) than WT littermates.", "source": "Figure 2G; Results, second section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-contralateral-visual", "statement": "Visual cortex (VISp) responds robustly to contralateral visual stimuli.", "source": "Figure 3B; Results, third section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_davatolhagh_2025.ipynb", "notes": "Under the criterion, the right-minus-left and left-minus-right peaks both fall at the left edge of the frame (columns 0 and 2, rows 0 and 539), on the same side of the estimated midline (column 316), with trial tests at p = 0.053 and 0.14. These corner pixels are darker in the mean image (534 and 926) than 95% of the frame (5th percentile 1538), outside the imaged brain; the spatial components cover the whole frame with no mask. In a variant restricted to bright pixels 20 or more from the edge, the right-minus-left peak lies left of the midline (column 199) and the left-minus-right peak right of it (column 481), p = 8.1e-15 and 1.6e-17; the variant does not decide the outcome. It does not show that the lateralization is visual. At these two pixels the side difference exceeds 3 standard errors from 0.128 s after the stimulus, while the median movement onset is 0.086 s. Only 27 trials (13 right, 14 left) have no movement before 0.4 s; on them the difference at the two pixels points the same way (p = 0.02 and 0.091), but a masked peak search on these trials alone puts the peaks on the reverse sides (columns 550 and 72, p = 0.0062 and 0.012), which is not explained here. The slow trials exclude only wheel movement. In the same window paw speed and camera motion energy rise on 0.90 to 0.96 of all trials at 25 or 100% contrast, and wheel velocity, the right paw in both side cameras and the left camera's motion energy differ between right and left stimulus trials (p = 0.0005 or less); on the 27 slow trials paw speed rises on 0.44 to 0.78 of trials and the right paw in the right camera still differs by side (p = 0.014). Neither VISp nor the hemispheres can be named without an atlas registration.", "deviations": [ "Tested in image coordinates, with a midline estimated from the mean image, as the dandiset has no atlas registration.", "The peak search of the criterion did not exclude pixels outside the brain; the masked search is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3c-ko-elevated-activity", "statement": "KO mice show elevated dF/F across cortex in the ITI (most prominent in motor regions), stimulus and feedback periods compared with WT.", "source": "Figure 3C; Results, third section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype. The atlas registration needed for regional measures is also missing.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-ko-higher-correlation", "statement": "KO mice show globally increased pairwise correlations between regional dF/F time series during the task.", "source": "Figure 3D (legend labelled E); Results, third section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes and the registration to Allen areas, neither of which is in the dandiset; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3e-ko-higher-variance", "statement": "KO mice show higher pixel-wise trial-to-trial variance across all cortical regions and task periods.", "source": "Figure 3E; Results, third section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-full-cvr2", "statement": "The full linear encoding model explains more than half of single-trial cortical variance (cvR2 0.60 +/- 0.02 in KO and 0.54 +/- 0.02 in WT).", "source": "Figure 4B and 4C; Results, fourth section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_davatolhagh_2025.ipynb", "notes": "Full-model cvR2 is 0.471 pooled in pixel space (reading a), 0.422 as the mean over pixels (b) and 0.126 as the mean over components (c); minus the intercept-only model (the time-point columns alone), 0.123, 0.133 and 0.078. None is within 0.486 to 0.660; reading (a) is above 0.3, which the criterion counts as partial. Without the body camera's video components the pooled cvR2 is 0.414. Variants that do not decide the outcome are as follows. With the video components of the left and right cameras added, as in the paper (encoding_all_cameras.ipynb), cvR2 is 0.574 (a) and 0.525 (b), within the range, and 0.208 (c). With folds that keep each trial's frames together and each frame once per trial, it is 0.422, 0.363 and 0.047 with the body camera only, and 0.472, 0.405 and 0.046 with all three cameras, below the range. Over the masked pixels of the fig3b variant (pixels brighter than the median of the mean image and 20 or more from the edge) reading (b) is 0.434. The paper's Results give 0.60 and 0.54 as the full model's cvR2 and say it accounts for more than half of the variance, while its Figure 4C legend says the full model is shown with the trial time regressor subtracted out. Under that reading the values here are 0.123 and 0.133 (a, b) with the body camera and 0.226 and 0.236 with all three cameras, far below the range.", "deviations": [ "One session of one mouse of unknown genotype; the expected range spans the WT and KO means.", "No video components from the left and right cameras in the design that decides the outcome (left out for runtime; the body camera's are included; a second notebook adds them as a variant), paw speeds from Lightning Pose where the paper uses DeepLabCut, ROI motion energies assumed to be the whisker pads and body.", "The subjective prior is an action-kernel model fitted here; trial windows, the penalty selection (generalized cross-validation) and the readings of cvR2 were chosen here, as the paper's widefield model code is not public." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4cd-movement-dominates", "statement": "Movement predictors account for most of the explained variance; shuffling them reduces cvR2 by much more than shuffling task predictors (delta R2 for movement 0.40 +/- 0.02 in KO and 0.33 +/- 0.02 in WT; task shuffle beta -0.02).", "source": "Figure 4C and 4D; Results, fourth section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_davatolhagh_2025.ipynb", "notes": "Shuffling movement predictors lowers cvR2 by 0.104 (a), 0.119 (b) and 0.067 (c); shuffling task predictors by 0.017, 0.015 and 0.013. Movement dominates under every reading and in every fold (smallest movement drop 0.065, largest task drop 0.019), but the movement drop is below 0.297 to 0.440 under every reading. Without the body camera's video components the movement drop is 0.042 against 0.021 for task pooled, and 0.010 against 0.015 over components. Variants that do not decide the outcome are as follows. With folds by trial and each frame once per trial, the movement drop is 0.049, 0.060 and -0.005 against 0.017, 0.016 and 0.012 for task, so over components task exceeds movement, which the criterion would count as not reproduced. With all three cameras the movement drop is 0.216, 0.232 and 0.161 against 0.008, 0.008 and 0.007 for task, still below the range; with folds by trial, 0.109, 0.115 and 0.008 against 0.008, 0.008 and 0.000.", "deviations": [ "As for fig4c-full-cvr2; the missing side-camera video components likely lower the movement contribution." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4cd-ko-more-movement", "statement": "KO mice lose more explained variance than WT when movement predictors are shuffled (Group x Movement beta = 0.071, p = 0.006; delta R2 KO 0.40 against WT 0.33, p = 0.032), with no group difference for task predictors; full-model cvR2 tends to be higher in KO (p = 0.076).", "source": "Figure 4C and 4D; Results, fourth section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs2-ko-elevated-motion", "statement": "KO mice show elevated baseline motion energy relative to WT, with comparable stimulus-evoked movement dynamics after baseline correction.", "source": "Supplementary Figure 2", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs3-ko-higher-unique", "statement": "Individual movement variables explain more unique variance in KO than in WT mice, and task variables explain little unique variance in either group.", "source": "Supplementary Figure 3; Results, fourth section", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Needs mice of both genotypes; see fig1d-psychometric-params-genotype.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds one session of one mouse (sub-FD-28). The paper analyses 10 sessions from each of 11 wild-type and 8 Nrxn1a knockout mice. Eleven of the paper's findings, all comparisons between genotypes, cannot be tested." }, { "kind": "metadata_insufficient", "statement": "The genotype of the mouse is not given in the NWB files, the dandiset metadata, or the public IBL database (subject FD_28 has an empty genotype list, from a query made by hand during the attempt). The subject description is the paper's general description of the cross. A comment in the conversion script lists the session under knockout sessions, but next to a note that the list is a placeholder." }, { "kind": "data_missing", "statement": "Neither NWB file holds the cortical landmarks or the registration to the Allen atlas that the conversion code's documentation describes for the processed file (lab_meta_data localization and atlas_registration), so no pixel can be assigned to a cortical area." }, { "kind": "metadata_error", "statement": "Both imaging planes give the indicator as GCaMP6f; the paper's Methods and the file's keywords give GCaMP6s (CamKII-tTA x TRE-GCaMP6s)." }, { "kind": "metadata_error", "statement": "The raw file's imaging planes state an imaging rate of 15 Hz; the timestamps give 31.2 Hz per channel (32.03 ms intervals), and the Methods give 30 Hz." }, { "kind": "metadata_error", "statement": "The dandiset's keywords and description name \"CNTNALP2\", which is neither the gene of the paper and the files (Nrxn1a) nor a correct spelling of Cntnap2." }, { "kind": "metadata_error", "statement": "The wheel series state that counter-clockwise is positive, but trials whose choice is labelled counter_clockwise turn the wheel with negative velocity (95.5% of them 0.1 to 0.3 s after movement onset). The choice labels agree with the rewards, so the sign convention of the wheel or of the labels is misdescribed." }, { "kind": "metadata_error", "statement": "The wheel movement onset is described as the first movement after the go cue, but 151 of 899 onsets precede the go cue (by up to 0.18 s)." }, { "kind": "metadata_insufficient", "statement": "The ROI motion energy series give the ROI position in pixels but not the body part it covers; the paper's model uses whisker-pad and body motion energy." }, { "kind": "metadata_insufficient", "statement": "The SVD spatial components cover the whole 540 x 640 frame with no brain mask, and the corners of the frame carry large values in stimulus-evoked maps." }, { "kind": "other", "statement": "The dandiset has no published version; only the draft exists, so no version can be cited or pinned." }, { "kind": "methods_unavailable", "statement": "The paper's analysis code is to be made public on publication. The encoding code it links (churchlandlab/chiCa) implements the model for single-cell data in another task, not the widefield analysis." }, { "kind": "paper_inconsistency", "statement": "In the Figure 3 legend the correlation panel is labelled (E) twice and (D) is missing, the correlation panel's legend says the KO minus WT matrix shows reduced inter-regional correlations while the Results say correlations are increased, and the legend of panel C describes variance difference maps, as does panel E." } ], "verifications": [ { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file. bioRxiv refused its requests, so it read only the abstract and relied on the claims file's account of the paper's methods. It queried the archive's metadata for the blocked claims and tested the helper functions on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; all 18 agree with the record.", "agreed": 18, "of": 18, "disagreements": [] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebooks of the revision (reproduce_davatolhagh_2025.ipynb and encoding_all_cameras.ipynb), the helper module, the claims file and this record. bioRxiv refused its requests and Europe PMC has no full text, so it could not read the paper. It queried the dandiset's metadata from the DANDI API and downloaded no data. It agreed with all 18 outcomes.", "agreed": 18, "of": 18, "disagreements": [] } ] }, { "id": "001754-knierim-2000-01", "dandiset": "001754", "dandiset_version": "0.260728.1352", "paper": "10.1038/72910", "paper_title": "Three-dimensional spatial selectivity of hippocampal neurons during space flight", "date": "2026-10-14", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "runs", "entry": "001754-knierim-2000", "entry_title": "Place cells during space flight on the Neurolab mission (Knierim et al. 2000)", "description": "Tests the findings of Knierim, McNaughton and Poe (2000) that can be tested on dandiset 001754, which holds sorted units, task epochs, rate maps and spike-time positions of three rats recorded before and during the Neurolab shuttle mission. It tests spatial selectivity on the Escher staircase in flight, spatial information in flight against preflight, and the stability of place fields across two sessions. The paper is not open access; claims come from its abstract, its figure titles and the dandiset's description. There is no EEG in the dandiset.", "notebooks": [ { "path": "reproduce_knierim_2000.ipynb", "title": "Reproducing Knierim et al. (2000) from dandiset 001754", "executed": "notebooks/001754-knierim-2000/reproduce_knierim_2000.html" } ], "outcomes": [ { "claim": "flight-spatial-code", "statement": "Hippocampal neurons recorded on the space shuttle form a robust spatial code on the three-dimensional Escher staircase track in weightlessness.", "source": "Abstract; dandiset description (\"Place cells eventually demonstrated normal spatially specific firing\")", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "The third verification round agreed with the change from partially_reproduced to not_reproduced. On flight day 9, 12 of 25 Rat1 units (0.48) have spatial information above the 95th percentile of 500 circular-shift shuffles on the Escher staircase (binomial p = 6.9e-10 against 0.05), and 3 of 28 Rat2 units (0.107, p = 0.16). By the criterion Rat1 is above chance but below 0.5 and Rat2 is not above chance, so neither the reproduced nor the partially reproduced rule is met. With spikes at the lost position given a neighbouring position, as in the first version, Rat1 had 13 of 25 (0.52), which gave partially_reproduced. Rat1 FD9 is close to the bound. 6 units have p between 0.01 and 0.1, repeats with 2000 shuffles and five other seeds give 11 or 12 of 25 (0.44 to 0.48), and the run of 200 shuffles in the data check, with the same lookup, gives 13 of 25 (0.52); across these seven runs the count is 11 to 13 of 25, on both sides of 0.5, so the outcome for Rat1 is not robust. The outcome follows the pre-specified run of 500 shuffles, with which the five repeats of 2000 shuffles agree. Rat2 FD9 gives 2 or 3 of 28 in every repeat. Shifted spikes are dropped for lack of a position more often in Rat2's ES epochs (median 0.307 on FD9) than in Rat1's (0.074), but a count-matched variant gives the same counts for Rat2. Rat2's units are not selective with the shared position trace in any window, and Rat1's units are selective in Rat2's FD4 ES epoch (6 of 15), so the trace in Rat2's epochs may not be Rat2's position; the files do not name the animal tracked. On flight day 4, 10 of 20 Rat1 units, 0 of 16 Rat2 units, and 10 of 16 and 1 of 19 Rat3 units in its two ES epochs are significant. In MC epochs 0 to 2 units per session are significant. The \"three orthogonal surfaces\" part of the abstract is tested apart, and blocked.", "deviations": [ "The paper's Methods were not available; the selection (50 spikes at a known position), the 32 x 32 binning, the shuffle and the thresholds are common choices fixed in the claims file.", "Occupancy is the original analysis's occupancy map for the epoch, and shuffled spikes take the nearest position sample within 0.25 s, as the dandiset gives position only at spike times. A spike whose nearest sample is the lost position is dropped.", "Robust is read as at least half of the units significant in each flight day 9 session.", "Rat2's flight day 9 session is judged although whose position the trace holds in it could not be established." ], "disagreed": true, "data": "dandiset", "where": null, "proposed": null }, { "claim": "three-orthogonal-surfaces", "statement": "The spatial code covers each of the three orthogonal surfaces of the Escher staircase.", "source": "Abstract", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The dandiset holds one two-dimensional pixel position per time from one camera. Nothing in the files or the dandiset metadata describes the camera's view or the track layout, and the conversion code describes the ES track only as a three-dimensional track with 90 degree yaw and pitch turns and the position as video tracker pixel coordinates (its lines are printed in the notebook), so pixels cannot be assigned to the three surfaces. The NASA record of the study (OSD-968) says position was recorded with two synchronised cameras (printed in the notebook); a second view is not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "si-comparable-to-preflight", "statement": "In flight, spatial information content of place cells is comparable to preflight levels.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "Flight day 9 ES rate maps (64, Rats 1 and 2) have a median spatial information of 1.385 bits/spike against 1.448 for preflight ES maps (53); two-sided Mann-Whitney p = 0.45, difference -0.064 bits/spike, ratio 0.96. Per rat, CEL-named maps only, maps with a peak of 1 Hz or more, MC maps, all flight maps, bins with 5 or more occupancy counts (p = 0.44) and information adjusted for rate x occupancy (p = 0.45), all give p of 0.20 or more. Rate x occupancy is proportional to the spike count in the flight maps (about 22 per spike) and is assumed to be so in the preflight maps, where it cannot be checked. Information falls with the spike count (Spearman rho -0.252 over all ES maps). Rat1's compared sessions have similar counts and Rat2's do not (median unit spikes 359 and 352 preflight, 437 and 205 on FD9; median rate x occupancy 7862 and 7628 against 9105 and 5226), so Rat2's FD9 maps rest on fewer spikes, which by sampling bias raises their spatial information. The rate maps are smoothed with an unstated kernel, so no shuffle-corrected value could be computed. The dandiset description says preflight was recorded on a flat rectangular track, so this may compare different apparatus. Rat2's FD9 ES maps have a median of 1.343 bits/spike although only 3 of its 28 units are significant against shuffles, so the rate maps' spatial information does not show that Rat2's cells were selective.", "deviations": [ "The source is the dandiset's description of the paper's findings, not the paper's text.", "The paper's test is unknown; a two-sided Mann-Whitney U test at 0.05 was fixed in advance.", "Spatial information comes from the original rate maps, without correction for the number of spikes, as the preflight files hold no position.", "The -999 bins and the lost-position bin [63, 0] are left out of each map.", "The preflight epochs labelled ES may have been recorded on a flat rectangular track, as the dandiset description says." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fd4-abnormal-selectivity", "statement": "On the first in-flight exposures (flight day 4) spatial selectivity was abnormal.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "Flight day 4 ES rate maps (107, Rats 1 to 3) have a median of 1.214 bits/spike against 1.441 preflight (98); one-sided Mann-Whitney p = 0.055, above the criterion's 0.05 (ratio 0.84). The FD4 median is lower in each rat (ratios 0.65 to 0.88), significantly only for Rat1 (p = 0.032); with maps of peak rate 1 Hz or more p = 0.0095, with information adjusted for rate x occupancy p = 0.0025, over bins with 5 or more occupancy counts p = 0.053. Rat1's and Rat2's FD4 maps have fewer spikes than preflight, so sampling bias works against the claim. FD4 against FD9 for Rats 1 and 2 gives 1.148 against 1.385 (p = 0.21); spike-based information minus the shuffle mean is lower on FD4 for Rats 1 and 2 (p = 0.015) and not with Rat3 included (p = 0.13). The spike-based fraction of significant units is 21 of 71 on FD4 and 15 of 53 on FD9 (p = 0.64). The direction agrees with the claim and the criterion's test falls just short.", "deviations": [ "The source is the dandiset's description of the paper's findings, not the paper's text.", "Abnormal is read as lower spatial information; the description does not say what was abnormal.", "The paper's test is unknown; a one-sided Mann-Whitney U test at 0.05 was fixed in advance.", "The preflight epochs labelled ES may have been recorded on a flat rectangular track, as the dandiset description says." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-stability-across-sessions", "statement": "Place fields are stable across sessions.", "source": "Figure 3 (title only; which sessions the figure compares is not known)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "In Rat3's two flight day 4 ES epochs, the 15 units with 50 or more spikes in each have a median rate-map correlation of 0.537 (range -0.107 to 0.849), above the 95th percentile of 1000 re-paired medians (0.102, p = 0.001) and above 0.5; 8 of 15 exceed 0.5. With smoothing of 0.5 to 2 bins and 50 or 100 spikes the median is 0.315 to 0.707, always above its null (p = 0.001); at 0.5 bins it is below 0.5. Mean rates are related across the epochs (Spearman rho 0.598, re-paired 95th percentile 0.339), consistent with the same neurons but not showing it. The dandiset's rate maps paired by their ~N names give a median of 0.157, as the names do not identify cells. In the second epoch 1 of 19 units is significant against 10 of 16 in the first, with similar occupancy and shuffle drops and more spikes per tested unit in the second (median 455 against 301); this is not explained. The original spike files in OSD-968 hold waveform amplitudes for each spike, according to the conversion notes, and could test the identity assumption; they were not used.", "deviations": [ "Only the title of Figure 3 was available; which sessions it compares is unknown. The test uses the only pair of same-track sessions with position on one day.", "Assumes that a tetrode and cluster id names the same neuron in both epochs; the dandiset does not say so and holds no waveforms to check it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "theta-normal", "statement": "Hippocampal EEG showed normal theta rhythm during locomotion in flight.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No file holds EEG or any continuous voltage. The unfiltered listing of every file shows an empty acquisition group and no ElectricalSeries or LFP; the files hold units, epochs, position and rate maps. The NASA record OSD-968 describes its files as spike files, rate-map files, legacy metadata and NWB copies, and its metadata does not mention EEG, theta, ripples or LFP (printed in the notebook). Its archives, including the 272 MB processed archive, were not opened, so an EEG file inside one cannot be ruled out.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ripples-normal", "statement": "Hippocampal EEG showed normal sharp waves and ripples during quiet rest in flight.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No EEG in the dandiset, nor listed in OSD-968 (see theta-normal).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The Rat1 and Rat2 files of each flight day hold the same position trace (98.6 to 98.8% of samples at common timestamps within 2 pixels), presented as each rat's position. Rat1's units are spatially selective with it, Rat2's are not in any window, and Rat1's units are also selective in Rat2's flight day 4 ES epoch. Each file samples the trace at its own units' spike times, and the files do not name the animal the tracker followed. Whose position the trace is during Rat2's task epochs is not stated and could not be established." }, { "kind": "data_missing", "statement": "Position is given only at spike times (taken from the spike files), so occupancy cannot be computed from the files' position, and the preflight files have no position at all." }, { "kind": "metadata_error", "statement": "The dandiset description says the preflight recordings were made on a flat rectangular track, but the preflight files label their epochs ES (Escher staircase) and MC (Magic Carpet) and hold ES and MC rate maps, as the flight files do. Which apparatus the preflight epochs were recorded on is not stated in the files." }, { "kind": "identifier_missing", "statement": "The rate-map `source_file` names are Windows 8.3 short names (ESCELL~1 to ~4, then hashed names such as ES2BC0~1), so `cell_number`, read from the ~N suffix, is not a cell number. It equals the cluster id of the best-matching unit in 84 of 211 unit-epochs, and the rate maps cannot be linked to units as the table's description says. The long names are in the NASA archive (OSD-968), whose description names files like BL2.cell5." }, { "kind": "metadata_insufficient", "statement": "The rate maps are smoothed (in the median well-matched map, 91% of the bins with a positive rate hold no spike of the unit), and the kernel is not stated." }, { "kind": "metadata_insufficient", "statement": "Rate maps use -999 for unvisited bins, which the column description (rate in Hz) does not state. The tracker's lost position (0, 255), 5 to 12% of position samples, is counted in the original occupancy maps (bin [63, 0], up to 19% of an occupancy map in flight)." }, { "kind": "other", "statement": "Eight rate maps are identical copies of another map in the same file, some stored under a different tetrode (for example Rat1 FD4 TT1 and TT11 ESCELL~1, and four maps of Rat2 FD4 under TT13, TT19 and TT22)." }, { "kind": "metadata_insufficient", "statement": "Units merge per-epoch spike files that share a tetrode and cluster id; nothing states that a cluster id names the same neuron in different epochs. The unit table lacks the `session_type` and `source_file` columns the conversion's README lists, so a unit's spikes cannot be traced to their spike file." }, { "kind": "data_missing", "statement": "The dandiset's description reports normal theta and sharp waves and ripples in the hippocampal EEG, but no EEG is in the dandiset." }, { "kind": "other", "statement": "Spike times are given to 10 ms in five files and to 1 ms or finer in three; 2 to 15% of within-unit intervals are zero, in every epoch type and not mainly in overlapping epochs; their cause is not resolved. In the Rat1 flight day 4 file two baseline epochs overlap (2525 to 3390 s and 2720 to 3390 s)." }, { "kind": "metadata_insufficient", "statement": "The age is \"/\" for every subject, and the position's pixel scale and camera view are not described." } ], "verifications": [ { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's abstract and figure titles from the publisher's page (the paper is not open access). The verifier checked the archive's asset metadata for the blocked claims and ran synthetic checks of skaggs_info, rma_info, merge_bins, bin_xy and PositionLookup.", "agreed": 7, "of": 7, "disagreements": [] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the first revision, with its conclusions and summary, the helper module, the claims file, the README and this attempt record, with the paper's abstract and figure titles from the publisher's page.", "agreed": 6, "of": 7, "disagreements": [ { "claim": "flight-spatial-code", "outcome": "not_reproduced", "reason": "Agrees with the proposed not_reproduced and no longer with partially_reproduced. The pre-specified run gives Rat1 FD9 12 of 25 (0.48) and Rat2 FD9 3 of 28 (p 0.16), and the criterion maps that to not_reproduced; the five repeats with 2000 shuffles give 11 or 12 of 25. The result still sits on the 0.5 bound, as cell 23, with the corrected lookup and 200 shuffles, gives 13 of 25 (0.52), and the conclusions, the summary and the proposed reason leave it out; across the seven runs the count is 11 to 13 of 25, which straddles the bound, so the proposed not_reproduced is not robust. Whose position the trace holds in Rat2's epochs is disclosed but unresolved, and decides whether Rat2 FD9 is a valid judged session." } ] }, { "date": "2026-10-14", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The proposed change of flight-spatial-code to not_reproduced, with the full executed notebook of the second revision, the helper module, the claims file and this attempt record.", "agreed": 1, "of": 1, "disagreements": [] } ] }, { "id": "001754-knierim-2000-02", "dandiset": "001754", "dandiset_version": "draft", "paper": "10.1038/72910", "paper_title": "Three-dimensional spatial selectivity of hippocampal neurons during space flight", "date": "2026-10-15", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "001754-knierim-2000", "entry_title": "Place cells during space flight on the Neurolab mission (Knierim et al. 2000)", "description": "Tests the findings of Knierim, McNaughton and Poe (2000) that can be tested on dandiset 001754, which holds sorted units, task epochs, rate maps and spike-time positions of three rats recorded before and during the Neurolab shuttle mission. It tests spatial selectivity on the Escher staircase in flight, spatial information in flight against preflight, and the stability of place fields across two sessions. The paper is not open access; claims come from its abstract, its figure titles and the dandiset's description. There is no EEG in the dandiset.", "notebooks": [ { "path": "reproduce_knierim_2000.ipynb", "title": "Reproducing Knierim et al. (2000) from dandiset 001754", "executed": "notebooks/001754-knierim-2000/reproduce_knierim_2000.html" } ], "outcomes": [ { "claim": "flight-spatial-code", "statement": "Hippocampal neurons recorded on the space shuttle form a robust spatial code on the three-dimensional Escher staircase track in weightlessness.", "source": "Abstract; dandiset description (\"Place cells eventually demonstrated normal spatially specific firing\")", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "On flight day 9, 10 of 25 Rat1 units (0.40) have spatial information above the 95th percentile of 500 circular-shift shuffles on the Escher staircase (binomial p = 1.6e-7 against 0.05), and 2 of 28 Rat2 units (0.071, p = 0.41). By the criterion Rat1 is above chance but below 0.5 and Rat2 is not above chance, so neither the reproduced nor the partially reproduced rule is met. Repeats with 2000 shuffles and five other seeds give 10 or 11 of 25 for Rat1 and 2 of 28 for Rat2, and the run of 200 shuffles in the data check gives 10 and 2; 5 Rat1 units have p between 0.01 and 0.1. The outcome is the same as in 001754-knierim-2000-01, which recorded 12 of 25 for Rat1 (11 to 13 over seven runs); on the earlier version's files the notebook gives 11 or 12 of 25 for Rat1 and 2 or 3 of 28 for Rat2 over five seeds. Every real spike has a sample at its own time in both versions; the draft's trace adds samples at the other rat's spike times in each window, so shifted spikes find a sample more often and the shuffles change. Shifted spikes are now dropped about as often in Rat2's FD9 ES epoch (median 0.058) as in Rat1's (0.060), against 0.306 to 0.307 and 0.074 to 0.075 on the earlier version's files, and a count-matched variant gives 12 of 25 (0.48) for Rat1 and 2 of 28 for Rat2. With each unit's spikes replaced by a Poisson train of the same mean count, 9 of 122 flight ES units are significant (0.074, binomial p = 0.16 against 0.05), and 12 of 125 (0.096, p = 0.023) when each spike is moved to its nearest position sample, which reproduces the real drop rates; per session the false-positive fraction is 0 to 0.21, and in the judged sessions 0.160 and 0.154 for Rat1 and 0.037 and 0.214 for Rat2. Against these fractions Rat1's 10 of 25 is still above chance (p = 0.0035 and 0.0026) and Rat2's 2 of 28 is not (p = 0.28 and 0.99), so the outcome is the same, though the criterion's 0.05 is below the false-positive fraction of some sessions. With each unit's real train reversed in time within its epoch, which keeps its bursts and changes in rate and breaks its relation to the position, 2 of 122 flight ES units are significant (1 of 25 in Rat1's FD9 session, 0 of 27 in Rat2's), and Rat3's ES1 trains against the ES2 trace and the reverse give 0 of 16 and 0 of 19, so with real temporal structure the test is conservative. A unit's 95th percentile of the shuffles is nearly the same for its reversed train (Spearman rho 0.995), 1.7 to 2.3 times that of a Poisson train of the same count per session, and higher the fewer 10 s periods hold its spikes (rho -0.874 with the effective fraction of 10 s bins filled) and the fewer spikes it has (rho -0.601); the two explain 80% of its variance on a log scale. Rat2's FD9 units are the most clumped (median 0.145 of the bins, against 0.190 to 0.358 in the other sessions) and have the highest median 95th percentile (3.572). The test has less power for such units, and its power was not measured, so a low fraction, Rat2's especially, is weak evidence against a spatial code; the criterion's rule decides the outcome. The trace moves as a tracked animal would in Rat2's windows (median step 0.50 pixels and path length 33.0 pixels per second in its FD9 ES window), and units of neither rat are selective in any MC window (0 to 2 of 11 to 32), so neither settles whose position it is. Rat2's units are not selective with the trace in any window (1 of 16 and 2 of 28 in their own ES epochs, 0 of 15 and 0 of 41 in Rat1's), and Rat1's units are selective in Rat2's FD4 ES epoch (10 of 15), so the trace in Rat2's epochs may not be Rat2's position; the files say it is taken to be, and that the source does not name the animal tracked. On flight day 4, 11 of 20 Rat1 units, 1 of 16 Rat2 units, and 11 of 16 and 1 of 19 Rat3 units in its ES1 and ES2 epochs are significant. In MC epochs 0 to 2 units per session are significant. The \"three orthogonal surfaces\" part of the abstract is tested apart, and blocked.", "deviations": [ "The paper's Methods were not available; the selection (50 spikes at a known position), the 32 x 32 binning, the shuffle and the thresholds are common choices fixed in the claims file.", "Occupancy is the original analysis's occupancy map for the epoch, and shuffled spikes take the nearest position sample within 0.25 s, as the dandiset gives position only at spike times. A spike whose nearest sample is the lost position is dropped.", "Robust is read as at least half of the units significant in each flight day 9 session.", "Rat2's flight day 9 session is judged although whose position the trace holds in it could not be established." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "three-orthogonal-surfaces", "statement": "The spatial code covers each of the three orthogonal surfaces of the Escher staircase.", "source": "Abstract", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The dandiset holds one two-dimensional pixel position per time from one camera. The draft's position reference frame says the camera view and the pixel size on the apparatus are not recorded in the source files, nothing in the files or the dandiset metadata describes the track layout in the image, and the conversion code at the new commit describes the ES track only as a three-dimensional track with 90 degree yaw and pitch turns (its lines are printed in the notebook), so pixels cannot be assigned to the three surfaces. The NASA record of the study (OSD-968) says position was recorded with two synchronised cameras (printed in the notebook); a second view is not in the dandiset. Same outcome as in 001754-knierim-2000-01.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "si-comparable-to-preflight", "statement": "In flight, spatial information content of place cells is comparable to preflight levels.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "Flight day 9 ES rate maps (64, Rats 1 and 2) have a median spatial information of 1.385 bits/spike against 1.448 for preflight ES maps (53); two-sided Mann-Whitney p = 0.45, difference -0.064 bits/spike, ratio 0.96. The main test's maps and numbers are the same as in 001754-knierim-2000-01, and so is the outcome. Per rat (p = 0.25 and 0.88), maps with archived names containing CEL (0.43), maps with a peak of 1 Hz or more (0.89), MC maps (0.92), all flight maps (0.12), bins with 5 or more occupancy counts (0.44) and information adjusted for rate x occupancy (0.37) all give p of 0.12 or more. Rate x occupancy is proportional to the spike count in the flight maps (about 22 per spike) and is assumed to be so in the preflight maps, where it cannot be checked. Information falls with the spike count (Spearman rho -0.226 over all ES maps). Rat1's compared sessions have similar counts and Rat2's do not (median unit spikes 359 and 352 preflight, 437 and 205 on FD9; median rate x occupancy 7862 and 7628 against 9105 and 5226), so Rat2's FD9 maps rest on fewer spikes, which by sampling bias raises their spatial information. The rate maps are smoothed with an unrecorded kernel, so no shuffle-corrected value could be computed. The dandiset description says preflight was recorded on a flat rectangular track, so this may compare different apparatus, and Rat2's preflight file shares no tetrode with its flight files. Rat2's FD9 ES maps have a median of 1.343 bits/spike although only 2 of its 28 units are significant against shuffles, so the rate maps' spatial information does not show that Rat2's cells were selective. Over the 124 tested flight ES units, the rate maps of units significant against shuffles have a higher median than the others (1.855 against 1.076, p = 9.0e-7), but Rat2's 26 non-significant FD9 units have a median of 1.283, close to the preflight 1.448. The bootstrap 95% interval of the FD9 minus preflight median difference is -0.425 to 0.312 bits/spike (-29% to +22% of the preflight median); for Rat1 alone it is -0.750 to 0.543 (p = 0.25). The test has no equivalence margin, so a drop of up to 29% of the preflight median (40% for Rat1 alone) is not excluded, and the result shows only that no difference was detected.", "deviations": [ "The source is the dandiset's description of the paper's findings, not the paper's text.", "The paper's test is unknown; a two-sided Mann-Whitney U test at 0.05 was fixed in advance.", "Spatial information comes from the original rate maps, without correction for the number of spikes, as the preflight files hold no position.", "The unvisited bins (NaN) and the lost-position bin [63, 0] are left out of each map.", "The preflight epochs labelled ES may have been recorded on a flat rectangular track, as the dandiset description says.", "The assignment of the preflight files to rats is taken from the files, though the conversion notes list it as an open question." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fd4-abnormal-selectivity", "statement": "On the first in-flight exposures (flight day 4) spatial selectivity was abnormal.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "Flight day 4 ES rate maps (104, Rats 1 to 3) have a median of 1.177 bits/spike against 1.441 preflight (98); one-sided Mann-Whitney p = 0.024, below the criterion's 0.05 (ratio 0.82). This differs from 001754-knierim-2000-01 (not_reproduced, 107 maps, p = 0.055) because the draft leaves out every copy in the groups of identical maps, and three Rat2 FD4 ES maps that the first attempt counted once each (7.583 bits/spike each, mean rate below 0.001 Hz) are no longer in the dandiset. On the earlier version's maps the test gives p = 0.055 with all 107 distinct maps and p = 0.024 with the 104 that are in the draft, so the outcome rests on whether those three maps are counted. The FD4 median is lower in each rat (ratios 0.65 to 0.88), significantly only for Rat1 (p = 0.032). The test passes with maps of peak rate 1 Hz or more (p = 0.0095), over bins with 5 or more occupancy counts (p = 0.023) and with information adjusted for rate x occupancy (p = 0.0011), and not with maps whose archived names contain CEL (p = 0.073) or with MC maps (p = 0.060). Rat1's and Rat2's FD4 maps have fewer spikes than preflight, so sampling bias works against the claim. FD4 against FD9 for Rats 1 and 2 gives 1.081 against 1.385 (p = 0.095); spike-based information minus the shuffle mean is 0.025 against 0.211 for Rats 1 and 2 (p = 0.13) and 0.232 against 0.211 with Rat3 (p = 0.31). The spike-based fraction of significant units is 24 of 71 on FD4 and 12 of 53 on FD9 (p = 0.94), so the spike-based measures do not show lower selectivity on flight day 4. Without Rat2, whose position trace could not be attributed, Rats 1 and 3 give 1.242 against 1.510 (p = 0.035), on the draft and on the earlier version alike, as the three left-out maps are Rat2's.", "deviations": [ "The source is the dandiset's description of the paper's findings, not the paper's text.", "Abnormal is read as lower spatial information; the description does not say what was abnormal.", "The paper's test is unknown; a one-sided Mann-Whitney U test at 0.05 was fixed in advance.", "The preflight epochs labelled ES may have been recorded on a flat rectangular track, as the dandiset description says.", "The draft leaves out all copies of identical maps; three Rat2 FD4 ES maps counted in the first attempt are not in the test." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3-stability-across-sessions", "statement": "Place fields are stable across sessions.", "source": "Figure 3 (title only; which sessions the figure compares is not known)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_knierim_2000.ipynb", "notes": "In Rat3's two flight day 4 ES epochs, the 15 units with 50 or more spikes in each have a median rate-map correlation of 0.537 (range -0.107 to 0.849), above the 95th percentile of 1000 re-paired medians (0.102, p = 0.001) and above 0.5; 8 of 15 exceed 0.5. These numbers and the outcome are the same as in 001754-knierim-2000-01. With smoothing of 0.5 to 2 bins and 50 or 100 spikes the median is 0.315 to 0.707, always above its null (p = 0.001); at 0.5 bins it is below 0.5. The dandiset's ES1 and ES2 rate maps, now linked to the same unit, give a median of 0.340 over 18 units (0.157 in the first attempt, when maps were paired by short names). A unit is the same sorted cluster in both epochs, as the units' description now states; mean rates are related across the epochs (Spearman rho 0.598, re-paired 95th percentile 0.339). In the first epoch 11 of 16 units are significant against shuffles and in the second 1 of 19, with similar occupancy and shuffle drops and more spikes per tested unit in the second (median 455 against 301). For several stable units the 95th percentile of the shuffles rises more than their information in the second epoch (TT4 cluster 1, information against 95th percentile, 2.449 against 1.326 and then 3.592 against 4.305; TT5 cluster 1, 0.910 against 0.504 and then 1.472 against 2.393); the epochs use 348 and 299 bins with 5 or more occupancy counts. Poisson trains give 0 to 2 false positives in either epoch. These units fire fewer spikes in fewer 10 s periods in the second epoch (TT4 cluster 1, 1582 spikes filling an effective 0.267 of the 10 s bins and then 423 filling 0.096; TT5 cluster 1, 8844 at 0.575 and then 2221 at 0.307), which raises the shuffles' 95th percentile (see flight-spatial-code); the stability measure does not use the shuffle test.", "deviations": [ "Only the title of Figure 3 was available; which sessions it compares is unknown. The test uses the only pair of same-track sessions with position on one day.", "Takes the same sorted cluster in both epochs to be the same neuron; the files hold no waveforms to check it." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "theta-normal", "statement": "Hippocampal EEG showed normal theta rhythm during locomotion in flight.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No file holds EEG or any continuous voltage. The unfiltered listing of every file shows an empty acquisition group and no ElectricalSeries or LFP, and the draft's experiment description says no EEG or other continuous voltage was archived. The NASA record OSD-968 describes its files as spike files, rate-map files, legacy metadata and NWB copies, and its metadata does not mention EEG, theta, ripples or LFP (printed in the notebook). Its archives were not opened, so an EEG file inside one cannot be ruled out. Same outcome as in 001754-knierim-2000-01.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ripples-normal", "statement": "Hippocampal EEG showed normal sharp waves and ripples during quiet rest in flight.", "source": "Dandiset description (not checked against the paper's text)", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No EEG in the dandiset, nor listed in OSD-968 (see theta-normal). Same outcome as in 001754-knierim-2000-01.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "Partly fixed since 001754-knierim-2000-01. Each flight file now holds the shared tracker's trace only within its own rat's ES and MC epochs and says the trace there is taken to be that rat's position, and that the source does not name the animal tracked. Rat2's units are not spatially selective with the trace in any window (1 of 16 and 2 of 28 in Rat2's ES epochs, 0 of 15 and 0 of 41 in Rat1's), and Rat1's units are selective in Rat2's flight day 4 ES epoch (10 of 15), when Rat1 is labelled as on baseline. The trace moves as a continuous track in Rat2's windows, and units of neither rat are selective in any MC window, so neither settles it. Whose position the trace is during Rat2's task epochs is still not established." }, { "kind": "data_missing", "statement": "Still present. Position is given only at spike times (taken from the spike files), so occupancy cannot be computed from the files' position, and the preflight files have no position at all. The draft's position description now states this." }, { "kind": "metadata_error", "statement": "Still present. The dandiset description says the preflight recordings were made on a flat rectangular track, but the preflight files label their epochs ES (Escher staircase) and MC (Magic Carpet) and hold ES and MC rate maps, as the flight files do. Which apparatus the preflight epochs were recorded on is not stated in the files." }, { "kind": "metadata_insufficient", "statement": "Partly fixed. The rate-map description now says the maps are smoothed, but the kernel is not recorded (in the median well-matched map, 91% of the bins with a positive rate hold no spike of the unit)." }, { "kind": "data_missing", "statement": "Partly fixed. The files' experiment description now says no EEG was archived, but the dandiset's description still reports normal theta and sharp waves and ripples in the hippocampal EEG, and no EEG is in the dandiset." }, { "kind": "metadata_insufficient", "statement": "Partly fixed. The age is still \"/\" for every subject, now with a subject description saying it is not recorded, and the position's reference frame now says the camera view and pixel size are not recorded; the map geometry is given in pixels. The age, pixel scale and camera view themselves are missing." }, { "kind": "metadata_insufficient", "statement": "New. Rat2's preflight units are on tetrodes TT0 to TT10 and its flight units on TT12 to TT22, with no tetrode in common, while Rat1's and Rat3's preflight and flight tetrodes overlap. The conversion notes list whether the preflight folders are assigned to the right rats as an open question, and nothing in the files settles it, so per-rat comparisons with preflight rest on an unconfirmed assignment." } ], "verifications": [ { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the draft with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's abstract and figure titles (the paper is not open access). The verifier queried the archive's asset metadata for the blocked claims and ran a synthetic calibration of the shuffle test and checks of skaggs_info, merge_bins and the PositionLookup test.", "agreed": 7, "of": 7, "disagreements": [] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the first revision of the draft, with its conclusions and summary, the helper module, the claims file, the README and this attempt record, with the paper's abstract and figure titles.", "agreed": 7, "of": 7, "disagreements": [] } ] }, { "id": "001878-sun-2021-01", "dandiset": "001878", "dandiset_version": "draft", "paper": "10.22002/d1.1991", "paper_title": "CalMS21 - Caltech Mouse Social Interactions (Sun et al., 2021)", "date": "2026-10-19", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001878-sun-2021", "entry_title": "CalMS21 mouse social behavior dataset (Sun et al. 2021)", "description": "Tests the claims of Sun et al. (2021), the paper describing the CalMS21 dataset of resident-intruder pose and behavior annotations, on dandiset 001878, which holds one CalMS21 sequence (Task 1 test sequence mouse071) with its video, and on the full dataset deposited on CaltechDATA. It checks the format, identities and annotations of the dandiset's sequence, links it to the deposit, and tests the dataset's counts and label fractions. The model benchmarks are not run.", "notebooks": [ { "path": "reproduce_sun_2021.ipynb", "title": "Reproducing Sun et al. (2021) from dandiset 001878 and the CalMS21 deposit", "executed": "notebooks/001878-sun-2021/reproduce_sun_2021.html" } ], "outcomes": [ { "claim": "format-keypoints", "statement": "Each frame holds seven MARS keypoints (nose, left ear, right ear, neck, left hip, right hip, tail base) for each of two mice, the resident (mouse 0) and the intruder (mouse 1), in pixel coordinates of a 1024 x 570 image, at 30 Hz, with a confidence score from 0 to 1 for each keypoint.", "source": "Section 3 and Figure 3; Appendix C (data format); Appendix D.1", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "The file holds 14 keypoint series named for the seven parts of the resident and the intruder, in pixels, at 30 Hz, with every coordinate inside the 1024 x 570 image (x 5.0 to 991.2, y 9.0 to 563.3). The confidence field is present for every keypoint but all 333,340 values are NaN, so the confidence part of the claim fails.", "deviations": [ "Judged on the one CalMS21 sequence in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "resident-is-black", "statement": "Mouse 0, the resident, is the black C57Bl/6J mouse, and mouse 1, the intruder, is the white BALB/c mouse.", "source": "Appendix C; Appendix B (Collection Process); Appendix D.1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "In 746 of 794 sampled frames (every 30th) the body centres are at least 60 px apart; in all of them the 12 px patch on the resident is darker than the one on the intruder (median grey level 46.4 against 250.9). With 8 and 24 px patches the fractions are 0.997 and 1.000, with separations of 30 and 120 px 0.999 and 1.000, and 1.0 in every minute.", "deviations": [ "The coat colour test (grey level of the video at the body centre) was chosen here; the paper states the identities without a test." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "task1-vocab", "statement": "Task 1 frames are annotated by one annotator (annotator id 0) with exactly one label per frame from the vocabulary attack 0, investigation 1, mount 2 and other 3.", "source": "Section 3; Appendix C (metadata and vocab)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "The catalogue holds attack 0, investigation 1, mount 2 and other 3; the bouts give the annotator as \"CalMS21 annotator 0\"; the 170 bouts tile the session from 0 to 793.67 s with no gaps, so all 23,810 frames have exactly one label. The session has no attack bouts.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "task1-video", "statement": "The source videos of Task 1 are released, recorded at 30 Hz and 1024 x 570 pixels.", "source": "Section 3.1; Appendix D.1", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "The video is 1024 x 570, h264, at 30 frames per second with 23,810 frames, equal to the pose. Its motion energy correlates best with the pose speed at lag 0 (r = 0.754, falling to 0.19 and 0.26 at 15 frames either way). It is 184,059,454 bytes against 964,451,532 for CaltechDATA's mouse071_task1_annotator1.mp4, so it was re-encoded; the two were not compared frame by frame.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "contact-during-social-behaviors", "statement": "Close investigation, attack and mount are behaviors in which the resident is in close contact with the intruder; other frames include the animals apart.", "source": "Appendix D.2 (behavior definitions)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "Median distance from the resident's nose to the nearest intruder keypoint is 21.4 px in 4,679 investigation frames and 15.0 px in 2,894 mount frames, against 376.0 px in 16,237 other frames (differences -354.6 and -361.0 px, 95% block bootstrap intervals -408.9 to -295.2 and -413.6 to -303.8, with blocks of contiguous session time). The centroid distance gives -307.2 and -355.5 px, with intervals excluding 0, and each half of the session gives the same order. Attack is absent from the session, so the attack part of the statement is untested.", "deviations": [ "The paper defines the behaviors in words; the distance measure, the comparison with other frames and the bootstrap were chosen here.", "One session, with no attack frames." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "pose-errors-close-fast", "statement": "Errors in pose estimation are most common on frames when the two animals are in close contact or moving very quickly.", "source": "Appendix B (Composition, errors and noise)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "657 of 23,810 frames (2.8%) have a body length outside the session's quartiles widened by 3 IQR. In the closest 10% of frames (centroid distance at most 66.4 px) the fraction is 0.131 against 0.016 elsewhere (difference 0.115, 95% interval 0.064 to 0.179). In the fastest 10% (at least 389 px/s) it is 0.010 against 0.030 (difference -0.020, interval -0.033 to -0.008), the reverse of the claim. Both directions hold at 5% and 20% and with a factor of 1.5. With the speed taken as the running median of the larger speed per frame, the fast difference is -0.020 (interval -0.033 to -0.008) at 10% and -0.011 (interval -0.025 to 0.001) at 20%. Error fractions by label are 0.045 (investigation), 0.105 (mount) and 0.009 (other), so a hunched posture in mount could give real outliers. Checked against the MARS confidence of the same frames, flagged close frames have a lower confidence than unflagged close frames (median 0.574 against 0.657, difference -0.082, interval -0.107 to -0.050), and in each of eight flagged close frames drawn at random and shown with the video, at least one segment visibly runs across the other mouse or the background (judged by eye). The flags in close frames therefore mark mostly tracking errors, though the share of real postures among them is not measured.", "deviations": [ "The dandiset has no confidence values, so pose errors are counted with an anatomical proxy chosen here; the paper gives no measure of pose error.", "The thresholds for close and fast frames were chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "link-mouse071", "statement": "The dandiset's CalMS21 sequence is the CalMS21 Task 1 test sequence mouse071, with the same keypoints, confidence scores and frame annotations.", "source": "Appendix C; CaltechDATA record 10.22002/D1.1991, file task1_classic_classification.zip", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "Matched by name to task1/test/mouse071_task1_annotator1 on CaltechDATA. Both have 23,810 frames; every keypoint coordinate is identical (largest difference 0 px), while swapping the mice or the axes gives differences of about 895 px. The frame labels from the bouts agree with the CaltechDATA annotations on all 23,810 frames (4,679 investigation, 2,894 mount, 16,237 other). CaltechDATA's confidence scores (0.030 to 0.980, all finite) are NaN in the dandiset. The same recording is also deposited on CaltechDATA as the Task 3 training sequence task3/groom/train/mouse002_task3_groom.", "deviations": [], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "pose-errors-close-fast-confidence", "statement": "Errors in pose estimation are most common on frames when the two animals are in close contact or moving very quickly, as shown by the MARS confidence scores.", "source": "Appendix B (Composition, errors and noise)", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "The mean confidence per frame (CaltechDATA scores, matched frame by frame) is lower in the closest 10% of frames (median 0.649 against 0.740, difference -0.091, 95% interval -0.107 to -0.074), most of all for the intruder (-0.149 against -0.031 for the resident). In the fastest 10% of frames it is higher (0.751 against 0.732, difference 0.018, interval 0.012 to 0.025), the reverse of the claim. Both hold at 5% and 20%. The confidence correlates with the body-length error flags of pose-errors-close-fast (point-biserial r = -0.366). With the speed taken as the running median of the larger speed per frame, the fast difference is 0.018 (interval 0.012 to 0.025). The link holds in full, so the match of scores to frames is exact.", "deviations": [ "Confidence is a proxy for pose error; the paper gives no measure.", "The confidence scores come from CaltechDATA, as the dandiset's are missing." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "table5-task1-counts", "statement": "Task 1 has 70 training sequences with 507,738 frames and 19 test sequences with 262,107 frames.", "source": "Table 5; Section 3.1; Figure 4A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "The training file holds 70 sequences with 507,738 frames and the test file 19 with 262,107, as reported. Annotation lengths equal the frame counts of the scores in every sequence, and the frame counts of the keypoints and the scores agree in all 574 sequences of the deposit.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table5-task2-counts", "statement": "Task 2 has, for annotators 1 to 5, 6 training sequences each with 139,112, 135,623, 107,420, 108,325 and 92,383 frames, and 13, 6, 4, 4 and 20 test sequences with 286,810, 150,919, 77,079, 76,174 and 364,007 frames.", "source": "Table 5; Section 3.2", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "19 of 20 counts match exactly. Annotator 1's training set has 139,122 frames where Table 5 gives 139,112 (10 frames, 0.007%); its six sequences match. The six sequences have the same frame counts in scores, keypoints and annotations; the paper gives no per-sequence counts, so the sequence that holds the 10 frames is not known. Annotator ids in the metadata agree with those in the keys.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table5-task3-counts", "statement": "Task 3 has, for approach, disengaged, grooming, intromission, mount attempt, sniff face and white rearing, 3, 2, 2, 1, 4, 3 and 2 training sequences with 20,624, 35,751, 45,174, 19,200, 46,847, 19,244 and 36,181 frames, and 25, 1, 13, 10, 12, 47 and 1 test sequences with 126,468, 19,088, 156,664, 55,218, 85,836, 251,793 and 17,939 frames.", "source": "Table 5; Section 3.3; Figure 4A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "All 28 counts match Table 5.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table6-task1-label-fractions", "statement": "In the Task 1 training set, 2.76% of frames are labelled attack, 28.9% investigation, 5.64% mount and 62.7% other.", "source": "Table 6; Figure 4B", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "Under reading (a), the training split, investigation, mount and other are within half a unit of the last reported digit; attack is 14,039 of 507,738 frames, 2.765009%, 0.005009 from 2.76 against a tolerance of 0.005. It rounds to 2.77 and truncates to the reported 2.76. All four are within 10% of the reported values. Reading (b), training and test, gives 3.46, 27.00, 7.85 and 61.68% and does not match.", "deviations": [ "The tolerance of half a unit of the last digit is tighter than the protocol's default of 10%, because these are percentages of a fixed file; under the default the claim would be reproduced." ], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "fig4b-task2-label-fractions", "statement": "The five Task 2 annotators label different fractions of frames as other, investigation, mount and attack (annotator 1 60.0, 20.6, 16.2 and 3.2%; annotator 2 65.5, 25.8, 3.4 and 5.3%; annotator 3 68.9, 13.5, 9.5 and 8.1%; annotator 4 75.2, 11.6, 4.5 and 8.7%; annotator 5 69.5, 26.4, 1.0 and 3.0%).", "source": "Figure 4B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "Under the training split with the class order of the Task 1 pie (other, investigation, mount, attack), all 20 percentages are within 0.05 of the figure's values; the best assignment of classes gives the same 20. The closest case is annotator 1 attack, 4,517 of 139,122 frames (3.2468%, 0.047 from 3.2), which would stay within 0.05 with up to 4 more attack frames. Training and test together match 1 of 20 under either class reading.", "deviations": [ "The Task 2 pies carry no class names; the order was read from the Task 1 pie, and the alternative reading (best assignment) was listed before the analysis. Both match." ], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table7-task3-label-fractions", "statement": "In Task 3 the behaviors occupy 3.25% (approach), 1.47% (disengaged), 14.0% (groom), 19.3% (intromission), 0.90% (mount attempt), 4.74% (sniff face) and 9.29% (white rearing) of frames.", "source": "Table 7; Figure 4B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "Under reading (a), the training split, all seven are within tolerance. Training and test together give values outside 10% for five of seven (for example groom 7.36%).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "dataset-size", "statement": "The unlabeled set has 282 videos and about 6 million frames; the dataset holds over 1 million annotated frames, over 70 hours of tracked poses and over 10 hours of frame-by-frame annotation.", "source": "Abstract; Section 3; Figure 4A; Section 5 (Discussion)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "The unlabeled set has 282 sequences and 5,952,058 frames (55.1 h), counted the same in the keypoints and the scores. Annotated frames are 769,845 (7.1 h) in Task 1, 3,243,734 (30.0 h) over all labelled sets, and 2,273,674 (21.1 h) with each recording counted once; tracked pose including the unlabeled set is 62.2, 85.2 and 76.2 h. So the three \"over\" statements (1 million annotated frames, 10 hours of annotation, 70 hours of pose) hold under readings (b) and (c) and none holds under reading (a).", "deviations": [ "The paper does not say which sets its totals cover; three readings were listed before the analysis." ], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table10-task3-difficulty", "statement": "On Task 3, classifier performance depends on the percentage of frames in which a behavior is observed and on its average bout duration, with shorter bouts giving lower performance.", "source": "Section 4.4; Tables 7 and 10", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_sun_2021.ipynb", "notes": "Across the seven behaviors the baseline F1 of Table 10 rises with the percentage of labelled frames (Spearman 0.786, exact one-sided p = 0.024 on the training split; 0.929, p = 0.003 on the test split) and with mean bout length, but the latter is not significant (0.321, p = 0.249; 0.607, p = 0.083). With the task programming model's F1 the bout-length correlations are 0.536 (p = 0.118) and 0.679 (p = 0.055). The direction of both parts of the statement holds; only the frequency part is significant with seven behaviors.", "deviations": [ "The paper states the dependence without a test; the correlation and the permutation test were chosen here, using the paper's published F1 scores with frequencies and bout lengths computed from the data." ], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table1-architectures", "statement": "Among baseline architectures trained on Task 1, the 1D convolutional network performs best (F1 0.793, MAP 0.856), ahead of fully connected (0.659), LSTM (0.675) and self-attention (0.610) models.", "source": "Table 1; Section 4.1", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs the four baseline networks trained on Task 1. The paper gives some settings (input window, skip factor, the ranges searched) and refers to the project code for the rest, but the code at gitlab.aicrowd.com/aicrowd/research/mab-e/mab-e-baselines did not answer, with or without the sandbox, and no copy was found in Software Heritage or on GitHub; the web archive holds its landing page only. The data are public on CaltechDATA. Training five runs of each network was also not attempted within the time limit.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table2-task-programming", "statement": "Adding task programming features learned from the unlabeled set raises Task 1 F1 from 0.793 to 0.829, and the challenge's top entry reaches 0.864.", "source": "Table 2 and Table 8; Section 4.2", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs the baseline network (code unavailable, see table1-architectures) and the challenge's top entry, whose code is not linked. The task programming code (GitHub neuroethology/TREBA) and precomputed features on CaltechDATA are public, but without the baseline classifier the comparison cannot be repeated.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table3-task2-style-transfer", "statement": "On Task 2 the fine-tuned baseline reaches an annotator-averaged F1 of 0.754, 0.774 with task programming features and 0.809 for the top entry, and all models do better on annotators 1 and 2 than on 3, 4 and 5.", "source": "Table 3 and Table 9; Section 4.3 and Appendix G.2", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs the fine-tuned baseline and the top entry; the baseline code is unavailable (see table1-architectures) and the top entry's code is not linked.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "table4-task3-new-behaviors", "statement": "On Task 3 the baseline reaches a behavior-averaged F1 of 0.338 (0.328 with task programming features, 0.319 for the top entry), far below Tasks 1 and 2.", "source": "Table 4 and Table 10; Section 4.4", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs the fine-tuned baseline with per-behavior learning rates hand-tuned on a validation set, and the top entry; neither's code is available (see table1-architectures).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "fig7-errors-at-transitions", "statement": "Many prediction errors of the baseline models fall around the boundaries between behaviors.", "source": "Figure 7; Section 4.2", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs the baseline model's predictions; its code is unavailable (see table1-architectures), so the claim depends on a blocked claim. The predictions are also not deposited in either archive (data_missing).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null }, { "claim": "fig11-annotator-similarity", "statement": "The annotator embedding learned by the top Task 2 entry places annotators 3 and 4 close to each other and apart from annotators 1, 2 and 5.", "source": "Figure 11; Section 4.3 and Appendix G.2", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs the trained top entry's annotator embedding; the entry's code is not linked and the paper describes the model only in outline. The learned matrix is also not deposited in either archive (data_missing).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "CaltechDATA doi:10.22002/D1.1991 (record s0vdx-0k302, version 1.0)", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The MARS confidence scores, which CalMS21 distributes with every keypoint, are missing from the dandiset's CalMS21 file; the confidence field of all 14 pose series is present but all 333,340 values are NaN. CaltechDATA's copy of the same sequence has them (0.03 to 0.98)." }, { "kind": "selection_undocumented", "statement": "For CalMS21 the dandiset holds one sequence, the Task 1 test sequence mouse071, out of 574 sequences on CaltechDATA. Its description presents a collection of datasets and does not say that only one CalMS21 sequence is included or why this one was chosen." }, { "kind": "metadata_insufficient", "statement": "The behavior catalogue (CalMS21_ethogram) has an empty definition for attack, investigation, mount and other, though the paper defines the three behaviors (Appendix D.2) and states that annotations refer to behaviors initiated by the resident." }, { "kind": "metadata_insufficient", "statement": "The two mice are stored as one subject with strain C57BL/6, sex unknown and age P0D/; the intruder's strain (BALB/c) and the residents' sex (male) are known from the paper but not recorded, and which series belongs to the black or white mouse is given only by the series names." }, { "kind": "metadata_error", "statement": "The session start time is 2024-01-01T00:00, a placeholder; CalMS21 gives no recording dates." }, { "kind": "metadata_insufficient", "statement": "The `centroid_speed` series, and the bout columns mean_speed, peak_speed and immobility_fraction that reduce it, are the speed of the mean of all 14 keypoints, which is the midpoint of the two mice, not the speed of either animal. The description (\"the pose centroid, mean over keypoints\") does not make this clear." }, { "kind": "other", "statement": "The dandiset's mouse071 video (184 MB) is a re-encoding of CaltechDATA's (964 MB). It has the same frame count, size and rate, and its motion follows the pose at lag 0, but the dandiset does not say it was re-encoded." }, { "kind": "metadata_insufficient", "statement": "The dandiset links the CalMS21 dataset DOI (10.22002/D1.1991) as IsDerivedFrom, but not the paper that describes the dataset and its benchmarks (arXiv 2104.02710, NeurIPS 2021 Datasets and Benchmarks)." }, { "kind": "other", "statement": "On CaltechDATA, 574 CalMS21 sequences hold 450 distinct recordings (identical keypoints over the whole sequence). 93 of the 109 Task 3 test sequences are Task 1 training recordings, five Task 1 test recordings (mouse071 among them) appear as six Task 3 training sequences, and four Task 2 recordings are in the training set of one of annotators 3 and 4 and the test set of the other. The paper describes each sequence as an independent observation and does not mention the overlap, and the CaltechDATA readme says that training and test sets are split by animal identity." }, { "kind": "paper_inconsistency", "statement": "The paper's datasheet says the dataset does not include the raw videos, while Section 3.1 says all source videos of Task 1 are released, and the deposit holds them. The datasheet also gives the licence as CC-BY-NC-SA, while the CaltechDATA record and the dandiset give CC-BY 4.0." }, { "kind": "other", "statement": "Table 5 gives 139,112 training frames for Task 2 annotator 1; the deposited file holds 139,122. The other 47 counts of Table 5 match." }, { "kind": "methods_unavailable", "statement": "The baseline code the paper links (gitlab.aicrowd.com/aicrowd/research/mab-e/mab-e-baselines) is not reachable and no archived copy of the repository was found; the code of the challenge's top entries is not linked. The paper leaves the architectures' settings to that code, so none of the benchmark results can be repeated." } ], "verifications": [ { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file (commit cf06231).", "agreed": 22, "of": 22, "disagreements": [] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the second run, with its conclusion cells and summary, the helper module, the claims file and the attempt record (commit c209e2e).", "agreed": 22, "of": 22, "disagreements": [] } ] }, { "id": "001888-hristova-2025-01", "dandiset": "001888", "dandiset_version": "draft", "paper": "10.1111/epi.18606", "paper_title": "Absence seizures and sleep-wake abnormalities in a rat model of GRIN2B neurodevelopmental disorder", "date": "2026-10-19", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001888-hristova-2025", "entry_title": "Absence seizures and sleep in Grin2b+/- rats (Hristova, Fasol et al. 2025)", "description": "Tests the EEG findings of Hristova, Fasol et al. (2025) on dandiset 001888, which holds the 24-h wireless EEG and EMG recordings, sleep scores and SWD events of 14 Grin2b+/- rats, 2 wild type rats and one rat without genotype. It compares SWD number, duration and timing, sleep-wake amounts and bouts, state spectra computed from the raw EEG, the state in which SWDs start, and the correlation of SWD time with sleep measures. The western blots, development measures, visual scoring and pharmacology recordings of the paper are not in the dandiset.", "notebooks": [ { "path": "reproduce_hristova_2025.ipynb", "title": "Reproducing Hristova, Fasol et al. (2025) from dandiset 001888", "executed": "notebooks/001888-hristova-2025/reproduce_hristova_2025.html" } ], "outcomes": [ { "claim": "fig2b-swd-hourly", "statement": "Grin2b+/- rats have more SWDs than WT across the 24-h day; hour of day has no effect and does not interact with genotype (linear mixed model, genotype F = 55.36, p < .00001; hour p = .16; interaction p = .49).", "source": "Figure 2B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Split-plot ANOVA on SWDs per ZT hour, genotype F = 11.45, p = 0.0045 (Het higher), hour p = 0.069, interaction p = 0.9998. Het hourly means 19.2 to 37.8, WT 0 to 8.2. With GRIN2B-132 as WT or Het the genotype effect holds (p = 0.0011, 0.013) and hour reaches p = 0.041. Without GRIN2B-228, GRIN2B-238 or both, genotype p = 0.0001, 0.048 and 0.0036, hour p 0.070 to 0.074. A fitted random-intercept model (MixedLM) gives the same genotype and interaction statistics. The paper's genotype F is 55.36 with 9 WT; here there are 2.", "deviations": [ "Two WT rats, where the paper has nine.", "The random-intercept mixed model is tested as a split-plot ANOVA." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-swd-number", "statement": "Grin2b+/- rats have more SWDs over 24 h than WT (Wilcoxon rank-sum, W = 4.5, p = .0002).", "source": "Figure 2C, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 690.6 SWDs per day, WT 56.3 (GRIN2B-238 none, GRIN2B-240 112.5); W = 1, p = 0.047. GRIN2B-240 ranks above one Het, GRIN2B-228, which has 1 SWD per day. With GRIN2B-132 as WT p = 0.020, as Het p = 0.062. Without GRIN2B-228 p = 0.034 (W = 0); with GRIN2B-238 left out one WT remains and p = 0.20.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-swd-mean-duration", "statement": "SWDs are longer on average in Grin2b+/- rats than in WT (two-sample t test, df = 22, T = -5.26, p = .00003).", "source": "Figure 2C, middle", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het mean SWD duration 4.54 s against 1.47 s in GRIN2B-240, the only WT rat with SWDs; t test p = 0.16 (df 13). With GRIN2B-132 (1.70 s) as WT p = 0.062; without GRIN2B-228 p = 0.090. A t test against a single WT value says little either way.", "deviations": [ "One WT rat has SWDs, so the WT group has one value." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-swd-total-duration", "statement": "The total time in SWDs over 24 h is higher in Grin2b+/- rats than in WT (Wilcoxon rank-sum, W = 5.5, p = .0002).", "source": "Figure 2C, right", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 57.77 min per day, WT 1.37 min; W = 1, p = 0.033. With GRIN2B-132 as WT p = 0.012, as Het p = 0.029. Without GRIN2B-228 p = 0.019; with GRIN2B-238 left out one WT remains and p = 0.27.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "disc-het-swd-minutes", "statement": "Over 24 h, Grin2b+/- rats spend on average 59.97 min in SWDs, while WT littermates average less than a minute.", "source": "Discussion, paragraph 2", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "The Het mean of 57.77 min per day (SEM 9.04, 14 rats) is within 59.97 +- 6.0. The WT mean is 1.37 min (0 and 2.75), not below 1 min. Without GRIN2B-228 the Het mean is 62.21, also within tolerance; without GRIN2B-238 the WT mean is 2.75. Counting the epochs SWD events overlap as 5 s each gives 110.57 min, and counting the epochs the scorer flags gives 60.2 min, so the paper's number fits both the event durations and the flags.", "deviations": [ "Two WT rats, where the paper has nine; the WT part rests on GRIN2B-240 alone." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5a-swd-light-dark", "statement": "The number of SWDs does not differ between the light and dark phases, and Grin2b+/- rats have more SWDs than WT in both (linear mixed model, genotype p < .00001, phase p = .28, interaction p = .53).", "source": "Figure S5A; Results 3.3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Phase F = 1.19, p = 0.29; genotype F = 11.45, p = 0.0045; interaction p = 0.86. Het 316.7 SWDs in the light and 373.9 in the dark, WT 12.5 and 43.8. Within Het, light minus dark median -79.8 (signed-rank p = 0.19). Without GRIN2B-228, GRIN2B-238 or both, phase p = 0.30 and genotype p = 0.0001, 0.048 and 0.0036.", "deviations": [ "Two WT rats; the mixed model is tested as a split-plot ANOVA." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs8-swd-sex", "statement": "Sex does not affect the number, mean duration or total duration of SWDs (two-way ANOVA sex x genotype, sex p = .74, .99 and .99).", "source": "Figure S8B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Sex term p = 0.29, 0.94 and 0.78 for number, mean duration and total duration. Within Het, females 763.3 SWDs per day against 617.9 in males (t test p = 0.31), 4.59 against 4.50 s, 60.3 against 55.2 min. Without GRIN2B-228, GRIN2B-238 or both the sex terms have p from 0.31 to 0.94.", "deviations": [ "The ANOVA has no sex by genotype interaction, as both WT are female; the paper's model has one." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-swd-spectrum-peak", "statement": "The EEG spectrum during SWDs has a clear peak in the theta range with a harmonic, in both genotypes.", "source": "Figure 2D; Results 3.3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "All 15 rats with at least 5 usable SWD epochs in the raw windows (13 Het, the WT GRIN2B-240 and GRIN2B-132) have a peak at 7.0 to 8.0 Hz and another at 14.0 to 16.0 Hz. The stored spectra show peaks near the same frequencies (7.4 to 8.2 and 14.4 to 16.2 Hz). GRIN2B-240 has 18 usable SWD epochs.", "deviations": [ "Spectra from about 4.8 h of raw EEG per rat (one 24-min chunk at six ZT hours of each day), on the SWD-detection channel, with a 2-s Welch segment chosen here.", "The peak rule (local maximum with prominence 0.1 in log10 power, harmonic within 1 Hz of twice the peak) was chosen here; the paper describes the peak by eye." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-swd-delta-power", "statement": "Delta power during SWDs is higher in Grin2b+/- rats than in WT (two-way ANOVA genotype x band, interaction p = .015; Tukey delta p = .039).", "source": "Figure 2E", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Only one WT rat (GRIN2B-240) has SWDs; GRIN2B-238 has none in either day, and the paper's other seven WT rats are not in the dandiset. The claim's rule needs at least two animals per genotype (also other, too few animals). A search of the archive for GRIN2B, Gonzalez-Sulser and the paper's DOI finds only this dandiset. As an illustration only, with GRIN2B-132 (no genotype) counted as WT, Het SWD delta power is lower than WT (-0.34, Tukey p = 1.0), against the paper's direction.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-rem-hourly", "statement": "Grin2b+/- rats have less REM sleep per hour than WT across the day, and the reduction is not specific to certain hours (linear mixed model, genotype F = 9.98, p = .0045; hour x genotype p = .53).", "source": "Figure 3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Genotype F = 4.69, p = 0.048 (Het lower); interaction p = 0.096. At the threshold; with GRIN2B-132 as WT p = 0.19, as Het p = 0.038 (interaction p = 0.071); with the scorer's flags or the stored scores p = 0.049 and 0.050. Without GRIN2B-228 genotype p = 0.060; without GRIN2B-238 or both genotype p = 0.019 and 0.025 but the interaction has p = 0.0001 and 0.00005. The outcome holds with all 16 rats and with GRIN2B-132 counted as Het, and not without GRIN2B-228 or GRIN2B-238. A fitted mixed model (MixedLM) gives genotype Wald p = 0.030 and interaction p = 0.086.", "deviations": [ "Two WT rats; the mixed model is tested as a split-plot ANOVA.", "SWD epochs are the epochs SWD events overlap; the lab's scorer uses its per-epoch flags." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-rem-total", "statement": "Grin2b+/- rats spend less total time in REM sleep over 24 h than WT (two-sample t test, df = 22, T = 3.16, p = .0045).", "source": "Figure 3G, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 44.8 min of REM per day, WT 69.7 (54.3 and 85.2); t = 2.16, df 14, p = 0.048. With GRIN2B-132 as WT p = 0.19, as Het p = 0.038; SWD-epoch variants p = 0.049 and 0.050, and 0.049 with only the SWD time removed. Without GRIN2B-228 p = 0.060; without GRIN2B-238 p = 0.019.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-rem-bouts", "statement": "Grin2b+/- rats have fewer REM bouts than WT (two-sample t test, df = 22, T = 3.94, p = .00069).", "source": "Figure 3G, middle", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 37.9 REM bouts per day, WT 74.0; t = 4.12, df 14, p = 0.0010. Both WT have more bouts than every Het. With GRIN2B-132 as WT p = 0.068. Without GRIN2B-228, GRIN2B-238 or both p <= 0.0017; with bouts not split by SWD epochs p = 0.0007.", "deviations": [ "Two WT rats; the bout definition (runs of one state, ended by SWD epochs) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-rem-bout-duration", "statement": "REM bouts are longer on average in Grin2b+/- rats than in WT (Wilcoxon rank-sum, W = 33, p = .043).", "source": "Figure 3G, right; Results 3.4", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het REM bouts 71.9 s, WT 56.8 s; W = 2, p = 0.067. With GRIN2B-132 (95.5 s) as WT the difference is 2.2 s (p = 0.59). Without GRIN2B-228 p = 0.076; with bouts not split by SWD epochs p = 0.067.", "deviations": [ "Two WT rats; bout definition chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-nrem-total", "statement": "Total NREM sleep over 24 h does not differ between genotypes (two-sample t test, df = 22, T = -.09, p = .93).", "source": "Figure 3H, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 450.5 min, WT 419.3 min, difference 31.2 min; t = -1.29, p = 0.22. With GRIN2B-132 as WT the difference is 48.4 min, p = 0.035. Without GRIN2B-238 the Het have 17.6 min less (p = 0.54); with only the SWD time removed p = 0.19. With two WT the test has little power to find a difference.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-nrem-bouts", "statement": "Grin2b+/- rats have fewer NREM bouts, which are longer, than WT (Wilcoxon rank-sum, bouts W = 29.5, p = .025; mean bout duration W = 26, p = .015).", "source": "Figure 3H, middle and right", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Mean NREM bout duration Het 127.1 s, WT 92.3 s, W = 0, p = 0.017. Number of NREM bouts Het 218.5, WT 273.0 per day, W = 25, p = 0.10. With the scorer's flags, the stored scores or bouts not split by SWD epochs both parts have p < 0.05 (bouts p = 0.032). Without GRIN2B-228 bouts p = 0.11, duration p = 0.019.", "deviations": [ "Two WT rats; bout definition chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3i-wake-total", "statement": "Grin2b+/- rats spend less total time awake over 24 h than WT (Welch t test, df = 10.25, T = 2.26, p = .047).", "source": "Figure 3I, left; Results 3.4", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 834.1 min awake per day, WT 944.9, difference -110.8 min; Welch p = 0.35. With the scorer's flags -68.1 min (p = 0.49), with only the SWD time removed -65.5 min (p = 0.50), with the stored scores -10.8 min (p = 0.89), so most of the difference is SWD time removed from wake. Without GRIN2B-228 -121.2 min (p = 0.33).", "deviations": [ "Two WT rats; SWD epochs are the epochs SWD events overlap." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3i-wake-bouts", "statement": "Grin2b+/- rats have more wake bouts of shorter duration than WT (Wilcoxon rank-sum, W = 18, p = .0035; Welch t test on mean bout duration, df = 8.91, T = 2.97, p = .016).", "source": "Figure 3I, middle and right", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 559.4 wake bouts per day against WT 294.5 (W = 2, p = 0.067); mean wake bout 100.6 s against 206.2 s (Welch p = 0.31). With the stored scores, where SWD epochs count as wake, both reverse (190.8 against 241.0 bouts, p = 0.017; 304.2 against 239.2 s), and they reverse with bouts not split by SWD epochs too (186.3 against 241.0 bouts, p = 0.017; 275.4 against 237.7 s). The outcome rests on SWD epochs ending wake bouts, which follows the Methods' exclusion of SWD times but builds part of the difference in. Without GRIN2B-228 the bout count has p = 0.019.", "deviations": [ "Two WT rats; bout definition chosen here; SWD epochs end wake bouts." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4a-rem-spectrum", "statement": "EEG spectral power during REM sleep does not differ between genotypes (two-way ANOVA genotype x band, genotype p = .14, interaction p = .69).", "source": "Figure 4A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Normalized REM band power, genotype F = 3.30, p = 0.073; interaction p = 0.998; Het lower by 0.19 on average. Contiguous bands give genotype p = 0.034, SWD epochs from flags p < 0.0001, the stored spectra p = 0.17, the cleaner S1 channel p = 0.067; the slope rejection removes no epoch. Without GRIN2B-228 p = 0.094, without GRIN2B-238 p = 0.19. The windows cover a median of 5 to 10% of each state's epochs (1.1% of GRIN2B-129's REM). With two WT the test has little power, and the band ANOVA treats an animal's five bands as separate observations, as the paper's does.", "deviations": [ "Spectra from about 4.8 h of raw EEG per rat on the SWD-detection channel; the paper used one representative channel and all epochs.", "Band limits (delta 1-4, theta 4-8, sigma 10-15, beta 15-30, gamma 30-48 Hz) and the Welch segment are not given in the paper. The spectral-slope rejection, read here as a slope below -5 of log10 power against log10 frequency or power at 1 Hz above 500 mV^2/Hz, removes no epoch.", "The paper chose the S1 channel with fewer artefacts by eye; that choice is not in the dandiset. The main channel is S1_Tr_R, and the per-animal channel with fewer artefact epochs is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-nrem-beta", "statement": "During NREM sleep Grin2b+/- rats have higher beta power than WT (two-way ANOVA genotype x band, interaction p = .038; Tukey beta p = .0008, other bands p >= .82).", "source": "Figure 4B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "NREM beta is lower in Het (difference -0.078 normalized, Tukey p = 1.0); interaction p = 0.90. Every variant with both WT (GRIN2B-132 either way, contiguous bands, SWD epochs from flags, slope rejection, cleaner S1 channel, stored spectra) has Het beta lower, by 0.0035 to 0.30. With GRIN2B-238 left out Het beta is higher in 7 of 12 variants, by 0.0032 to 0.147, with Tukey p >= 0.99 and interaction p >= 0.92.", "deviations": [ "As for fig4a-rem-spectrum; two WT rats." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-wake-power", "statement": "During wake, spectral power is reduced in Grin2b+/- rats overall, without a difference in single bands (two-way ANOVA genotype x band, genotype p = .01, interaction p = .86).", "source": "Figure 4C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Normalized wake power is higher in Het on average (+0.081; genotype F = 0.58, p = 0.45), and higher on average in every variant on the raw EEG with both WT (+0.0065 to +0.168). The stored spectra have Het lower on average (-0.027, p = 0.59; p = 0.0072 only with GRIN2B-132 counted as WT), as does the cleaner S1 channel without GRIN2B-238 (-0.0072, p = 0.93).", "deviations": [ "As for fig4a-rem-spectrum; two WT rats." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-swd-state-distribution", "statement": "Over both genotypes, SWDs occur mostly in wake (94.8%), then NREM (4.4%), and rarely in REM sleep (0.5%).", "source": "Figure 5A; Results 3.5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Reading (a) gives wake 94.18%, NREM 5.55%, REM 0.27% over 16 rats with SWDs; wake is within tolerance and the order holds, NREM and REM are not. Reading (b) 92.87, 6.81, 0.32; (c) 91.17, 8.64, 0.19; (d) 89.27, 10.50, 0.23. Readings (c) and (d) follow the Supplementary Methods' rule. No reading puts all three within tolerance. Without GRIN2B-228 the values move by at most 0.6 percentage points.", "deviations": [ "The paper's text allows four readings of how the percentages are formed; all are shown.", "Two of the paper's nine WT rats; GRIN2B-132 is included." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-het-more-nrem-swds", "statement": "Compared with WT, Grin2b+/- rats have a higher share of SWDs in NREM and a lower share in wake (two-way ANOVA genotype x state, interaction p = .00008; Tukey NREM p = .0011, wake p = .0022).", "source": "Figure 5A", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Only one WT rat has SWDs (GRIN2B-240, 0% of its SWDs after NREM), and the paper's other seven WT rats are not in the dandiset, so the per-state comparison between genotypes cannot be tested under the claim's rule of two animals per group (also other, too few animals). As an illustration only, with GRIN2B-132 (no genotype) counted as WT, 6.30% of Het SWDs follow NREM against 0.23% in the two WT (interaction p = 0.013, Tukey NREM p = 0.29).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-transition-swds", "statement": "All Grin2b+/- rats have SWDs that start at wake-NREM transitions, against 3 of 9 WT rats (Fisher's exact test, p = .00062).", "source": "Figure 5C; Results 3.5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "13 of 14 Het rats have at least one SWD at a wake-NREM transition, 0 of 2 WT; Fisher p = 0.025. GRIN2B-228 (2 SWDs in two days, none after NREM) has none. The claim's statement that all Het have such SWDs does not hold for GRIN2B-228; it may not be one of the paper's rats. Without GRIN2B-228 13 of 13 Het count (Fisher p = 0.0095), which would meet the criterion; the outcome is judged on all 16 rats.", "deviations": [ "The definition of a wake-NREM transition (a wake epoch followed by an NREM epoch within the six epochs before the SWD) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5b-transition-percent", "statement": "In Grin2b+/- rats 24.2% of SWDs occur during the wake-NREM transition, similar to the 22.39% of the WT rats that have such SWDs (two-sample t test, p = .74).", "source": "Results 3.5; Figure S5B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Reading (i), the share of NREM-initiated SWDs that are transitional, with an SWD initiated in NREM when any of the six epochs before it is NREM (the Supplementary Methods), gives 22.93% (SEM 1.97, 13 Het), within 24.2 +- 2.42. Reading (ii), the share of all SWDs, gives 2.23%. With NREM taken from the epoch before the SWD, the rule of the first criterion, reading (i) gives 36.31%. Leaving out GRIN2B-228 does not change reading (i). The claim's WT part is not tested, as no WT rat has transitional SWDs, so the WT value and the t test were not computed.", "deviations": [ "The denominator is not stated; two readings are shown.", "The criterion's NREM rule was corrected after verification round 1, once the analysis had been seen, to the six-epoch rule the Supplementary Methods state; the first rule gave 36.31%.", "The transition definition (a wake epoch followed by an NREM epoch within the six epochs before the SWD) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-swd-wake-correlation", "statement": "In Grin2b+/- rats, total SWD duration is negatively correlated with total time awake (Pearson, R = -.51, p = .048).", "source": "Figure 5F, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "R = -0.81, p = 0.0005 over 14 Het (-0.82 with GRIN2B-132, -0.73 without GRIN2B-228). With the scorer's flags R = -0.75; with the stored scores R = -0.06 (p = 0.83); with only the SWD time removed from wake R = -0.74 (p = 0.0024). The correlation arises from SWD time being taken out of wake. In Het the SWD epochs removed total 110.6 min per day against 57.8 min of SWD time.", "deviations": [ "14 Het, where the paper has 15." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5def-no-other-correlations", "statement": "In Grin2b+/- rats, total SWD duration is not correlated with total REM or NREM time, the number of REM, NREM or wake bouts, or the mean REM, NREM or wake bout duration (Pearson, all p >= .066).", "source": "Figure 5D-F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Two of the eight measures correlate with total SWD time, the number of wake bouts (R = 0.54, p = 0.046) and mean wake bout duration (R = -0.58, p = 0.028); the other six have p from 0.16 to 0.96. With the scorer's flags the same two correlate (R = 0.82, -0.72); with the stored scores, with bouts not split by SWD epochs or without GRIN2B-228 none does. The paper gives R = 0.17 and -0.25 for these two.", "deviations": [ "14 Het; the criterion grades eight tests (none significant reproduced, one or two partial)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-glun2b-reduced", "statement": "GluN2B protein is reduced by about 50% in somatosensory cortex and hippocampus of Grin2b+/- rats (homogenate t test p = .000104; synaptosome Wilcoxon p = .00094).", "source": "Figure 1C; Figure S2C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The western blot quantification is not in the dandiset, which holds only EEG/EMG files, and the paper's data statement says raw data are available on request.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1df-other-proteins-unchanged", "statement": "GluN2A, GluR1 and PSD95 expression are unchanged in Grin2b+/- rats.", "source": "Figure 1D-F; Figure S2D-F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Western blot data not in the dandiset (see fig1c-glun2b-reduced).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4-normal-development", "statement": "Grin2b+/- rats survive, grow and develop motor reflexes like WT littermates (survival 48% and 52%; body weight, righting reflex and negative geotaxis do not differ).", "source": "Results 3.2; Figure S4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Survival, body weight, righting reflex and negative geotaxis measures are not in the dandiset or any public archive the paper names.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-scorer-agreement", "statement": "The automated sleep scorer agrees with visual scoring on 90.8% of epochs (Cohen's kappa 0.83).", "source": "Supplementary Methods; Table S1; Figure S1", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The visual scores of the 4-h validation periods are not in the dandiset; the files hold only the automated scores.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6b-systemic-etx-number", "statement": "Systemic ethosuximide reduces the number of SWDs relative to saline and memantine in both genotypes (linear mixed model, treatment p = .0049; ethosuximide-saline p = .0081).", "source": "Figure 6B", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The pharmacology recordings (2-channel EEG of 17 rats over baseline, treatment and washout days) are not in the dandiset, whose 17 files are 73 to 99 h recordings with the 14-channel grid, each holding two 24-h baseline windows. No other dandiset for this paper was found.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-systemic-duration", "statement": "Systemic ethosuximide and memantine reduce the mean SWD duration in Grin2b+/- rats but not in WT (treatment x genotype p = .044).", "source": "Figure 6C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Pharmacology recordings not in the dandiset (see fig6b-systemic-etx-number).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-systemic-total", "statement": "Systemic ethosuximide reduces the total SWD duration in both genotypes (treatment p = .0011; ethosuximide-saline p = .0005).", "source": "Figure 6D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Pharmacology recordings not in the dandiset (see fig6b-systemic-etx-number).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7c-nrt-infusion", "statement": "Infusion of ethosuximide or memantine into the reticular thalamic nucleus reduces the number and total duration of SWDs in Grin2b+/- rats but not their mean duration.", "source": "Figure 7C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The intrathalamic infusion recordings of 4 Grin2b+/- rats are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds 2 of the paper's 9 analysed wild type rats (14 or 15 of its 15 Grin2b+/-), so genotype comparisons rest on two WT, one of which has no SWDs. The pharmacology and intrathalamic infusion recordings (Figures 6, 7, S11, S12), western blots (Figures 1, S2, S3), development measures (Figure S4) and the visual scoring used to validate the scorer (Table S1) are not in it. The paper says raw data are available on request." }, { "kind": "metadata_insufficient", "statement": "GRIN2B-132 has no genotype and sex U, so it cannot be placed in either group. The conversion repository marks both as still to be confirmed by the lab." }, { "kind": "selection_undocumented", "statement": "The paper analysed 15 Grin2b+/- and 9 WT rats and excluded 4 and 9 descendants of one founder. The dandiset does not say which of its rats the paper analysed, and holds a Grin2b+/- rat (GRIN2B-228) with 1 SWD per day, unlike the paper's statement that all Grin2b+/- rats had SWDs at wake-NREM transitions." }, { "kind": "metadata_error", "statement": "The sleep_states description gives code 4 for SWD epochs, but no file holds code 4; the stored scores are the scorer's output before SWD epochs are set, so SWD epochs are scored as wake, NREM or REM." }, { "kind": "metadata_error", "statement": "swd_epoch_counts is described as the number of SWD events per 5-s epoch but holds the scorer's flags (6 for an SWD epoch, 4 otherwise). The flagged epochs cover a median of 51% (0 to 73%) of the epochs SWD events overlap, mostly the last epoch of each SWD, and only about a tenth of SWD onsets fall in a flagged epoch." }, { "kind": "metadata_error", "statement": "In seizure_totals_by_zt the per-hour SWD counts are in spike_wave_discharge, while number_of_seizure_events and Day hold the day's total in the first row and 0 elsewhere; the description itself marks the columns as unconfirmed." }, { "kind": "metadata_error", "statement": "sleep_state_power_spectra is described as a baseline-corrected PSD normalized to the average over states, with units to be confirmed. The lab's scorer writes the mean log10 multitaper amplitude referenced to each frequency's 5th percentile over the day, which is what the values (0 to about 1.6) fit; the paper's Welch spectra are not in the dandiset." }, { "kind": "format_error", "statement": "The raw EEG and EMG are stored as unsigned 12-bit codes with offset 0, so every channel reads about +8 mV of DC in volts. Signal loss is written as 32767 on all channels at once, and some files hold other values outside 0 to 4095; neither is described. In the windows read, 21 to 73% of 5-s epochs per rat contain such samples (73% for GRIN2B-238)." }, { "kind": "metadata_error", "statement": "The dandiset's assets summary counts 16 files and 16 subjects, while the draft holds 17 NWB files of 17 rats." }, { "kind": "code_mismatch", "statement": "The Methods exclude SWD times from the sleep states, while the lab's scorer replaces only the flagged epochs, which cover about half of the epochs SWD events overlap. The paper's wake results depend on this; with the stored scores (SWD epochs as wake) the wake bout differences reverse and the correlation of SWD time with wake time disappears." }, { "kind": "paper_inconsistency", "statement": "In the Figure 5 legend, NREM time gives T = -1.47 with R = -0.13 and df = 13, which implies T = -0.47; REM bouts give T = 0.704 with R = -0.19, of opposite sign; and REM bout duration and wake bouts have identical statistics (T = 0.61, R = 0.17, p = 0.55). The Figure 5A ANOVA gives genotype F = 1 with p = 0.98, which do not match for df = 1." }, { "kind": "paper_inconsistency", "statement": "The Figure 3 legend says no net differences between genotypes were observed for wake, while reporting a genotype effect on hourly wake time of F = 7.14, p = 0.014, and the Results say Grin2b+/- rats spent less time awake." }, { "kind": "metadata_insufficient", "statement": "The Supplementary Methods chose, by eye and per animal, the S1 EEG channel (left or right) and the EMG channel with fewer artefacts for sleep scoring; the dandiset does not record which channels were used." }, { "kind": "methods_unavailable", "statement": "The paper does not give its frequency band limits, Welch segment length, bout definition or the rule for wake-NREM transitions, and neither linked repository holds the statistics or figure code." } ], "verifications": [ { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper and its Supplementary Methods. The verifier had no attempt record and took its counts from the claims file. It gave its own outcome for each claim; all 34 agree with the record as it stood then. It checked the blocked claims against the archive's file list and metadata.", "agreed": 34, "of": 34, "disagreements": [] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file, the attempt record and the README, with the paper and its Supplementary Methods. The verifier agreed with all 34 outcomes, including the change of figs5b-transition-percent to reproduced, and found all round-1 points resolved. It found sentences the outputs did not support. The disc-het-swd-minutes conclusion said the paper's 59.97 min does not match the scorer's flags; cell 32 now prints the flagged epochs as 60.2 min, and the conclusion says the figure fits both. The fig4c range now ends at +0.168. The fig3d conclusion now says the outcome also holds with GRIN2B-132 counted as Het. The summary now names fig5def-no-other-correlations among the claims that would change without GRIN2B-228, and the fig3d interaction without GRIN2B-238. The README run time and the description of the recordings (73 to 99 h, each with two 24-h baseline windows) are corrected, as is the same description in the fig6b note and the claims-file comment. No outcome changed, and none is proposed to change.", "agreed": 34, "of": 34, "disagreements": [] } ] }, { "id": "001933-chen-2026-01", "dandiset": "001933", "dandiset_version": "0.260825.1457", "paper": "10.1038/s41467-026-75194-3", "paper_title": "Leucine-rich repeat kinase 2 impairs the release sites of Parkinson\u2019s disease vulnerable dopamine axons", "date": "2026-10-15", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "001933-chen-2026", "entry_title": "LRRK2-G2019S and dopamine release from Anxa1+ and Calb1+ neurons (Chen, He et al. 2026)", "description": "Tests the findings of Chen, He et al. (2026). On dandiset 001933, which holds GRAB-DA3m fiber photometry in the dorsal striatum during optogenetic stimulation of Anxa1+ (15 mice) or Calb1+ (12 mice) SNc dopamine neurons in LRRK2-WT and LRRK2-G2019S mice, it compares evoked and spontaneous dopamine release between genotypes, per power and per mouse, and links the dandiset to the paper's published source data. The imaging, proteomics and western blots of Figures 1 to 5 are not in the dandiset; their claims are tested on the data the paper deposited on Zenodo, in PRIDE and in the BioImage Archive, and counted apart.", "notebooks": [ { "path": "reproduce_chen_2026.ipynb", "title": "Reproducing Chen, He et al. (2026) from dandiset 001933", "executed": "notebooks/001933-chen-2026/reproduce_chen_2026.html" } ], "outcomes": [ { "claim": "source-data-link", "statement": "The dandiset's recordings are those behind the paper's Figure 6 and Supplementary Figures 7 and 8, and the paper's published per-stimulation traces, evoked integrals and spontaneous transient integrals can be recomputed from them.", "source": "Figure 6C to 6F, Supplementary Figures 7B, 7C, 8C to 8E; Source Data (Zenodo 10.5281/zenodo.19930567)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "All 27 mice of the source data are in the dandiset with the same genotype and line. The Anxa1 half links. 120 of 120 traces of Figure 6C and 479 of 480 of Supplementary Figure 7B equal the dandiset's dF/F from 1 s before onset (largest difference among matched traces 5.7e-13 in each), the evoked integrals equal the code's measure times 0.0001 for all Anxa1 records but one, and the transient counts match for 15 of 15 mice. The one miss in each is the last 4 mW stimulation of mouse 4398, whose processed series ends 0.8 s after onset. The Calb1 half does not link; 0 of 384 traces, 0 of 384 integrals and the transient counts of 1 of 12 mice match. dF/F recomputed from the raw signal with the code's processing reproduces the stored Calb1 series (largest difference 1.47 % dF/F) but not the published traces (median differences 66 to 519 % dF/F; 22 to 88 at the best background fraction per mouse). The published spontaneous values are 0.005 times the mean dF/F over each transient (ratio 0.004994 to 0.004999), so part (4) as fixed, with integrals, matches for no mouse; with the transient mean it matches for 13 of 27 mice within 1% (Anxa1 13 of 15; 4398 and 4007 each fail by one sorted value, 1.03% and 1.67%), and for none within the 1e-4 of part (3); integrals match for none at either tolerance. The four parts match for 1.0, 0.609, 0.609 and 0 of their records (0.481 with the transient mean), so the outcome is not reproduced under either measure. The Calb1 mismatch is not one of epoch or power labels; searched over all 64 epochs and 8 powers of each mouse, no epoch is within 1e-6 of any of the 384 S8D traces (closest 15.7 to 150.8 % dF/F), and against the matched epochs the per-mouse median slopes are 0.21 to 0.75 and offsets -13.8 to 16.2 % dF/F. The Figure 6E integrals match the 0.5 mW epochs (120 of 120) and none of the 4 mW ones. The published values reproduce the paper's statistics (Figure 6E p = 1.1e-20, Cohen's d 2.06 and 0.765), so the Calb1 differences come from the data, not from the paper's computation on them.", "deviations": [ "The criterion fixed the integral of each spontaneous transient; the published values turned out to be the mean dF/F over the transient. The mean is shown as a variant and does not change the outcome." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig6e-anxa1-evoked-reduced", "statement": "Optogenetically evoked dopamine release in the dorsolateral striatum (Anxa1+ projection region) at 0.5 mW is lower in LRRK2-G2019S than in LRRK2-WT mice (64 against 56 stimulations, p = 1.10e-20, one-tailed two-sample t-test).", "source": "Figure 6E (left), Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Light-on integrals at 0.5 mW, GS 48.8 against WT 128.0 % dF/F x s, one-tailed p = 1.16e-22 (paper 1.10e-20), Cohen's d 2.21. The code's window gives p = 1.1e-20, the paper's value. It holds at 4 mW (p = 4.08e-18), without the two GS mice given 0.33 s trains (p = 4.16e-17), and with mouse means (Welch p = 0.000434). The window chunking_index.m computes as written reverses the sign (p = 1).", "deviations": [ "The integral is over each train's light-on period, as the Methods state; the paper's values come from the code's window, -0.1 to 1.0 s, shown as a variant. The baseline, which the Methods do not give, is the code's.", "The paper's plotting code selects power code 'h' for this panel; the panel is tested at the 0.5 mW of the legend, which the source data confirm, and 4 mW is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6e-anxa1-evoked-per-mouse", "statement": "Seven of eight individual G2019S mice show significantly reduced evoked dopamine release at 0.5 mW compared with the WT group; mouse 3743 does not.", "source": "Figure 6E (right) and legend; Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Under all four readings (Welch or Student, one- or two-tailed) 7 of 8 GS mice are below the WT group at p < 0.05/8 and 3743 is the exception (mean 125 against 128, Welch one-tailed p = 0.362). The count is the same with the code's window. Two of the seven, 3742 and 4885, received the paper's powers as 0.33 s trains, unlike every WT mouse, and their responses do not follow the labelled power; the other five significant mice were stimulated as the WT mice were.", "deviations": [ "The Methods name Welch's test, the legend's p-values are one-tailed and the code runs a two-tailed Student test; all four readings are shown and all give 7." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp7c-anxa1-evoked-all-powers", "statement": "The reduction of evoked dopamine release in Anxa1 G2019S mice holds at each of the four stimulation powers, 0.1, 0.5, 1 and 4 mW (p from 1.29e-15 to 1.10e-20).", "source": "Supplementary Figure 7C; Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "GS lower at all four powers, one-tailed p from 3.13e-15 to 1.16e-22 with the light-on window. With the code's window the p-values at 0.1, 0.5 and 1 mW equal the paper's (1.29e-15, 1.1e-20, 1.22e-17); at 4 mW it is 5.62e-16 against 2.39e-16, as that window, which runs to 1.0 s after onset, leaves 55 WT stimulations there (the processed series of mouse 4398 ends 0.8 s after its last onset). The Methods window keeps all 56.", "deviations": [ "In the code's window variant, 55 WT stimulations at 4 mW in place of 56, as one falls at the end of a truncated series." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6f-anxa1-spontaneous-reduced", "statement": "Spontaneous dopamine transients in the dorsolateral striatum are smaller in G2019S than in WT mice (1064 against 798 transients, p = 2.75e-177, one-tailed two-sample t-test), with 57 to 285 transients per mouse.", "source": "Figure 6F (left) and legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "The Methods' detection gives the paper's counts exactly (1064 and 798, 57 to 285 per mouse). Integrals GS 131.9 against WT 302.9 % dF/F x s, one-tailed p = 4.85e-72 (paper 2.75e-177). With the mean dF/F over each transient, the measure of the published values, p = 2.23e-177. With mouse means, Welch p = 0.0318.", "deviations": [ "The integral of each transient is used, as the Methods state; the paper's values are 0.005 times the mean dF/F over the transient, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6f-anxa1-spontaneous-per-mouse", "statement": "Six of eight individual G2019S mice show significantly smaller spontaneous dopamine transients than the WT group; mice 4651 and 3743 do not.", "source": "Figure 6F (right) and legend; Results, last section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "By the integral 5 of 8 GS mice are below the WT group under every reading; the exceptions are 3743 (p = 0.431), 4651 (mean 417, above the WT mean of 303) and 4652 (p = 0.0128). With the transient mean, the paper's measure, the one-tailed Student test gives 6 of 8 with 3743 and 4651 as the exceptions and p-values close to the legend's (4651 0.00819 against 0.008, 3742 5.38e-88 against 5.28e-88); the Welch tests give 7 there. The difference from the paper comes from the measure; the paper's count follows the Student test of its legend.", "deviations": [ "The integral of each transient is used, as the Methods state; the paper's measure is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp8c-calb1-spontaneous-not-reduced", "statement": "In the dorsomedial striatum (Calb1+ projection region), spontaneous dopamine transients are not reduced in G2019S mice (970 against 682 transients, p = 0.98).", "source": "Supplementary Figure 8C; Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "The paper's test does not find the effect, one-tailed p = 0.0509, difference of means 21.1 % dF/F x s, Cohen's d 0.085; the result sits at the threshold. With the transient mean GS are lower at p = 2.25e-09 (d 0.306), with the code's exclusion window as written at p = 1.81e-05, and with mouse means Welch p = 0.402. The counts are within tolerance but differ from the paper's 970 and 682, and the Calb1 dF/F in the dandiset is not the one the paper analysed (source-data-link); the published values give p = 0.989.", "deviations": [ "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp8e-calb1-evoked-reduced", "statement": "Evoked dopamine release in the dorsomedial striatum from Calb1+ neuron stimulation is reduced in G2019S mice at each of four powers (56 against 40 stimulations per power, p from 6.45e-05 to 0.001).", "source": "Supplementary Figure 8E (left); Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "GS lower at all four powers, one-tailed p from 4.38e-07 to 6.29e-10, smaller than the paper's 6.45e-05 to 0.001. The p-values differ because the dandiset's Calb1 dF/F is not the paper's (source-data-link). With one value per mouse (7 GS, 5 WT), Welch one-tailed p is 0.0424, 0.0413, 0.0726 and 0.0916 at 0.1, 0.5, 1 and 4 mW.", "deviations": [ "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp8e-calb1-few-mice-reduced", "statement": "Only 2 of 7 G2019S mice show reduced Calb1+ evoked dopamine release relative to the WT group.", "source": "Supplementary Figure 8E (right); Results, last section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "At 0.5 mW, 7 (Welch one-tailed), 6 (Welch two-tailed) and 4 (Student, either tail) of 7 GS mice are below the WT group at p < 0.05/7, against the paper's 2; the closest reading gives 4, recorded as measured. Student tests give 2 at 0.1 and 1 mW. The panel's power is not stated, and the dandiset's Calb1 dF/F is not the paper's.", "deviations": [ "The legend does not state the power of the per-mouse panel; 0.5 mW was fixed before the analysis and the other powers are shown.", "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "cohens-d-anxa1-larger", "statement": "The G2019S reduction of evoked release at 0.5 mW is much larger for Anxa1+ (Cohen's d = 2.05) than for Calb1+ stimulation (d = 0.76).", "source": "Results, last section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Anxa1 d = 2.21 is within tolerance; Calb1 d = 1.40 is not (0.684 to 0.836), and the ratio 1.58 is under the factor of 2 the criterion asks. With the code's window, 2.06 and 1.25. The paper's published integrals give 2.06 and 0.765, so the miss is consistent with the Calb1 dF/F in the dandiset not being the paper's. The Anxa1 effect is larger than the Calb1 effect at every power and window that starts by onset (ratio 1.29 to 1.74), so the direction of the paper's comparison holds, with a smaller gap.", "deviations": [ "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-lrrk2-enriched-vulnerable", "statement": "LRRK2 immunolabeling intensity is higher in Aldh1a1+ (vulnerable) than in Aldh1a1- SNc dopamine neurons (p = 0.0008).", "source": "Figure 1B and 1D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The immunostaining images are not in the dandiset, which holds only the photometry. They are in the BioImage Archive (S-BIAD2070, S-BIAD2071, S-BIAD2072 and S-BIAD2074) and per-section values in the Zenodo source data.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2070 (images); Zenodo doi:10.5281/zenodo.19930567 (per-section values)", "proposed": null }, { "claim": "fig2b-rab3-phosphorylation", "statement": "LRRK2 kinase inhibition with MLi-2 changes 289 phosphopeptides in striatal synaptosomes of G2019S mice, including RAB3 T86.", "source": "Figure 2A to 2C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The phosphoproteomics are not in the dandiset; they are in PRIDE (PXD065003, PXD065006, PXD065125).", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "PRIDE PXD065006", "proposed": null }, { "claim": "fig2eg-prab3-increased", "statement": "Phosphorylation of RAB3A and RAB3C is increased in the SNc of G2019S mice and returns to WT levels with MLi-2.", "source": "Figure 2D to 2G", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The western blots are not in the dandiset; blot images and values are in the Zenodo source data.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.19930567", "proposed": null }, { "claim": "fig3d-rim-binds-unphosphorylated", "statement": "RIM1 and RIM2 bind unphosphorylated RAB3A in preference to RAB3A phosphorylated at T86, while RILPL1 and RILPL2 prefer the phosphorylated form.", "source": "Figure 3D to 3F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The affinity purification mass spectrometry is not in the dandiset; it is in PRIDE.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "PRIDE PXD065125", "proposed": null }, { "claim": "fig4d-fewer-active-zones", "statement": "Fewer TH+/VAMP2+ striatal synaptosomes from G2019S mice contain bassoon, and the remaining bassoon clusters are larger.", "source": "Figure 4D and 4E", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The synaptosome images are not in the dandiset; they are in the BioImage Archive.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2074 (images); Zenodo doi:10.5281/zenodo.19930567 (per-area values)", "proposed": null }, { "claim": "fig4i-rim1-reduced", "statement": "RIM1 is reduced in striatal synaptosomes of G2019S mice (p = 0.0245) but not in other striatal fractions or the SNc.", "source": "Figure 4H to 4L", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The western blots are not in the dandiset; they are in the Zenodo source data.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.19930567", "proposed": null }, { "claim": "fig5-bassoon-vulnerable-axons", "statement": "Bassoon cluster density is reduced and cluster volume increased in Aldh1a1+ but not Aldh1a1- dopamine axons of G2019S mice, and the same holds in Anxa1+ axons.", "source": "Figure 5D, 5E, 5G and 5H", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The SIM images are not in the dandiset; they are in the BioImage Archive.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2071 (images); Zenodo doi:10.5281/zenodo.19930567 (per-section values)", "proposed": null }, { "claim": "fig5j-no-axon-loss", "statement": "The volume occupied by TH+ fibres in the dorsal striatum does not differ between G2019S and WT mice.", "source": "Figure 5I and 5J", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The confocal images are not in the dandiset; they are in the BioImage Archive.", "deviations": [], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2072 (images); Zenodo doi:10.5281/zenodo.19930567 (per-section values)", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The Calb1 dF/F in the dandiset is not the trace behind Supplementary Figure 8. None of the 384 published Calb1 triggered traces or evoked integrals match it, no epoch of any power matches a published trace, the transient counts match for 1 of 12 mice, and dF/F recomputed from the deposited raw signal with the published code reproduces the dandiset's series, not the paper's, at any single background fraction. The processing the paper used for Calb1 is neither deposited nor described, so the Calb1 results of the paper cannot be recomputed from the dandiset." }, { "kind": "data_missing", "statement": "The dandiset holds only the fiber photometry of Figure 6 and Supplementary Figures 7 and 8. The imaging, proteomics and western blots of Figures 1 to 5 are elsewhere (BioImage Archive, PRIDE, Zenodo), so eight of the paper's main findings cannot be tested on it." }, { "kind": "other", "statement": "The processed series of mouse 4398 ends 0.8 s after its last onset, a 4 mW stimulation, while the paper's trace for that stimulation is complete and differs from the dandiset's in the samples both hold." }, { "kind": "metadata_error", "statement": "The OptogeneticEpochsTable description gives 8 ms on and 8 ms off for 500 ms, four powers and trains at least 20 s apart. The tables hold eight powers, two kinds of train in Anxa1 files (9 ms pulses every 10 ms for 0.33 s, and 8 ms every 16 ms for 0.51 s), and pairs of trains 15.3 s apart (51% of gaps under 20 s). One train each in mice 4652 and 740 has a pulse length of 0, no period and one pulse." }, { "kind": "other", "statement": "Two Anxa1 G2019S mice (3742 and 4885) received the paper's four powers as 0.33 s trains of 9 ms pulses, while every other mouse received them as 0.51 s trains of 8 ms pulses. Neither the paper nor the dandiset says so. In these two mice the response does not follow the labelled power (in 3742 the 0.5 mW trains give the smallest response, median 5.7 against 33.5 % dF/F x s at 0.1 mW), so the data cannot confirm their power labels. Leaving the two mice out does not change the Anxa1 result." }, { "kind": "metadata_error", "statement": "The dF/F series (FiberPhotometryResponseSeriesDfOverF) is stated in a.u.; its description and its values are percent dF/F." }, { "kind": "metadata_error", "statement": "The archive's summary of the dandiset lists only a behavioral approach and BehavioralTimeSeries; the files hold fiber photometry and optogenetics." }, { "kind": "selection_undocumented", "statement": "The dandiset holds the 27 mice the paper kept after excluding four on histology (one Anxa1 G2019S, one Calb1 G2019S, two Calb1 WT). It does not say that mice were left out or why." }, { "kind": "code_mismatch", "statement": "chunking_index.m computes the start of each window as trigger - fs*ti, so with ti = -1 the window used for the evoked integral and for the spontaneous exclusion starts 1 s after onset. The source data show that the figures used the intended window starting 1 s before onset; the code as published gives the reverse sign." }, { "kind": "code_mismatch", "statement": "plot_results.m selects power code 'h' for Figure 6E, which the lab's stimulation key, as used by the conversion, maps to 4 mW; the figure, its legend and the source data are at 0.5 mW." }, { "kind": "code_mismatch", "statement": "The Methods and transient_by_threshold.m give the integral of dF/F over each spontaneous transient; the published values of Figure 6F and Supplementary Figure 8C are 0.005 times the mean dF/F over each transient, a duration-normalized integral. The code that computes them is not in the repository." }, { "kind": "paper_inconsistency", "statement": "For the per-mouse comparisons the Methods and the asterisks name Welch's test, the legends give one-tailed two-sample t-test p-values, and the code runs a two-tailed Student test. The Figure 6F count of 6 of 8 follows the one-tailed Student test; Welch's test gives 7." }, { "kind": "other", "statement": "The paper does not cite the dandiset; its data statement names Zenodo, PRIDE and the BioImage Archive." } ], "verifications": [ { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook (commit 6a2acb7) with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's main text. The verifier listed the version's assets through the DANDI API and ran synthetic checks of double_threshold, _movmean, evoked_integrals, spontaneous_transients, cohens_d and one_tailed_less.", "agreed": 18, "of": 18, "disagreements": [] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full re-executed notebook of the first revision (commit 0c6b642) with its conclusions and summary, the README, the attempt record, the helper module and the claims file. The verifier checked every Result paragraph and the summary against the printed outputs and recomputed 131.9 and 302.9 from the per-mouse table. It did not read the Supplementary Figure 7 and 8 legends.", "agreed": 18, "of": 18, "disagreements": [] } ] }, { "id": "001933-chen-2026-02", "dandiset": "001933", "dandiset_version": "0.260825.1457", "paper": "10.1038/s41467-026-75194-3", "paper_title": "Leucine-rich repeat kinase 2 impairs the release sites of Parkinson\u2019s disease vulnerable dopamine axons", "date": "2026-10-15", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001933-chen-2026", "entry_title": "LRRK2-G2019S and dopamine release from Anxa1+ and Calb1+ neurons (Chen, He et al. 2026)", "description": "Tests the findings of Chen, He et al. (2026). On dandiset 001933, which holds GRAB-DA3m fiber photometry in the dorsal striatum during optogenetic stimulation of Anxa1+ (15 mice) or Calb1+ (12 mice) SNc dopamine neurons in LRRK2-WT and LRRK2-G2019S mice, it compares evoked and spontaneous dopamine release between genotypes, per power and per mouse, and links the dandiset to the paper's published source data. The imaging, proteomics and western blots of Figures 1 to 5 are not in the dandiset; their claims are tested on the data the paper deposited on Zenodo, in PRIDE and in the BioImage Archive, and counted apart.", "notebooks": [ { "path": "reproduce_chen_2026.ipynb", "title": "Reproducing Chen, He et al. (2026) from dandiset 001933", "executed": "notebooks/001933-chen-2026/reproduce_chen_2026.html" } ], "outcomes": [ { "claim": "source-data-link", "statement": "The dandiset's recordings are those behind the paper's Figure 6 and Supplementary Figures 7 and 8, and the paper's published per-stimulation traces, evoked integrals and spontaneous transient integrals can be recomputed from them.", "source": "Figure 6C to 6F, Supplementary Figures 7B, 7C, 8C to 8E; Source Data (Zenodo 10.5281/zenodo.19930567)", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "All 27 mice of the source data are in the dandiset with the same genotype and line. The Anxa1 half links. 120 of 120 traces of Figure 6C and 479 of 480 of Supplementary Figure 7B equal the dandiset's dF/F from 1 s before onset (largest difference among matched traces 5.7e-13 in each), the evoked integrals equal the code's measure times 0.0001 for all Anxa1 records but one, and the transient counts match for 15 of 15 mice. The one miss in each is the last 4 mW stimulation of mouse 4398, whose processed series ends 0.8 s after onset. The Calb1 half does not link; 0 of 384 traces, 0 of 384 integrals and the transient counts of 1 of 12 mice match. dF/F recomputed from the raw signal with the code's processing reproduces the stored Calb1 series (largest difference 1.47 % dF/F) but not the published traces (median differences 66 to 519 % dF/F; 22 to 88 at the best background fraction per mouse). The published spontaneous values are 0.005 times the trapezoid integral of each transient divided by its number of samples (within-mouse spread of the ratio at most 2.2e-15; 15 of 15 Anxa1 mice and 0 of 12 Calb1 mice match at 1e-4), so part (4) as fixed, with integrals, matches for no mouse at either tolerance. The four parts match for 1.0, 0.609, 0.609 and 0 of their records, so the outcome is not reproduced. With the published measure in part (4) they match for 1.0, 0.609, 0.609 and 0.556, which would be partially reproduced; the criterion fixed integrals, so this is a variant. The mean dF/F over each transient comes close (13 of 15 Anxa1 mice within 1%, none within 1e-4). The Calb1 mismatch is not one of epoch or power labels; searched over all 64 epochs and 8 powers of each mouse, no epoch is within 1e-6 of any of the 384 S8D traces (closest 15.7 to 150.8 % dF/F), and against the matched epochs the per-mouse median slopes are 0.21 to 0.75 and offsets -13.8 to 16.2 % dF/F. The Figure 6E integrals match the 0.5 mW epochs (120 of 120) and none of the 4 mW ones. The published values reproduce the paper's statistics (Figure 6E p = 1.1e-20, Figure 6F p = 2.75e-177, Cohen's d 2.06 and 0.765), so the Calb1 differences come from the data, not from the paper's computation on them.", "deviations": [ "The criterion fixed the integral of each spontaneous transient; the published values turned out to be 0.005 times the integral divided by the number of samples in the transient. That measure, and the mean dF/F, are shown as variants and do not change the outcome." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig6e-anxa1-evoked-reduced", "statement": "Optogenetically evoked dopamine release in the dorsolateral striatum (Anxa1+ projection region) at 0.5 mW is lower in LRRK2-G2019S than in LRRK2-WT mice (64 against 56 stimulations, p = 1.10e-20, one-tailed two-sample t-test).", "source": "Figure 6E (left), Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Light-on integrals at 0.5 mW, GS 48.8 against WT 128.0 % dF/F x s, one-tailed p = 1.16e-22 (paper 1.10e-20), Cohen's d 2.21. The code's window gives p = 1.1e-20, the paper's value. It holds at 4 mW (p = 4.08e-18), without the two GS mice given 0.33 s trains (p = 4.16e-17), and with mouse means (Welch p = 0.000434). The window chunking_index.m computes as written reverses the sign (p = 1).", "deviations": [ "The integral is over each train's light-on period, as the Methods state; the paper's values come from the code's window, -0.1 to 1.0 s, shown as a variant. The baseline, which the Methods do not give, is the code's.", "The paper's plotting code selects power code 'h' for this panel; the panel is tested at the 0.5 mW of the legend, which the source data confirm, and 4 mW is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6e-anxa1-evoked-per-mouse", "statement": "Seven of eight individual G2019S mice show significantly reduced evoked dopamine release at 0.5 mW compared with the WT group; mouse 3743 does not.", "source": "Figure 6E (right) and legend; Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Under all four readings (Welch or Student, one- or two-tailed) 7 of 8 GS mice are below the WT group at p < 0.05/8 and 3743 is the exception (mean 125 against 128, Welch one-tailed p = 0.362). The count is the same with the code's window. Two of the seven, 3742 and 4885, received the paper's powers as 0.33 s trains, unlike every WT mouse, and their responses do not follow the labelled power; the other five significant mice were stimulated as the WT mice were.", "deviations": [ "The Methods name Welch's test, the legend's p-values are one-tailed and the code runs a two-tailed Student test; all four readings are shown and all give 7." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp7c-anxa1-evoked-all-powers", "statement": "The reduction of evoked dopamine release in Anxa1 G2019S mice holds at each of the four stimulation powers, 0.1, 0.5, 1 and 4 mW (p from 1.29e-15 to 1.10e-20).", "source": "Supplementary Figure 7C; Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "GS lower at all four powers, one-tailed p from 3.13e-15 to 1.16e-22 with the light-on window. With the code's window the p-values at 0.1, 0.5 and 1 mW equal the paper's (1.29e-15, 1.1e-20, 1.22e-17); at 4 mW it is 5.62e-16 against 2.39e-16, as that window, which runs to 1.0 s after onset, leaves 55 WT stimulations there (the processed series of mouse 4398 ends 0.8 s after its last onset). The Methods window keeps all 56.", "deviations": [ "In the code's window variant, 55 WT stimulations at 4 mW in place of 56, as one falls at the end of a truncated series." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6f-anxa1-spontaneous-reduced", "statement": "Spontaneous dopamine transients in the dorsolateral striatum are smaller in G2019S than in WT mice (1064 against 798 transients, p = 2.75e-177, one-tailed two-sample t-test), with 57 to 285 transients per mouse.", "source": "Figure 6F (left) and legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "The Methods' detection gives the paper's counts exactly (1064 and 798, 57 to 285 per mouse). Integrals GS 131.9 against WT 302.9 % dF/F x s, one-tailed p = 4.85e-72 (paper 2.75e-177). With the measure of the published values, 0.005 times the integral divided by the number of samples, p = 2.747e-177, the paper's value. With mouse means, Welch p = 0.0318.", "deviations": [ "The integral of each transient is used, as the Methods state; the paper's values are 0.005 times the integral divided by the number of samples in the transient, shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6f-anxa1-spontaneous-per-mouse", "statement": "Six of eight individual G2019S mice show significantly smaller spontaneous dopamine transients than the WT group; mice 4651 and 3743 do not.", "source": "Figure 6F (right) and legend; Results, last section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "By the integral 5 of 8 GS mice are below the WT group under every reading; the exceptions are 3743 (p = 0.431), 4651 (mean 417, above the WT mean of 303) and 4652 (p = 0.0128). With the paper's measure, 0.005 times the integral divided by the number of samples, the one-tailed Student test gives 6 of 8 with 3743 and 4651 as the exceptions and the legend's p-values (3742 5.28e-88, 4004 1.24e-95, 4652 6.21e-13, 4885 1.44e-49; 4651 0.00844 against 0.008); the Welch tests give 7 there. The difference from the paper comes from the measure; the paper's count follows the Student test of its legend.", "deviations": [ "The integral of each transient is used, as the Methods state; the paper's measure is shown as a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp8c-calb1-spontaneous-not-reduced", "statement": "In the dorsomedial striatum (Calb1+ projection region), spontaneous dopamine transients are not reduced in G2019S mice (970 against 682 transients, p = 0.98).", "source": "Supplementary Figure 8C; Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "The paper's test does not find the effect, one-tailed p = 0.0509, difference of means 21.1 % dF/F x s, Cohen's d 0.085; the result sits at the threshold and is fragile. Moving either end of the exclusion window by up to 10 samples gives p from 0.0403 to 0.0792, below 0.05 in 59 of 121 windows. With the published measure (0.005 times the integral divided by the number of samples) GS are lower at p = 2.45e-09 (d 0.305), with the transient mean at p = 2.25e-09, with the code's exclusion window as written at p = 1.81e-05, and with mouse means Welch p = 0.402. The counts are within tolerance but differ from the paper's 970 and 682, and the Calb1 dF/F in the dandiset is not the one the paper analysed (source-data-link); the published values give p = 0.989.", "deviations": [ "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp8e-calb1-evoked-reduced", "statement": "Evoked dopamine release in the dorsomedial striatum from Calb1+ neuron stimulation is reduced in G2019S mice at each of four powers (56 against 40 stimulations per power, p from 6.45e-05 to 0.001).", "source": "Supplementary Figure 8E (left); Results, last section", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "GS lower at all four powers, one-tailed p from 4.38e-07 to 6.29e-10, smaller than the paper's 6.45e-05 to 0.001. The p-values differ because the dandiset's Calb1 dF/F is not the paper's (source-data-link). With one value per mouse (7 GS, 5 WT), Welch one-tailed p is 0.0424, 0.0413, 0.0726 and 0.0916 at 0.1, 0.5, 1 and 4 mW.", "deviations": [ "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "supp8e-calb1-few-mice-reduced", "statement": "Only 2 of 7 G2019S mice show reduced Calb1+ evoked dopamine release relative to the WT group.", "source": "Supplementary Figure 8E (right); Results, last section", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "At 0.5 mW, 7 (Welch one-tailed), 6 (Welch two-tailed) and 4 (Student, either tail) of 7 GS mice are below the WT group at p < 0.05/7, against the paper's 2; the closest reading gives 4, recorded as measured. Student tests give 2 at 0.1 and 1 mW. The panel's power is not stated, and the dandiset's Calb1 dF/F is not the paper's.", "deviations": [ "The legend does not state the power of the per-mouse panel; 0.5 mW was fixed before the analysis and the other powers are shown.", "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "cohens-d-anxa1-larger", "statement": "The G2019S reduction of evoked release at 0.5 mW is much larger for Anxa1+ (Cohen's d = 2.05) than for Calb1+ stimulation (d = 0.76).", "source": "Results, last section", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Anxa1 d = 2.21 is within tolerance; Calb1 d = 1.40 is not (0.684 to 0.836), and the ratio 1.58 is under the factor of 2 the criterion asks. With the code's window, 2.06 and 1.25. The paper's published integrals give 2.06 and 0.765, so the miss is consistent with the Calb1 dF/F in the dandiset not being the paper's. The Anxa1 effect is larger than the Calb1 effect at every power and window that starts by onset (ratio 1.29 to 1.74), so the direction of the paper's comparison holds, with a smaller gap.", "deviations": [ "Run on the dandiset's Calb1 dF/F, which differs from the trace behind Supplementary Figure 8." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1d-lrrk2-enriched-vulnerable", "statement": "LRRK2 immunolabeling intensity is higher in Aldh1a1+ (vulnerable) than in Aldh1a1- SNc dopamine neurons (p = 0.0008).", "source": "Figure 1B and 1D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Over the 16 sections of the source data (5, 6 and 5 from three mice), LRRK2 intensity is higher in Aldh1a1+ than in Aldh1a1- neurons, 1.049 against 0.973, two-tailed unpaired Student p = 4.65e-06, Cohen's d 1.97; higher in 15 of 16 sections and in each mouse. The paper's p = 0.0008 matches a paired test over sections (0.000759) or an unpaired test of the three mouse means (0.000822), not the unpaired test over sections its legend names. Attempt -01 blocked this claim with data_missing under pilot-6, as the data are not in the dandiset; under pilot-7 it is a claim on data elsewhere and is tested.", "deviations": [ "The test starts from the paper's per-section values. The images (S-BIAD2070) are matched by mouse but not segmented again, as the Methods' analysis runs in Imaris 10.1, a commercial program, with automatic thresholds." ], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2070 (images); Zenodo doi:10.5281/zenodo.19930567 (per-section values)", "proposed": null }, { "claim": "fig2b-rab3-phosphorylation", "statement": "LRRK2 kinase inhibition with MLi-2 changes 289 phosphopeptides in striatal synaptosomes of G2019S mice, including RAB3 T86.", "source": "Figure 2A to 2C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "On the log2 abundances as deposited, 1694 (reading a, all six values) or 1810 (reading b, two per group) phosphopeptides pass p <= 0.05 and |difference| > 0.58, against 289, and nearly all are lower with vehicle (1673 and 1785), as the samples labelled MLi-2 have higher abundances overall (median log2 17.84 to 18.12 against 17.25 to 17.47). The RAB3 T86 peptide passes (p = 0.00892) but is lower with vehicle (difference -1.31), so neither part of the criterion holds. Centring each sample on its median, a step the criterion did not fix, gives 243 and 282 peptides (282 within tolerance) and RAB3 T86 still higher with MLi-2 (difference -0.693, p = 0.0238). The paper's volcano table holds MLi-2 minus vehicle as the samples are labelled; on the 4340 peptides with all six values its difference equals that difference plus a constant to within 1.6e-06, and against vehicle minus MLi-2 the residual reaches 13. Its p-values are near those of a t-test on median-centred values but not equal (median gap in -log10 p 0.0088 Welch, 0.0161 Student). It gives 254 peptides at the legend's thresholds, and RAB3 T86 +0.688, which the legend reads as higher with vehicle. As the samples are labelled, the RAB3 T86 phosphopeptide rises after MLi-2. RAB10 T73 does not change (0.15, p = 0.775), so the data cannot tell whether the labels or the figure's direction are swapped. If the labels are swapped, the median-centred reading b gives 282 peptides and RAB3 T86 higher with vehicle (+0.693), which would reproduce the claim, so the outcome rests on a labelling question the data cannot answer. Attempt -01 blocked this claim with data_missing under pilot-6; under pilot-7 it is tested on the PRIDE data.", "deviations": [ "The criterion fixed log2 abundances without normalisation; the paper's volcano table follows median-centred values. The median-centred result is shown as a variant and does not change the outcome.", "The legend does not say which peptides were tested; two readings (all six values, two per group) are shown.", "The search (Proteome Discoverer with Byonic and Sequest, commercial) is not re-run; the test starts from the deposited abundances." ], "disagreed": false, "data": "elsewhere", "where": "PRIDE PXD065006", "proposed": null }, { "claim": "fig2eg-prab3-increased", "statement": "Phosphorylation of RAB3A and RAB3C is increased in the SNc of G2019S mice and returns to WT levels with MLi-2.", "source": "Figure 2D to 2G", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "With contrasts on the pooled variance, Sidak-adjusted over the three pairs, GS is above WT and above GS with MLi-2 for RAB3A (p = 0.0202 and 0.00688) and RAB3C (0.00358 and 0.0415), with F = 8.593, 11.33, 14.76 and 7.398, the legend's values. GS with MLi-2 does not differ from WT (adjusted p = 0.963 and 0.622). Over two pairs the p-values are 0.0135, 0.00459, 0.00239 and 0.0279. Attempt -01 blocked this claim with data_missing under pilot-6; under pilot-7 it is tested on the Zenodo data.", "deviations": [ "The test starts from the deposited ratios; the uncropped blots are not quantified again, as the Methods do not say how bands were measured.", "The legend's two-way ANOVA has genotype and treatment factors on three groups; it is run as the equivalent one-way model with contrasts, which gives the legend's F values." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.19930567", "proposed": null }, { "claim": "fig3d-rim-binds-unphosphorylated", "statement": "RIM1 and RIM2 bind unphosphorylated RAB3A in preference to RAB3A phosphorylated at T86, while RILPL1 and RILPL2 prefer the phosphorylated form.", "source": "Figure 3D to 3F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "RIM1 (Q99NE5-7) and RIM2 are higher with RAB3A (log2 differences 2.42 and 2.17, paired p = 0.00361 and 0.0124) and RILPL1 higher with p-RAB3A (-6.02, p = 9.8e-05). RILPL2 is detected in all six p-RAB3A and in none of the RAB3A pulldowns, so the criterion's paired test has no pair and does not find it higher with p-RAB3A; three of four comparisons hold. With the Methods' imputation (seeded), a variant, it is higher with p-RAB3A (-7.92, p = 1.21e-08), and the limma table gives logFC -7.58, so the data point the way of the claim for RILPL2. The paper's p-values for RIM2 and RILPL1 (0.011, 0.002) are those of the paired test on intensities without the log (0.0109, 0.0022). The deposited limma table agrees in direction for every group. Its counts at the text's p-value < 0.05 and |log2FC| >= 1 are 121 and 32; the paper's 69 and 16 are the counts at adjusted p < 0.05. Attempt -01 blocked this claim with data_missing under pilot-6; under pilot-7 it is tested on the PRIDE data.", "deviations": [ "RILPL2 has no pair for the criterion's paired test and is counted as not holding; the Methods' imputation followed by an unpaired t-test, which gives four of four, is shown as a variant.", "The tests use log2 intensities; the paper's p-values follow intensities without the log. Both are shown.", "Replicates are paired in run order, as the paper does not give the pairing." ], "disagreed": true, "data": "elsewhere", "where": "PRIDE PXD065125", "proposed": null }, { "claim": "fig4d-fewer-active-zones", "statement": "Fewer TH+/VAMP2+ striatal synaptosomes from G2019S mice contain bassoon, and the remaining bassoon clusters are larger.", "source": "Figure 4D and 4E", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Part A holds. In the source data fewer TH+/VAMP2+ synaptosomes contain bassoon in GS (12.0 against 21.4 %, p = 6.38e-05; 0.000118 without the GS value under 1 %) and the bassoon area is larger (0.0862 against 0.0750 um2, p = 0.0301, the paper's value); with one value per mouse p = 0.263 and 0.474. Part B does not. The Methods' FIJI procedure as re-implemented here gives, GS against WT, 48.8 against 52.4 % with bassoon (p = 0.459) and a bassoon area of 0.0682 against 0.0696 um2 (overlap, p = 0.805) or 0.132 against 0.141 um2 (bassoon particle, p = 0.206). The re-implementation keeps a median of 183 VAMP2 particles per image against the legend's about 1000; the Default threshold alone gives a median of 1186 objects, of which the size limit keeps 193 and the circularity limit 183. Its percentages are more than twice the paper's, so part B may fail because of this attempt's segmentation, and its null result is weak evidence against the claim. The OME metadata of 165 of 168 images confirm the channel order. Attempt -01 blocked this claim with data_missing under pilot-6; under pilot-7 it is tested on the Zenodo values and the BioImage Archive images.", "deviations": [ "The FIJI procedure is re-implemented in Python (rolling ball as ImageJ shrinks it, ImageJ's Default threshold, scikit-image perimeters); it is not FIJI, and its particle counts are far below the paper's.", "The images cannot be matched to the published areas one by one; part B compares genotypes over the deposited images (35 GS and 39 WT for the percentage, 49 and 43 for the area, one image in each folder with nothing to measure)." ], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2074 (images); Zenodo doi:10.5281/zenodo.19930567 (per-area values)", "proposed": null }, { "claim": "fig4i-rim1-reduced", "statement": "RIM1 is reduced in striatal synaptosomes of G2019S mice (p = 0.0245) but not in other striatal fractions or the SNc.", "source": "Figure 4H to 4L", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "RIM1 in synaptosomes is lower in GS, 0.206 against 0.319, two-tailed p = 0.0245 (the paper's value), Cohen's d -1.53. RIM1 in the S1 fraction (p = 0.896) and in the SNc (p = 0.936) does not differ, nor do synaptophysin (4G, p = 0.445) and the protein of 4H (p = 0.634). Attempt -01 blocked this claim with data_missing under pilot-6; under pilot-7 it is tested on the Zenodo data.", "deviations": [ "The test starts from the deposited band values; the uncropped blots are not quantified again, as the Methods do not say how bands were measured." ], "disagreed": false, "data": "elsewhere", "where": "Zenodo doi:10.5281/zenodo.19930567", "proposed": null }, { "claim": "fig5-bassoon-vulnerable-axons", "statement": "Bassoon cluster density is reduced and cluster volume increased in Aldh1a1+ but not Aldh1a1- dopamine axons of G2019S mice, and the same holds in Anxa1+ axons.", "source": "Figure 5D, 5E, 5G and 5H", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "Five of six parts hold. With section 5 of WT mouse 1723 counted once (its four values equal those of section 4), Aldh1a1+ density is lower in GS (0.164 against 0.217) at Sidak p = 0.058, so part 1 fails; Aldh1a1- density does not differ (p = 0.713); bassoon volume is larger in GS Aldh1a1+ axons (p = 0.0425) and not in Aldh1a1- axons (p = 0.699); in Anxa1+ axons density is lower (p = 0.0374) and volume larger (p = 0.0148). As deposited, with the section twice, all six hold and the ANOVA gives the legend's numbers (5D Sidak p 0.0344, 5E 0.0385). Attempt -01 blocked this claim with data_missing under pilot-6; under pilot-7 it is tested on the Zenodo values.", "deviations": [ "The analysis starts from the per-section values; the 542 GB of SIM images (S-BIAD2071) are matched by file name and not analysed again, as the Methods' analysis runs in Imaris 10.1.", "One section that appears twice in the source data is counted once, as the claims file fixes; the paper counts it twice." ], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2071 (images); Zenodo doi:10.5281/zenodo.19930567 (per-section values)", "proposed": null }, { "claim": "fig5j-no-axon-loss", "statement": "The volume occupied by TH+ fibres in the dorsal striatum does not differ between G2019S and WT mice.", "source": "Figure 5I and 5J", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_chen_2026.ipynb", "notes": "The paper's test does not find a difference in TH volume, two-tailed p = 0.117 over 12 sections per genotype; GS is 7.1 % lower (0.929 against 1.000), Cohen's d -0.67. Attempt -01 blocked this claim with data_missing under pilot-6; under pilot-7 it is tested on the Zenodo values.", "deviations": [ "The test starts from the per-section values; the images (S-BIAD2072) are matched by file name and not analysed again, as the Methods' analysis runs in Imaris 10.1." ], "disagreed": false, "data": "elsewhere", "where": "BioImage Archive S-BIAD2072 (images); Zenodo doi:10.5281/zenodo.19930567 (per-section values)", "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "Still present from attempt -01. The Calb1 dF/F in the dandiset is not the trace behind Supplementary Figure 8. None of the 384 published Calb1 triggered traces is within 1e-6 of any epoch of its mouse (closest 15.7 % dF/F), none of the evoked integrals match, the transient counts match for 1 of 12 mice, and dF/F recomputed from the deposited raw signal with the published code reproduces the dandiset's series, not the paper's. The processing the paper used for Calb1 is neither deposited nor described." }, { "kind": "other", "statement": "Still present from attempt -01, where it was recorded as data_missing. The dandiset holds only the fiber photometry of Figure 6 and Supplementary Figures 7 and 8. The imaging, proteomics and western blots of Figures 1 to 5 are public on Zenodo, in PRIDE and in the BioImage Archive, but neither the dandiset's description nor its related resources name those deposits." }, { "kind": "other", "statement": "Still present from attempt -01. The processed series of mouse 4398 ends 0.81 s after its last onset, a 4 mW stimulation, while the paper's trace for that stimulation is complete." }, { "kind": "metadata_error", "statement": "Still present from attempt -01. The OptogeneticEpochsTable description gives 8 ms on and 8 ms off for 500 ms, four powers and trains at least 20 s apart. The tables hold eight powers, two kinds of train in Anxa1 files (0.33 s and 0.51 s), and pairs of trains 15.3 s apart. Two trains have a pulse length of 0." }, { "kind": "other", "statement": "Still present from attempt -01. Two Anxa1 G2019S mice (3742 and 4885) received the paper's four powers as 0.33 s trains of 9 ms pulses, while every other mouse received them as 0.51 s trains of 8 ms pulses. Neither the paper nor the dandiset says so, and in these two mice the response does not follow the labelled power." }, { "kind": "metadata_error", "statement": "Still present from attempt -01. The dF/F series (FiberPhotometryResponseSeriesDfOverF) is stated in a.u.; its description and its values are percent dF/F." }, { "kind": "metadata_error", "statement": "Still present from attempt -01. The archive's summary of the dandiset lists only a behavioral approach and BehavioralTimeSeries; the files hold fiber photometry and optogenetics." }, { "kind": "selection_undocumented", "statement": "Still present from attempt -01. The dandiset holds the 27 mice the paper kept after excluding four on histology, and does not say that mice were left out or why." }, { "kind": "code_mismatch", "statement": "Still present from attempt -01 (the repository is at the same commit). chunking_index.m computes the start of each window as trigger - fs*ti, so with ti = -1 the window starts 1 s after onset; the figures used the intended window starting 1 s before onset." }, { "kind": "code_mismatch", "statement": "Still present from attempt -01. plot_results.m selects power code 'h' (4 mW) for Figure 6E; the figure, its legend and the source data are at 0.5 mW." }, { "kind": "code_mismatch", "statement": "Still present from attempt -01, and made more exact. The Methods and transient_by_threshold.m give the integral of dF/F over each spontaneous transient; the published values of Figure 6F and Supplementary Figure 8C are 0.005 times the trapezoid integral divided by the number of samples in the transient (exact to 2.2e-15 in every Anxa1 mouse; attempt -01 described them as about 0.005 times the mean dF/F), and the code that computes them is not in the repository." }, { "kind": "paper_inconsistency", "statement": "Still present from attempt -01. For the per-mouse comparisons of Figure 6 the Methods and the asterisks name Welch's test, the legends give one-tailed two-sample t-test p-values, and the code runs a two-tailed Student test." }, { "kind": "other", "statement": "Still present from attempt -01. The paper does not cite the dandiset (none of its 99 references names DANDI); its data statement names Zenodo, PRIDE and the BioImage Archive." }, { "kind": "paper_inconsistency", "statement": "New. In the synaptosome phosphoproteomics (PRIDE PXD065006, equal to Supplementary data 1) the RAB3 T86 phosphopeptide is higher in the samples labelled MLi-2 than in those labelled vehicle (median-centred log2 difference vehicle minus MLi-2 of -0.693, p = 0.0238), and the paper's volcano table holds MLi-2 minus vehicle (equal to it up to a constant within 1.6e-06 on 4340 peptides), while the Figure 2B legend reads a positive difference as higher with vehicle and the text reports less RAB3 phosphorylation with MLi-2. Either the sample labels of the deposit or the direction of Figure 2B is swapped." }, { "kind": "paper_inconsistency", "statement": "New. The paper's volcano table (Supplementary data 1) gives 254 phosphopeptides at the legend's thresholds (p <= 0.05, |difference| > 0.58), where the text gives 289." }, { "kind": "paper_inconsistency", "statement": "New. The text gives 69 and 16 proteins preferring RAB3A and p-RAB3A at p-value < 0.05 and |log2FC| = 1; the deposited limma table (PRIDE PXD065125) gives 121 and 32 at that p-value, and 69 and 16 at adjusted p < 0.05. The Figure 3E and 3F p-values are of paired tests on intensities without the log, which the legend does not say." }, { "kind": "paper_inconsistency", "statement": "New. The Figure 1D legend gives a two-tailed unpaired t-test over 16 sections with p = 0.0008; on the source data that test gives p = 4.65e-06, and 0.0008 matches a paired test over sections or an unpaired test of the three mouse means." }, { "kind": "other", "statement": "New. In the source data of Figure 5D and 5E, sections 4 and 5 of WT mouse 1723 carry the same four values to six digits, so one section appears to have been entered twice. Counted once, the Aldh1a1+ density comparison has Sidak p = 0.058 in place of 0.0344." }, { "kind": "paper_inconsistency", "statement": "New. The source data and the legends differ in counts. Figure 4E has 51 G2019S areas against the legend's 57 (the source data give the legend's p = 0.0301); Figure 5E has 21 G2019S Aldh1a1+ sections against 20; and the 5E legend gives a genotype F of 1.277, the 5D value, where the data give 5.234 with the legend's p = 0.0252. One Figure 4D value (0.0766 %) is of the size of the Figure 4E areas and may have been pasted from there." }, { "kind": "identifier_missing", "statement": "New. The source data of Figure 5G, 5H and 5J give one animal column holding WT IDs for both genotypes, so the G2019S animals are not identified. The BioImage Archive names them (S-BIAD2071 1019, 1020, 1022, 1052; S-BIAD2072 3243, 3246, 4120, 4369). S-BIAD2071 names a WT mouse 1923 where the source data name 1723, and two of its files carry no mouse ID. S-BIAD2074 names mice only by a number from 1 to 5 per genotype." }, { "kind": "selection_undocumented", "statement": "New. The image studies hold images the figures do not use, without saying which were used. S-BIAD2070 has 7 images per mouse for Figure 1D, which has 5 or 6 sections per mouse; S-BIAD2071 has a fourth Anxa1 WT mouse (1018) not in Figure 5G and 5H; S-BIAD2072 has 64 volume images per genotype where the legend gives 96; and the synaptosome images of S-BIAD2074 differ in number per mouse from the published areas (G2019S 14, 10 and 12 images against 14, 11 and 10 areas in Figure 4D; 50 images against 51 areas in Figure 4E)." }, { "kind": "methods_unavailable", "statement": "New. The image analyses of Figures 1 and 5 ran in Imaris 10.1 with automatic or manually adjusted thresholds that are not deposited, and the Methods do not say how western blot bands were quantified, so these values cannot be recomputed from the images and blots that are deposited." }, { "kind": "metadata_error", "statement": "New. In BioImage Archive S-BIAD2074, the OME metadata of three images (BSN-area Export_ki4_BSN2, BSN3 and BSN4) give an excitation of 488 nm for all three channels, where the other 165 images give 488, 561 and 640 nm and the archive annotates bassoon, TH and VAMP2." } ], "verifications": [ { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The executed notebook of the first run with the conclusion cells and the summary removed, the helper modules and the claims file, with the paper. The verifier tested double_threshold, evoked_integrals, cohens_d, twoway_anova and sidak_within on synthetic inputs, checked the column labels of the Figure 1D sheet and the OME metadata of one synaptosome image. Report in transcripts/001933/verifier-1-report.md.", "agreed": 17, "of": 18, "disagreements": [ { "claim": "fig3d-rim-binds-unphosphorylated", "outcome": "partially_reproduced", "reason": "Cell 59: RIM1, RIM2 and RILPL1 hold under the paired test. RILPL2 has no values in the RAB3A pulldowns, so the paired test is undefined: 3 of 4. The closing decision replaces the criterion's paired test with the imputation variant for RILPL2, turning 3 of 4 into 4 of 4. RILPL2 is present in 6 of 6 p-RAB3A pulldowns and 0 of 6 RAB3A pulldowns, which supports the claim qualitatively, but the criterion's test cannot score it (problem 4)." } ] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the revised run, with its conclusion cells and summary, the helper modules, the README, this record and the claims file, with the paper. The verifier checked every Result cell, the summary, the notes and the findings against the printed outputs, viewed the overlay figure of cell 21 and checked that the round-1 reasons were stated faithfully. Report in transcripts/001933/verifier-2-report.md.", "agreed": 18, "of": 18, "disagreements": [] } ] }, { "id": "002013-amjad-2025-01", "dandiset": "002013", "dandiset_version": "0.261012.0921", "paper": "10.1021/acschemneuro.5c00071", "paper_title": "Microinvasive Probes for Monitoring Electrical and Chemical Neural Activity in Nonhuman Primates", "date": "2026-10-15", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "002013-amjad-2025", "entry_title": "Microinvasive probes for dopamine, LFP and spikes in monkeys (Amjad et al. 2025)", "description": "Tests the findings of Amjad, Mahajan, Choi, Shrivastav, Murray, Somich, Coyne and Schwerdt (2025) on dandiset 002013, which holds the three example sessions of the paper. It checks the recording parameters and task structure, the dopamine response to large and small reward cues at site c8dg, beta-band LFP suppression by reward and cue side at c3bs-c3a, beta bursts around the cue, and the isolation of the sorted unit of monkey P, and compares the dandiset with the paper's Zenodo deposit.", "notebooks": [ { "path": "reproduce_amjad_2025.ipynb", "title": "Reproducing Amjad et al. (2025) from dandiset 002013", "executed": "notebooks/002013-amjad-2025/reproduce_amjad_2025.html" } ], "outcomes": [ { "claim": "insertion-yield", "statement": "Insertion yields were low, 21.4% (3 of 14 sensors) in monkey T and 33% (3 of 9) in monkey P, counted as recording sites that stayed functional after insertion until the end of the study.", "source": "Results and Discussion, second paragraph", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds one or two sites per session and no list of the implanted sensors or of which kept working, in its files or its metadata. None of the ten file names of the paper's Zenodo deposit, printed in the data check, points to such a list.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "chronic-duration", "statement": "The s-\u00b5IPs kept recording for more than a year after implantation; the example sites were recorded 483 days (c8dg), 496 days (c3bs-c3a) and 390 days (monkey P) after implantation.", "source": "Figure 3 to 5 legends; Results and Discussion", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The subject, device and electrode fields of the files hold no implantation date, and none of the mentions of implantation in the files' general section or the dandiset metadata (all printed in the data check) comes with a date, so days post-implant cannot be computed. The two Monkey T sessions are 13 days apart, which matches the difference between the 483 and 496 days of the legends.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fscv-waveform", "statement": "FSCV applied a triangular waveform from -0.4 to 1.3 V at 400 V/s, every 100 ms (10 Hz).", "source": "Methods, FSCV and EPhys Recordings", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "The applied voltage runs from -0.347 to 1.340 V at 400.5 V/s, one scan every 0.1 s. Three of four values are within tolerance; the lowest potential is outside -0.4 +- 0.04 V. The dandiset's own description (-0.35 to 1.34 V) agrees with the data, so the Methods state the nominal waveform. The data of the applied voltage have conversion 1 and offset 0, so the values are read as stored.", "deviations": [ "Measured on session 09/13/2024 only, the only FSCV session in the dandiset." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "ephys-acquisition", "statement": "EPhys was sampled at 30 kHz in monkey P and 32 kHz in monkey T, and band-pass filtered from 0.1 to 7500 Hz.", "source": "Methods, FSCV and EPhys Recordings", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "Monkey P's raw timestamps have a median interval of 33.333 \u00b5s (30 kHz) and Monkey T's series a rate of 32000 Hz. The Neuralynx settings of both Monkey T channels give a low cut of 0.1 Hz and a high cut of 8000 Hz, inside the tolerance of 7500 Hz but not equal to it; the dandiset's description also says 0.1 to 7500 Hz (printed). Monkey P's file stores no filter settings; its notes, printed in full, and its electrode columns name no filter or cut-off.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "shape-task-structure", "statement": "In the shape task, forced trials made up 25% of all trials, and the cue-reward association was reversed after blocks of 50 to 300 trials.", "source": "Methods, Behavioral Tasks", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "Forced trials are 358 of 1468 (24.4%). The eight complete blocks of the cue-reward association are 71 to 273 trials long; the first and last blocks, cut by the file, are 61 and 194 trials.", "deviations": [ "Blocks are found from the image codes of successful forced trials, as choice trials carry no feedback code; a reversal is placed after the last forced trial of the earlier association, so block edges are uncertain by the gap between forced trials." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "zenodo-link", "statement": "The dandiset reproduces the processed data the paper deposited on Zenodo; the trial selections and the beta power of the paper's example trial computed from the dandiset agree with the paper's own files.", "source": "Data Availability Statement (doi:10.5281/zenodo.14826579)", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "Trials are matched by number. The decoded selections agree with the four Zenodo lists for 569 of 570, 602 of 602, 594 of 594 and 577 of 578 trials; the only difference is trial 1501, the last of the session, absent from the Zenodo large-reward and right lists. The Zenodo example \"trial35\" is the 35th trial of the large-reward list (trial 84). Beta power computed here correlates with its trace at r = 0.943 at a lag of 6 ms, with a median amplitude ratio of 0.943, so the dandiset's LFP, its trial times and the beta pipeline used here agree with the paper's files. The Zenodo example's raw LFP variable is a copy of its time variable, so the LFP trace itself could not be compared. The criterion tests only r and was written after r = 0.94 was known. The amplitudes differ (maximum 2184 \u00b5V\u00b2 here against 1560 \u00b5V\u00b2 in the Zenodo trace), so the paper's filter or envelope probably differs from the one used here.", "deviations": [ "The beta filter (4th-order Butterworth, forwards and backwards, squared Hilbert envelope) is a common choice; the paper's code is not public, and r = 0.943 suggests its filter differs somewhat." ], "disagreed": false, "data": "with_inputs", "where": null, "proposed": null }, { "claim": "fig3a-dual-channel", "statement": "Dopamine was measured from two neighbouring channels of one dual-channel s-\u00b5IP (sites c8dg and c8ds, 0.1 to 0.2 mm apart), and both showed dopamine increases after the value cue in a single forced large-reward trial.", "source": "Figure 3A; Results and Discussion", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds FSCV from site c8dg only. Site c8ds is not in it, and the Zenodo deposit holds processed FSCV of c8dg only; its one FSCV file is FSCV_trlists_c8dg_09132024_firsthalf.mat (file list printed in the data check). The c8dg half can be tested and holds; the mean of the re-referenced dopamine over 0 to 3 s is above zero in 56 of 85 large-reward forced trials (65.9%), and in 58 of 85 with a baseline of the mean over -1 to 0 s.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3a-redox-peaks", "statement": "The single-trial FSCV colour plot shows dopamine redox current, with changes near 0.6 V (oxidation) and -0.2 V (reduction) after the value cue.", "source": "Figure 3A", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": null, "notes": "The raw FSCV current is in the dandiset, but its timing could not be linked to the trials. Its scan times are an exact 0.1 s grid starting at the first trial start and running 24120 s, past the last trial; at 0.6 V it does not match the stored oxidation current of any of six rows tested at the stored times (|r| below 0.06) or anywhere in the record (best r 0.16 to 0.20 at offsets that differ from row to row); and it shows no large-against-small contrast at the stored value cue times (p = 0.46). The same search at 0.50 V, 0.70 V and -0.19 V gives best r 0.17 to 0.22 at offsets that differ from row to row. Computed at the stored times (not deciding), the background-subtracted voltammogram of 164 large-reward forced trials has its largest rising-sweep value at -0.24 V (at 0.6 V it is -0.033) and its most negative value at the switching potential, 1.34 V, with an SD of 0.042 over the scan; it does not meet the criterion. A colour plot of a forced large-reward trial therefore cannot be placed in the trial.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3b-beta-bursts", "statement": "Single-trial bipolar LFP from site c3bs-c3a shows beta bursts (one to a few cycles of high beta power) whose frequency changes around the cue and other task events.", "source": "Figure 3B; Results and Discussion", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "With the threshold at the 75th percentile (356 \u00b5V\u00b2) and bursts of at least 50 ms, the burst rate of 570 large-reward trials is 1.51 per s in the second before the value cue and 1.21 in the second after it (Wilcoxon p = 9.5e-10). The rate changes around the cue at the 50th and 90th percentiles too (p below 1e-40), rising at the 50th and falling at the 90th, so its direction depends on the threshold while the change does not. The rate dips just after the cue (0.51 per s in 0 to 0.25 s) and falls again from 6 s after it, after the feedback. On the smoothed power 95.1% of runs above the 75th percentile last at least 50 ms (median 206 ms), so the minimum length does little; on the unsmoothed envelope the rate also falls after the cue (3.07 to 2.11 per s, p = 6.8e-34). At the deciding threshold the fall in bursts coincides with the drop in beta power after the cue, so it is not separate evidence from the suppression of fig4b-beta-reward.", "deviations": [ "The paper shows a single trial and does not define a burst; the threshold, minimum length and test were chosen here before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4a-dopamine-reward", "statement": "Trial-averaged dopamine at site c8dg is higher after large-reward than after small-reward value cues, in successful forced trials of the shape task.", "source": "Figure 4A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "Over 0 to 3 s after the value cue, the re-referenced dopamine has a median of 1.28 in 85 large-reward trials and 0.19 in 80 small-reward trials (Mann-Whitney p = 0.023; 3 trials of 168 have no valid samples in the window). The difference lies in 1.5 to 3 s (p = 0.0072), not 0 to 1.5 s (p = 0.41). The effect is weak. Before the cue the groups differ the other way (p = 0.064). Without re-referencing (the stored da) there is no difference (p = 0.3), nor in the re-referenced oxidation current (p = 0.41). It holds in trials 1 to 367 (p = 0.013) and not in trials 368 to 734 (p = 0.51). With a baseline of the mean over -1 to 0 s in place of the sample at the cue the result is the same (1.38 against 0.10, p = 0.022).", "deviations": [ "Only the first 734 of 1468 trials of the session have trial-aligned FSCV in the dandiset, so 168 successful forced trials are used.", "The stored da is not referenced at the value cue; it is re-referenced here by subtracting its value at the cue, which equals background subtraction there only if the PCA projection was linear and the nulling (NaN) masks are ignored.", "Small reward is inferred from the absence of the big-reward code, confirmed by the cue condition codes 35 and 36 in all 303 successful forced trials.", "The paper gives no window or test; 0 to 3 s and the Mann-Whitney test were chosen before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-beta-reward", "statement": "Beta-band LFP power at c3bs-c3a in the direction task is more suppressed (stronger event-related desynchronization) after large-reward than after small-reward value cues, in a brief window after the cue.", "source": "Figure 4B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "Over 0 to 0.5 s after the value cue, median beta power is 275 \u00b5V\u00b2 in 570 large-reward trials and 327 \u00b5V\u00b2 in 602 small-reward trials (ratio 0.84, Mann-Whitney p = 1e-08), with no difference before the cue (ratio 1.006, p = 0.82). It holds relative to pre-cue power (ratio 0.82, p = 1.1e-06) and on each side (left p = 0.0016, right p = 1e-07). It is confined to a brief window, as the legend says; over 0 to 1 s large is slightly higher (ratio 1.04, p = 0.09) and over 0.25 to 0.75 s there is no difference (p = 0.66). The 0.25 s smoothing does not carry the difference from before the cue; on the unsmoothed envelope it holds over 0 to 0.5 s (ratio 0.834, p = 1.9e-08) and 0.125 to 0.5 s (ratio 0.671, p = 4.8e-19); in 0.1 s bins large and small do not differ before the cue (ratios 0.95 to 1.05), large is lower from 0.1 to 0.4 s (0.85, 0.59, 0.60) and higher from 0.5 s on (1.32 to 1.49). The criterion, lower power over 0 to 0.5 s, is met; the bins fit a deeper suppression after large-reward cues and equally an earlier suppression with an earlier rebound, so the part of the claim saying the suppression is greater is not shown. The LFP's 1497 joins do not step (largest change at a join 20.3 \u00b5V, below the 99.9th percentile of 26.0 \u00b5V over all samples), and 118 of 1172 successful trials have one within -0.5 to 1 s of the cue, 23 to 36 in each reward and side condition. Trial 1501, absent from the Zenodo lists, is included; one trial of 570 cannot change the result.", "deviations": [ "The paper does not give the window highlighted in Figure 4B or a test; 0 to 0.5 s and the Mann-Whitney test were chosen before the analysis." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-beta-side", "statement": "With the reward fixed at large, beta-band LFP power is more suppressed when the cue is on the left (contralateral) than on the right (ipsilateral).", "source": "Figure 4C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "Among large-reward trials, median beta power over 0 to 0.5 s is 245 \u00b5V\u00b2 for left cues and 301 \u00b5V\u00b2 for right cues (282 and 288 trials, ratio 0.81, Mann-Whitney p = 1.6e-06). Before the cue left is slightly higher (ratio 1.095, p = 0.013), so relative to pre-cue power the difference is larger (ratio 0.71, p = 2.1e-09). It holds over 0 to 1 s (p = 0.019), not over 0.25 to 0.75 s (p = 0.75), and also in small-reward trials (p = 1.5e-10). On the unsmoothed envelope left is lower over 0 to 0.5 s (ratio 0.807, p = 1.7e-06) and 0.125 to 0.5 s (ratio 0.688, p = 3.2e-17), most from 0.1 to 0.3 s (ratios 0.54 and 0.55).", "deviations": [ "Left is taken as contralateral, as the Methods state; the files do not say which hemisphere was implanted.", "Window and test chosen before the analysis, as for fig4b-beta-reward." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-spike-reward", "statement": "Spikes recorded from an s-\u00b5IP in the caudate of monkey P (site c33, 390 days post implant) fire at a different rate for large and small reward during the value cue fixation of the direction task.", "source": "Figure 5A; Results and Discussion", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Monkey P's file has no trials table and no events, so value cue times and reward sizes are not in the dandiset. The paper's Zenodo deposit has the session's raw Neuralynx events (session126_events.mat) as TTL values without names; their codes differ from those of the Monkey T sessions, so they could not be decoded (metadata insufficient). The notebook now reads that file, with 20812 events with 36 distinct TTL values and no names; the trial-start code 128 does not occur and the value cue code 23 occurs 20 times.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5bc-unit-isolation", "statement": "The s-\u00b5IP recorded a spike-sorted unit in monkey P, shown by its average waveform and its interspike interval histogram.", "source": "Figure 5B and 5C", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_amjad_2025.ipynb", "notes": "Plexon unit 1 has 31247 spikes at 2.61 Hz. One of 31246 interspike intervals is under 1 ms (0.003%), and its mean waveform trough (-30.6 \u00b5V) is 5.66 times the raw noise level (5.41 \u00b5V, 300 to 6000 Hz, 600 s). The units table's unit 0 (unsorted and poor-quality spikes merged) has 11.65% of intervals under 1 ms and is not a unit.", "deviations": [ "The noise level and the two thresholds are common choices; the paper shows the waveform and histogram without numbers.", "The paper names the site c33; the file names it cl3. The session is taken as the paper's." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "format_error", "statement": "Each event is stored about five times in the events tables of both Monkey T sessions (85665 stored times, 17686 distinct, in 09/13/2024; 59702 and 12434 in 09/26/2024), once for every overlapping 60 s trial window that contains it." }, { "kind": "metadata_insufficient", "statement": "The trials tables hold only times, no trial conditions. Conditions must be decoded from the event codes. Session 09/13/2024 has no small-reward code, and the labels of codes 35 and 36 (\"right cue reward condition 1/2\") do not say that they code large and small reward, which the data show in all 303 successful forced trials." }, { "kind": "data_missing", "statement": "The trial-aligned FSCV table of session 09/13/2024 has rows for only the first 734 of its 1468 trials (from a source file named \"firsthalf\"), and the dandiset has FSCV from c8dg only; the second site of Figure 3A (c8ds) is missing." }, { "kind": "metadata_insufficient", "statement": "The trial-aligned FSCV columns (da, ph, m, iox) carry no units, and da is not referenced at the value cue as the Methods describe; the reference point is not stated." }, { "kind": "metadata_error", "statement": "The raw FSCV current is labelled amperes, but its values range from -1527 to 1557; the unit is likely nA or the data are not current." }, { "kind": "metadata_error", "statement": "The raw FSCV scan times are an exact 0.1 s grid starting at the first trial start and running 24120 s, past the last trial, and the raw current cannot be matched to the trial-aligned oxidation current at any offset or to the task at the stored times. The conversion notes say the times were interpolated between trial-start codes; the data do not support that they are on the trial clock." }, { "kind": "metadata_error", "statement": "The bipolar LFP of session 09/26/2024 stores values already in volts (around 1e-4) with a conversion factor of 3.05e-8, so that read as NWB prescribes it is in picovolts." }, { "kind": "metadata_error", "statement": "The raw ephys of session 09/26/2024 has starting_time 0 and no timestamps, but it matches the stored LFP (r 0.92 to 0.98) only when read 9831.35 s later on the trial clock, consistently from the first trial to the last." }, { "kind": "metadata_error", "statement": "In Monkey P's file the spike times (6800 to 18785 s) are 6800.666 s later than the raw signal's timestamps (0 to 11985 s); the spike-triggered average of the raw signal shows the spike only with that shift. The file does not say the two use different clocks." }, { "kind": "format_error", "statement": "In Monkey P's units table, unit 0 merges the unsorted (0) and poor-quality (-1) thresholded spikes, including 7 spike times below 1 s and 3 repeated times; the poor-quality spikes of the thresholded table are not in time order." }, { "kind": "data_missing", "statement": "Monkey P's file has no trials or events, so the reward-related firing of Figure 5A cannot be tested. The paper's Zenodo events for this session are raw TTL values without a code map." }, { "kind": "metadata_insufficient", "statement": "No implantation dates are given, so the days post-implant of each session cannot be checked." }, { "kind": "metadata_error", "statement": "Monkey P's site is named cl3 in the file and dandiset description, c33 in the Figure 5 legend; the files' related_publications cite the bioRxiv preprint, not the article; the acquisition high cut is 8000 Hz in the Neuralynx settings, not the 7500 Hz the description states." }, { "kind": "other", "statement": "The applied FSCV waveform runs from -0.347 to 1.340 V, as the dandiset description says; the paper's Methods give -0.4 to 1.3 V." } ], "verifications": [ { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text (PMC12183687). The verifier read the archive's file list and metadata through the DANDI API and tested the helpers on synthetic inputs (beta_power, burst_onsets, window_mean, codes_per_trial, rereference, fscv_window_mean, best_lag, reward_blocks). It had no attempt record and took the claims from the claims file.", "agreed": 14, "of": 14, "disagreements": [] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the first revision, the helper module, the claims file, the attempt record, the README and its own round-1 report, with the paper's full text (PMC12183687).", "agreed": 14, "of": 14, "disagreements": [] } ] }, { "id": "002014-choi-2025-01", "dandiset": "002014", "dandiset_version": "0.261012.0921", "paper": "10.1016/j.jneumeth.2025.110467", "paper_title": "Aseptic, semi-sealed cranial chamber implants for chronic multi-channel neurochemical and electrophysiological neural recording in nonhuman primates", "date": "2026-10-15", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-6" }, "tier": "agent_verified", "entry": "002014-choi-2025", "entry_title": "Dopamine, spikes and LFP through an aseptic cranial chamber in a rhesus monkey (Choi et al. 2025)", "description": "Tests the recording findings of Choi et al. (2025) on dandiset 002014, which holds one session of monkey T recorded through the paper's semi-sealed chamber. It compares dopamine and beta-band LFP power between large and small reward trials, aligns spikes to the value cue, and checks the unit's waveform and interspike intervals. The surgical, culture, drainage and yield results, and monkey J, are not in the dandiset.", "notebooks": [ { "path": "reproduce_choi_2025.ipynb", "title": "Reproducing Choi et al. (2025) from dandiset 002014", "executed": "notebooks/002014-choi-2025/reproduce_choi_2025.html" } ], "outcomes": [ { "claim": "fig8a-single-trial-dopamine", "statement": "In a single trial (trial 133 of the session), dopamine concentration changes at site c8ds fluctuate, especially after the value cue display.", "source": "Figure 8A and its legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_choi_2025.ipynb", "notes": "In trial 133 (1-based, a successful large reward trial) the SD of dopamine referenced at V over the 5 s after V is 2.02 times that over the 5 s before. Under the other reading (index 133, trial 134) the ratio is 2.04, with 36% and 46% of samples NaN. The test is weak. Of the 889 successful trials with a reference at V, the median ratio is 1.27, 64% exceed 1, and trial 133's ratio is above 76.9% of them. The criterion was written after trial 133's values had been printed.", "deviations": [ "The paper shows the trial as a figure with no measure; the SD ratio and its windows were chosen here.", "The paper's trial numbering is not stated; both 1-based and 0-based readings are shown, and both match." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig8b-dopamine-large-vs-small", "statement": "Trial-averaged dopamine at site c8ds, aligned to the value cue, increases more for large than for small reward trials, especially between the value cue display and reward.", "source": "Figure 8B and its legend", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_choi_2025.ipynb", "notes": "From V to reward, dopamine referenced at V averages 1.88 in large and 1.10 in small reward trials (difference 0.78 in the file's unstated unit, Cohen's d 0.19, Mann-Whitney p = 0.0035, 429 and 460 trials, 23 and 39 dropped for lack of a reference at V). Shuffling the labels within blocks of 50 consecutive trials, which keeps the drift across the session in the null, gives p = 0.0045. The difference is small in the first 2 s after V (p = 0.44) and largest from reward to 3 s after (difference 1.59, p = 0.0001, within blocks p = 0.0010); before V there is none (p = 0.50). It holds in the second half of the session (p = 0.0125) and not significantly in the first (p = 0.075). Without trial 1411, p = 0.0031.", "deviations": [ "The PCA dopamine estimate at V is subtracted, in place of subtracting the background voltammogram at V before the PCA; the two agree if the PCA model is linear, which the dandiset does not let us check.", "The window (V to each trial's reward) and the test were chosen here; the paper states none.", "Trial 1411, which the paper's large reward list leaves out, is included (one trial of 452); without it p = 0.0031.", "Where dopamine is NaN at V, the reference is interpolated between the nearest valid samples if both lie within 0.2 s; none of the 62 such trials has them, so all are dropped." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig9a-spikes-task-aligned", "statement": "Spikes recorded at site c5d on a chamber-implanted CFE can be shown as a raster and a peristimulus time histogram aligned to the value cue display, for large and small reward trials.", "source": "Figure 9A and its legend; Results, section 3.5", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_choi_2025.ipynb", "notes": "With the spike times moved to the trial clock by the offset measured in the data check (11812.11 s), all successful trials have a spike within V - 1 s to V + 3 s, and the variance across 100 ms bins of the PSTH is 0.49 against a 95th percentile of 0.06 over random alignments (p = 0.005 with 200); 0.48 with the 7 ms lag also corrected. The rate falls from 5.63 spikes/s before V to 4.58 in the first 0.2 s and rises to 7.70 at 0.3 to 0.5 s. Large and small trials do not differ over 0 to 1 s (5.69 against 5.66 spikes/s, p = 0.90); the paper states no difference. The Plexon unit gives 0.17 against 0.06. With the spike times as stored, 42% of trials have a spike in the window and the variance is 0.01 against 0.03, so the claim fails on the file as published.", "deviations": [ "The spike times are moved by an offset measured from the data (the raw ephys located in the stored LFP); the file places them 11812.11 s early.", "The spikes are those of the thresholded table (the paper's Zenodo file); the Plexon unit is a variant.", "The paper states no effect for this panel; the criterion (spikes in most trials, and a rate locked to V beyond chance) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig9bc-unit-waveform-isi", "statement": "The spikes at site c5d have a consistent waveform (mean and standard deviation) and an interspike interval distribution (1 ms bins) consistent with a single unit.", "source": "Figure 9B and 9C and their legends", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_choi_2025.ipynb", "notes": "The criterion holds, but the evidence for a single unit is weak. No ISI is under 1 ms (9 of 101732 under 2 ms), and the mean waveform's trough of -56.4 \u00b5V is 4.79 times the SD across spikes at that sample. Neither part could easily fail. The shortest ISI, 1.562 ms, just exceeds the 48-sample (1.50 ms) waveform, so the detector's dead time excludes ISIs under 1 ms, and every one of the 101733 spikes exceeds the 40 \u00b5V threshold (smallest peak 40.3 \u00b5V), which nearly forces the trough above twice the SD. Above the dead time, ISIs per ms at 1.56 to 3 ms are 0.106 times those at 10 to 30 ms (Plexon unit 0.204), which fits a refractory period in most spikes but does not rule out other units. Only 54411 of the Plexon unit's 90912 spikes lie within 0.2 ms of a spike of thresholded unit 1 (101733 spikes). The Plexon unit has 1 ISI under 1 ms, 14 (0.015%) under 1.56 ms and 39 (0.04%) under 2 ms.", "deviations": [ "The paper states no measure for these panels; the 1% ISI rule and the trough-to-SD ratio are common choices made here.", "The waveforms are read as microvolts, although the file states volts." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig9d-beta-suppression-large", "statement": "Trial-averaged beta-band LFP power at c7b referenced to c5c is suppressed more in the brief window after the value cue for large than for small reward cues.", "source": "Figure 9D and its legend", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_choi_2025.ipynb", "notes": "Beta power (13 to 30 Hz) falls after V in both conditions (median log10 ratio of 0 to 0.5 s after V to 0.5 s before, -0.158 for large and -0.125 for small, each p < 0.001 against 0). The fall is larger for large cues, but not significantly (difference of medians -0.033, Mann-Whitney p = 0.108; 452 and 499 trials, none dropped; shuffling within blocks of 50 trials, p = 0.19). Averaged over trials, as in the paper's figure, power over 0 to 0.5 s is 0.839 of the baseline for large (95% CI 0.782 to 0.903) and 0.885 for small (0.831 to 0.940), a difference of -0.046 (-0.125 to 0.036). No variant reaches p < 0.05 (15 to 30 Hz, p = 0.063; 1 s baseline, p = 0.108; 12 to 25 Hz, p = 0.19; windows of 0 to 0.3 s and 0 to 1 s, p = 0.59 and 0.84; without baseline, p = 0.17). The paper states no test for this panel.", "deviations": [ "The band, the filter, the power measure, the baseline, the window and the test were chosen here; the paper gives none.", "The stored series, described as beta-band LFP, is broadband and was band-passed here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "recordings-two-monkeys", "statement": "The chamber system provided recordings of dopamine and electrical neural activity in two monkeys (T and J).", "source": "Abstract; Results, section 3.5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds one session of monkey T only (one NWB file). No recording of monkey J is in it or in the paper's Zenodo record, which also holds monkey T only. The monkey T part is tested by the Figure 8 and 9 claims.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "scfe-functional-yield", "statement": "53% (21/40) and 25% (13/51) of implanted sCFEs retained functionality (background current above 500 nA and noise below 0.05 nA) in monkeys T and J.", "source": "Results, section 3.5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The per-electrode background current and noise measured at implantation and during recovery, for 40 and 51 sCFEs, are not in the dandiset, which holds one FSCV electrode (c8ds) on one day. Not found in the Zenodo record either.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "scfe-background-yield", "statement": "73% (29/40) and 39% (20/51) of implanted sCFEs retained background current above 500 nA in monkeys T and J, of which 28% and 35% had noise above 0.05 nA.", "source": "Results, section 3.5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "As for scfe-functional-yield; the electrode-level background and noise measurements are not deposited.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "mcfe-functional-yield", "statement": "21.4% (3/14) and 14.2% (2/14) of mCFEs retained functionality in monkeys T and J.", "source": "Results, section 3.5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "No mCFE measurements are in the dandiset or the Zenodo record.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "dopamine-signal-yield", "statement": "Of the functional CFEs, 63% (15/24) and 53% (8/15) in monkeys T and J displayed visible dopamine signals and were used during task performance.", "source": "Results, section 3.5", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The dandiset holds the FSCV of one electrode; the 24 and 15 functional CFEs and which of them showed dopamine signals are not deposited.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "asepsis-cultures", "statement": "Monkey T kept negative bacterial cultures for all samples; in monkey J, staphylococcus cultured at 29 days post-implant was cleared by 39 to 44 days and the chamber stayed aseptic for 286 days after treatment.", "source": "Results, section 3.2; Abstract", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The culture results (IDEXX BioAnalytics) are not in the dandiset, the Zenodo record or the protocols.io protocols the paper cites.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6-drainage-volume", "statement": "Fluid aspirated from the chamber per session ranged from 0.3 to 4.8 mL in monkey T and 0.2 to 9.8 mL in monkey J, and was sanguinous for the first 18 (T) and 217 (J) days.", "source": "Results, section 3.2; Figure 6", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The aspirated volumes per session are not in the dandiset or the Zenodo record.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7-bone-growth-margins", "statement": "Bone growth was observed within and around the chamber in both monkeys, and the chamber margins stayed relatively healthy.", "source": "Results, sections 3.3 and 3.4; Figure 7", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The observations are photographs and surgical notes, which are not deposited.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "format_error", "statement": "The raw ephys and the spike times are not on the clock of the trials, events, LFP and FSCV table. The raw ephys is stored with a starting time of 0 s and a rate, and the spike times count from its first sample. Locating the raw c7b minus c5c signal in the stored LFP puts raw time 0 at 11812.11 s on the trial clock (correlation 0.98 to 1.00 at eight points, drift about 4 ms per hour). Without this correction spikes cannot be aligned to the task. The dandiset description says all data are expressed relative to the start of the Neuralynx recording, which the data contradict." }, { "kind": "metadata_error", "statement": "The absolute times disagree. On the trial clock the raw samples run from 12:06:44 to 17:12:20, while the Neuralynx header gives the recording as opened at 08:49:52 (the session start) and closed at 15:12:24, two hours before the raw samples end. The header span (22952 s) is also longer than the raw samples (18336 s)." }, { "kind": "other", "statement": "The stored spike times of the thresholded units are about 7.1 ms after the spike troughs in raw c5d (in one 300 s segment of 1633 spikes, per-spike trough lags of -7.4 to -6.9 ms from the 10th to the 90th percentile, 98.8% within 0.5 ms of -7.1 ms)." }, { "kind": "metadata_error", "statement": "The series \"bipolar_lfp_series\" is described as beta-band LFP but is broadband with line noise removed. Its values are already in volts, while it carries the raw int16 conversion factor (3.05e-8), which would scale them about 3e7 times too small." }, { "kind": "metadata_error", "statement": "The thresholded spike waveforms are stated in volts but hold microvolts (mean trough about -56), and the raw FSCV current is stated in amperes but holds nanoamperes (values around 1000)." }, { "kind": "metadata_insufficient", "statement": "The columns of the trial-aligned FSCV table (da, ph, m, iox) state no units, and the `good` column is true for every trial." }, { "kind": "metadata_error", "statement": "The subject description (\"Two adult female rhesus monkeys were used for in vivo validation of the s-\u00b5IP device\"), the session and experiment descriptions and the keyword \"micro-invasive neural implant\" describe the lab's micro-invasive probe study, not this paper's chamber." }, { "kind": "format_error", "statement": "The event table stores each event once per overlapping 60 s trial window, about five copies of each (7221 stored trial-start events for 1412 distinct ones), and its event times are not sorted. The Plexon units table's spike times are not sorted either." }, { "kind": "metadata_insufficient", "statement": "The trial tags are all \"initial cue display\" and carry no trial type. Reward size and outcome can be rebuilt from the events, and they then match the paper's Zenodo trial lists except trial 1411, which the events mark as a successful large reward trial and the list leaves out." }, { "kind": "metadata_insufficient", "statement": "The paper says the reward size depends on whether the target is at the top or bottom of the screen. The events code left and right conditions, and both reward sizes occur on both sides, so the target position that sets the reward is not in the dandiset." }, { "kind": "other", "statement": "The raw FSCV minute files are joined without their gaps (328 min of scans against 302 min of trials, placed from a single starting time), and the trial-aligned oxidation current cannot be located in them, so the raw FSCV's clock could not be established." }, { "kind": "data_missing", "statement": "Only one session of monkey T is deposited. The data behind the electrode yields, cultures, drainage volumes and bone growth, and all of monkey J, are not, so eight of the thirteen claims cannot be tested." } ], "verifications": [ { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text (PMC13250822). The verifier listed the version's assets and metadata through the archive API, and tested psth, window_mean, trial_table, band_power_around and reference_at on synthetic inputs.", "agreed": 13, "of": 13, "disagreements": [] }, { "date": "2026-10-15", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "The full executed notebook of the revision with its conclusions and summary, the helper module, the claims file, the README and this record.", "agreed": 13, "of": 13, "disagreements": [] } ] } ], "entries": [ { "name": "000003-senzai-2017", "type": "reproduction", "title": "Granule cells and mossy cells of the dentate gyrus (Senzai and Buzsaki 2017)", "description": "Tests the findings of Senzai and Buzsaki (2017) on dandiset 000003, which holds silicon probe recordings of the dentate gyrus and CA3 in 16 mice, in 101 files from 94 recording days, with labelled granule cells, mossy cells, CA3 pyramidal cells and interneurons, sleep states, dentate spikes, light pulses, and positions on a circular T-maze and in open fields. It covers firing by brain state, theta and gamma phase locking, recruitment by dentate spikes, optogenetic tagging, monosynaptic transmission, place fields and remapping, and, on the 17 files that give each unit's shank, depth and the classification of granule and mossy cells.", "dandisets": [ "000003" ], "papers": [ "10.1016/j.neuron.2016.12.011" ], "derived_from": [], "notebooks": [ { "path": "reproduce_senzai_2017.ipynb", "title": "Reproducing Senzai and Buzsaki (2017) from dandiset 000003", "executed": "notebooks/000003-senzai-2017/reproduce_senzai_2017.html" } ] }, { "name": "000004-chandravadia-2020", "type": "reproduction", "title": "Human single neurons during a recognition memory task (Chandravadia et al. 2020)", "description": "Tests the data descriptor of Chandravadia et al. (2020) on dandiset 000004, which holds 87 sessions of 59 epilepsy patients with single units from the amygdala and hippocampus during a new/old recognition task. It checks the files against the paper's description of the data records and subjects, and repeats the behavioural results (AUC, ROC asymmetry, accuracy by confidence) and the proportions of visually and memory selective cells of Figure 5.", "dandisets": [ "000004" ], "papers": [ "10.1038/s41597-020-0415-9" ], "derived_from": [], "notebooks": [ { "path": "reproduce_chandravadia_2020.ipynb", "title": "Reproducing Chandravadia et al. (2020) from dandiset 000004", "executed": "notebooks/000004-chandravadia-2020/reproduce_chandravadia_2020.html" } ] }, { "name": "000006-economo-2018", "type": "reproduction", "title": "Two types of pyramidal tract neuron in mouse motor cortex (Economo et al. 2018)", "description": "Tests the findings in the abstract of Economo et al. (2018) that dandiset 000006 can test. The dandiset holds silicon probe recordings from the anterior lateral motor cortex of 12 mice in a delayed response task, with tagged PTupper and PTlower units. The notebook measures the selectivity for lick direction of the tagged units in the sample, delay and response epochs, and compares the two types. The transcriptomic and anatomical findings are not testable on it.", "dandisets": [ "000006" ], "papers": [ "10.1038/s41586-018-0642-9" ], "derived_from": [], "notebooks": [ { "path": "reproduce_economo_2018.ipynb", "title": "Reproducing Economo et al. (2018) from dandiset 000006", "executed": "notebooks/000006-economo-2018/reproduce_economo_2018.html" } ] }, { "name": "000035-scala-2021", "type": "reproduction", "title": "Patch-seq neurons of mouse motor cortex at physiological temperature (Scala, Kobak et al. 2021)", "description": "Tests the findings of Scala, Kobak et al. (2021) that can be tested on dandiset 000035, which holds the paper's follow-up recordings at 34 degrees C (185 neurons, mostly layer 5 Sst and excitatory cells). It extracts the paper's 17 electrophysiological features from the traces, checks the cohort and the stimulus against the Methods, tests whether IT and ET neurons overlap electrophysiologically, and compares Sst t-types between temperatures using the paper's published room-temperature features. The findings on the main room-temperature data set are in dandiset 000008 and are not tested here.", "dandisets": [ "000035" ], "papers": [ "10.1038/s41586-020-2907-3" ], "derived_from": [], "notebooks": [ { "path": "reproduce_scala_2021.ipynb", "title": "Reproducing Scala, Kobak et al. (2021) from dandiset 000035", "executed": null } ] }, { "name": "000041-watson-2016", "type": "reproduction", "title": "Firing rates across sleep states in rat frontal cortex (Watson et al. 2016)", "description": "Tests the findings of Watson, Levenstein, Greene, Gelinas and Buzsaki (2016) on dandiset 000041, which holds silicon probe recordings of units, LFP and sleep states from the frontal cortex of 10 rats in their home cage. It compares firing rates and bursting across WAKE, nonREM and REM, how rates of fast and slow firing cells change over sleep and within nonREM packets, how they relate to LFP band power, and the rate changes across state triplets. UP and DOWN state and spindle analyses are blocked, as their methods are in the unavailable supplement.", "dandisets": [ "000041" ], "papers": [ "10.1016/j.neuron.2016.03.036" ], "derived_from": [], "notebooks": [ { "path": "reproduce_watson_2016.ipynb", "title": "Reproducing Watson et al. (2016) from dandiset 000041", "executed": "notebooks/000041-watson-2016/reproduce_watson_2016.html" } ] }, { "name": "000044-grosmark-2016", "type": "reproduction", "title": "Rigid and plastic hippocampal sequences (Grosmark and Buzsaki 2016)", "description": "Tests the findings of Grosmark and Buzsaki (2016) on dandiset 000044, which holds eight sessions of CA1 units, LFP, sleep states and track positions from four rats, each with sleep before and after exploring a novel track. It decodes candidate ripple events with a Bayesian decoder, compares sequence scores across PRE, MAZE and POST, estimates each place cell's contribution to sequences, and relates firing rate and ripple gain to coactivation and replay.", "dandisets": [ "000044" ], "papers": [ "10.1126/science.aad1935" ], "derived_from": [], "notebooks": [ { "path": "reproduce_grosmark_2016.ipynb", "title": "Reproducing Grosmark and Buzsaki (2016) from dandiset 000044", "executed": "notebooks/000044-grosmark-2016/reproduce_grosmark_2016.html" } ] }, { "name": "000056-peyrache-2015", "type": "reproduction", "title": "Head-direction cells across waking and sleep (Peyrache et al. 2015)", "description": "Tests the findings of Peyrache, Lacroix, Petersen and Buzsaki (2015) on dandiset 000056, which holds spike times, LED positions and sleep states from 40 sessions of 7 mice recorded in the anterior thalamus and post-subiculum. It classifies head-direction cells, compares their rates and pairwise correlations across waking, REM and slow-wave sleep, estimates the speed of the internal head-direction signal from cross-correlograms, and tests noise correlations and decoding. The units carry no brain region, so the comparisons between the two structures cannot be made.", "dandisets": [ "000056" ], "papers": [ "10.1038/nn.3968" ], "derived_from": [], "notebooks": [ { "path": "reproduce_peyrache_2015.ipynb", "title": "Reproducing Peyrache et al. (2015) from dandiset 000056", "executed": "notebooks/000056-peyrache-2015/reproduce_peyrache_2015.html" } ] }, { "name": "000059-petersen-2020", "type": "reproduction", "title": "Cooling of the medial septum, hippocampal theta and place cell timing (Petersen & Buzsaki 2020)", "description": "Tests the findings of Petersen and Buzsaki (2020) on dandiset 000059, which holds 50 sessions of five rats running a spatial alternation task on a figure-8 maze while the medial septum was cooled, with MS temperature, trials, position, LFP, wide-band data and sorted units. It tests the slowing of theta with temperature, the increase of choice errors, the oscillation frequency of place cells against LFP theta, place field features, and the time and phase lags of place cell pairs. The hippocampal temperature recordings of the control experiment are not in the dandiset.", "dandisets": [ "000059" ], "papers": [ "10.1016/j.neuron.2020.05.023" ], "derived_from": [], "notebooks": [ { "path": "reproduce_petersen_2020.ipynb", "title": "Reproducing Petersen & Buzsaki (2020) from dandiset 000059", "executed": "notebooks/000059-petersen-2020/reproduce_petersen_2020.html" } ] }, { "name": "000061-girardeau-2017", "type": "reproduction", "title": "Hippocampus and amygdala reactivation during sleep (Girardeau et al. 2017)", "description": "Tests the findings stated in the abstract of Girardeau, Inema and Buzsaki (2017) on dandiset 000061, which holds sorted units of the hippocampus and the amygdala, sleep states, ripple, air-puff and reward events from four rats on an air-puff linear track task. It tests the reactivation of joint hippocampus and BLA patterns in sleep after the run, its peak at ripples, the BLA cells modulated by ripples and their weight in the patterns, and the difference between the air-puff and the safe run direction. The paper's full text was not available, so the methods are common choices fixed before the analysis.", "dandisets": [ "000061" ], "papers": [ "10.1038/nn.4637" ], "derived_from": [], "notebooks": [ { "path": "reproduce_girardeau_2017.ipynb", "title": "Reproducing Girardeau et al. (2017) from dandiset 000061", "executed": "notebooks/000061-girardeau-2017/reproduce_girardeau_2017.html" } ] }, { "name": "000067-fujisawa-2008", "type": "reproduction", "title": "Prefrontal assemblies and monosynaptic dynamics in a working memory task (Fujisawa et al. 2008)", "description": "Tests the findings of Fujisawa, Amarasingham, Harrison and Buzsaki (2008) on dandiset 000067, which holds recordings of three rats from a 64-site prefrontal probe and a CA1 probe during an odor-place matching task. Units are placed on the probes from their waveforms in the wideband signal. It tests the population activity, field sizes and trajectory selectivity of prefrontal neurons, monosynaptic connections found with a jitter test, the cell classes and distances they imply, and the task dependence, short-term plasticity and summation of the connections. The paper's example session and fourth rat are not in the dandiset.", "dandisets": [ "000067" ], "papers": [ "10.1038/nn.2134" ], "derived_from": [], "notebooks": [ { "path": "reproduce_fujisawa_2008.ipynb", "title": "Reproducing Fujisawa et al. (2008) from dandiset 000067", "executed": "notebooks/000067-fujisawa-2008/reproduce_fujisawa_2008.html" } ] }, { "name": "000070-churchland-2012", "type": "reproduction", "title": "Rotational dynamics of motor cortex during reaching (Churchland et al. 2012)", "description": "Tests the findings of Churchland, Cunningham, Kaufman, Foster, Nuyujukian, Ryu and Shenoy (2012) that can be tested on dandiset 000070, which holds the paper's two Utah array datasets (monkeys J and N, 108 maze conditions each) and eight further array sessions. It runs jPCA on condition-averaged rates around movement onset and tests the consistency of rotations across conditions, the variance the jPCA planes capture, the fit of rotational dynamics, the shuffle controls, the separate PMd and M1 arrays, and simulated kinematic populations. The single-electrode datasets, EMG, leech and walking-monkey data are not in the dandiset.", "dandisets": [ "000070" ], "papers": [ "10.1038/nature11129" ], "derived_from": [], "notebooks": [ { "path": "reproduce_churchland_2012.ipynb", "title": "Reproducing Churchland et al. (2012) from dandiset 000070", "executed": "notebooks/000070-churchland-2012/reproduce_churchland_2012.html" } ] }, { "name": "000114-carcea-2021", "type": "reproduction", "title": "PVN units and maternal behaviour in co-housed virgin mice (Carcea et al. 2021)", "description": "Tests the findings of Carcea et al. (2021) that dandiset 000114 can support. The dandiset holds PVN single units and video annotations from virgin mice co-housed with a dam and litter, and fibre photometry from virgins watching dam retrievals. The entry tests the fraction of units activated during nest entry, shepherding and dam retrieval, the firing after shepherded against voluntary nest entries, and the rates of shepherding and dam retrieval. OT-PVN identity, the behavioural cohorts and the auditory cortex data are not in the dandiset.", "dandisets": [ "000114" ], "papers": [ "10.1038/s41586-021-03814-7" ], "derived_from": [], "notebooks": [ { "path": "reproduce_carcea_2021.ipynb", "title": "Reproducing Carcea et al. (2021) from dandiset 000114", "executed": "notebooks/000114-carcea-2021/reproduce_carcea_2021.html" } ] }, { "name": "000121-even-chen-2019", "type": "reproduction", "title": "Structure and variability of delay activity in premotor cortex (Even-Chen et al. 2019)", "description": "Tests the findings of Even-Chen, Sheffer, Vyas, Ryu and Shenoy (2019) on dandiset 000121, which holds 12 sessions of delayed center-out reaching with Utah arrays in two monkeys (all 7 of R, 5 of the 16 of J). It checks the sessions and trial counts, the behaviour, the low-dimensional structure of PMd delay activity (PCA, the spatial plane, its time course, the speed axis), the variability of single-trial neural states on and off the reach axis, and SVM decoding of reach direction and distance.", "dandisets": [ "000121" ], "papers": [ "10.1371/journal.pcbi.1006808" ], "derived_from": [], "notebooks": [ { "path": "reproduce_even_chen_2019.ipynb", "title": "Reproducing Even-Chen et al. (2019) from dandiset 000121", "executed": "notebooks/000121-even-chen-2019/reproduce_even_chen_2019.html" } ] }, { "name": "000127-chowdhury-2020", "type": "reproduction", "title": "Active and passive arm movements in somatosensory area 2 (Chowdhury et al. 2020)", "description": "Tests the active/passive findings of Chowdhury, Glaser and Miller (2020) on dandiset 000127, which holds one of the paper's twelve sessions. It compares hand and arm kinematics between active reaches and passive bumps, measures how well single neurons tell the two apart, and fits hand-only and whole-arm models of each neuron's firing. The paper's two-workspace experiment cannot be tested because those sessions are not in the dandiset.", "dandisets": [ "000127" ], "papers": [ "10.7554/elife.48198" ], "derived_from": [], "notebooks": [ { "path": "reproduce_chowdhury_2020.ipynb", "title": "Reproducing Chowdhury, Glaser & Miller (2020) from dandiset 000127", "executed": "notebooks/000127-chowdhury-2020/reproduce_chowdhury_2020.html" } ] }, { "name": "000130-sohn-2019", "type": "reproduction", "title": "Bayesian computation through cortical latent dynamics (Sohn et al. 2019)", "description": "Tests the findings of Sohn, Narain, Meirhaeghe and Jazayeri (2019) on dandiset 000130, the Neural Latents Benchmark's DMFC_RSG set, which holds one session of monkey H performing the Ready-Set-Go task with 54 units from dorsomedial frontal cortex. It tests the behaviour and the Bayesian observer model, single-unit sensitivity to the prior and elapsed time, the geometry and speed of population trajectories, the alternative mechanisms, and single-trial GPFA trajectories. Monkey G and the recurrent network models are not in the dandiset.", "dandisets": [ "000130" ], "papers": [ "10.1016/j.neuron.2019.06.012" ], "derived_from": [], "notebooks": [ { "path": "reproduce_sohn_2019.ipynb", "title": "Reproducing Sohn et al. (2019) from dandiset 000130", "executed": "notebooks/000130-sohn-2019/reproduce_sohn_2019.html" } ] }, { "name": "000147-guan-2022", "type": "reproduction", "title": "Finger representations in human posterior parietal cortex after paralysis (Guan et al. 2022)", "description": "Tests the findings of Guan, Aflalo et al. (2022) that dandiset 000147 can support. It checks online and offline finger decoding, single-unit tuning and whether the cue location can be decoded, builds the cross-validated finger RDMs of the ten sessions, compares them with the able-bodied fMRI models from the authors' repository, and tests whether the representation changed across sessions and runs. The calibration and control tasks, the component model RDMs and sorting quality metrics are not in the dandiset, so the claims that need them are blocked.", "dandisets": [ "000147" ], "papers": [ "10.7554/elife.74478" ], "derived_from": [], "notebooks": [ { "path": "reproduce_guan_2022.ipynb", "title": "Reproducing Guan, Aflalo et al. (2022) from dandiset 000147", "executed": "notebooks/000147-guan-2022/reproduce_guan_2022.html" } ] }, { "name": "000207-zheng-2022", "type": "reproduction", "title": "Cognitive boundaries and human medial temporal lobe neurons (Zheng et al. 2022)", "description": "Tests the findings of Zheng et al. (2022) that can be tested on dandiset 000207, which holds spike times of medial temporal lobe neurons and the behaviour of 19 patients in a task with video clips that contain no boundary, a soft boundary or a hard boundary. It compares memory for temporal order and for scenes across the three kinds of clip, looks for boundary cells and event cells with the paper's definitions, counts neurons that respond to clip onsets, and measures how far the population state moves after a boundary. Eleven of the paper's twenty findings cannot be tested, because the dandiset has no local field potentials, no neurons outside the medial temporal lobe, no labels for the paper's cell classes, and no way to link test trials with soft or hard boundaries to the clips they came from.", "dandisets": [ "000207" ], "papers": [ "10.1038/s41593-022-01020-w" ], "derived_from": [], "notebooks": [ { "path": "reproduce_zheng_2022.ipynb", "title": "Reproducing Zheng et al. (2022) from dandiset 000207", "executed": "notebooks/000207-zheng-2022/reproduce_zheng_2022.html" } ] }, { "name": "000213-tingley-2018", "type": "reproduction", "title": "Spatial phase coding in the lateral septum (Tingley and Buzsaki 2018)", "description": "Tests the findings of Tingley and Buzsaki (2018) on dandiset 000213, which holds 67 sessions of simultaneous hippocampal and lateral septum recordings from five rats running on alternation mazes and a linear track. It decodes position from the spike rate and the spike theta phase of each LS and hippocampal unit, finds place fields, measures spatial information, relates phase coding to recording depth, and measures hippocampal-LS theta coherence and theta-gamma coupling, and detects hippocampal-LS cell assemblies on a random sample of pairs.", "dandisets": [ "000213" ], "papers": [ "10.1016/j.neuron.2018.04.028" ], "derived_from": [], "notebooks": [ { "path": "reproduce_tingley_2018.ipynb", "title": "Reproducing Tingley and Buzsaki (2018) from dandiset 000213", "executed": "notebooks/000213-tingley-2018/reproduce_tingley_2018.html" } ] }, { "name": "000218-tingley-2019", "type": "reproduction", "title": "Lateral septum HFOs and hippocampal ripples (Tingley and Buzsaki 2019)", "description": "Tests the findings of Tingley and Buzsaki (2019) on dandiset 000218, which holds LFP, sorted units, sleep states and trials from simultaneous recordings of the lateral septum and hippocampus in 6 rats. LS high-frequency oscillations and CA1 ripples are detected from the LFP, as the files hold no detected events, and the notebook tests their properties, their coupling and state dependence, the phase locking and co-activation of LS neurons, and which ripple features predict LS firing. The optogenetic experiments are not in the dandiset.", "dandisets": [ "000218" ], "papers": [ "10.1016/j.neuron.2019.10.012" ], "derived_from": [], "notebooks": [ { "path": "reproduce_tingley_2019.ipynb", "title": "Reproducing Tingley and Buzsaki (2019) from dandiset 000218", "executed": "notebooks/000218-tingley-2019/reproduce_tingley_2019.html" } ] }, { "name": "000226-severson-2017", "type": "reproduction", "title": "Merkel and other whisker afferents during active touch and whisking (Severson et al. 2017)", "description": "Tests the findings of Severson, Xu, Van de Loo, Bai, Ginty and O'Connor (2017) on dandiset 000226, which holds 56 trigeminal afferent recordings with high-speed whisker video and 4 EMG sessions. It checks the recordings against the paper's Table S1, the spike rates during non-whisking, whisking in air and touch, the classes of afferents, direction selectivity, the statistical and viscoelastic models of touch responses, phase tuning during whisking in air, the nasolabialis motor units and the curvature noise. The cutting conditions of the progressive cutting experiment, the intrinsic protractor EMG and the optogenetic tagging data are not in the dandiset.", "dandisets": [ "000226" ], "papers": [ "10.1016/j.neuron.2017.03.045" ], "derived_from": [], "notebooks": [ { "path": "reproduce_severson_2017.ipynb", "title": "Reproducing Severson et al. (2017) from dandiset 000226", "executed": "notebooks/000226-severson-2017/reproduce_severson_2017.html" } ] }, { "name": "000232-chang-2023", "type": "reproduction", "title": "Rule-based modulation of a sensorimotor transformation across cortical areas (Chang et al. 2023)", "description": "Tests the findings of Chang, Finkel, Xu and O'Connor (bioRxiv 2023, version 2) on dandiset 000232, which holds silicon-probe recordings from S1, S2, MM, ALM and AMM of mice performing a cross-modal sensory selection task, and the behaviour of optogenetic inhibition sessions in that task and in a tactile detection task. It covers behavioural performance, single-neuron rule and stimulus discrimination, population decoding of the rule, neural trajectories and subspaces, coding dimensions, rule transitions and the effects of optogenetic inhibition.", "dandisets": [ "000232" ], "papers": [ "10.1101/2023.08.21.554194" ], "derived_from": [], "notebooks": [ { "path": "reproduce_chang_2023.ipynb", "title": "Reproducing Chang et al. (2023) from dandiset 000232", "executed": "notebooks/000232-chang-2023/reproduce_chang_2023.html" } ] }, { "name": "000239-xu-2022", "type": "reproduction", "title": "Cortical processing of flexible sensorimotor sequences (Xu et al. 2022)", "description": "Tests the findings of Xu, Dong, Chen, Delgado, Hughes, Zhang and O'Connor (2022) on dandiset 000239, which holds the trial tables, tongue tracking and sorted spikes of mice performing a sequence licking task. It decodes tongue kinematics, sequence identity and sequence time from S1TJ, M1TJ, ALM and S1BF populations, classifies backtracking and zigzag sequence context, and checks the behavioural measures and unit counts. The optogenetic and control experiments cannot be tested, as the files do not say which region was inhibited or which condition each session was.", "dandisets": [ "000239" ], "papers": [ "10.1038/s41586-022-04478-7" ], "derived_from": [], "notebooks": [ { "path": "reproduce_xu_2022.ipynb", "title": "Reproducing Xu et al. (2022) from dandiset 000239", "executed": "notebooks/000239-xu-2022/reproduce_xu_2022.html" } ] }, { "name": "000350-mu-2019", "type": "reproduction", "title": "Futility-induced passivity and whole-brain neuronal and glial activity in zebrafish (Mu et al. 2019)", "description": "Tests the findings of Mu, Bennett, Rubinov et al. (2019) that dandiset 000350 can test. The dandiset holds 12 light-sheet sessions of paralysed larval zebrafish swimming fictively in virtual reality, with swim bouts, stimulus signals and, in 8 of them, segmented neuronal or neuronal and glial traces. The entry measures passive and active epochs, swim intervals and vigor in closed and open loop, and whole-brain neuronal and glial activity around passivity onset. The perturbation and noradrenergic imaging experiments of Figures 4 to 6 are not in the dandiset.", "dandisets": [ "000350" ], "papers": [ "10.1016/j.cell.2019.05.050" ], "derived_from": [], "notebooks": [ { "path": "reproduce_mu_2019.ipynb", "title": "Reproducing Mu et al. (2019) from dandiset 000350", "executed": "notebooks/000350-mu-2019/reproduce_mu_2019.html" } ] }, { "name": "000409-ibl-2025", "type": "reproduction", "title": "The IBL brain-wide map of neural activity (International Brain Laboratory et al. 2025)", "description": "Tests the findings of the IBL brain-wide map paper (Nature 2025) on dandiset 000409, which holds 459 sessions of Neuropixels recordings from 139 mice performing the IBL decision-making task. It checks the dataset's composition and inclusion counts, the behavioural results of Figure 1, and, on a fixed set of regions, the decoding of stimulus, choice and feedback, single-cell selectivity, the latencies of stimulus trajectories and the feedback oscillations related to licking, and over all canonical regions the number with significant stimulus trajectories.", "dandisets": [ "000409" ], "papers": [ "10.1038/s41586-025-09235-0" ], "derived_from": [], "notebooks": [ { "path": "reproduce_ibl_2025.ipynb", "title": "Reproducing the IBL brain-wide map (2025) from dandiset 000409", "executed": "notebooks/000409-ibl-2025/reproduce_ibl_2025.html" } ] }, { "name": "000552-huszar-2022", "type": "reproduction", "title": "Birthdated CA1 pyramidal neurons in freely moving mice (Huszar et al. 2022)", "description": "Tests the findings of Huszar, Zhang, Blockus and Buzsaki (2022) that can be tested on dandiset 000552, which holds sleep states, sharp-wave ripples, spike-sorted units and position from 17 mice electroporated at E13.5 to E16.5. It checks the description of the dataset and tests the findings on all pyramidal neurons on familiar and novel mazes (population-vector decorrelation, firing rates, spatial information and ratemap correlations). The units carry no light-responsiveness label and no optogenetic pulse times are stored, so the comparisons of same- and different-birthdate neurons are blocked.", "dandisets": [ "000552" ], "papers": [ "10.1038/s41593-022-01138-x" ], "derived_from": [], "notebooks": [ { "path": "reproduce_huszar_2022.ipynb", "title": "Reproducing Huszar et al. (2022) from dandiset 000552", "executed": "notebooks/000552-huszar-2022/reproduce_huszar_2022.html" } ] }, { "name": "000559-markowitz-2023", "type": "reproduction", "title": "Dopamine and spontaneous behaviour in mice (Markowitz, Gillis, Jay et al. 2023)", "description": "Tests the findings of Markowitz, Gillis, Jay et al. (2023) on dandiset 000559, which holds the dLight photometry, MoSeq syllables and closed-loop optogenetic sessions of the paper. It relates DLS dopamine to velocity, syllable identity, syllable use and sequence entropy, compares DMS with DLS, and tests the reinforcement of target syllables by closed-loop dopamine release. The modelling of Figures 4 and 5 is not attempted.", "dandisets": [ "000559" ], "papers": [ "10.1038/s41586-022-05611-2" ], "derived_from": [], "notebooks": [ { "path": "reproduce_markowitz_2023.ipynb", "title": "Reproducing Markowitz, Gillis, Jay et al. (2023) from dandiset 000559", "executed": "notebooks/000559-markowitz-2023/reproduce_markowitz_2023.html" } ] }, { "name": "000568-valero-2022", "type": "reproduction", "title": "Pulsed optogenetics in hippocampal CA1 (Valero et al. 2022)", "description": "Tests the findings of Valero, Zutshi, Yoon and Buzsaki (2022) on dandiset 000568, which holds 28 sessions of CA1 units recorded with uLED probes in four CaMKIIa-Cre::Ai32 mice. Pulse times and laps are in two sessions only, so the light responses during ripples, theta and place fields are tested on those two; the ripple modulation of firing is tested on all sessions. The intracellular recordings and the light intensity levels are not in the dandiset.", "dandisets": [ "000568" ], "papers": [ "10.1126/science.abm1891" ], "derived_from": [], "notebooks": [ { "path": "reproduce_valero_2022.ipynb", "title": "Reproducing Valero et al. (2022) from dandiset 000568", "executed": "notebooks/000568-valero-2022/reproduce_valero_2022.html" } ] }, { "name": "000582-sargolini-2006", "type": "reproduction", "title": "Grid, head-direction and conjunctive cells by entorhinal layer (Sargolini et al. 2006)", "description": "Tests three conclusions of Sargolini et al. (2006) on dandiset 000582, which holds spike times and tracked positions for 620 cell-sessions from the medial entorhinal cortex of 15 rats. For every cell it computes a grid score, head-direction tuning and speed tuning, with chance levels from time-shifted spike trains, and compares the cell types found in each cortical layer.", "dandisets": [ "000582" ], "papers": [ "10.1126/science.1125572" ], "derived_from": [], "notebooks": [ { "path": "reproduce_sargolini_2006.ipynb", "title": "Reproducing Sargolini et al. (2006) from dandiset 000582", "executed": "notebooks/000582-sargolini-2006/reproduce_sargolini_2006.html" } ] }, { "name": "000625-geiller-2020", "type": "reproduction", "title": "Molecularly identified CA1 interneurons during random foraging (Geiller, Vancura et al. 2020)", "description": "Tests the findings of Geiller, Vancura et al. (2020) that can be tested on dandiset 000625, which holds three random-foraging sessions of one mouse with 231 interneurons, 74 of them assigned one of the paper's six subtypes. It checks the imaging clock against the behaviour, then measures each interneuron's correlation with running speed, run-stop responses, spatial selectivity, position decoding and the stability of tuning curves within and across sessions. The sharp-wave ripple, novel-context, goal-oriented learning and VIP experiments are not in the dandiset.", "dandisets": [ "000625" ], "papers": [ "10.1016/j.neuron.2020.09.013" ], "derived_from": [], "notebooks": [ { "path": "reproduce_geiller_2020.ipynb", "title": "Reproducing Geiller, Vancura et al. (2020) from dandiset 000625", "executed": "notebooks/000625-geiller-2020/reproduce_geiller_2020.html" } ] }, { "name": "000691-scherrer-2023", "type": "reproduction", "title": "Imaging thousands of neurons in a freely moving mouse with a large-FOV head-mounted microscope (Scherrer et al. 2023)", "description": "Tests the findings of Scherrer, Lynch, Zhang and Fee (2023) that can be tested on dandiset 000691, which holds one session of one mouse imaged with the large-FOV head-mounted microscope while it explores a looped maze, with 2948 EXTRACT footprints and a behaviour video. It counts the footprints, tracks the mouse from the video, decodes its position and direction from the activity, maps local decoding across the field of view, looks for footprints with localized activity and for the spread of coactive populations, and tests the illumination profiles of Extended Data Fig. 2 on images in the paper's code repository. The other mice, the birds and the optical tests are not in the dandiset.", "dandisets": [ "000691" ], "papers": [ "10.1038/s41592-023-01806-1" ], "derived_from": [], "notebooks": [ { "path": "reproduce_scherrer_2023.ipynb", "title": "Reproducing Scherrer et al. (2023) from dandiset 000691", "executed": "notebooks/000691-scherrer-2023/reproduce_scherrer_2023.html" } ] }, { "name": "000718-zaki-2024", "type": "reproduction", "title": "Offline ensemble co-reactivation in the EEG/EMG experiment (Zaki et al. 2024)", "description": "Tests the findings of Zaki et al. (2024) that can be tested on dandiset 000718, which holds two of the nine mice of the paper's calcium imaging and EEG/EMG experiment (one high-shock, one low-shock) with their encoding and recall sessions, the first offline recording after encoding, and cell registration for the high-shock mouse. It checks the deposited freezing against the paper's per-mouse values, compares freezing between the two mice, tests offline population bursts and their skew against shuffled activity and against movement, and compares overlap-neutral with overlap-aversive co-bursting in wake. The one-hour offline, behaviour-only, inhibitory tagging and no-shock experiments are not in the dandiset.", "dandisets": [ "000718" ], "papers": [ "10.1038/s41586-024-08168-4" ], "derived_from": [], "notebooks": [ { "path": "reproduce_zaki_2024.ipynb", "title": "Reproducing Zaki et al. (2024) from dandiset 000718", "executed": "notebooks/000718-zaki-2024/reproduce_zaki_2024.html" } ] }, { "name": "000727-brezovec-2022", "type": "reproduction", "title": "Brain-wide neural correlates of walking in Drosophila (Brezovec et al. 2022)", "description": "Tests the findings of Brezovec, Berger, Druckmann and Clandinin (2022) on dandiset 000727, which holds whole-brain two-photon imaging and ball tracking of nine walking flies. It streams 12 planes of the authors' processed volumes in the Functional Drosophila Atlas for all flies, and tests the voxel correlations with forward and turning velocity, their symmetry, the principal components and the models that predict velocity from them, the demixing of velocity components, and the timing of neural activity relative to behaviour. Region-level results cannot be tested, as the dandiset has no neuropil labels.", "dandisets": [ "000727" ], "papers": [ "10.1101/2022.03.20.485047" ], "derived_from": [], "notebooks": [ { "path": "reproduce_brezovec_2022.ipynb", "title": "Reproducing Brezovec et al. (2022) from dandiset 000727", "executed": "notebooks/000727-brezovec-2022/reproduce_brezovec_2022.html" } ] }, { "name": "000947-schwab-2020", "type": "reproduction", "title": "GPi and VLa activity during reaching in macaques (Schwab et al. 2020)", "description": "Tests the findings of Schwab, Kase, Zimnik, Rosenbaum, Codianni, Rubin and Turner (2020) on the pre-MPTP recordings of dandiset 000947, single units from the internal globus pallidus and the ventrolateral anterior thalamus of two monkeys performing a reaching task. It compares rates, spike widths, peri-movement responses and their latencies, spike and rate correlations of simultaneously recorded pairs, and the effect of GPi bursts and pauses on VLa activity, and links the dandiset's units to the paper's own unit list.", "dandisets": [ "000947" ], "papers": [ "10.1371/journal.pbio.3000829" ], "derived_from": [], "notebooks": [ { "path": "reproduce_schwab_2020.ipynb", "title": "Reproducing Schwab et al. (2020) from dandiset 000947", "executed": "notebooks/000947-schwab-2020/reproduce_schwab_2020.html" } ] }, { "name": "000971-seiler-2022", "type": "reproduction", "title": "Dorsomedial striatal dopamine and compulsive reward seeking (Seiler et al. 2022)", "description": "Tests the findings of Seiler, Cosme, Sherathiya, Schaid, Bianco, Bridgemohan and Lerner (2022) on dandiset 000971, which holds the operant behavior of a fiber photometry cohort and three optogenetic cohorts, dual-site photometry from DMS and DLS dopamine axons during RI60 and RR20 training, and western blot images. It tests the shock probe phenotypes and their behavior, the DMS and DLS rewarded-unrewarded peak scores, and the effects of DMS and DLS terminal manipulations. RI30 and shock probe photometry, fear conditioning, open field and histology are not in the dandiset.", "dandisets": [ "000971" ], "papers": [ "10.1016/j.cub.2022.01.055" ], "derived_from": [], "notebooks": [ { "path": "reproduce_seiler_2022.ipynb", "title": "Reproducing Seiler et al. (2022) from dandiset 000971", "executed": "notebooks/000971-seiler-2022/reproduce_seiler_2022.html" } ] }, { "name": "001038-azcorra-2023", "type": "reproduction", "title": "Functional responses of genetic subtypes of dopamine neurons (Azcorra, Gaertner et al. 2023)", "description": "Tests the fiber photometry findings of Azcorra, Gaertner et al. (2023) on dandiset 001038, which holds the recordings from striatal axons and SNc somas of Vglut2, Calb1, Anxa1, Aldh1a1 and DAT mice running on a treadmill and receiving rewards and air puffs. It covers locomotion signaling (Figures 2, 3 and 5), reward and air puff responses (Figure 4), clustering (Figure 6), soma and axon correlation (Figure 7) and Extended Data Figures 1 and 6 to 9. Two snRNA-seq claims of Figure 1 are tested on the paper's GEO matrices.", "dandisets": [ "001038" ], "papers": [ "10.1038/s41593-023-01401-9" ], "derived_from": [], "notebooks": [ { "path": "reproduce_azcorra_2023.ipynb", "title": "Reproducing Azcorra, Gaertner et al. (2023) from dandiset 001038", "executed": "notebooks/001038-azcorra-2023/reproduce_azcorra_2023.html" } ] }, { "name": "001075-randi-2023", "type": "reproduction", "title": "Neural signal propagation atlas of C. elegans (Randi et al. 2023)", "description": "Tests the findings of Randi, Sharma, Dvali and Leifer (2023) on dandiset 001075, which holds the 113 wild-type-background recordings of whole-brain calcium imaging during single-neuron optogenetic stimulation, 110 of them with extracted traces. It checks the recordings, the number of measured neuron pairs, three example connections of Figure 1, the spatial specificity of the stimulation, the responses to RID stimulation in WT and, from the paper's OSF export, in unc-31 animals, and how the per-pair measurements and recordings link to the paper's Source Data and OSF export. The q values, the spontaneous recordings and the kernel analyses are not testable.", "dandisets": [ "001075" ], "papers": [ "10.1038/s41586-023-06683-4" ], "derived_from": [], "notebooks": [ { "path": "reproduce_randi_2023.ipynb", "title": "Reproducing Randi et al. (2023) from dandiset 001075", "executed": "notebooks/001075-randi-2023/reproduce_randi_2023.html" } ] }, { "name": "001084-vu-2024", "type": "reproduction", "title": "Striatal dopamine release patterns and targeted stimulation through micro-fiber arrays (Vu et al. 2024)", "description": "Tests the findings of Vu, Brown, Wen et al. (2024) on dandiset 001084, which holds multi-fiber photometry from mice with arrays of 30 to 103 fibers across the striatum. It re-runs the paper's GLM of dopamine release to light and tone in 280 fibers of 7 mice (amplitude maps, latencies and their spatial gradients), the isosbestic controls, the D1 calcium correlations, the chronic reward responses, and the spread of release evoked by single-fiber stimulation with its controls. The freely moving, histology and jaw movement data of Figures 3, 7 and S1 are not in the dandiset.", "dandisets": [ "001084" ], "papers": [ "10.1016/j.neuron.2023.12.011" ], "derived_from": [], "notebooks": [ { "path": "reproduce_vu_2024.ipynb", "title": "Reproducing Vu et al. (2024) from dandiset 001084", "executed": "notebooks/001084-vu-2024/reproduce_vu_2024.html" } ] }, { "name": "001097-liu-2024", "type": "reproduction", "title": "A hypothalamic line attractor for female mating (Liu, Nair et al. 2024)", "description": "Tests the findings of Liu, Nair et al. (2024) on dandiset 001097, which holds miniscope imaging of VMHvl alpha-cells in female mice during mating, with annotations of male and female behaviour. It tests the behavioural dynamics of mating, single-cell tuning, GLM fits and persistence, and, with the authors' deposited rSLDS weights for two mice, how the receptive-day integration dimension and its cells behave across the oestrus cycle. Claims that need new rSLDS fits are blocked, as the model cannot be built or fit within the registry's environment and time limit.", "dandisets": [ "001097" ], "papers": [ "10.1038/s41586-024-07916-w" ], "derived_from": [], "notebooks": [ { "path": "reproduce_liu_2024.ipynb", "title": "Reproducing Liu, Nair et al. (2024) from dandiset 001097", "executed": "notebooks/001097-liu-2024/reproduce_liu_2024.html" } ] }, { "name": "001170-ling-2023", "type": "reproduction", "title": "ON and OFF odor responses in the mouse olfactory bulb and locust antennal lobe (Ling et al. 2023)", "description": "Tests the findings of Ling, Moss, Smith, Deng, Kroeger, Reimer, Raman and Arenkiel (bioRxiv 2023, v2 2024) on dandiset 001170, which holds two-photon imaging of olfactory bulb glomeruli in awake mice, seven sessions from four mice under the paper's block protocol and five random-order sessions. It compares glomerular ON and OFF responses, contrast enhancement between sequential odors, and odor classification after offset, and tests the locust findings on the recordings the paper deposited on Figshare.", "dandisets": [ "001170" ], "papers": [ "10.1101/2023.04.24.538157" ], "derived_from": [], "notebooks": [ { "path": "reproduce_ling_2023.ipynb", "title": "Reproducing Ling et al. (2023) from dandiset 001170", "executed": "notebooks/001170-ling-2023/reproduce_ling_2023.html" } ] }, { "name": "001172-lohani-2022", "type": "reproduction", "title": "Cholinergic and calcium dynamics across behavioural states (Lohani, Moberly et al. 2022)", "description": "Tests the findings of Lohani, Moberly et al. (2022) on dandiset 001172, which holds dual-colour mesoscopic imaging of ACh3.0 and jRCaMP1b with face video, pupil and wheel data from 4 of the paper's 6 mice. It tests the regression of both signals on behaviour, transients at face movement and locomotion onsets, amplitudes in sustained states, and the state dependence of correlations between areas and between the two signals, using the Allen parcel masks of the paper's code. ECoG, pharmacology, control mice and cholinergic axon imaging are not in the dandiset.", "dandisets": [ "001172" ], "papers": [ "10.1038/s41593-022-01202-6" ], "derived_from": [], "notebooks": [ { "path": "reproduce_lohani_2022.ipynb", "title": "Reproducing Lohani, Moberly et al. (2022) from dandiset 001172", "executed": "notebooks/001172-lohani-2022/reproduce_lohani_2022.html" } ] }, { "name": "001453-fouke-2025", "type": "reproduction", "title": "Optomotor swimming of zebrafish and Danionella cerebrum (Fouke et al. 2025)", "description": "Tests the freely swimming findings of Fouke, He, Loring and Naumann (2025) on dandiset 001453, which holds the tracking data of 25 zebrafish and 12 Danionella cerebrum larvae during the optomotor protocol. It compares swimming speed, turning and angular acceleration between species and stimuli, the response to monocular stimuli, and how steady the swimming is. The imaging and head-fixed tail tracking of the paper's Figures 2 to 4 are not in the dandiset.", "dandisets": [ "001453" ], "papers": [ "10.1016/j.cub.2025.04.027" ], "derived_from": [], "notebooks": [ { "path": "reproduce_fouke_2025.ipynb", "title": "Reproducing Fouke et al. (2025) from dandiset 001453", "executed": "notebooks/001453-fouke-2025/reproduce_fouke_2025.html" } ] }, { "name": "001528-hadjas-2025", "type": "reproduction", "title": "Responses of SNr GABA and SNc dopamine neuron subtypes to STN and PPN input (Hadjas et al. 2025)", "description": "Tests the mouse fiber photometry findings of Hadjas et al. (2025) on dandiset 001528, which holds recordings from 120 mice during optogenetic stimulation of STN or PPN inputs to the substantia nigra. It compares responses of SNr GABA neurons, SNc pan-DA neurons, striatal dopamine release in TS and DLS, DA terminals, and Vglut2+ and Anxa1+ DA neurons across train durations and frequencies, using the lab's dF/F stored in the files. The human tissue counts of Figure 1 are not in the dandiset.", "dandisets": [ "001528" ], "papers": [ "10.1101/2025.06.03.657460" ], "derived_from": [], "notebooks": [ { "path": "reproduce_hadjas_2025.ipynb", "title": "Reproducing Hadjas et al. (2025) from dandiset 001528", "executed": "notebooks/001528-hadjas-2025/reproduce_hadjas_2025.html" } ] }, { "name": "001538-zhai-2025", "type": "reproduction", "title": "State-dependent modulation of spiny projection neurons in levodopa-induced dyskinesia (Zhai et al. 2025)", "description": "Tests the findings of Zhai, Cui, Wokosin, Sun, Tkatch, Crittenden, Graybiel and Surmeier (2025) on dandiset 001538. It measures somatic excitability (rheobase and spike counts) and the dendritic excitability index of dSPNs and iSPNs in the LID off- and on-states and under D1R, D2R and M1R antagonists, CDGI deletion and M1R deletion, and evoked ACh release with GRAB-ACh3.0. It links the recordings to the paper's per-cell tables on Zenodo. The Sr2+-oEPSC, ACh and AIM data hold too few cells or mice for most of the paper's tests, and the spine data are raw stacks only.", "dandisets": [ "001538" ], "papers": [ "10.1126/sciadv.adv8224" ], "derived_from": [], "notebooks": [ { "path": "reproduce_zhai_2025.ipynb", "title": "Reproducing Zhai et al. (2025) from dandiset 001538", "executed": "notebooks/001538-zhai-2025/reproduce_zhai_2025.html" } ] }, { "name": "001550-pagan-2025", "type": "reproduction", "title": "Context-dependent evidence accumulation in rats (Pagan et al. 2025)", "description": "Tests the findings of Pagan, Tang, Aoi, Pillow, Mante, Sussillo and Brody (2025) on dandiset 001550, which holds the behaviour of 26 rats trained on a task that switches between accumulating location and frequency evidence. It links the dandiset to the paper's published behavioural tables, checks the session statistics and selection, fits the behavioural pulse kernels and their slope indices, tests the optogenetic inactivation, and, with the paper's neural data from GitHub, the link between behavioural and neural slope indices.", "dandisets": [ "001550" ], "papers": [ "10.1038/s41586-024-08433-6" ], "derived_from": [], "notebooks": [ { "path": "reproduce_pagan_2025.ipynb", "title": "Reproducing Pagan et al. (2025) from dandiset 001550", "executed": "notebooks/001550-pagan-2025/reproduce_pagan_2025.html" } ] }, { "name": "001616-gerken-2025", "type": "reproduction", "title": "Single units of the human medial temporal lobe during a full-length movie (Gerken, Darcher et al. 2025)", "description": "Tests the findings of Gerken, Darcher et al. (eLife reviewed preprint 106758, 2025) on dandiset 001616 (SUMMER), which holds 2286 units from 29 patients watching \"500 Days of Summer\" with 53 frame-wise annotations. It counts units responsive to the onsets of movie features, runs the cluster permutation test by region, and decodes characters, location and cuts with the paper's logistic regression, pooled, per patient, per region and on subsets of units. The paper's LSTM is not run.", "dandisets": [ "001616" ], "papers": [ "10.7554/elife.106758.1" ], "derived_from": [], "notebooks": [ { "path": "reproduce_gerken_2025.ipynb", "title": "Reproducing Gerken, Darcher et al. (2025) from dandiset 001616", "executed": "notebooks/001616-gerken-2025/reproduce_gerken_2025.html" }, { "path": "top_ranked_units.ipynb", "title": "Top-ranked units for decoding Summer (Figure 7)", "executed": "notebooks/001616-gerken-2025/top_ranked_units.html" }, { "path": "responsive_zeta_cuts.ipynb", "title": "Responsive units by the dataset code's ZETA test, camera and scene cuts (variant)", "executed": "notebooks/001616-gerken-2025/responsive_zeta_cuts.html" }, { "path": "responsive_zeta_labels.ipynb", "title": "Responsive units by the dataset code's ZETA test, character, person and location labels (variant)", "executed": "notebooks/001616-gerken-2025/responsive_zeta_labels.html" } ] }, { "name": "001636-pasquereau-2013", "type": "reproduction", "title": "M1 responses to muscle stretch in the parkinsonian monkey (Pasquereau and Turner 2013)", "description": "Tests the findings of Pasquereau and Turner (2013) on dandiset 001636, which holds single-unit recordings from M1 of two monkeys before and after MPTP, with torque perturbations, joint angle and EMG. Only monkey V can be tested, as the monkey L files mark no perturbation. The notebook checks the cells, resting rates and antidromic latencies, detects torque responses, and compares the torque-evoked movements and triceps EMG before and after MPTP.", "dandisets": [ "001636" ], "papers": [ "10.3389/fnsys.2013.00098" ], "derived_from": [], "notebooks": [ { "path": "reproduce_pasquereau_2013.ipynb", "title": "Reproducing Pasquereau and Turner (2013) from dandiset 001636", "executed": "notebooks/001636-pasquereau-2013/reproduce_pasquereau_2013.html" } ] }, { "name": "001692-bouabid-2026", "type": "reproduction", "title": "Striatal dopamine-acetylcholine hotspot (Bouabid, Vu et al. 2026)", "description": "Tests the findings of Bouabid, Vu et al. (2026) on dandiset 001692, which holds multi-fiber photometry of dopamine and acetylcholine across the striatum of 17 mice. It reproduces the spontaneous cross-correlations and their anterior dorsolateral hotspot, paired transients, reward, Pavlovian cue, locomotion and optogenetic stimulation analyses, and the control mice, and tests the ex vivo slice statistics of Figure 8 on the paper's source data on Zenodo.", "dandisets": [ "001692" ], "papers": [ "10.64898/2026.01.20.700614" ], "derived_from": [], "notebooks": [ { "path": "reproduce_bouabid_2026.ipynb", "title": "Reproducing Bouabid, Vu et al. (2026) from dandiset 001692", "executed": "notebooks/001692-bouabid-2026/reproduce_bouabid_2026.html" } ] }, { "name": "001699-moore-2025", "type": "reproduction", "title": "Head-direction coding in juvenile and adult Fmr1-/y rats (Moore et al. 2025)", "description": "Tests the findings of Moore, Duszkiewicz, Asiminas, Dudchenko, Peyrache and Wood (bioRxiv 2025) on dandiset 001699, which holds silicon-probe recordings of the postsubiculum of 24 juvenile and adult Fmr1-/y and wild-type rats during open-field exploration and sleep. It recomputes the cell selection, head-direction tuning, its stability within and between sessions, decoder drift, and tuning to the Isomap angle of waking and REM population activity, and compares genotypes in each age group.", "dandisets": [ "001699" ], "papers": [ "10.1101/2025.01.09.632139" ], "derived_from": [], "notebooks": [ { "path": "reproduce_moore_2025.ipynb", "title": "Reproducing Moore et al. (2025) from dandiset 001699", "executed": "notebooks/001699-moore-2025/reproduce_moore_2025.html" } ] }, { "name": "001712-davatolhagh-2025", "type": "reproduction", "title": "Prior use and cortical dynamics in a Nrxn1a mouse model (Davatolhagh et al. 2025)", "description": "Tests the findings of Davatolhagh et al. (2025) that can be tested on dandiset 001712, which holds one widefield imaging and behaviour session of one mouse of unstated genotype in the IBL biased choice task. It tests the psychometric curve, reaction times, the use of the block prior, adaptation after block switches, lateralized visual responses and a linear encoding model of the imaging with task and movement predictors. The comparisons between knockout and wild-type mice cannot be tested.", "dandisets": [ "001712" ], "papers": [ "10.1101/2025.09.12.675910" ], "derived_from": [], "notebooks": [ { "path": "reproduce_davatolhagh_2025.ipynb", "title": "Reproducing Davatolhagh et al. (2025) from dandiset 001712", "executed": "notebooks/001712-davatolhagh-2025/reproduce_davatolhagh_2025.html" }, { "path": "encoding_all_cameras.ipynb", "title": "Encoding model with the video components of all three cameras (variant)", "executed": "notebooks/001712-davatolhagh-2025/encoding_all_cameras.html" } ] }, { "name": "001754-knierim-2000", "type": "reproduction", "title": "Place cells during space flight on the Neurolab mission (Knierim et al. 2000)", "description": "Tests the findings of Knierim, McNaughton and Poe (2000) that can be tested on dandiset 001754, which holds sorted units, task epochs, rate maps and spike-time positions of three rats recorded before and during the Neurolab shuttle mission. It tests spatial selectivity on the Escher staircase in flight, spatial information in flight against preflight, and the stability of place fields across two sessions. The paper is not open access; claims come from its abstract, its figure titles and the dandiset's description. There is no EEG in the dandiset.", "dandisets": [ "001754" ], "papers": [ "10.1038/72910" ], "derived_from": [], "notebooks": [ { "path": "reproduce_knierim_2000.ipynb", "title": "Reproducing Knierim et al. (2000) from dandiset 001754", "executed": "notebooks/001754-knierim-2000/reproduce_knierim_2000.html" } ] }, { "name": "001878-sun-2021", "type": "reproduction", "title": "CalMS21 mouse social behavior dataset (Sun et al. 2021)", "description": "Tests the claims of Sun et al. (2021), the paper describing the CalMS21 dataset of resident-intruder pose and behavior annotations, on dandiset 001878, which holds one CalMS21 sequence (Task 1 test sequence mouse071) with its video, and on the full dataset deposited on CaltechDATA. It checks the format, identities and annotations of the dandiset's sequence, links it to the deposit, and tests the dataset's counts and label fractions. The model benchmarks are not run.", "dandisets": [ "001878" ], "papers": [ "10.22002/d1.1991" ], "derived_from": [], "notebooks": [ { "path": "reproduce_sun_2021.ipynb", "title": "Reproducing Sun et al. (2021) from dandiset 001878 and the CalMS21 deposit", "executed": "notebooks/001878-sun-2021/reproduce_sun_2021.html" } ] }, { "name": "001888-hristova-2025", "type": "reproduction", "title": "Absence seizures and sleep in Grin2b+/- rats (Hristova, Fasol et al. 2025)", "description": "Tests the EEG findings of Hristova, Fasol et al. (2025) on dandiset 001888, which holds the 24-h wireless EEG and EMG recordings, sleep scores and SWD events of 14 Grin2b+/- rats, 2 wild type rats and one rat without genotype. It compares SWD number, duration and timing, sleep-wake amounts and bouts, state spectra computed from the raw EEG, the state in which SWDs start, and the correlation of SWD time with sleep measures. The western blots, development measures, visual scoring and pharmacology recordings of the paper are not in the dandiset.", "dandisets": [ "001888" ], "papers": [ "10.1111/epi.18606" ], "derived_from": [], "notebooks": [ { "path": "reproduce_hristova_2025.ipynb", "title": "Reproducing Hristova, Fasol et al. (2025) from dandiset 001888", "executed": "notebooks/001888-hristova-2025/reproduce_hristova_2025.html" } ] }, { "name": "001933-chen-2026", "type": "reproduction", "title": "LRRK2-G2019S and dopamine release from Anxa1+ and Calb1+ neurons (Chen, He et al. 2026)", "description": "Tests the findings of Chen, He et al. (2026). On dandiset 001933, which holds GRAB-DA3m fiber photometry in the dorsal striatum during optogenetic stimulation of Anxa1+ (15 mice) or Calb1+ (12 mice) SNc dopamine neurons in LRRK2-WT and LRRK2-G2019S mice, it compares evoked and spontaneous dopamine release between genotypes, per power and per mouse, and links the dandiset to the paper's published source data. The imaging, proteomics and western blots of Figures 1 to 5 are not in the dandiset; their claims are tested on the data the paper deposited on Zenodo, in PRIDE and in the BioImage Archive, and counted apart.", "dandisets": [ "001933" ], "papers": [ "10.1038/s41467-026-75194-3", "10.5281/zenodo.19930567" ], "derived_from": [], "notebooks": [ { "path": "reproduce_chen_2026.ipynb", "title": "Reproducing Chen, He et al. (2026) from dandiset 001933", "executed": "notebooks/001933-chen-2026/reproduce_chen_2026.html" } ] }, { "name": "002013-amjad-2025", "type": "reproduction", "title": "Microinvasive probes for dopamine, LFP and spikes in monkeys (Amjad et al. 2025)", "description": "Tests the findings of Amjad, Mahajan, Choi, Shrivastav, Murray, Somich, Coyne and Schwerdt (2025) on dandiset 002013, which holds the three example sessions of the paper. It checks the recording parameters and task structure, the dopamine response to large and small reward cues at site c8dg, beta-band LFP suppression by reward and cue side at c3bs-c3a, beta bursts around the cue, and the isolation of the sorted unit of monkey P, and compares the dandiset with the paper's Zenodo deposit.", "dandisets": [ "002013" ], "papers": [ "10.1021/acschemneuro.5c00071" ], "derived_from": [], "notebooks": [ { "path": "reproduce_amjad_2025.ipynb", "title": "Reproducing Amjad et al. (2025) from dandiset 002013", "executed": "notebooks/002013-amjad-2025/reproduce_amjad_2025.html" } ] }, { "name": "002014-choi-2025", "type": "reproduction", "title": "Dopamine, spikes and LFP through an aseptic cranial chamber in a rhesus monkey (Choi et al. 2025)", "description": "Tests the recording findings of Choi et al. (2025) on dandiset 002014, which holds one session of monkey T recorded through the paper's semi-sealed chamber. It compares dopamine and beta-band LFP power between large and small reward trials, aligns spikes to the value cue, and checks the unit's waveform and interspike intervals. The surgical, culture, drainage and yield results, and monkey J, are not in the dandiset.", "dandisets": [ "002014" ], "papers": [ "10.1016/j.jneumeth.2025.110467" ], "derived_from": [], "notebooks": [ { "path": "reproduce_choi_2025.ipynb", "title": "Reproducing Choi et al. (2025) from dandiset 002014", "executed": "notebooks/002014-choi-2025/reproduce_choi_2025.html" } ] } ], "targets": [ { "dandiset": "000003", "name": "Physiological Properties and Behavioral Correlates of Hippocampal Granule Cells and Mossy Cells", "size_gb": 2559.25, "files": 101, "status": "attempted", "paper": "10.1016/j.neuron.2016.12.011", "paper_title": "Physiological Properties and Behavioral Correlates of Hippocampal Granule Cells and Mossy Cells", "papers": [ "10.1016/j.neuron.2016.12.011" ], "n_papers": 1, "technique": [ "behavioral", "electrophysiological" ], "species": [ "House mouse" ], "catalystneuro": [ "contributor Baker, Cody of CatalystNeuro" ] }, { "dandiset": "000004", "name": "A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task", "size_gb": 6.2, "files": 87, "status": "attempted", "paper": "10.1038/s41597-020-0415-9", "paper_title": "A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task", "papers": [ "10.1038/s41597-020-0415-9" ], "n_papers": 1, "technique": [ "electrophysiological" ], "species": [ "Human" ], "catalystneuro": [ "contributor Dichter, Benjamin of CatalystNeuro" ] }, { "dandiset": "000005", "name": "Electrophysiology data from thalamic and cortical neurons during somatosensation", "size_gb": 46.44, "files": 148, "status": "open", "paper": "10.1038/nn.4412", "paper_title": "Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation", "papers": [ "10.1038/nn.4412" ], "n_papers": 1, "technique": [ "electrophysiological", "optogenetic" ], "species": [ "House mouse" ], "catalystneuro": [] }, { "dandiset": "000006", "name": "Mouse anterior lateral motor cortex (ALM) in delay response task", "size_gb": 0.14, "files": 53, "status": "attempted", "paper": "10.1038/s41586-018-0642-9", "paper_title": "Distinct descending motor cortex pathways and their roles in movement", "papers": [ 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