{ "dandiset": "000218", "page": "dandisets/000218/", "generated": "2026-10-19T16:23:39+00:00", "caution": "A failure to reproduce is not a finding that the paper is wrong. It may be a failure of the attempt.", "outcome_counts": { "reproduced": 4, "partially_reproduced": 7, "not_reproduced": 10, "blocked": 10 }, "outcome_counts_with_outside_data": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_elsewhere": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "attempts": [ { "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": [] } ] } ], "entries": [ { "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" } ] } ] }