{ "dandiset": "001699", "page": "dandisets/001699/", "generated": "2026-10-19T12:04:40+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": 14, "partially_reproduced": 7, "not_reproduced": 5, "blocked": 1 }, "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": "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": [] } ] } ], "entries": [ { "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" } ] } ] }