{ "dataset": { "archive": "dandi", "id": "000041", "label": "DANDI:000041" }, "page": "datasets/dandi/000041/", "generated": "2026-10-20T19:09:16+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": 8, "partially_reproduced": 9, "not_reproduced": 15, "blocked": 7 }, "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 }, "outcome_counts_links": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "attempts": [ { "id": "000041-watson-2016-01", "dataset": { "archive": "dandi", "id": "000041", "version": "0.250624.0419", "doi": "10.48324/dandi.000041/0.250624.0419" }, "key": "dandi:000041", "label": "DANDI:000041", "dataset_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" }, "runner": { "platform": "GitHub Actions", "url": "https://github.com/catalystneuro/reproduction-registry/actions/runs/38839151188" }, "tier": "agent_verified", "deprecated": "", "deprecated_on": null, "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, paragraph 1; Results, Assessment of firing patterns in different brain states, paragraph 1; Experimental Procedures", "quote": "We recorded across different brain states from 11 rats ... Recordings from 27 sessions (294\u00b1137 min) ... This resulted in 995 putative pyramidal (pE) cells ... and 126 putative interneurons (pI)", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 2; Figure 2A", "quote": "Median rates (\u00b1SD) of putative pyramidal cells in each state were: WAKE: 0.76\u00b11.53 Hz, nonREM: 0.69\u00b10.86 Hz, REM: 0.88\u00b11.33 Hz; and for putative interneurons were: WAKE: 5.59\u00b17.25 Hz, nonREM: 4.69\u00b15.62 Hz, REM 4.25\u00b19.43 Hz.", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 2; Figure 2A", "quote": "the distribution of per-cell mean firing rates for putative pyramidal neurons was strongly positively skewed ... spanning three orders of magnitude range from 0.05 Hz to 5 Hz (Figure 2A)", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 2; Figure 2A", "quote": "The right tail extended toward higher rates during WAKE and REM compared to nonREM (Figure 2A; fraction of >2 Hz neurons: WAKE= 19.2%; REM= 19.2%; nonREM= 8.8%; Chi-Square Test", "statistics": [ { "test": "Chi-Square Test", "p": 1e-10, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 2; Figure 2B", "quote": "Whereas nonREM and WAKE firing rates remained highly correlated on a per-cell basis (R = 0.82 ... the slope of this relationship significantly deviated from 1 (Figure 2B) ... (95% confidence interval of slope: 0.66 \u2013 0.71)", "statistics": [ { "about": "correlation of nonREM and WAKE rates", "statistic": "R = 0.82", "p": 1e-10, "p_relation": "<" }, { "about": "slope of the nonREM against WAKE rate relation", "ci": { "level": 0.95, "low": 0.66, "high": 0.71 } } ], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 3", "quote": "Burst index was highest during nonREM (median in nonREM = 11.8%) and lowest during WAKE (4.0 %), with REM (5.5 %) slightly higher than WAKE (p < 0.05; Kruskal-Wallis test).", "statistics": [ { "test": "Kruskal-Wallis test", "p": 0.05, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 3; Figure 2C", "quote": "a large peak occurred at approximately 8ms inter-spike interval during nonREM, whereas smaller peaks were present at ~125 ms (i.e., theta frequency) during REM and WAKE (Figure 2C)", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 3; Figure 2C", "quote": "Time decay of the autocorrelograms of pyramidal neurons was significantly faster during nonREM compared to WAKE and REM (Figure 2C; decay fit exponent median nonREM = \u2013 1.35, WAKE = \u2013 0.83, REM = \u2013 0.80; p < 0.05; Kruskal-Wallis test).", "statistics": [ { "test": "Kruskal-Wallis test", "p": 0.05, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 5; Figure 2F", "quote": "the fastest and slowest firing neurons tended to be positively correlated within groups, but were actually negatively correlated across groups (Figure 2F).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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, paragraph 2", "quote": "There were a total of 790 MAs in our dataset (median duration = 15.9\u00b13.3sec; frequency = 0.32\u00b10.12 per minute; 9.1\u00b13.5% of time in SLEEP).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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, paragraph 2", "quote": "Over nonREM episodes the fraction of time occupied by MAs decreased (correlation versus normalized nonREM episode time: R = \u22120.85", "statistics": [ { "statistic": "R = -0.85", "p": 1e-10, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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, paragraph 3", "quote": "We found that the duration of packets was distributed over two orders of magnitude, with a median of 111 seconds.", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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, paragraph 3; Results, Assessment of firing patterns in different brain states, paragraph 1; Results, Firing pattern and LFP changes across the course of sleep, paragraph 1", "quote": "Sessions without full WAKE-SLEEP cycles (Supplementary Materials) were also discarded. ... We identified 54 WAKE-SLEEP episodes in our dataset, or an average of 2.0 episodes per neuron recorded (27 sessions)", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 the course of sleep, paragraph 1; Figure 3B", "quote": "the arithmetic mean of the population firing rates of pE cells declined over the course of sleep using a test of correlation of spike rate versus time (Figure 3A\u2013B; R = \u2013 0.11", "statistics": [ { "statistic": "R = -0.11", "p": 0.001, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 the course of sleep, paragraph 1", "quote": "Comparison of the population discharge rates in the first and last nonREM packets of SLEEP episodes showed an overall mean rate decrease (1.04\u00b11.20 Hz versus 0.88\u00b10.91 Hz; p < 0.02; Wilcoxon test)", "statistics": [ { "test": "Wilcoxon test", "p": 0.02, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 the course of sleep, paragraph 2; Figure 3D", "quote": "we assessed spike rates of the same neurons in the first versus the last nonREM packets of SLEEP and found the slope of this correlation significantly departed from unity (slope 95% confidence interval 0.827\u20130.880)", "statistics": [ { "ci": { "level": 0.95, "low": 0.827, "high": 0.88 } } ], "kind": "finding", "inferred": "", "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": "dataset", "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 and LFP changes across the course of sleep, paragraph 1; Results, Sleep sub-states induce differential lasting firing rate changes, paragraph 2; Figure 3E", "quote": "the significantly decreased discharge rate of pE neurons in a 5-min post-sleep WAKE compared to a 5-min pre-sleep WAKE epoch ... a significant decrease firing in the top three sextile groups and an increase in the lowest sextile group (all ps < 0.05", "statistics": [ { "about": "population, post-sleep against pre-sleep WAKE", "test": "Wilcoxon test", "p": 1e-06, "p_relation": "<" }, { "about": "each of the top three sextiles and the lowest sextile", "p": 0.05, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 and LFP changes across the course of sleep, paragraph 2; Figure 3B", "quote": "The mean spike discharge rate of highest-firing rate sextile groups significantly decreased over sleep whereas the activity of the lowest-firing rate sextile showed a marginal increase (Figure 3B; Pearson correlations versus normalized time).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 and LFP changes across the course of sleep, paragraph 2", "quote": "the coefficient of firing rate variation also showed a significantly decreasing slope over the course of SLEEP (R = \u2013 0.05; p < 0.01).", "statistics": [ { "statistic": "R = -0.05", "p": 0.01, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 5; Figure 4A and 4B, panel iv", "quote": "Firing rates of the fastest-firing sextile groups decreased, whereas those of the slowest-firing sextile groups increased within both nonREM episodes and packets (Figure 4A, B iv; R and p values in figure)", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 5; Figure 4A and 4B, panel v", "quote": "resulting in a decreasing coefficient of variation of binned population firing rates (Figure 4 A\u2013B v; Repisode= \u22120.13 ... Rpacket= \u2013 0.12", "statistics": [ { "about": "nonREM episodes", "statistic": "R = -0.13", "p": 1e-10, "p_relation": "<" }, { "about": "nonREM packets", "statistic": "R = -0.12", "p": 1e-10, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 5; Figure 4A and 4B, panel vi", "quote": "the 15ms spike burst index of pyramidal neurons, also showed a positive slope within both nonREM episodes and packets (Figure 4 A\u2013B vi; Repisode= 0.09 ... Rpacket = 0.08", "statistics": [ { "about": "nonREM episodes", "statistic": "R = 0.09", "p": 1e-10, "p_relation": "<" }, { "about": "nonREM packets", "statistic": "R = 0.08", "p": 1e-10, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 2; Figure 4A and 4B, panel i", "quote": "Over nonREM episodes and packets, delta and sigma band power steadily increased (Trachsel et al., 1988), whereas gamma power decreased over episodes but not packets (Figure 4 A\u2013B i).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 2", "quote": "Mean delta power within whole packets (normalized by nonREM delta power) was positively correlated with packet length (R = 0.31; p < 0.05).", "statistics": [ { "statistic": "R = 0.31", "p": 0.05, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 6; Figure 4C and 4D", "quote": "Per-packet firing rate of the top sextile group was negatively correlated with ... whole-packet delta power ... R= \u2013 0.28 ... and gamma power (Figure 4D; R = 0.44 ... the bottom sextile group and sigma power in the last 20 sec of the packet (R = 0.25", "statistics": [ { "about": "sextile 6 rate against packet delta power", "statistic": "R = -0.28", "p": 1e-10, "p_relation": "<" }, { "about": "sextile 6 rate against packet gamma power", "statistic": "R = 0.44", "p": 1e-10, "p_relation": "<" }, { "about": "sextile 1 rate against sigma power in the last 20 s", "statistic": "R = 0.25", "p": 1e-10, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 3; Figure 5B", "quote": "Firing rates in the top two firing rate sextiles were significantly reduced by the intervening nonREM packet (both p < 0.01; Figure 5B, blue)", "statistics": [ { "p": 0.01, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 4; Figure 5B", "quote": "WAKE episodes increased the activity of the fastest-firing sextile group of pyramidal cells from nonREM packetn to packetn+1 (Figure 5B, black) ... uninterrupted nonREM-WAKE-nonREM triplets (n = 24)", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 5; Figure 5B", "quote": "MA epochs between packets did not affect fast-firing neurons but significantly increased the rate of slow-firing neurons from packetn to packetn+1 (Figure 5B, yellow).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 5; Figure 5B", "quote": "Finally, REM episodes decreased the spike rates from packetn to packetn+1 in all sextile groups (Figure 5B, red).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 5; Figure 5C", "quote": "Longer REM episodes exerted a proportionally larger effect on rate changes from packetn to packetn+1 for all sextile groups (Figure 5C; R = \u2013 0.22", "statistics": [ { "test": "t-test", "statistic": "R = -0.22", "p": 0.01, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 3; Figure 5C", "quote": "sigma power in the last 20 seconds of nonREM packets was correlated with a greater increase in the lowest firing-rate sextile group in the MAn versus MAn+1 analysis (Figure 5C; R = 0.181, p < 0.01).", "statistics": [ { "statistic": "R = 0.181", "p": 0.01, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 5; Figure 5C", "quote": "The increase of spike rate from packetn to packetn+1 in the slowest sextile group was positively correlated with the delta power change from packetn to packetn+1 (Figure 5C).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 8 (Figure S5A and S5B)", "quote": "entry into WAKE corresponded with an increase in firing rate of the highest sextile two groups and a drop in firing rate of the lowest two sextile groups (Figure S5A) ... During REM, all sextile groups except the fourth showed an increase in firing rate (Figure S5B)", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 differential lasting firing rate changes, paragraph 4; Figure 5C", "quote": "Furthermore, WAKE periods with more movement had a proportionally larger effect (Figure 5C; R = 0.43; p < 0.05).", "statistics": [ { "statistic": "R = 0.43", "p": 0.05, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 4 (Figure S4A)", "quote": "The durations of DOWN states of \u2018slow oscillations\u2019 showed a skewed distribution (median = 0.19s) and so did the UP states (median = 0.47s; Figure S4A).", "statistics": [], "kind": "finding", "inferred": "", "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": "dataset", "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 the course of sleep, paragraph 3; Figure 3C", "quote": "Incidence of spindles (1.94\u00b10.39/min) decreased ... while spindle duration (0.52\u00b10.32 sec), frequency (13.93\u00b10.93 Hz) and amplitude (203.3\u00b187.71 \u00b5V) did not change over SLEEP. Incidence of both UP states (R = \u2013 0.10 ... and DOWN states (R = \u2013 0.08 ... while the duration of DOWN states increased", "statistics": [ { "about": "spindle incidence", "statistic": "R = -0.093", "p": 1e-05, "p_relation": "<" }, { "about": "UP state incidence", "statistic": "R = -0.10", "p": 1e-06, "p_relation": "<" }, { "about": "DOWN state incidence", "statistic": "R = -0.08", "p": 0.0001, "p_relation": "<" }, { "about": "DOWN state duration", "statistic": "Rslope = 0.09", "p": 0.0001, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 episodes and packets, paragraph 2 and 3; Figure 4A and 4B, panels ii and iii", "quote": "The incidence of both UP states (R = 0.05 ... and DOWN states (R = 0.08 ... increased significantly within packets, whereas the duration of UP states decreased (R = \u2013 0.02 ... and DOWN states increased (R = 0.07 ... and packets (R = 0.7 ... Spindle duration also increased", "statistics": [ { "about": "UP state incidence", "statistic": "R = 0.05", "p": 0.001, "p_relation": "<" }, { "about": "DOWN state incidence", "statistic": "R = 0.08", "p": 1e-10, "p_relation": "<" }, { "about": "UP state duration", "statistic": "R = -0.02", "p": 0.01, "p_relation": "<" }, { "about": "DOWN state duration", "statistic": "R = 0.07", "p": 1e-10, "p_relation": "<" }, { "about": "spindle incidence, packets", "statistic": "R = 0.7", "p": 1e-10, "p_relation": "<" }, { "about": "spindle duration, packets", "statistic": "R = 0.07", "p": 0.0001, "p_relation": "<" } ], "kind": "finding", "inferred": "", "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": "dataset", "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 in different brain states, paragraph 5; Figure 2D and 2E", "quote": "pyramidal neurons fired in reliable spatiotemporal sequences during the early part of the UP state (<200 msec) and these stereotypical sequences remained stable across the entirety of sleep (Figure 2D). Additionally, the spike onset times of individual neurons in the sequences were negatively correlated with their firing rates (Figure 2E)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs UP state onsets (see updown-durations).", "deviations": [], "disagreed": false, "data": "dataset", "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, Firing pattern and LFP changes across the course of sleep, paragraph 3; Results, Firing rate and LFP changes within nonREM episodes and packets, paragraph 7; Figure 3F and Figure 4E", "quote": "the firing rates of the fastest sextile group and putative interneurons decreased later in sleep, whereas firing of the slowest sextile increased (Figure 3F) ... showed a drop in firing rate for the fastest sextile group ... an increase in firing rate of putative interneurons", "statistics": [ { "about": "fastest sextile, first against second third of packets", "test": "Wilcoxon rank-sum test", "p": 1e-08, "p_relation": "<" }, { "about": "putative interneurons, first against second third of packets", "p": 0.001, "p_relation": "<" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": null, "notes": "Needs UP state detection (see updown-durations).", "deviations": [], "disagreed": false, "data": "dataset", "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": [] } ] } ], "entries": [ { "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.", "datasets": [ "dandi: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" } ] } ] }