{ "dandiset": "001888", "page": "dandisets/001888/", "generated": "2026-10-19T13:42:58+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": 13, "partially_reproduced": 9, "not_reproduced": 2, "blocked": 10 }, "outcome_counts_with_outside_data": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_elsewhere": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "attempts": [ { "id": "001888-hristova-2025-01", "dandiset": "001888", "dandiset_version": "draft", "paper": "10.1111/epi.18606", "paper_title": "Absence seizures and sleep-wake abnormalities in a rat model of GRIN2B neurodevelopmental disorder", "date": "2026-10-19", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code (GitHub Actions)", "model": "claude-opus-5-5", "protocol": "pilot-7" }, "tier": "agent_verified", "entry": "001888-hristova-2025", "entry_title": "Absence seizures and sleep in Grin2b+/- rats (Hristova, Fasol et al. 2025)", "description": "Tests the EEG findings of Hristova, Fasol et al. (2025) on dandiset 001888, which holds the 24-h wireless EEG and EMG recordings, sleep scores and SWD events of 14 Grin2b+/- rats, 2 wild type rats and one rat without genotype. It compares SWD number, duration and timing, sleep-wake amounts and bouts, state spectra computed from the raw EEG, the state in which SWDs start, and the correlation of SWD time with sleep measures. The western blots, development measures, visual scoring and pharmacology recordings of the paper are not in the dandiset.", "notebooks": [ { "path": "reproduce_hristova_2025.ipynb", "title": "Reproducing Hristova, Fasol et al. (2025) from dandiset 001888", "executed": "notebooks/001888-hristova-2025/reproduce_hristova_2025.html" } ], "outcomes": [ { "claim": "fig2b-swd-hourly", "statement": "Grin2b+/- rats have more SWDs than WT across the 24-h day; hour of day has no effect and does not interact with genotype (linear mixed model, genotype F = 55.36, p < .00001; hour p = .16; interaction p = .49).", "source": "Figure 2B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Split-plot ANOVA on SWDs per ZT hour, genotype F = 11.45, p = 0.0045 (Het higher), hour p = 0.069, interaction p = 0.9998. Het hourly means 19.2 to 37.8, WT 0 to 8.2. With GRIN2B-132 as WT or Het the genotype effect holds (p = 0.0011, 0.013) and hour reaches p = 0.041. Without GRIN2B-228, GRIN2B-238 or both, genotype p = 0.0001, 0.048 and 0.0036, hour p 0.070 to 0.074. A fitted random-intercept model (MixedLM) gives the same genotype and interaction statistics. The paper's genotype F is 55.36 with 9 WT; here there are 2.", "deviations": [ "Two WT rats, where the paper has nine.", "The random-intercept mixed model is tested as a split-plot ANOVA." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-swd-number", "statement": "Grin2b+/- rats have more SWDs over 24 h than WT (Wilcoxon rank-sum, W = 4.5, p = .0002).", "source": "Figure 2C, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 690.6 SWDs per day, WT 56.3 (GRIN2B-238 none, GRIN2B-240 112.5); W = 1, p = 0.047. GRIN2B-240 ranks above one Het, GRIN2B-228, which has 1 SWD per day. With GRIN2B-132 as WT p = 0.020, as Het p = 0.062. Without GRIN2B-228 p = 0.034 (W = 0); with GRIN2B-238 left out one WT remains and p = 0.20.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-swd-mean-duration", "statement": "SWDs are longer on average in Grin2b+/- rats than in WT (two-sample t test, df = 22, T = -5.26, p = .00003).", "source": "Figure 2C, middle", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het mean SWD duration 4.54 s against 1.47 s in GRIN2B-240, the only WT rat with SWDs; t test p = 0.16 (df 13). With GRIN2B-132 (1.70 s) as WT p = 0.062; without GRIN2B-228 p = 0.090. A t test against a single WT value says little either way.", "deviations": [ "One WT rat has SWDs, so the WT group has one value." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2c-swd-total-duration", "statement": "The total time in SWDs over 24 h is higher in Grin2b+/- rats than in WT (Wilcoxon rank-sum, W = 5.5, p = .0002).", "source": "Figure 2C, right", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 57.77 min per day, WT 1.37 min; W = 1, p = 0.033. With GRIN2B-132 as WT p = 0.012, as Het p = 0.029. Without GRIN2B-228 p = 0.019; with GRIN2B-238 left out one WT remains and p = 0.27.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "disc-het-swd-minutes", "statement": "Over 24 h, Grin2b+/- rats spend on average 59.97 min in SWDs, while WT littermates average less than a minute.", "source": "Discussion, paragraph 2", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "The Het mean of 57.77 min per day (SEM 9.04, 14 rats) is within 59.97 +- 6.0. The WT mean is 1.37 min (0 and 2.75), not below 1 min. Without GRIN2B-228 the Het mean is 62.21, also within tolerance; without GRIN2B-238 the WT mean is 2.75. Counting the epochs SWD events overlap as 5 s each gives 110.57 min, and counting the epochs the scorer flags gives 60.2 min, so the paper's number fits both the event durations and the flags.", "deviations": [ "Two WT rats, where the paper has nine; the WT part rests on GRIN2B-240 alone." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5a-swd-light-dark", "statement": "The number of SWDs does not differ between the light and dark phases, and Grin2b+/- rats have more SWDs than WT in both (linear mixed model, genotype p < .00001, phase p = .28, interaction p = .53).", "source": "Figure S5A; Results 3.3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Phase F = 1.19, p = 0.29; genotype F = 11.45, p = 0.0045; interaction p = 0.86. Het 316.7 SWDs in the light and 373.9 in the dark, WT 12.5 and 43.8. Within Het, light minus dark median -79.8 (signed-rank p = 0.19). Without GRIN2B-228, GRIN2B-238 or both, phase p = 0.30 and genotype p = 0.0001, 0.048 and 0.0036.", "deviations": [ "Two WT rats; the mixed model is tested as a split-plot ANOVA." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs8-swd-sex", "statement": "Sex does not affect the number, mean duration or total duration of SWDs (two-way ANOVA sex x genotype, sex p = .74, .99 and .99).", "source": "Figure S8B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Sex term p = 0.29, 0.94 and 0.78 for number, mean duration and total duration. Within Het, females 763.3 SWDs per day against 617.9 in males (t test p = 0.31), 4.59 against 4.50 s, 60.3 against 55.2 min. Without GRIN2B-228, GRIN2B-238 or both the sex terms have p from 0.31 to 0.94.", "deviations": [ "The ANOVA has no sex by genotype interaction, as both WT are female; the paper's model has one." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2d-swd-spectrum-peak", "statement": "The EEG spectrum during SWDs has a clear peak in the theta range with a harmonic, in both genotypes.", "source": "Figure 2D; Results 3.3", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "All 15 rats with at least 5 usable SWD epochs in the raw windows (13 Het, the WT GRIN2B-240 and GRIN2B-132) have a peak at 7.0 to 8.0 Hz and another at 14.0 to 16.0 Hz. The stored spectra show peaks near the same frequencies (7.4 to 8.2 and 14.4 to 16.2 Hz). GRIN2B-240 has 18 usable SWD epochs.", "deviations": [ "Spectra from about 4.8 h of raw EEG per rat (one 24-min chunk at six ZT hours of each day), on the SWD-detection channel, with a 2-s Welch segment chosen here.", "The peak rule (local maximum with prominence 0.1 in log10 power, harmonic within 1 Hz of twice the peak) was chosen here; the paper describes the peak by eye." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig2e-swd-delta-power", "statement": "Delta power during SWDs is higher in Grin2b+/- rats than in WT (two-way ANOVA genotype x band, interaction p = .015; Tukey delta p = .039).", "source": "Figure 2E", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Only one WT rat (GRIN2B-240) has SWDs; GRIN2B-238 has none in either day, and the paper's other seven WT rats are not in the dandiset. The claim's rule needs at least two animals per genotype (also other, too few animals). A search of the archive for GRIN2B, Gonzalez-Sulser and the paper's DOI finds only this dandiset. As an illustration only, with GRIN2B-132 (no genotype) counted as WT, Het SWD delta power is lower than WT (-0.34, Tukey p = 1.0), against the paper's direction.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3d-rem-hourly", "statement": "Grin2b+/- rats have less REM sleep per hour than WT across the day, and the reduction is not specific to certain hours (linear mixed model, genotype F = 9.98, p = .0045; hour x genotype p = .53).", "source": "Figure 3D", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Genotype F = 4.69, p = 0.048 (Het lower); interaction p = 0.096. At the threshold; with GRIN2B-132 as WT p = 0.19, as Het p = 0.038 (interaction p = 0.071); with the scorer's flags or the stored scores p = 0.049 and 0.050. Without GRIN2B-228 genotype p = 0.060; without GRIN2B-238 or both genotype p = 0.019 and 0.025 but the interaction has p = 0.0001 and 0.00005. The outcome holds with all 16 rats and with GRIN2B-132 counted as Het, and not without GRIN2B-228 or GRIN2B-238. A fitted mixed model (MixedLM) gives genotype Wald p = 0.030 and interaction p = 0.086.", "deviations": [ "Two WT rats; the mixed model is tested as a split-plot ANOVA.", "SWD epochs are the epochs SWD events overlap; the lab's scorer uses its per-epoch flags." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-rem-total", "statement": "Grin2b+/- rats spend less total time in REM sleep over 24 h than WT (two-sample t test, df = 22, T = 3.16, p = .0045).", "source": "Figure 3G, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 44.8 min of REM per day, WT 69.7 (54.3 and 85.2); t = 2.16, df 14, p = 0.048. With GRIN2B-132 as WT p = 0.19, as Het p = 0.038; SWD-epoch variants p = 0.049 and 0.050, and 0.049 with only the SWD time removed. Without GRIN2B-228 p = 0.060; without GRIN2B-238 p = 0.019.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-rem-bouts", "statement": "Grin2b+/- rats have fewer REM bouts than WT (two-sample t test, df = 22, T = 3.94, p = .00069).", "source": "Figure 3G, middle", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 37.9 REM bouts per day, WT 74.0; t = 4.12, df 14, p = 0.0010. Both WT have more bouts than every Het. With GRIN2B-132 as WT p = 0.068. Without GRIN2B-228, GRIN2B-238 or both p <= 0.0017; with bouts not split by SWD epochs p = 0.0007.", "deviations": [ "Two WT rats; the bout definition (runs of one state, ended by SWD epochs) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3g-rem-bout-duration", "statement": "REM bouts are longer on average in Grin2b+/- rats than in WT (Wilcoxon rank-sum, W = 33, p = .043).", "source": "Figure 3G, right; Results 3.4", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het REM bouts 71.9 s, WT 56.8 s; W = 2, p = 0.067. With GRIN2B-132 (95.5 s) as WT the difference is 2.2 s (p = 0.59). Without GRIN2B-228 p = 0.076; with bouts not split by SWD epochs p = 0.067.", "deviations": [ "Two WT rats; bout definition chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-nrem-total", "statement": "Total NREM sleep over 24 h does not differ between genotypes (two-sample t test, df = 22, T = -.09, p = .93).", "source": "Figure 3H, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 450.5 min, WT 419.3 min, difference 31.2 min; t = -1.29, p = 0.22. With GRIN2B-132 as WT the difference is 48.4 min, p = 0.035. Without GRIN2B-238 the Het have 17.6 min less (p = 0.54); with only the SWD time removed p = 0.19. With two WT the test has little power to find a difference.", "deviations": [ "Two WT rats, where the paper has nine." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3h-nrem-bouts", "statement": "Grin2b+/- rats have fewer NREM bouts, which are longer, than WT (Wilcoxon rank-sum, bouts W = 29.5, p = .025; mean bout duration W = 26, p = .015).", "source": "Figure 3H, middle and right", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Mean NREM bout duration Het 127.1 s, WT 92.3 s, W = 0, p = 0.017. Number of NREM bouts Het 218.5, WT 273.0 per day, W = 25, p = 0.10. With the scorer's flags, the stored scores or bouts not split by SWD epochs both parts have p < 0.05 (bouts p = 0.032). Without GRIN2B-228 bouts p = 0.11, duration p = 0.019.", "deviations": [ "Two WT rats; bout definition chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3i-wake-total", "statement": "Grin2b+/- rats spend less total time awake over 24 h than WT (Welch t test, df = 10.25, T = 2.26, p = .047).", "source": "Figure 3I, left; Results 3.4", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 834.1 min awake per day, WT 944.9, difference -110.8 min; Welch p = 0.35. With the scorer's flags -68.1 min (p = 0.49), with only the SWD time removed -65.5 min (p = 0.50), with the stored scores -10.8 min (p = 0.89), so most of the difference is SWD time removed from wake. Without GRIN2B-228 -121.2 min (p = 0.33).", "deviations": [ "Two WT rats; SWD epochs are the epochs SWD events overlap." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig3i-wake-bouts", "statement": "Grin2b+/- rats have more wake bouts of shorter duration than WT (Wilcoxon rank-sum, W = 18, p = .0035; Welch t test on mean bout duration, df = 8.91, T = 2.97, p = .016).", "source": "Figure 3I, middle and right", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Het 559.4 wake bouts per day against WT 294.5 (W = 2, p = 0.067); mean wake bout 100.6 s against 206.2 s (Welch p = 0.31). With the stored scores, where SWD epochs count as wake, both reverse (190.8 against 241.0 bouts, p = 0.017; 304.2 against 239.2 s), and they reverse with bouts not split by SWD epochs too (186.3 against 241.0 bouts, p = 0.017; 275.4 against 237.7 s). The outcome rests on SWD epochs ending wake bouts, which follows the Methods' exclusion of SWD times but builds part of the difference in. Without GRIN2B-228 the bout count has p = 0.019.", "deviations": [ "Two WT rats; bout definition chosen here; SWD epochs end wake bouts." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4a-rem-spectrum", "statement": "EEG spectral power during REM sleep does not differ between genotypes (two-way ANOVA genotype x band, genotype p = .14, interaction p = .69).", "source": "Figure 4A", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Normalized REM band power, genotype F = 3.30, p = 0.073; interaction p = 0.998; Het lower by 0.19 on average. Contiguous bands give genotype p = 0.034, SWD epochs from flags p < 0.0001, the stored spectra p = 0.17, the cleaner S1 channel p = 0.067; the slope rejection removes no epoch. Without GRIN2B-228 p = 0.094, without GRIN2B-238 p = 0.19. The windows cover a median of 5 to 10% of each state's epochs (1.1% of GRIN2B-129's REM). With two WT the test has little power, and the band ANOVA treats an animal's five bands as separate observations, as the paper's does.", "deviations": [ "Spectra from about 4.8 h of raw EEG per rat on the SWD-detection channel; the paper used one representative channel and all epochs.", "Band limits (delta 1-4, theta 4-8, sigma 10-15, beta 15-30, gamma 30-48 Hz) and the Welch segment are not given in the paper. The spectral-slope rejection, read here as a slope below -5 of log10 power against log10 frequency or power at 1 Hz above 500 mV^2/Hz, removes no epoch.", "The paper chose the S1 channel with fewer artefacts by eye; that choice is not in the dandiset. The main channel is S1_Tr_R, and the per-animal channel with fewer artefact epochs is a variant." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4b-nrem-beta", "statement": "During NREM sleep Grin2b+/- rats have higher beta power than WT (two-way ANOVA genotype x band, interaction p = .038; Tukey beta p = .0008, other bands p >= .82).", "source": "Figure 4B", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "NREM beta is lower in Het (difference -0.078 normalized, Tukey p = 1.0); interaction p = 0.90. Every variant with both WT (GRIN2B-132 either way, contiguous bands, SWD epochs from flags, slope rejection, cleaner S1 channel, stored spectra) has Het beta lower, by 0.0035 to 0.30. With GRIN2B-238 left out Het beta is higher in 7 of 12 variants, by 0.0032 to 0.147, with Tukey p >= 0.99 and interaction p >= 0.92.", "deviations": [ "As for fig4a-rem-spectrum; two WT rats." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig4c-wake-power", "statement": "During wake, spectral power is reduced in Grin2b+/- rats overall, without a difference in single bands (two-way ANOVA genotype x band, genotype p = .01, interaction p = .86).", "source": "Figure 4C", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Normalized wake power is higher in Het on average (+0.081; genotype F = 0.58, p = 0.45), and higher on average in every variant on the raw EEG with both WT (+0.0065 to +0.168). The stored spectra have Het lower on average (-0.027, p = 0.59; p = 0.0072 only with GRIN2B-132 counted as WT), as does the cleaner S1 channel without GRIN2B-238 (-0.0072, p = 0.93).", "deviations": [ "As for fig4a-rem-spectrum; two WT rats." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-swd-state-distribution", "statement": "Over both genotypes, SWDs occur mostly in wake (94.8%), then NREM (4.4%), and rarely in REM sleep (0.5%).", "source": "Figure 5A; Results 3.5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Reading (a) gives wake 94.18%, NREM 5.55%, REM 0.27% over 16 rats with SWDs; wake is within tolerance and the order holds, NREM and REM are not. Reading (b) 92.87, 6.81, 0.32; (c) 91.17, 8.64, 0.19; (d) 89.27, 10.50, 0.23. Readings (c) and (d) follow the Supplementary Methods' rule. No reading puts all three within tolerance. Without GRIN2B-228 the values move by at most 0.6 percentage points.", "deviations": [ "The paper's text allows four readings of how the percentages are formed; all are shown.", "Two of the paper's nine WT rats; GRIN2B-132 is included." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5a-het-more-nrem-swds", "statement": "Compared with WT, Grin2b+/- rats have a higher share of SWDs in NREM and a lower share in wake (two-way ANOVA genotype x state, interaction p = .00008; Tukey NREM p = .0011, wake p = .0022).", "source": "Figure 5A", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Only one WT rat has SWDs (GRIN2B-240, 0% of its SWDs after NREM), and the paper's other seven WT rats are not in the dandiset, so the per-state comparison between genotypes cannot be tested under the claim's rule of two animals per group (also other, too few animals). As an illustration only, with GRIN2B-132 (no genotype) counted as WT, 6.30% of Het SWDs follow NREM against 0.23% in the two WT (interaction p = 0.013, Tukey NREM p = 0.29).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5c-transition-swds", "statement": "All Grin2b+/- rats have SWDs that start at wake-NREM transitions, against 3 of 9 WT rats (Fisher's exact test, p = .00062).", "source": "Figure 5C; Results 3.5", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "13 of 14 Het rats have at least one SWD at a wake-NREM transition, 0 of 2 WT; Fisher p = 0.025. GRIN2B-228 (2 SWDs in two days, none after NREM) has none. The claim's statement that all Het have such SWDs does not hold for GRIN2B-228; it may not be one of the paper's rats. Without GRIN2B-228 13 of 13 Het count (Fisher p = 0.0095), which would meet the criterion; the outcome is judged on all 16 rats.", "deviations": [ "The definition of a wake-NREM transition (a wake epoch followed by an NREM epoch within the six epochs before the SWD) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs5b-transition-percent", "statement": "In Grin2b+/- rats 24.2% of SWDs occur during the wake-NREM transition, similar to the 22.39% of the WT rats that have such SWDs (two-sample t test, p = .74).", "source": "Results 3.5; Figure S5B", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Reading (i), the share of NREM-initiated SWDs that are transitional, with an SWD initiated in NREM when any of the six epochs before it is NREM (the Supplementary Methods), gives 22.93% (SEM 1.97, 13 Het), within 24.2 +- 2.42. Reading (ii), the share of all SWDs, gives 2.23%. With NREM taken from the epoch before the SWD, the rule of the first criterion, reading (i) gives 36.31%. Leaving out GRIN2B-228 does not change reading (i). The claim's WT part is not tested, as no WT rat has transitional SWDs, so the WT value and the t test were not computed.", "deviations": [ "The denominator is not stated; two readings are shown.", "The criterion's NREM rule was corrected after verification round 1, once the analysis had been seen, to the six-epoch rule the Supplementary Methods state; the first rule gave 36.31%.", "The transition definition (a wake epoch followed by an NREM epoch within the six epochs before the SWD) was chosen here." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5f-swd-wake-correlation", "statement": "In Grin2b+/- rats, total SWD duration is negatively correlated with total time awake (Pearson, R = -.51, p = .048).", "source": "Figure 5F, left", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "R = -0.81, p = 0.0005 over 14 Het (-0.82 with GRIN2B-132, -0.73 without GRIN2B-228). With the scorer's flags R = -0.75; with the stored scores R = -0.06 (p = 0.83); with only the SWD time removed from wake R = -0.74 (p = 0.0024). The correlation arises from SWD time being taken out of wake. In Het the SWD epochs removed total 110.6 min per day against 57.8 min of SWD time.", "deviations": [ "14 Het, where the paper has 15." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig5def-no-other-correlations", "statement": "In Grin2b+/- rats, total SWD duration is not correlated with total REM or NREM time, the number of REM, NREM or wake bouts, or the mean REM, NREM or wake bout duration (Pearson, all p >= .066).", "source": "Figure 5D-F", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_hristova_2025.ipynb", "notes": "Two of the eight measures correlate with total SWD time, the number of wake bouts (R = 0.54, p = 0.046) and mean wake bout duration (R = -0.58, p = 0.028); the other six have p from 0.16 to 0.96. With the scorer's flags the same two correlate (R = 0.82, -0.72); with the stored scores, with bouts not split by SWD epochs or without GRIN2B-228 none does. The paper gives R = 0.17 and -0.25 for these two.", "deviations": [ "14 Het; the criterion grades eight tests (none significant reproduced, one or two partial)." ], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1c-glun2b-reduced", "statement": "GluN2B protein is reduced by about 50% in somatosensory cortex and hippocampus of Grin2b+/- rats (homogenate t test p = .000104; synaptosome Wilcoxon p = .00094).", "source": "Figure 1C; Figure S2C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The western blot quantification is not in the dandiset, which holds only EEG/EMG files, and the paper's data statement says raw data are available on request.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig1df-other-proteins-unchanged", "statement": "GluN2A, GluR1 and PSD95 expression are unchanged in Grin2b+/- rats.", "source": "Figure 1D-F; Figure S2D-F", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Western blot data not in the dandiset (see fig1c-glun2b-reduced).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs4-normal-development", "statement": "Grin2b+/- rats survive, grow and develop motor reflexes like WT littermates (survival 48% and 52%; body weight, righting reflex and negative geotaxis do not differ).", "source": "Results 3.2; Figure S4", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Survival, body weight, righting reflex and negative geotaxis measures are not in the dandiset or any public archive the paper names.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "figs1-scorer-agreement", "statement": "The automated sleep scorer agrees with visual scoring on 90.8% of epochs (Cohen's kappa 0.83).", "source": "Supplementary Methods; Table S1; Figure S1", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The visual scores of the 4-h validation periods are not in the dandiset; the files hold only the automated scores.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6b-systemic-etx-number", "statement": "Systemic ethosuximide reduces the number of SWDs relative to saline and memantine in both genotypes (linear mixed model, treatment p = .0049; ethosuximide-saline p = .0081).", "source": "Figure 6B", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The pharmacology recordings (2-channel EEG of 17 rats over baseline, treatment and washout days) are not in the dandiset, whose 17 files are 73 to 99 h recordings with the 14-channel grid, each holding two 24-h baseline windows. No other dandiset for this paper was found.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6c-systemic-duration", "statement": "Systemic ethosuximide and memantine reduce the mean SWD duration in Grin2b+/- rats but not in WT (treatment x genotype p = .044).", "source": "Figure 6C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Pharmacology recordings not in the dandiset (see fig6b-systemic-etx-number).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig6d-systemic-total", "statement": "Systemic ethosuximide reduces the total SWD duration in both genotypes (treatment p = .0011; ethosuximide-saline p = .0005).", "source": "Figure 6D", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "Pharmacology recordings not in the dandiset (see fig6b-systemic-etx-number).", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null }, { "claim": "fig7c-nrt-infusion", "statement": "Infusion of ethosuximide or memantine into the reticular thalamic nucleus reduces the number and total duration of SWDs in Grin2b+/- rats but not their mean duration.", "source": "Figure 7C", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The intrathalamic infusion recordings of 4 Grin2b+/- rats are not in the dandiset.", "deviations": [], "disagreed": false, "data": "dandiset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds 2 of the paper's 9 analysed wild type rats (14 or 15 of its 15 Grin2b+/-), so genotype comparisons rest on two WT, one of which has no SWDs. The pharmacology and intrathalamic infusion recordings (Figures 6, 7, S11, S12), western blots (Figures 1, S2, S3), development measures (Figure S4) and the visual scoring used to validate the scorer (Table S1) are not in it. The paper says raw data are available on request." }, { "kind": "metadata_insufficient", "statement": "GRIN2B-132 has no genotype and sex U, so it cannot be placed in either group. The conversion repository marks both as still to be confirmed by the lab." }, { "kind": "selection_undocumented", "statement": "The paper analysed 15 Grin2b+/- and 9 WT rats and excluded 4 and 9 descendants of one founder. The dandiset does not say which of its rats the paper analysed, and holds a Grin2b+/- rat (GRIN2B-228) with 1 SWD per day, unlike the paper's statement that all Grin2b+/- rats had SWDs at wake-NREM transitions." }, { "kind": "metadata_error", "statement": "The sleep_states description gives code 4 for SWD epochs, but no file holds code 4; the stored scores are the scorer's output before SWD epochs are set, so SWD epochs are scored as wake, NREM or REM." }, { "kind": "metadata_error", "statement": "swd_epoch_counts is described as the number of SWD events per 5-s epoch but holds the scorer's flags (6 for an SWD epoch, 4 otherwise). The flagged epochs cover a median of 51% (0 to 73%) of the epochs SWD events overlap, mostly the last epoch of each SWD, and only about a tenth of SWD onsets fall in a flagged epoch." }, { "kind": "metadata_error", "statement": "In seizure_totals_by_zt the per-hour SWD counts are in spike_wave_discharge, while number_of_seizure_events and Day hold the day's total in the first row and 0 elsewhere; the description itself marks the columns as unconfirmed." }, { "kind": "metadata_error", "statement": "sleep_state_power_spectra is described as a baseline-corrected PSD normalized to the average over states, with units to be confirmed. The lab's scorer writes the mean log10 multitaper amplitude referenced to each frequency's 5th percentile over the day, which is what the values (0 to about 1.6) fit; the paper's Welch spectra are not in the dandiset." }, { "kind": "format_error", "statement": "The raw EEG and EMG are stored as unsigned 12-bit codes with offset 0, so every channel reads about +8 mV of DC in volts. Signal loss is written as 32767 on all channels at once, and some files hold other values outside 0 to 4095; neither is described. In the windows read, 21 to 73% of 5-s epochs per rat contain such samples (73% for GRIN2B-238)." }, { "kind": "metadata_error", "statement": "The dandiset's assets summary counts 16 files and 16 subjects, while the draft holds 17 NWB files of 17 rats." }, { "kind": "code_mismatch", "statement": "The Methods exclude SWD times from the sleep states, while the lab's scorer replaces only the flagged epochs, which cover about half of the epochs SWD events overlap. The paper's wake results depend on this; with the stored scores (SWD epochs as wake) the wake bout differences reverse and the correlation of SWD time with wake time disappears." }, { "kind": "paper_inconsistency", "statement": "In the Figure 5 legend, NREM time gives T = -1.47 with R = -0.13 and df = 13, which implies T = -0.47; REM bouts give T = 0.704 with R = -0.19, of opposite sign; and REM bout duration and wake bouts have identical statistics (T = 0.61, R = 0.17, p = 0.55). The Figure 5A ANOVA gives genotype F = 1 with p = 0.98, which do not match for df = 1." }, { "kind": "paper_inconsistency", "statement": "The Figure 3 legend says no net differences between genotypes were observed for wake, while reporting a genotype effect on hourly wake time of F = 7.14, p = 0.014, and the Results say Grin2b+/- rats spent less time awake." }, { "kind": "metadata_insufficient", "statement": "The Supplementary Methods chose, by eye and per animal, the S1 EEG channel (left or right) and the EMG channel with fewer artefacts for sleep scoring; the dandiset does not record which channels were used." }, { "kind": "methods_unavailable", "statement": "The paper does not give its frequency band limits, Welch segment length, bout definition or the rule for wake-NREM transitions, and neither linked repository holds the statistics or figure code." } ], "verifications": [ { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper and its Supplementary Methods. The verifier had no attempt record and took its counts from the claims file. It gave its own outcome for each claim; all 34 agree with the record as it stood then. It checked the blocked claims against the archive's file list and metadata.", "agreed": 34, "of": 34, "disagreements": [] }, { "date": "2026-10-19", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file, the attempt record and the README, with the paper and its Supplementary Methods. The verifier agreed with all 34 outcomes, including the change of figs5b-transition-percent to reproduced, and found all round-1 points resolved. It found sentences the outputs did not support. The disc-het-swd-minutes conclusion said the paper's 59.97 min does not match the scorer's flags; cell 32 now prints the flagged epochs as 60.2 min, and the conclusion says the figure fits both. The fig4c range now ends at +0.168. The fig3d conclusion now says the outcome also holds with GRIN2B-132 counted as Het. The summary now names fig5def-no-other-correlations among the claims that would change without GRIN2B-228, and the fig3d interaction without GRIN2B-238. The README run time and the description of the recordings (73 to 99 h, each with two 24-h baseline windows) are corrected, as is the same description in the fig6b note and the claims-file comment. No outcome changed, and none is proposed to change.", "agreed": 34, "of": 34, "disagreements": [] } ] } ], "entries": [ { "name": "001888-hristova-2025", "type": "reproduction", "title": "Absence seizures and sleep in Grin2b+/- rats (Hristova, Fasol et al. 2025)", "description": "Tests the EEG findings of Hristova, Fasol et al. (2025) on dandiset 001888, which holds the 24-h wireless EEG and EMG recordings, sleep scores and SWD events of 14 Grin2b+/- rats, 2 wild type rats and one rat without genotype. It compares SWD number, duration and timing, sleep-wake amounts and bouts, state spectra computed from the raw EEG, the state in which SWDs start, and the correlation of SWD time with sleep measures. The western blots, development measures, visual scoring and pharmacology recordings of the paper are not in the dandiset.", "dandisets": [ "001888" ], "papers": [ "10.1111/epi.18606" ], "derived_from": [], "notebooks": [ { "path": "reproduce_hristova_2025.ipynb", "title": "Reproducing Hristova, Fasol et al. (2025) from dandiset 001888", "executed": "notebooks/001888-hristova-2025/reproduce_hristova_2025.html" } ] } ] }