Where the author or a verifier believed the claims file misread the paper, they asked, citing the paper, and a reader who had not seen the data answered from the paper alone, amending the claims file where it was wrong. The author then ran the claim as answered. Attempts before protocol pilot-11 also asked here for method details the claims file did not give.
Part (iii) of the criterion requires PAX6 to have the highest median initial firing rate (first_isi_inv_hero) of the four subclasses. The paper says PAX6 cells have a "high initial firing rate" and does not compare them with L1 VIP cells on this feature. Should (iii) be read as PAX6 above LAMP5 and MC4R, the subclasses the paragraph contrasts it with, in place of the highest of all four?
Passage. PAX6 cells had similar axons to LAMP5 cells, occasionally with descending branches, and sparse downward dendrites, along with minimal sag and high initial firing rate at the onset of response to depolarizing current injection (Fig. 2A-B). (Results, Morpho-electric diversity in human L1, paragraph 2)
Why it matters. The median initial firing rate is 49.3 Hz in PAX6 and 54.6 Hz in L1 VIP (Dunn FDR p 0.39 to 1 between them), so (iii) fails and the claim is not reproduced. PAX6 is above LAMP5 (about 32 Hz) and MC4R (about 29 to 31 Hz) with Dunn FDR p of 3.4e-5 or less, so under the narrower reading parts (i) to (iii) all hold and the claim would be reproduced.
The reader’s answer. Changed. The paper says PAX6 cells have "minimal sag and high initial firing rate at the onset of response to depolarizing current injection (Fig. 2A-B)" right after describing LAMP5 cells, and it nowhere ranks PAX6 above L1 VIP on this feature, so "highest of the four" read more into the text than it states. Part (iii) of the criterion now requires the PAX6 median first_isi_inv_hero to exceed those of LAMP5 and of MC4R, which keeps "high" as above most other subclasses without a comparison with L1 VIP that the paper does not make.
The criterion requires that "cells with more sag show less change of spike upstroke from the first to the third spike". The paper says only that spike adaptation properties show a "strong inverse relationship" with sag. With the upstroke adaptation ratio as third spike over first, the order that matches the paper's per-cell table, all ratios are below 1 and the slope on sag is negative, so cells with more sag have a larger fall of upstroke, which is more change. Should the direction part of the criterion be read as a negative slope of the ratio on sag (the inverse relationship the paper states), in place of less change with more sag?
Passage. Spike adaptation properties showed a strong inverse relationship with sag across the dataset (Fig. S3A). (Results, Morpho-electric diversity in human L1, paragraph 1); Trendline from linear regression (right) with shading showing bootstrapped 95% CI (R2=0.74, p<10-13). (Fig. S3 legend, panel A)
Why it matters. The slope is -0.61 on the features computed here and -0.64 on the paper's values, so the direction holds under the paper's words and fails under the criterion's. It cannot change the outcome of this attempt, which fails on R2 (0.33 and 0.36 against 0.74 +/- 0.074), but a later attempt that matched R2 would be judged on the direction.
No reader has answered it yet.
The criterion blocks the claim as data_missing when the dandiset does not hold the held-out Amsterdam and Szeged cells. DANDI 000228 (version 0.260829.2040, contributors include Chartrand, Tamas and Molnar) holds 91 Szeged files from the donors of 15 of the 17 held-out Szeged cells, and DANDI 000337 (version 0.260917.2218, Mansvelder lab) holds 21 Amsterdam files. Neither is cited by the paper. Should the claims file name them as outside inputs for this claim, with a link claim that matches their files to the held-out cells?
Passage. After excluding features for which the distributions strongly differed from the primary dataset, we found comparable classification performance (81%, Fig. S8B) (Results, Cross-modality relationships of L1 subclasses and t-types, paragraph 2)
Why it matters. The 000228 file paths carry no session id (subjects are named by donor), so a link would have to match their features to the paper's tamas_features_E.csv within each donor; none of the 9 held-out Amsterdam cells has its LIMS session id among the 000337 files. If the files can be linked, the Szeged half of the held-out test could be run, and the claim would no longer be blocked as data_missing.
No reader has answered it yet.
The criterion requires the median first_isi_inv_hero of the mouse Lamp5 Krt73 cells to exceed that of every other mouse subclass, L1 VIP included. The paper says only that these cells "tended to fire in doublets at stimulus onset" and does not compare their initial firing rate with L1 VIP cells. Should the doublet part be read as Lamp5 Krt73 above LAMP5 and MC4R, the comparison a reader adopted for part (iii) of fig2b-subclass-ephys-profiles, in place of above every other subclass?
Passage. In mouse L1, the homologous PAX6 subclass was extremely rare, comprising only a few cells in the Lamp5 Krt73 t-type. These cells tended to fire in doublets at stimulus onset ... sometimes followed by a delayed ADP (Fig. 5C). (Results, Bursting PAX6 TNFAIP8L3 cells, paragraph 2)
Why it matters. The Lamp5 Krt73 median initial firing rate is 97.7 Hz (two cells with a value), above LAMP5 (20 Hz) and MC4R (26 Hz) but below L1 VIP (171 to 177 Hz), so the claim fails only on the comparison with L1 VIP and is not reproduced. The depolarizing sag ratio part holds. Under the narrower reading both parts hold and the claim would be reproduced.
No reader has answered it yet.
The criterion requires sag and first_isi_inv_hero each to have FDR p < 0.001 in the code's run_correlations test (cell 59, filter_dropouts=False, Benjamini-Hochberg across features). On the paper's own per-cell values this test gives sag FDR p = 0.0020 over the 96 Seattle LAMP5 cells and 0.0039 with the 14 Amsterdam and Szeged cells added. Does the criterion prescribe the test that produced the paper's "p<10−3" (for example the cell set, the features corrected over, or the dropout filter), or should sag be read under a different test?
Passage. Within the LAMP5 subclass, sag and initial firing rate decreased from the NMBR t-type to DBP to LCP2 t-types (Fig. 2C: strip plots within boxplot; Spearman correlation FDR-corrected p<10−3). (Results, Morpho-electric diversity in human L1, paragraph 2)
Why it matters. Raised by the round-3 verifier. Sag fails the threshold under every reading, including the paper's own values, so either the criterion's method differs from what produced the paper's statement or the statement does not hold for sag. The claim is not reproduced on the criterion as written.
No reader has answered it yet.
The criterion tests "the only within-subclass pair with high d' is LAMP5 NMBR against LAMP5 LCP2" on the electrophysiological d' matrix alone. In the paper the sentence follows the cross-modality comparison (Fig. 6B). Should it be read as referring to the transcriptomic matrix, or to both matrices, in place of the electrophysiological one alone?
Passage. Of note, d’ metrics were highly correlated between modalities ... (Pearson r=0.59, p=0.00016; Fig. 6B). The single within-subclass pair with a high d’ was LAMP5 NMBR and LAMP5 LCP2, which sit at opposite ends of the LAMP5 continuum. (Results, Cross-modality relationships of L1 subclasses and t-types, paragraph 1)
Why it matters. Raised by the round-3 verifier. On the electrophysiological matrix the claim fails under the criterion's second reading of high (above the median between-subclass d', 2.40 to 2.62), where no within-subclass pair is high, NMBR against LCP2 included (2.39). If the sentence is about the transcriptomic matrix, this part of the claim would need the transcriptomic d', which the dandiset does not hold.
No reader has answered it yet.