{
 "dandiset": "001528",
 "page": "dandisets/001528/",
 "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": 12,
  "partially_reproduced": 5,
  "not_reproduced": 3,
  "blocked": 5
 },
 "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": "001528-hadjas-2025-01",
   "dandiset": "001528",
   "dandiset_version": "draft",
   "paper": "10.1101/2025.06.03.657460",
   "paper_title": "Parkinson\u2019s Disease-vulnerable and -resilient dopamine neurons display opposite responses to excitatory input",
   "date": "2026-10-18",
   "kind": "agent",
   "accountable": "CatalystNeuro",
   "agent": {
    "harness": "Claude Code (GitHub Actions)",
    "model": "claude-opus-5-5",
    "protocol": "pilot-7"
   },
   "tier": "agent_verified",
   "entry": "001528-hadjas-2025",
   "entry_title": "Responses of SNr GABA and SNc dopamine neuron subtypes to STN and PPN input (Hadjas et al. 2025)",
   "description": "Tests the mouse fiber photometry findings of Hadjas et al. (2025) on dandiset 001528, which holds recordings from 120 mice during optogenetic stimulation of STN or PPN inputs to the substantia nigra. It compares responses of SNr GABA neurons, SNc pan-DA neurons, striatal dopamine release in TS and DLS, DA terminals, and Vglut2+ and Anxa1+ DA neurons across train durations and frequencies, using the lab's dF/F stored in the files. The human tissue counts of Figure 1 are not in the dandiset.",
   "notebooks": [
    {
     "path": "reproduce_hadjas_2025.ipynb",
     "title": "Reproducing Hadjas et al. (2025) from dandiset 001528",
     "executed": "notebooks/001528-hadjas-2025/reproduce_hadjas_2025.html"
    }
   ],
   "outcomes": [
    {
     "claim": "cohort-sizes",
     "statement": "The number of mice per experimental group is as given in the figure legends; SNr GABA neurons STN 7 and PPN 8 (Figure 2); SNc pan-DA neurons STN 11 and PPN 9 (Figure 3); GRAB-DA in TS and DLS, STN 6 and 7, PPN 9 and 9 (Figure 4); DA terminals in TS and DLS with STN stimulation, 9 and 9 (Figure S3); Vglut2+ DA neurons STN 10 and PPN 10, Anxa1+ terminals in DLS STN 8 and PPN 10 (Figure 5); Anxa1+ cell bodies in SNc STN 5 and PPN 4 (Figure S4).",
     "source": "Legends of Figures 2 to 5, S3 and S4",
     "outcome": "not_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "10 of 16 counts match. SNr GABA, pan-DA and GRAB-DA groups match exactly, as do DA terminals in TS and Vglut2 with PPN. DA terminals in DLS have 8 mice (paper 9) and Vglut2 with STN 9 (paper 10). The Anxa1 groups have DLS recordings for 5 (STN) and 4 (PPN) mice against the paper's 8 and 10, and SNc recordings for 8 and 10 against 5 and 4. All four Anxa1 counts would match if the nine recordings without a site suffix were DLS recordings; their signals resemble the SNc recordings, and the paper's cell-body statistics are matched by the dual mice's SNc recordings alone, so the DLS recordings of those nine mice appear to be missing. For Vglut2 STN the paper's own Wilcoxon statistics fit 9 mice (W = 41, 43, -5 give exact p = 0.0117, 0.0078, 0.82 with n = 9, the paper's values, and 0.037, 0.027, 0.85 with n = 10), so the legend's 10 is likely an error; counted that way 11 of 16 match, still below 12.",
     "deviations": [
      "Counted from the durations protocol; the frequencies protocol gives the same counts."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig2-gaba-excited",
     "statement": "Optogenetic stimulation of STN or PPN inputs increases SNr GABA neuron activity (paired t-test on the 1 s train, STN t = 3.8, p = 0.008; PPN t = 9.2, p < 0.0001).",
     "source": "Results, second section; Figure 2B and 2E with insets",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "1 s 40 Hz trains, mean during the train against the 1 s before onset. STN mean 18.89 % dF/F, paired t = 3.86, p = 0.0083, n = 7 (paper t = 3.8, p = 0.008); PPN 6.45 %, t = 9.19, p = 3.7e-05, n = 8 (paper t = 9.2). The 0.25 and 4 s trains also give significant increases (p 1.4e-05 to 0.0066).",
     "deviations": [
      "The response window (mean during the train) and pre-stimulus window (same length, before onset) are choices; the paper does not state them.",
      "All seven STN mice have 10 trials per condition, where the Methods state 5."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig2-gaba-frequency",
     "statement": "The SNr GABA response scales with stimulation frequency from 5 to 40 Hz (Friedman test on 1 s trains, STN F = 21.0, p = 0.0001; PPN F = 18.2, p = 0.0004).",
     "source": "Results, second section; Figure 2C and 2F",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "1 s trains of the frequencies protocol. STN means rise from 4.07 to 32.66 % between 5 and 40 Hz, Friedman 21.00, p = 0.00011, 7 of 7 mice higher at 40 than 5 Hz; PPN 1.57 to 6.10 %, Friedman 18.15, p = 0.00041, 8 of 8 (paper 21.0 and 18.2). A repeated-measures ANOVA variant gives p = 0.014 and 0.0001.",
     "deviations": [
      "The conversion code names the STN 1 s block of these mice as 10 mW, while the files and the Methods give 5 mW; the analysis takes the files as they are."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig3b-da-stn-250ms-peak",
     "statement": "A 250 ms 40 Hz train of STN inputs elicits a net increase in SNc pan-DA neuron activity that peaks after stimulus offset (latency to peak 0.50 +/- 0.03 s, mean +/- SEM).",
     "source": "Results, third section; Figure 3B",
     "outcome": "partially_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "With the window fixed in the criterion (peak from onset to 2.25 s) the mean latency is 0.786 s, SEM 0.204, n = 11, outside 0.50 +/- 0.03 s, because two mice peak at 2.03 and 2.24 s. Ten of 11 mice peak after offset and the net response over 0 to 1.25 s is positive (2.89 %, t = 3.28, p = 0.0083). With a window ending at 1.25 s, a variant, the mean latency is 0.492 s, SEM 0.033, the paper's value. The two late-peaking mice (C4217, B8612) have small responses, an early local maximum at 0.41 and 0.62 s, and a slow rise that continues past the window (maximum over 0 to 5 s at 2.97 and 2.78 s), which looks like a late rebound or drift.",
     "deviations": [
      "The paper does not give the window in which the peak is sought; the criterion fixed 0 to 2.25 s, and the variant 0 to 1.25 s matches the paper."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig3c-da-stn-duration",
     "statement": "For SNc pan-DA neurons the STN-evoked response varies with train duration; with 1 and 4 s trains an initial increase is followed by inhibition (Friedman test, F = 13.0, p = 0.005).",
     "source": "Results, third section; Figure 3B and 3C",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "Means during 0.25, 1 and 4 s trains are 0.52, 0.97 and -3.13 %, n = 11. Reading (a), Friedman over three durations, 13.64, p = 0.0011; reading (b), with the pre-stimulus window as a fourth group, 12.93, p = 0.0048, matching the paper's F = 13.0, p = 0.005; reading (c), area under the curve, p = 0.06. In 4 s trains the first 0.5 s (0.71 %) is above the last 1 s (-5.05 %) in all 11 mice, paired t = 4.81, p = 0.00071.",
     "deviations": [
      "The paper's F and p fit four groups while three durations were tested; readings (a) and (b) match, and (b) gives the paper's value."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig3d-da-stn-frequency-ns",
     "statement": "The amplitude of the SNc pan-DA response during STN stimulation does not scale with frequency (Friedman test, F = 4.2, p = 0.24).",
     "source": "Results, third section; Figure 3D",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "1 s trains, Friedman 4.20, p = 0.24, n = 11 (paper F = 4.2, p = 0.24); 40 minus 5 Hz 0.21 % dF/F. Variants with 0.25 s (p = 0.31) and 4 s trains (p = 0.18, 5 mice with all four frequencies) also find no effect.",
     "deviations": [
      "The paper does not say which train duration Figure 3D shows; the 1 s train was fixed in the criterion."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig3g-da-ppn-duration",
     "statement": "PPN stimulation also evokes SNc pan-DA responses that vary with train duration (Friedman test, F = 11.5, p = 0.009).",
     "source": "Results, third section; Figure 3F and 3G",
     "outcome": "not_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "Means during 0.25, 1 and 4 s PPN trains are -0.60, 1.03 and 0.70 %, n = 9. Friedman p = 0.26, 0.25 and 0.46 under readings (a) to (c), where the paper reports F = 11.5, p = 0.009. Without the three PPN recordings whose clock could not be shown from the response (C3164, C5007, C5008), n = 6, readings (a) and (b) give p = 0.11 and 0.14.",
     "deviations": [
      "The paper's measure for this comparison is not stated; the mean during the train (and the area under the curve) were used, as for the STN comparison, which matches the paper there."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig3h-da-ppn-frequency-ns",
     "statement": "The SNc pan-DA response to PPN stimulation does not vary with frequency (repeated-measures one-way ANOVA, F2,15 = 1.35, p = 0.28).",
     "source": "Results, third section; Figure 3H",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "1 s trains, repeated-measures ANOVA F = 1.35 on Greenhouse-Geisser corrected df 1.85 and 14.8, p = 0.29, n = 9 (paper F2,15 = 1.35, p = 0.28); 40 minus 5 Hz 1.30 %. Variants with 0.25 and 4 s trains give p = 0.83 and 0.32.",
     "deviations": [
      "The 1 s train was fixed in the criterion, as the paper does not name the duration."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig4cf-ts-dls-opposite",
     "statement": "STN or PPN stimulation evokes opposite DA release in TS (increase) and DLS (decrease) (two-way ANOVA, striatal site, STN F1,11 = 40.9, PPN F1,16 = 36.4, p < 0.0001; site by time interaction of the same size).",
     "source": "Results, fourth section; Figure 4C and 4F",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "GRAB-DA, 1 s 40 Hz trains. STN, TS 12.45 % (6 of 6 above 0), DLS -8.91 % (7 of 7 below 0), site by time interaction F(1, 11) = 40.9, p = 5.1e-05; PPN, TS 11.39 % (9 of 9), DLS -5.75 % (9 of 9), F(1, 16) = 36.4, p = 1.7e-05, the paper's values. The 0.25 and 4 s trains give the same pattern.",
     "deviations": [],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig4dg-ts-frequency",
     "statement": "In TS, the DA increase evoked by either input scales with frequency, for all train durations (STN, repeated-measures ANOVA, 0.25 s F2,8 = 7.5, 1 s F2,7 = 13.6, 4 s F2,9 = 16.9; PPN, Friedman, F = 20.0, 24.0, 23.2).",
     "source": "Results, fourth section; Figure 4D and 4G; Figure S3C, S3D, S3I and S3J",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "All six tests hold, with the 40 Hz mean above the 5 Hz mean. STN repeated-measures ANOVA F = 7.62, 13.76, 17.31 for 0.25, 1 and 4 s (p = 0.019, 0.0044, 0.0011; paper 7.5, 13.6, 16.9); PPN Friedman 19.80, 24.33, 23.27 (p at most 0.0002; paper 20.0, 24.0, 23.2).",
     "deviations": [],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig4eh-dls-frequency",
     "statement": "In DLS, the DA inhibition scales with frequency and is most prominent at higher frequencies (STN, repeated-measures ANOVA, 0.25 s F = 7.5, 1 s F = 12.8, 4 s F = 46.8; PPN, 0.25 s Friedman F = 12.3, 1 s and 4 s repeated-measures ANOVA F = 12.8 and 10.2).",
     "source": "Results, fourth section; Figure 4E and 4H; Figure S3E, S3F, S3K and S3L",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "All six tests hold, with the 40 Hz mean below the 5 Hz mean (p below 0.0001 to 0.013). STN 0.25 and 4 s F = 7.89 and 47.23 (paper 7.5, 46.8); PPN 0.25 s Friedman 11.53 (paper 12.3), PPN 1 and 4 s F = 12.98 and 15.92 (paper 12.8, 10.2). STN 1 s gives F = 26.17 where the paper gives F1,11 = 12.8, p = 0.0005, the same F and df it gives for PPN 1 s.",
     "deviations": [],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig4eh-dls-5hz-increase",
     "statement": "Low-frequency (5 Hz) stimulation of either STN or PPN increases DLS dopamine.",
     "source": "Results, fourth section; Figure 4E and 4H; Figure S3F and S3L",
     "outcome": "not_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "1 s trains at 5 Hz (Figure 4E and 4H), mean GRAB-DA in DLS during the train, STN 1.51 % (4 of 7 above 0, p = 0.22), PPN 1.40 % (6 of 9, p = 0.13). The sentence also cites Figure S3F and S3L, the 4 s DLS panels; for 4 s trains, a variant, STN 5.41 % (7 of 7, p = 0.00062) and PPN 2.01 % (6 of 9, p = 0.07), one input of two, which would be partially reproduced under that reading. The 1 s after offset is positive in all six conditions (0.96 to 6.76 %).",
     "deviations": [
      "The paper does not state the window or test for this observation; the mean during 1 s trains (Figure 4E and 4H) against 0 was fixed in the criterion. The sentence cites both the 1 s panels and the 4 s panels (Figure S3F and S3L), and its account of summation over pulses fits longer trains; under the 4 s reading the effect holds for STN only."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig4cf-dls-rebound",
     "statement": "In DLS the DA inhibition is followed by a post-stimulus rebound above baseline.",
     "source": "Results, fourth section; Figure 4C and 4F",
     "outcome": "partially_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "After 1 s 40 Hz trains, PPN 4.53 % (8 of 9 above 0, p = 0.017), STN 0.87 % (5 of 7, p = 0.29). After 0.25 and 4 s trains the rebound is significant for both inputs (p 0.0039 to 0.015).",
     "deviations": [
      "The rebound window (1 s after offset) and test are choices; the paper gives no statistic."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "figs3-terminals-opposite",
     "statement": "Calcium in DA terminals in TS and DLS shows opposite responses to STN stimulation, as the GRAB-DA recordings do.",
     "source": "Results, fourth section; Figure S3N and S3O",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "DA terminal GCaMP, 1 s trains, TS 8.96 % (9 of 9 above 0), DLS -4.41 % (7 of 8 below 0), site by time interaction F(1, 15) = 26.2, p = 0.00013. The DLS terminals rebound after offset (6.73 %, 8 of 8 above 0).",
     "deviations": [
      "8 DLS mice, where the paper has 9."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig5-vglut2-excited",
     "statement": "Stimulation of STN or PPN inputs increases the activity of Vglut2+ DA neurons in SNc (STN, Wilcoxon, 0.25 s W = 41, p = 0.012, 1 s W = 43, p = 0.008, 4 s W = -5, p = 0.82; PPN, paired t-test, 0.25 s t = 2.9, p = 0.02, 1 s t = 3.4, p = 0.008, 4 s t = 3.0, p = 0.01).",
     "source": "Results, fifth section; Figure 5B, 5C, 5G and 5H; Figure S4A and S4D",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "STN Wilcoxon W = 43 and 43 for 0.25 and 1 s (p = 0.0078 each, n = 9; paper 41 and 43); PPN paired t = 2.89 and 3.42 (p = 0.018 and 0.0076, n = 10; paper 2.9 and 3.4). For 4 s trains STN W = -5, p = 0.82 as in the paper, and PPN t = 2.56, p = 0.031 (paper 3.0, p = 0.01).",
     "deviations": [
      "9 STN mice, where the legend gives 10; the paper's W and p values are the exact values for 9 mice."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig5-vglut2-frequency",
     "statement": "The Vglut2+ DA neuron increase scales with frequency for short STN trains and for all PPN durations (Friedman, STN 0.25 s F = 15.5, p = 0.001, 1 s F = 5.9, p = 0.11, 4 s F = 7.0, p = 0.07; PPN F = 18.8, 24.8, 20.2, p <= 0.0003).",
     "source": "Results, fifth section; Figure 5D, 5E, 5I and 5J",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "STN 0.25 s Friedman 13.53, p = 0.0036; PPN 0.25, 1 and 4 s 11.23, 17.91, 16.20 (p = 0.011, 0.0005, 0.0010), all with the 40 Hz mean above the 5 Hz mean. STN 1 and 4 s are not significant (p = 0.43 and 0.16), as in the paper (0.11 and 0.07).",
     "deviations": [
      "The PPN tests use the 7 of 10 mice that have all four frequencies; C3412, C3798 and C4707 have no 5 Hz trains in the dandiset. The paper's PPN 1 s Friedman statistic of 24.8 needs at least 9 mice (the maximum is 3n), so the paper had 5 Hz trains that are not deposited."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig5-anxa1-dls-inhibited",
     "statement": "In DLS terminals of SNc Anxa1+ neurons, STN and PPN stimulation produce inhibition (STN, 0.25 s t = 6.4, p = 0.0004, 1 s W = -36, p = 0.005, 4 s W = -36, p = 0.008; PPN, 0.25 s t = 3.9, p = 0.004, 1 s W = -55, p = 0.002, 4 s t = 3.8, p = 0.004).",
     "source": "Results, fifth section; Figure 5L, 5M, 5Q and 5R; Figure S4B and S4E",
     "outcome": "blocked",
     "blocked_by": "data_missing",
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "The dandiset holds Anxa1 DLS recordings for 5 (STN) and 4 (PPN) mice where the paper has 8 and 10. At these numbers the Wilcoxon tests the paper uses for three of the six conditions cannot reach p < 0.05 (smallest p 0.0625 and 0.125), so reproduced (6 of 6) cannot be reached with the deposited mice. The three t-tests can reach it, so partially reproduced (3 to 5 of 6) was reachable and was not reached; 2 of 6 tests are significant (STN 0.25 s t = -6.14, p = 0.0036; PPN 0.25 s t = -3.46, p = 0.041; PPN 4 s p = 0.13). No STN mouse goes up in any condition, and one PPN mouse in 4 s trains. With the nine recordings without a site suffix added to DLS, a variant, all 6 tests are significant. Its STN 4 s W = -36 (p = 0.0078) is the paper's, but the other two W (-34 and -51 against -36 and -55) and the t values (2.65, 2.47, 2.98 against 6.4, 3.9, 3.8) differ, while the cell-body statistics match closely with the dual mice (p to two digits, t within 0.08). The paper's statistics fix its n; W = -36 and -55 equal -n(n+1)/2 for n = 8 and 10, and t = 6.4 with p = 0.0004 needs 7 df (4 df give p = 0.0031). The DLS recordings of nine of the paper's mice are not in the dandiset.",
     "deviations": [],
     "disagreed": true,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig5-anxa1-dls-frequency",
     "statement": "The Anxa1+ terminal inhibition scales with frequency (STN, 0.25 s F = 18.0, 1 s F = 15.5, 4 s F = 15.3; PPN, 0.25 s F = 11.5, 1 s F2,15 = 11.0, 4 s F2,18 = 7.2).",
     "source": "Results, fifth section; Figure 5N, 5O, 5S and 5T",
     "outcome": "partially_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "With the dandiset's DLS recordings (5 STN, 4 PPN mice) 5 of 6 tests hold (p 0.0043 to 0.026, 40 Hz below 5 Hz); PPN 4 s does not (F = 1.95, p = 0.24). With the unsuffixed recordings added, 3 of 6 hold. The paper's F2,15 and F2,18 for PPN 1 and 4 s imply about 8.5 and 10 mice (6.8 to 13.3 with the dfs rounded), against 4 here, so the samples are smaller than the paper's for the reason given under fig5-anxa1-dls-inhibited.",
     "deviations": [
      "5 and 4 mice, where the paper has 8 and 10 (see fig5-anxa1-dls-inhibited)."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig5-anxa1-dls-rebound",
     "statement": "Anxa1+ terminals in DLS show a transient increase in activity at stimulus offset, for both inputs.",
     "source": "Results, fifth section; Figure 5L and 5Q",
     "outcome": "partially_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "After 1 s trains, STN 1.02 % (5 of 5 above 0, p = 0.0044), PPN 0.57 % (3 of 4, p = 0.14). The 0.25 and 4 s trains give the same picture (STN p = 0.036 and 0.026, PPN p = 0.20 and 0.11).",
     "deviations": [
      "5 and 4 mice, where the paper has 8 and 10.",
      "The rebound window (1 s after offset) and test are choices; the paper gives no statistic."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "figs4-anxa1-soma-inhibited",
     "statement": "Anxa1+ SNc cell bodies show stimulation-induced inhibition (paired t-test, STN 0.25 s t = 3.1, 1 s t = 4.0, 4 s t = 7.2, n = 5; PPN t = 4.8, 8.4, 3.3, n = 4) followed by post-stimulus rebound activation.",
     "source": "Results, fifth section; Figure S4C and S4F",
     "outcome": "partially_reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "With all SNc-labelled recordings (8 STN, 10 PPN mice) 5 of 6 tests show a significant decrease (p 0.0003 to 0.014); STN 0.25 s does not (t = -1.56, p = 0.16). Restricted to the mice with both a DLS and an SNc file (5 and 4, the paper's n), a variant, all 6 are significant with the paper's statistics (t = 3.13, 3.98, 7.26, 4.72, 8.35, 3.33 against 3.1, 4.0, 7.2, 4.8, 8.4, 3.3). The statement's post-stimulus rebound is not seen in the cell bodies after 1 s trains (STN -0.08 %, PPN 0.03 %, p = 0.65 and 0.80; dual mice p = 0.53 and 0.16).",
     "deviations": [
      "The dandiset labels 8 and 10 mice as SNc where the paper analysed 5 and 4; the outcome uses the dandiset's labels as fixed in the criterion."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig5-opposite-subtypes",
     "statement": "Excitatory inputs from STN and PPN activate PD-resilient Vglut2+ DA neurons but inhibit PD-vulnerable Anxa1+ DA neurons.",
     "source": "Title; Abstract; Results, fifth section; Figure 5",
     "outcome": "reproduced",
     "blocked_by": null,
     "notebook": "reproduce_hadjas_2025.ipynb",
     "notes": "1 s 40 Hz trains. STN, Vglut2 6.54 % against Anxa1 DLS -1.73 % (Welch t = 3.56, p = 0.0066); PPN 9.35 % against -1.48 % (t = 3.90, p = 0.0032). It holds with the unsuffixed Anxa1 recordings added to DLS (p = 0.0097 and 0.005) and against the Anxa1 SNc recordings (p = 0.017 and 0.0065).",
     "deviations": [
      "Anxa1 DLS recordings of 5 and 4 mice, where the paper has 8 and 10."
     ],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig1de-th-anxa1-reduced",
     "statement": "In human SNc, TH+ neurons (Mann-Whitney U = 2.0, p = 0.002) and TH+/ANXA1+ neurons (U = 1.0, p < 0.0001) are fewer in PD cases (n = 7) than in controls (n = 12).",
     "source": "Results, first section; Figure 1D and 1E",
     "outcome": "blocked",
     "blocked_by": "data_missing",
     "notebook": null,
     "notes": "The human RNAscope counts are not in the dandiset, which holds mouse photometry only. The preprint has no data availability statement, and the dandiset metadata and the conversion repository link no other deposit.",
     "deviations": [],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "fig1f-anxa1-de-enriched",
     "statement": "Among remaining DA neurons in PD, ANXA1+ neurons are de-enriched to 10 +/- 7% of control, ALDH1A1+ to 41 +/- 12%, while CALB1+ neurons trend toward enrichment (301 +/- 103%).",
     "source": "Results, first section; Figure 1F",
     "outcome": "blocked",
     "blocked_by": "data_missing",
     "notebook": null,
     "notes": "Human tissue counts are not in the dandiset nor in any deposit the paper or the dandiset names (see fig1de-th-anxa1-reduced).",
     "deviations": [],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "figs1-calb1-aldh1a1-counts",
     "statement": "TH+/CALB1+ neuron counts are not significantly changed in PD (U = 19.5, p = 0.08) while TH+/ALDH1A1+ counts are reduced (U = 1.0, p < 0.0001).",
     "source": "Results, first section; Figure S1B to S1F",
     "outcome": "blocked",
     "blocked_by": "data_missing",
     "notebook": null,
     "notes": "Human tissue counts are not in the dandiset nor in any deposit the paper or the dandiset names (see fig1de-th-anxa1-reduced).",
     "deviations": [],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    },
    {
     "claim": "figs1-if-aldh1a1",
     "statement": "Immunofluorescence confirms fewer TH+ and TH+/ALDH1A1+ neurons and a lower fraction of TH+ neurons expressing ALDH1A1 in PD (n = 11) than in controls (n = 15), and counts agree with RNAscope in four cases processed both ways.",
     "source": "Results, first section; Figure S1G to S1J",
     "outcome": "blocked",
     "blocked_by": "data_missing",
     "notebook": null,
     "notes": "Human immunofluorescence counts are not in the dandiset nor in any deposit the paper or the dandiset names (see fig1de-th-anxa1-reduced).",
     "deviations": [],
     "disagreed": false,
     "data": "dandiset",
     "where": null,
     "proposed": null
    }
   ],
   "findings": [
    {
     "kind": "data_missing",
     "statement": "For the Anxa1 mice the dandiset holds DLS terminal recordings for 5 (STN) and 4 (PPN) mice where the paper analyses 8 and 10. Nine mice (C5903, C5906, C5992, C6900, C6902, C7244, C7245, C7248, C7249) have only recordings labelled SNc, without a site suffix in the file name. Their signals resemble SNc recordings, and the paper's cell-body statistics are reproduced closely by the other nine mice's SNc recordings (p to two digits, t within 0.08), so the DLS recordings of these nine mice appear not to be deposited, and the nine SNc recordings were not used in the paper."
    },
    {
     "kind": "selection_undocumented",
     "statement": "The dandiset includes Anxa1 SNc recordings from nine mice that the paper's cell-body analysis (n = 5 and 4) leaves out, and it does not say which recordings the paper used."
    },
    {
     "kind": "data_missing",
     "statement": "The human RNAscope and immunofluorescence counts of Figure 1 and Figure S1 and the histology of Figure S2 are not in the dandiset, and the preprint has no data availability statement."
    },
    {
     "kind": "data_missing",
     "statement": "DA terminals in DLS have 8 mice where Figure S3 gives 9."
    },
    {
     "kind": "paper_inconsistency",
     "statement": "The Figure 5 legend gives 10 mice for Vglut2+ neurons with STN stimulation, while the paper's Wilcoxon statistics (W = 41, 43, -5 with p = 0.012, 0.008, 0.82) are the exact values for 9 mice; the dandiset holds 9."
    },
    {
     "kind": "data_missing",
     "statement": "Three Vglut2 PPN mice (C3412, C3798, C4707) have no 5 Hz trains in their frequencies sessions, while the paper's Friedman statistic for PPN 1 s (24.8) needs at least 9 mice with all four frequencies."
    },
    {
     "kind": "data_missing",
     "statement": "Subject C4608 (SNr GABA, PPN) has no 4 s trains in its frequencies session; the conversion notes say they were recorded in a separate session, which is not in the dandiset."
    },
    {
     "kind": "metadata_error",
     "statement": "The dF/F series are stated in a.u. but hold percent (100 times (Gc - fit) / fit); a recomputation from the stored signals agrees with a median correlation of 0.9999 (durations) and 0.9988 (frequencies)."
    },
    {
     "kind": "metadata_error",
     "statement": "Every session start time carries the offset -00:01, the local mean time of London that pytz gives when a time zone is attached with replace; the true offset is lost."
    },
    {
     "kind": "metadata_error",
     "statement": "The session description of the frequencies protocol gives an interval of 10 s between trains; the epochs and the Methods give 20 s."
    },
    {
     "kind": "other",
     "statement": "Thirteen mice (SNr GABA and pan-DA, ids starting with B) have 10 trials per condition where the Methods state 5, and 30 mice have 16 s trains that the paper does not mention."
    },
    {
     "kind": "code_mismatch",
     "statement": "The conversion code names the 1 s block of the STN to SNr GABA frequencies sessions s1s10mW, suggesting 10 mW, while the epoch tables and the Methods give 5 mW."
    },
    {
     "kind": "code_mismatch",
     "statement": "The conversion repository's Python re-implementation of the dF/F forces the robust fit through the origin, saying the MATLAB version does so, while its own description of the MATLAB scripts includes an intercept."
    },
    {
     "kind": "metadata_error",
     "statement": "The files describe the modulation inconsistently. The excitation source descriptions give 465 nm modulated at 210 Hz and 405 nm at 330 Hz, as the Methods do, while the processed series descriptions give the calcium signal as demodulated at 330 Hz and the isosbestic signal at 210 Hz, as the conversion repository's description of the MATLAB scripts does. This attempt did not check which is right against the raw signal."
    },
    {
     "kind": "metadata_insufficient",
     "statement": "The file names and session ids of nine Anxa1 mice carry no recording site, and every Anxa1 file lists both an SNc and a DLS fiber in its fiber photometry table, so the site rests on the name of the dF/F series alone."
    },
    {
     "kind": "other",
     "statement": "Eight subject ids are written in lower case (c3015, c3016, c4379, c4708, c4709, c4977, c4978, c5113) while the others are upper case."
    },
    {
     "kind": "paper_inconsistency",
     "statement": "The Results give F1,11 = 12.8 for the DLS frequency effect with 1 s trains for both STN (p = 0.0005) and PPN (p = 0.002); F(1, 11) = 12.8 gives p = 0.0043, and the data give F = 26.2 for STN. Two Friedman entries for Anxa1 terminals also do not fit their p-values (F = 11.5 with p = 0.0002, F = 15.5 with p = 0.015; with 3 df these give 0.0093 and 0.0014). F1,11 is also not possible for a one-way repeated-measures ANOVA in 7 or 9 mice. The Figure 5 legend says the Anxa1 STN frequency panels (N, O) show no significant effect of frequency, while the Results report significant effects for all three STN durations."
    },
    {
     "kind": "methods_unavailable",
     "statement": "The lab's MATLAB analysis scripts are not public; the preprint names custom MATLAB code and has no code availability statement. The conversion repository describes them."
    },
    {
     "kind": "other",
     "statement": "The dandiset has no published version; this attempt used the draft as modified on 2026-09-01T15:27:47Z."
    }
   ],
   "verifications": [
    {
     "date": "2026-10-18",
     "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. The verifier queried the archive's asset list and metadata and tested the helper functions on synthetic inputs. It gave its own outcome for each claim; 24 of 25 agree with the record. It would give not_reproduced for fig5-anxa1-dls-inhibited, which the record has as blocked.",
     "agreed": 24,
     "of": 25,
     "disagreements": [
      {
       "claim": "fig5-anxa1-dls-inhibited",
       "outcome": "not_reproduced",
       "reason": "2 of 6 significant with the DLS labels, n 5 and 4. Every mouse decreases except one in PPN 4 s, so the failure comes from sample size. With n = 5 the smallest two-sided Wilcoxon p is 0.0625 and with n = 4 it is 0.125, so three of the six tests cannot pass whatever the data show. The paper's W = -36 and -55 equal -n(n+1)/2 for n = 8 and 10, and t 6.4 with p 0.0004 needs df 7, so the paper analysed 8 and 10 DLS mice. The unsuffixed-recordings variant does not reproduce these statistics, so those recordings are not the paper's DLS data. The outcome reflects data missing from the archive, which the notebook never states as such."
      }
     ]
    },
    {
     "date": "2026-10-18",
     "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, the helper module, the claims file and the attempt record, with the paper. The verifier checked every conclusion, the Summary, the README and the record's notes and findings against the printed outputs, and gave its own outcome for each claim; it agrees with all 25. It found wording to correct in cell 70, cell 0, the README run time, and the word exactly for the cell-body match. In reply the README now gives about seven minutes (6.9 min in the round-2 run); the other changes are under the claims below.",
     "agreed": 25,
     "of": 25,
     "disagreements": []
    }
   ]
  }
 ],
 "entries": [
  {
   "name": "001528-hadjas-2025",
   "type": "reproduction",
   "title": "Responses of SNr GABA and SNc dopamine neuron subtypes to STN and PPN input (Hadjas et al. 2025)",
   "description": "Tests the mouse fiber photometry findings of Hadjas et al. (2025) on dandiset 001528, which holds recordings from 120 mice during optogenetic stimulation of STN or PPN inputs to the substantia nigra. It compares responses of SNr GABA neurons, SNc pan-DA neurons, striatal dopamine release in TS and DLS, DA terminals, and Vglut2+ and Anxa1+ DA neurons across train durations and frequencies, using the lab's dF/F stored in the files. The human tissue counts of Figure 1 are not in the dandiset.",
   "dandisets": [
    "001528"
   ],
   "papers": [
    "10.1101/2025.06.03.657460"
   ],
   "derived_from": [],
   "notebooks": [
    {
     "path": "reproduce_hadjas_2025.ipynb",
     "title": "Reproducing Hadjas et al. (2025) from dandiset 001528",
     "executed": "notebooks/001528-hadjas-2025/reproduce_hadjas_2025.html"
    }
   ]
  }
 ]
}