Dandisets / 001636

Dandiset 001636

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Pyramidal tract and corticostriatal neuron recordings in MPTP-treated macaque performing visuomotor tasks

behavioral electrophysiological Rhesus monkey Converted by CatalystNeuro 6.4 GB 447 files
  • 4 reproduced
  • 3 partially reproduced
  • 3 not reproduced
  • 18 blocked

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Claims

From the paper Primary motor cortex of the parkinsonian monkey: altered neuronal responses to muscle stretch

Reproducing Pasquereau and Turner (2013) from dandiset 001636 26

Notebook reproduce_pasquereau_2013.ipynb

  • Not reproducedResults, Behavioral effects of MPTP; Figure 1

    After MPTP, torque-induced displacements were slower and smaller; mean peak velocity fell by 16.2% and amplitude by 6.6% (ANOVA, F > 515 and F > 49).

    Over 294 monkey V sessions (repeated files left out), torque-induced movements are faster and larger after MPTP; session-mean peak velocity +28.8% and amplitude +15.2% (flexion +30.3% and +12.0%), MPTP F = 103 and 26, p < 0.0001. The torque command's pulse is about four times larger in most post-MPTP sessions; in the sessions with the same command size (43 pre, 12 post) the increases are +101.9% and +113.4%. The mean of the session-mean peak velocities is 58.7 deg/s, and only one response comes from a session in the paper's 130 to 200 deg/s window of matched sessions; mean displacements (3.09 deg) are smaller than its 10 deg. The angle's scale agrees with the files' own kinematic columns (active movements measured here within 2% of derived_peak_velocity and derived_movement_amplitude), so the small movements are in the data. The torque command differs between the states, so the change cannot be attributed to MPTP.

    How the test differed from the paper’s method

    • Monkey V only; the paper's ANOVA has animal as a third factor.
    • The peak velocity and amplitude windows (0 to 200 and 0 to 300 ms) and the FIR length are choices; the Methods give the filter and velocity threshold only.
    • Perturbations with the joint moving before onset (490 of 5413) are kept.
  • Not reproducedResults, Behavioral effects of MPTP; Figure 1

    The latency of torque-induced displacements did not change after MPTP (F < 0.2, p > 0.05).

    Movement onset is earlier after MPTP (session means 9.8 and 3.2 ms for flexion, 11.0 and 6.0 ms for extension; MPTP F = 1032, p < 0.0001), with an MPTP by direction interaction (F = 19.1; the paper reports F > 94). In sessions with the same command size it does not differ (7.81 and 7.73 ms, p = 0.79). The zero-phase filter can move an onset earlier, and 219 of 5413 perturbations have a latency of 0 ms. With a causal 10 ms average of the unfiltered velocity the session means are 12.6 to 18.6 ms and still shorter after MPTP (F = 781); without the trials already moving before onset F = 1037 (filtered) and 743 (causal). At the middle command size the causal variant gives p = 0.25, and 0.026 without the trials moving before onset. The difference goes with the torque command, so it cannot be attributed to MPTP.

    How the test differed from the paper’s method

    • Monkey V only.
    • Zero-phase (forward and backward) filtering; the Methods do not say how the filter was applied.
  • Not reproducedResults, Behavioral effects of MPTP

    The latency of the earliest EMG responses did not change after MPTP (p > 0.05).

    EMG responses start earlier after MPTP (40.8 against 24.0 ms, Kolmogorov-Smirnov p = 5.5e-21), in the same direction at 1.5 and 3 SD. At the middle command size the onsets do not differ (28.8 and 45.6 ms, p = 0.18), the post-MPTP onset being the later one there.

    How the test differed from the paper’s method

    • The paper does not name its test here; the Kolmogorov-Smirnov test it uses for the other EMG measures is used.
  • Partially reproducedResults, Database; Table 1

    PTN antidromic latencies did not change after MPTP (1.9 ms, p = 0.9), while CSN latencies were longer (5.1 against 6.1 ms, p < 0.05/3).

    The four means are within tolerance and PTN latencies do not differ (p = 0.54). CSN latencies are longer after MPTP with p = 0.018, just above the paper's 0.05/3 = 0.0167, so one test fails. With every monkey L PTN and CSN unit added (their selection by perturbations cannot be made), p = 0.0071 for CSNs and 0.91 for PTNs, and the post-MPTP CSN mean (7.01 ms) is outside tolerance. 18 PTNs and CSNs studied have no antidromic latency.

    How the test differed from the paper’s method

    • Monkey V cells studied, against expected values that pool both monkeys.
  • Partially reproducedResults, Behavioral effects of MPTP; Figure 2

    The total duration of EMG responses to torque increased after MPTP, from 57 +/- 6 to 79 +/- 3 ms (Kolmogorov-Smirnov, p < 0.001).

    Responses last longer after MPTP (24.5 against 50.4 ms, Kolmogorov-Smirnov p = 1.8e-39, 283 and 281 channel-sessions), but both means are outside tolerance (57 +/- 6 and 79 +/- 3); thresholds of 1.5 and 3 SD give 16.4 against 48.5 and 17.3 against 49.5 ms. At the middle command size they do not differ (28.4 and 27.9 ms, p = 0.96). Before MPTP 63.6% of the durations are 10 ms or less (median 9 ms, against 59 ms after).

    How the test differed from the paper’s method

    • The response threshold (2 SD of the baseline) and the pooling of three triceps channels are choices; the Methods cite an earlier paper for the EMG analysis.
  • Partially reproducedResults, Behavioral effects of MPTP; Figure 2

    The short-latency m1 component (15 to 40 ms) was poorly formed and generally much smaller than the m2 component.

    After MPTP, m2 exceeds m1 in 96.5% of 282 channel-sessions, median m1 / m2 0.22 (0.23 over channel-sessions with m2 > 0). Before MPTP the median ratio is 0.10 (0.09 with m2 > 0) but m2 exceeds m1 in 73.5% of 310, below the criterion's 75%.

  • ReproducedSupplementary table (monkey V); Results, Database; Table 1

    In monkey V, 112 neurons were studied before MPTP and 159 after, of which 49 and 54 were PTNs and 31 and 48 CSNs; three neurons in all were activated from both the peduncle and the putamen.

    Monkey V units with at least 5 perturbations of each direction number 112 before and 159 after MPTP, with 49 and 54 PTNs and 31 and 48 CSNs, exactly the supplementary table's counts. The files hold 3 units activated from both the peduncle and the putamen, all in monkey V and all among the cells studied. Dropping the two unit copies found in repeated files gives 53 post-MPTP PTNs.

    How the test differed from the paper’s method

    • The paper's location and isolation criteria cannot be applied; the units in the dandiset are taken as the selected units, which the matching counts support.
  • ReproducedSupplementary table; Table 1; Results, Database

    Before torque onset, the firing rate of M1 neurons was lower after MPTP, because PTN rates fell (Mann-Whitney p < 0.001) while CSN rates did not change (p = 0.5). In monkey V the rates were 12.6 and 8.9 spikes/s for all cells, 20.3 and 14.8 for PTNs, and 3.5 and 3.4 for CSNs, before and after MPTP.

    All six monkey V means are within tolerance. PTN rates are lower after MPTP (Mann-Whitney p = 0.034), CSN rates do not differ (p = 0.73), and the M1 rate is lower (p = 0.0033, below the paper's 0.05/2). The statement's p < 0.001 for PTNs, from both monkeys, is not reached in monkey V alone.

    How the test differed from the paper’s method

    • Monkey V only.
    • The baseline is the mean SDF over the 500 ms before onset over all perturbation trials, a reading of the Methods.
  • ReproducedResults, Database; Table 1

    Before MPTP, PTNs fired much faster than CSNs at rest (Mann-Whitney p < 0.001).

    Pre-MPTP monkey V PTNs 18.03 spikes/s (n = 49), CSNs 3.42 (n = 31), Mann-Whitney p = 1.3e-11. The paper's pooled means differ between its text (16.3 and 3.6) and Table 1 (18.3 and 3.2).

    How the test differed from the paper’s method

    • Monkey V only.
  • ReproducedResults, Behavioral effects of MPTP; Figure 2

    The long-latency (m2, 41 to 80 ms) EMG response of the stretched triceps was larger after MPTP (Kolmogorov-Smirnov, p < 0.05).

    For flexion torques the m2 response is larger after MPTP in both triceps longus channels and the triceps lateralis (medians 3.0 against 164.2, 3.1 against 297.5 and 5.2 against 76.2 A/D units; Kolmogorov-Smirnov p = 1.1e-58, 1.9e-50, 4.7e-15). The increase follows the torque command; median m2 is 0.61 at the smallest command size (pre only), 40.8 (pre) and 1.81 (post) at the middle, and 17.09 (pre, n = 5) and 194.6 (post) at the largest, so within a state it does not rise simply with command size, and in the middle-size sessions m2 is not larger after MPTP (triceps longus 1 median 46.7 against 1.3, p = 0.013, with 40 and 6 sessions). The outcome is the criterion's comparison; as the torque command is about four times larger in most post-MPTP sessions, the increase cannot be attributed to MPTP.

    How the test differed from the paper’s method

    • EMG in A/D units; the paper reports microvolts.
  • BlockedMethods, Data analysis· Methods underspecifiedverifier disagreed at first

    The detection threshold, p < 0.01 divided by 5 independent comparisons, holds the chance of a false response over the 200 ms epoch near 0.01.

    The analysis ran. At a pseudo onset 600 ms before the torque, a threshold crossing in the 200 ms epoch occurs in 0.22 of the 542 monkey V cell-directions with the main detection and 0.46 with the t-test variant; unperturbed trials taken at the usual torque time give 0.19 and 0.45. A response with onset in 20 to 60 ms occurs in 0.044 (pseudo onset) and 0.047 (unperturbed trials), against 0.37 at the true onset. The paper's threshold implies 0.01; the rates here are about 20 times higher, so the procedure differs from the paper's in a way the Methods do not settle (how the SDF values are compared with the baseline, and any minimum duration), and this claim and those that rest on the selection are blocked. Stationary Poisson spike trains at each cell-direction's baseline rate give 0.15 (main) and 0.49 (t-test), so most of the excess comes from the detection procedure, though about a third of the observed 0.22 is not explained by the Poisson trains, and the rate does not fall with baseline rate (0.17 to 0.27 by quartile) or number of trials (0.21 to 0.24). The pseudo-onset rate of responses is 0.12 of the true-onset rate. 14 cell-directions (10 CSN) have no baseline spike and cannot respond. A threshold calibrated to a pseudo-onset rate of 0.01 (t = 6.67 against 3.11) finds 30.4% and 32.7% of M1 cells torque-related. Whether the paper's procedure differs or its stated rate does not hold cannot be told from this analysis.

    How the test differed from the paper’s method

    • The detection compares the trial-averaged SDF with mean +/- t * SD of its baseline values, a reading of the Methods; a t-test across trials is shown as a variant.
    • A response's onset is its first crossing within 20 to 60 ms; the Methods define the onset as the first crossing, so a variant takes the first crossing anywhere in 0 to 200 ms (6 of 202 responses have an earlier crossing).
  • BlockedResults, Torque-evoked neuronal responses, pre- vs. post-MPTP; Figure 3A· Methods underspecified

    MPTP did not change the fraction of torque-related neurons, in M1, in PTNs or in CSNs (chi-square, p > 0.05/3).

    Blocked as the selection is. With the main detection the paper's test finds no change in M1 (-7.3 points, p = 0.29), PTNs (-4.8 points, p = 0.76) or CSNs (+0.5 points, p = 1.0). The t-test variant finds increases in M1 (+20.5 points, p = 0.0014) and PTNs (+25.3 points, p = 0.016), both below 0.05/3.

  • BlockedResults, Torque-evoked neuronal responses, prevalence; Figure 3A· Methods underspecified

    PTNs responded to torque more often than CSNs (68% against 31% over both monkeys, chi-square 32.3, p < 0.001).

    Blocked as the selection is. PTNs 71 of 103 (68.9%) against CSNs 13 of 79 (16.5%), chi-square 47.5, p = 5.6e-12; both fractions are outside tolerance (PTNs above 62.1 +/- 6.2, CSNs below 30.4 +/- 3.0). The t-test variant gives 60.2% and 32.9% (p = 0.00046).

  • BlockedResults, Torque-evoked neuronal responses, prevalence· Methods underspecified

    About half of the torque-related cells (124 of 284, 44%) responded to only one direction of rotation.

    Blocked as the selection is. 70 of 136 torque-related cells (51.5%) respond to one direction only (59.0% pre, 45.3% post); the t-test variant gives 63.3%.

  • BlockedTable 1; Results, Torque-evoked neuronal responses, pre- vs. post-MPTP· Methods underspecified

    Most torque responses were increases in firing (86% of M1 responses before and 88% after MPTP; 70% and 75% for PTNs), and MPTP did not change the PTN balance (chi-square 0.1, p = 0.7).

    Blocked as the selection is. Increases are 82.6% and 76.7% of M1 responses and 68.1% and 59.3% of PTN responses; the PTN balance does not change (chi-square 0.53, p = 0.47). The paper's Table 1 marks its CSN change p < 0.01, but its own counts (23 of 24 against 19 of 22) give p = 0.54 with the Yates-corrected chi-square test that reproduces its other values.

  • BlockedResults, Torque-evoked neuronal responses, pre- vs. post-MPTP; Figure 4A· Methods underspecified

    The magnitude of torque responses did not differ before and after MPTP, for M1 cells or for PTNs, by any of three measures (mean change, maximum change, area; Kolmogorov-Smirnov and Mann-Whitney, all p > 0.15).

    Blocked as the selection is. With the main detection, responses are smaller after MPTP; 11 of the 12 tests (directions pooled) have p < 0.05, for example M1 maximum change 43.7 against 32.4 spikes/s (Kolmogorov-Smirnov p = 0.0017) and PTN mean change 23.4 against 15.4 (Mann-Whitney p = 0.0001).

  • BlockedSupplementary table· Methods underspecified

    In monkey V, the mean response magnitudes were 42.4 and 37.9 spikes/s for M1 flexion responses, 50.9 and 42.6 for M1 extension responses, 33.4 and 26.1 for PTN flexion and 38.8 and 29.3 for PTN extension responses, before and after MPTP.

    Blocked as the selection is. Under reading (a), maximum change, the four pre-MPTP means are within tolerance and none of the post-MPTP ones; readings (b) and (c) match 1 and 0 of 8.

  • BlockedResults, Torque-evoked neuronal responses, pre- vs. post-MPTP; Figure 4B; supplementary table· Methods underspecified

    Response latencies were shorter after MPTP for M1 cells and for PTNs, for flexion and extension (Kolmogorov-Smirnov, all p < 0.05). In monkey V the means were 39.2 and 34.6 ms (M1 flexion), 40.4 and 33.4 ms (M1 extension), 43.9 and 35.5 ms (PTN flexion) and 44.4 and 36.7 ms (PTN extension), before and after MPTP.

    Blocked as the selection is. With the main detection all four comparisons are shorter after MPTP (Kolmogorov-Smirnov p = 0.0086, 0.0048, 0.022, 0.0023) and all eight means are within tolerance; pooled, M1 responses 41.8 and 35.9 ms and PTN responses 45.0 and 37.8 ms (earliest per cell 40.9 and 34.7, 44.2 and 35.4). The t-test variant finds no significant shortening (p 0.27 to 0.87).

  • BlockedResults, Torque-evoked neuronal responses, pre- vs. post-MPTP· Methods underspecified

    The latency shortening was not a history effect; latencies did not correlate with the days of training (monkey V Spearman |rho| = 0.02, p = 0.85).

    Blocked as the selection is. Over both states latency correlates with the recording day (Spearman rho = -0.26, p = 0.0022, n = 136), as post-MPTP sessions come later and have shorter latencies; within each state it does not (rho = 0.11, p = 0.42; rho = -0.15, p = 0.21).

  • BlockedResults, Torque-evoked neuronal responses, pre- vs. post-MPTP; supplementary table· Methods underspecified

    Torque-evoked increases in PTN firing were briefer after MPTP; the FWHM fell from 73 to 50 ms over both monkeys (Mann-Whitney, p < 0.05 for each direction). In monkey V the PTN FWHM was 97 and 52 ms for flexion and 57 and 41 ms for extension, before and after MPTP.

    Blocked as the selection is. PTN increases are briefer after MPTP for flexion (p = 0.039) but not for extension (p = 0.39); over all PTN responses the means are 97.4 and 52.3 ms for flexion and 56.9 and 60.7 ms for extension.

  • BlockedResults, Response directionality; Figure 6· Methods underspecified

    Directional selectivity fell after MPTP; reciprocal and unidirectional responses became less common and bidirectional and non-directional ones more common (by about 10% of torque-related M1 cells; chi-square 22.2, p < 0.001).

    Blocked as the selection is. Reciprocal and unidirectional cells fall from 59.0% to 52.0% of torque-related cells (-7.0 points), chi-square 6.26 (3 dof), p = 0.10. For PTNs they fall from 65.7% to 50.0% (p = 0.015). With categories set from the DSI value as the paper words them, 62.3% and 50.7% (p = 0.42). There is no reciprocal cell before MPTP; the smallest expected count is 2.2.

    How the test differed from the paper’s method

    • Categories are set from which directions respond and their signs, as fixed in the claims file; the paper words them by DSI value. The DSI value reading is shown as a variant.
  • BlockedSupplementary table· Methods underspecified

    In monkey V the mean DSI of torque-related cells was 0.72 and 0.66 for M1, 0.73 and 0.75 for PTNs and 0.81 and 0.83 for CSNs, before and after MPTP.

    Blocked as the selection is. Three of six means are within tolerance (PTN pre and both CSN values).

  • BlockedResults, Response directionality· Methods underspecified

    The loss of selectivity was not due to resting rates, as pre-torque rates did not differ between directional categories (one-way ANOVA, F = 0.77, p = 0.46).

    Blocked as the selection is. Baseline rates do not differ between the four categories (F = 0.58, p = 0.63) or three groups (F = 0.69, p = 0.50).

  • BlockedResults, Torque-evoked neuronal responses, pre- vs. post-MPTP; Supplementary Figure 1· Methods underspecified

    In sessions with equivalent torque-induced velocities (130 to 200 deg/s), MPTP did not change the magnitude of responses (Mann-Whitney, p = 0.19 for flexion and 0.46 for extension, with 24 and 33 flexion and 22 and 31 extension responses).

    Blocked as the selection is. Also, only one response comes from a session whose mean peak velocity is between 130 and 200 deg/s (session means reach 145.3 deg/s), so the matched groups cannot be formed on this velocity scale.

  • BlockedResults, Analysis of neural-behavioral correlations· Methods underspecified

    Across sessions, the mean PTN response latency did not correlate with the peak velocity of the torque-induced movement (|rho| < 0.18) or with the m2 EMG response (|rho| < 0.26; Spearman, p > 0.05 with threshold 0.05/4).

    Blocked as the selection is. Over 67 sessions mean PTN latency against mean peak velocity gives rho = -0.22, p = 0.080; against triceps longus 1 m2 (64 sessions) rho = -0.32, p = 0.011, below the paper's 0.0125. Within each state neither correlates (p 0.36 to 0.997).

Not tested in a notebook 2

1 data missing from the dandiset, 1 methods underspecified
  • BlockedSupplementary table (monkey L); Table 1· Data missing from the dandiset

    In monkey L, 57 of 115 neurons before MPTP and 35 of 73 after responded to torque perturbations of the wrist, and the monkey L responses enter all pooled results.

    No monkey L (Leu) file marks a torque perturbation; torque_perturbation_type is "none" and the onset NaN in every Leu trial. The Leu torque command is NaN in all 98 pre-MPTP files with analog data, and 15 of 51 post-MPTP Leu files have no analog data. The joint moves by more than 2 deg in the hold window in 15% (pre) and 1% (post) of Leu trials, against 66 to 86% of monkey V perturbed trials. The 35 post-MPTP Leu files with a torque command show 91 to 413 command excursions per file, starting a median 0.31 to 0.84 s after the lateral target appears, during the active movement; one of their 2048 trials has an excursion starting in the hold window. In monkey V such an excursion starts in the hold window in 1811 and 3563 trials, against 1862 and 3649 labelled perturbations. The perturbations may exist in the lab's source files; they are not in the dandiset.

  • BlockedResults, Analysis of neural-behavioral correlations· Methods underspecified

    Trial by trial, PTN response latencies did not correlate with the peak velocity or the m2 EMG response (Spearman |rho| < 0.34, p > 0.05).

    The Methods define response onset on the trial-averaged SDF and give no single-trial latency, which the test needs. No analysis code is published.

Findings about the data

What attempts found about the dandiset itself, for its owner and the archive.

  • Data missingThe monkey L (Leu) files mark no torque perturbation; torque_perturbation_type is "none" in every Leu trial, the Leu torque command is NaN in every pre-MPTP file, and 15 of 51 post-MPTP Leu files have no analog data. The monkey L half of the paper (115 and 73 cells, and its EMG and kinematics) cannot be tested.
  • File format errorThe analog streams (ElbowAngle, ElbowTorque, ElbowVelocity, EMG) are not on the clock of the trials table and spikes. The conversion lays each trial's analog samples end to end by sample count, while trials and spikes use the behavioural trial end, about 5 ms later per trial, so the stored analog clock falls behind by up to 365 ms within a session. Moving each analog segment to its trial's start puts the torque command step 4 to 7 ms after every labelled onset; on the stored clock it falls up to 108 ms before it.
  • OtherThe torque command's 50 ms pulse has three sizes (about 46, 91 and 183 units above rest). Most pre-MPTP monkey V sessions have the smallest (108 of 157) and most post-MPTP sessions the largest (129 of 141), and post-MPTP pulses are followed by an opposite swing. The paper describes one 0.1 Nm, 50 ms impulse; the command's scale is not given, so the change may be of the torque or of the command's recording. Movement and EMG results differ between command sizes.
  • Metadata errorThe ElbowAngle reference_frame says positive is extension; active flexion movements and flexion torques raise the angle in both monkeys, so positive is flexion. The series are named Elbow for monkey L, whose task used the wrist.
  • Metadata errorFour monkey V files (v4527b, v4810b, v5604b, v5812) repeat a block of another file's trials. In two of them the same unit, with identical spikes in every repeated trial, is stored twice with different projection types (v4527 unit 2 not_tested and v4527b unit 2 a PTN; v5811 unit 2 a PTN and v5812 unit 2 no_response).
  • Metadata errorunit_also_in_session_id uses the prefixes V and L where session ids use Venus and Leu, and 35 of its 43 references name files that are not in the dandiset. Where the file is present, it holds a different unit (another unit number, spike count and often projection type), not the same neuron.
  • Metadata errorThe dandiset description says MPTP was given systemically, that both monkeys made elbow movements and that Leu was recorded in 1993. The files and the paper say unilateral intracarotid MPTP, monkey L used the wrist, and Leu files date from August 1992.
  • OtherThe monkey L analog streams are sampled at 100 Hz; the paper says 200 Hz. The EMG is described as sample-hold integrated over 10 ms in the files and low-pass filtered at 100 Hz in the paper, and is stored in uncalibrated A/D units.
  • OtherThe torque onset comes 1.70 to 1.73 s after center_target_appearance_time in 90% of monkey V perturbations, where the Methods put it 1 to 2 s after center capture at random. Either the column marks another event or the torque was predictable from the target's appearance.
  • Methods not availableNo analysis code is published. The response detection as described gives a false-positive rate near 0.2 over the 200 ms epoch, against the 0.01 its threshold implies, and stationary Poisson spike trains give 0.15, most of it, so the paper's exact procedure cannot be recovered, and single-trial latencies are not defined.
  • Paper inconsistentThe pre-MPTP PTN and CSN resting rates are 16.3 and 3.6 spikes/s in the text and 18.3 and 3.2 in Table 1. Table 1 marks the CSN change in the fraction of excitatory responses p < 0.01, but its own counts (23 of 24 against 19 of 22) give p = 0.54 with the Yates-corrected chi-square test that reproduces its other chi-square values.

Notebooks

Every registered entry that uses this dandiset. An entry can hold several notebooks, and can use more than one dandiset.

Reproduction M1 responses to muscle stretch in the parkinsonian monkey (Pasquereau and Turner 2013)

Tests the findings of Pasquereau and Turner (2013) on dandiset 001636, which holds single-unit recordings from M1 of two monkeys before and after MPTP, with torque perturbations, joint angle and EMG. Only monkey V can be tested, as the monkey L files mark no perturbation. The notebook checks the cells, resting rates and antidromic latencies, detects torque responses, and compares the torque-evoked movements and triceps EMG before and after MPTP. All files

Verification

  • Round 1
    2026-10-15    Agreed with 27 of 28 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's full text. The verifier streamed 7 monkey L files and ran synthetic checks of stretch.detect (stationary Poisson spike trains) and stretch.kinematics.
    • false-positive-rate: the verifier’s outcome was “Not reproduced”. Cell 27: the any-crossing rate over 0 to 200 ms is 0.22 (main) and 0.46 (t-test variant). Unperturbed trials give 0.19, and stationary Poisson spike trains through detect give 0.13 to 0.20 (the verifier's test), so the excess comes from the threshold procedure, whose threshold is t times the SD over time of the trial-averaged SDF and is not a test of trial-to-trial variance. A single run cannot tell whether the paper's claim is wrong or its procedure differs. The Methods' literal reading, a 2-tailed t-test against the baseline, is closer to the t-test variant, which also fails (0.46). The response rate at the pseudo onset is 0.044 against 0.37 at the true onset, so about 12% of detected responses are expected to be false. It asked for example mean SDFs with their thresholds drawn, and the pseudo-onset false-positive rate split by baseline rate and by number of trials.
  • Round 2
    2026-10-15    Agreed with 28 of 28 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: Round 2. The full executed notebook with conclusions and summary, the attempt record, the README, the helper module, the claims file, the round-1 report and the paper's full text from Europe PMC. It checked the paper_inconsistency finding against the paper and found it supported. Other changes in reply are the README run time (the verifier saw 1.5 min printed by cell 104; this run printed 2.4 min) and the round-1 false-positive-rate reason, which now carries two points from its round-1 problem 1 that it found left out. It did not inspect the plotted figures.

Method differences

How the tests differed from the paper’s method or data, and the claims each applies to.

  • Monkey V only.baseline-rate ptn-faster-than-csn kinematic-latency-unchanged
  • The paper's location and isolation criteria cannot be applied; the units in the dandiset are taken as the selected units, which the matching counts support.cell-counts
  • The baseline is the mean SDF over the 500 ms before onset over all perturbation trials, a reading of the Methods.baseline-rate
  • Monkey V cells studied, against expected values that pool both monkeys.antidromic-latency
  • The detection compares the trial-averaged SDF with mean +/- t * SD of its baseline values, a reading of the Methods; a t-test across trials is shown as a variant.false-positive-rate
  • A response's onset is its first crossing within 20 to 60 ms; the Methods define the onset as the first crossing, so a variant takes the first crossing anywhere in 0 to 200 ms (6 of 202 responses have an earlier crossing).false-positive-rate
  • Categories are set from which directions respond and their signs, as fixed in the claims file; the paper words them by DSI value. The DSI value reading is shown as a variant.dsi-reduced
  • Monkey V only; the paper's ANOVA has animal as a third factor.kinematics-slower
  • The peak velocity and amplitude windows (0 to 200 and 0 to 300 ms) and the FIR length are choices; the Methods give the filter and velocity threshold only.kinematics-slower
  • Perturbations with the joint moving before onset (490 of 5413) are kept.kinematics-slower
  • Zero-phase (forward and backward) filtering; the Methods do not say how the filter was applied.kinematic-latency-unchanged
  • EMG in A/D units; the paper reports microvolts.emg-m2-larger
  • The response threshold (2 SD of the baseline) and the pooling of three triceps channels are choices; the Methods cite an earlier paper for the EMG analysis.emg-duration-longer
  • The paper does not name its test here; the Kolmogorov-Smirnov test it uses for the other EMG measures is used.emg-onset-unchanged

Provenance

Attempt record
001636-pasquereau-2013-01
Paper
Primary motor cortex of the parkinsonian monkey: altered neuronal responses to muscle stretch
Date
2026-10-15
Made by
An agent, run by CatalystNeuro
Dandiset version
0.260518.1819
Harness
Claude Code (GitHub Actions)
Model
claude-opus-5-5
Protocol
pilot-6

Transcripts of the agent runs

Each run’s prompt, messages and tool calls, with long output cut and the text of the paper left out, and its final report.

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