Behavioral correlates of Purkinje cell ensemble covariance.

Code ↔ Paper

1 match between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 1 match · it ties a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted

[1] § Methods › Data acquisition › Dynamic Clamp ↔ Figure4/simulateModulatedSpikes.m, the whole file · a weak match · score 0.54 · instantaneous rates, trace, trains, simulated, firing rates, modulate

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

MATLAB · 26 lines · 1018 B · no license · 1 match

function spikeTrains = simulateModulatedSpikes(realTrace, fs, baselineRate, modulationStrength, nNeurons, dt)
% realTrace: vector of your real trace (e.g., stimulus), size [1 x T]
% fs: sampling rate of realTrace (Hz)
% baselineRate: constant baseline firing rate (Hz)
% modulationStrength: scalar to tune modulation effect
% nNeurons: number of neurons to simulate
% dt: time step (s), e.g., 1/fs
T = length(realTrace);
t = (0:T-1) * dt;
% Normalize and scale the real trace to a modulation in rate
modSignal = (realTrace - mean(realTrace)) / std(realTrace);
% instantaneous rate across time (Hz)
instantRate = baselineRate * (1 + modulationStrength * modSignal);
instantRate(instantRate < 0) = 0; % no negative rates
spikeTrains = zeros(nNeurons,length(realTrace));
for neuronIdx = 1:nNeurons
% For each time bin, draw from Poisson
lambda = instantRate * dt; % probability per dt
spikes = rand(1, T) < lambda;
spikeTrains(neuronIdx,:) = spikes; % spike times (s)
end
end

simulateModulatedSpikes.m at commit 05f3c13, no license · at the source

Overview

Authors: Abdulraheem Nashef¹, Michael S. Spindle¹, Dylan J. Calame¹, Abigail L. Person¹

ORCID iDs: Abdulraheem Nashef, Abigail L. Person

Department of Physiology and Biophysics, Anschutz Medical Campus, University of Colorado,Aurora, CO USA

Institutions: University of Colorado Anschutz (United States)

Journal: Nature communications, volume 17, issue 1, article 7755

Dates: received 25 June 2025; accepted 8 June 2026; published online 19 June 2026

Type: Research article · Language: English

License: CC BY-NC-ND

Identifiers: DOI 10.1038/s41467-026-74576-x · PMID 42321245 · PMCID PMC13434793 · OpenAlex W7165370685

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: mouse (organism), systems (subfield)

Methods: Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, Single-unit activity, calcium imaging

Keywords: Cerebellum, Computational neuroscience, Neuroscience, Motor control

MeSH: Behavior, Animal*, Purkinje Cells*, Action Potentials, Animals, Biomechanical Phenomena, Cerebellar Nuclei, Forelimb, Male, Mice, Mice, Inbred C57BL, Movement (* major topic)

Topic: Vestibular and auditory disorders (Neurology, Neuroscience), according to OpenAlex

Funding: NINDS (NS131839, NS114430)

Citations: not cited yet (Europe PMC); 86 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

AbedNashef/Synchrony_paper

License: none: the authors keep all their rights

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 05f3c13f3441672ff2aea7d27e6de33883623293, 5 June 2026

Languages: MATLAB (42)

Size: 82 files, 42 scripts

Software Heritage: not archived

Found in: “Code availability”

Holds: README

Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Statistics and Machine Learning Toolbox (27 files), Image Processing Toolbox (10 files), Signal Processing Toolbox (3 files)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

43 files

Figure1/Bhv2clusterProp.m, MATLAB, 105 lines
Figure1/Fig1_Clustering.m, MATLAB, 84 lines
Figure1/get_activity_clusters.m, MATLAB, 89 lines
Figure2/Fig2_xcorr.m, MATLAB, 325 lines
Figure2/get_anti_diag.m, MATLAB, 25 lines
Figure2/get_peakiness.m, MATLAB, 22 lines
Figure2/get_width.m, MATLAB, 28 lines
Figure2/plot_all_diagonals4bfrMove.m, MATLAB, 97 lines
Figure2/plot_all_jpsth.m, MATLAB, 45 lines
Figure3/Cluster2dec_jPSTHs.m, MATLAB, 273 lines
Figure3/Cluster2maxV_jPSTHs.m, MATLAB, 238 lines
Figure3/Controls/isi_shuffle.m, MATLAB, 13 lines
Figure3/Controls/jitter_spikes.m, MATLAB, 26 lines
Figure3/Controls/jitter_spikes_isi.m, MATLAB, 12 lines
Figure3/Controls/montecarlo_jitter_spikes.m, MATLAB, 23 lines
Figure3/Controls/run_jpsth_shuffle.m, MATLAB, 168 lines
Figure3/Controls/run_sync2fr_4randomPairs.m, MATLAB, 84 lines
Figure3/Controls/run_sync2fr_4randomPairs_noCluster.m, MATLAB, 85 lines
Figure3/jPSTH2DecGain.m, MATLAB, 267 lines
Figure3/jPSTH2Endpoint.m, MATLAB, 222 lines
Figure4/Corr_cofiring2xcorr.m, MATLAB, 184 lines
Figure4/FigS9/Sync_and_fr_to_ISI.m, MATLAB, 400 lines
Figure4/Nuclear_Model_allData.m, MATLAB, 410 lines
Figure4/calculate_exc_conductance_stretched_ex.m, MATLAB, 873 lines
Figure4/cmpr_PSTHCorr.m, MATLAB, 524 lines
Figure4/get_ccg.m, MATLAB, 18 lines
Figure4/get_ccg_5ms.m, MATLAB, 18 lines
Figure4/get_null_fr.m, MATLAB, 14 lines
Figure4/jPSTH2CCG_corr.m, MATLAB, 235 lines
Figure4/jpsth_jitter_plot.m, MATLAB, 476 lines
Figure4/simulateModulatedSpikes.m, MATLAB, 26 lines, 1 match
Figure5/Corr_cofiring2xcorr.m, MATLAB, 184 lines
Figure5/Nuclear_Model_allData.m, MATLAB, 412 lines
Figure5/calculate_exc_conductance_stretched_ex.m, MATLAB, 873 lines
Figure5/cmpr_PSTHCorr.m, MATLAB, 524 lines
Figure5/get_ccg.m, MATLAB, 18 lines
Figure5/get_ccg_5ms.m, MATLAB, 18 lines
Figure5/get_null_fr.m, MATLAB, 14 lines
Figure5/jPSTH2CCG_corr.m, MATLAB, 235 lines
Figure5/jpsth_jitter_plot.m, MATLAB, 476 lines
Figure5/run_jpsth4highGain_basedOnAvg.m, MATLAB, 376 lines
Figure5/simulateModulatedSpikes.m, MATLAB, 26 lines
README.md, Text, 30 lines

At the source: github.com/AbedNashef/Synchrony_paper

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

it points to the authors' code: AbedNashef/Synchrony_paper

Read it in the paper: doi.org/10.1038/s41467-026-74576-x.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
42 scripts, each with its path and the digest of its content;
1 match between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

it points to the authors' code: AbedNashef/Synchrony_paper
it says that the data are available on request

Read it in the paper: doi.org/10.1038/s41467-026-74576-x.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 4 keywords, 11 MeSH terms, 1 funder, 86 references.

Cite

This paper

Nashef, A., Spindle, M. S., Calame, D. J., & Person, A. L. (2026). Behavioral correlates of Purkinje cell ensemble covariance. Nature communications, 17(1), 7755. https://doi.org/10.1038/s41467-026-74576-x

BibTeX

@article{nashef2026behavioral, author = {Nashef, Abdulraheem and Spindle, Michael S. and Calame, Dylan J. and Person, Abigail L.}, title = {{Behavioral correlates of Purkinje cell ensemble covariance}}, journal = {Nature communications}, year = {2026}, month = jun, volume = {17}, number = {1}, pages = {7755}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-026-74576-x}, url = {https://doi.org/10.1038/s41467-026-74576-x}, pmid = {42321245}, pmcid = {PMC13434793} }

RIS

TY - JOUR AU - Nashef, Abdulraheem AU - Spindle, Michael S. AU - Calame, Dylan J. AU - Person, Abigail L. TI - Behavioral correlates of Purkinje cell ensemble covariance T2 - Nature communications J2 - Nat Commun PY - 2026 DA - 2026/06/19 VL - 17 IS - 1 SP - 7755 SN - 2041-1723 PB - Nature Publishing Group DO - 10.1038/s41467-026-74576-x UR - https://doi.org/10.1038/s41467-026-74576-x LA - en ER -

CSL-JSON

{ "id": "10.1038/s41467-026-74576-x", "type": "article-journal", "title": "Behavioral correlates of Purkinje cell ensemble covariance", "container-title": "Nature communications", "author": [ { "family": "Nashef", "given": "Abdulraheem" }, { "family": "Spindle", "given": "Michael S." }, { "family": "Calame", "given": "Dylan J." }, { "family": "Person", "given": "Abigail L." } ], "container-title-short": "Nat Commun", "volume": "17", "issue": "1", "page": "7755", "DOI": "10.1038/s41467-026-74576-x", "PMID": "42321245", "PMCID": "PMC13434793", "ISSN": "2041-1723", "publisher": "Nature Publishing Group", "URL": "https://doi.org/10.1038/s41467-026-74576-x", "language": "en", "issued": { "date-parts": [ [ 2026, 6, 19 ] ] } }

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