OSCR

Thalamic modulation of cortical linearity across arousal states.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

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

The paper is loaded when this pane is shown.

The authors' code

MATLAB · 71 lines · 1.9 KB · CC-BY-4.0

  1. function [lmse,msd] = run_LFA(data_ts,n_lag, exp_var_lim)
  2. %RUN_LFA Summary of this function goes here
  3. % Detailed explanation goes here
  4. %
  5. %
  6. % Input:
  7. % data_ts = 3d matrix(double); variable x time x subj/trial/run
  8. %
  9. % n_lag = Number of future timepoints to predict (scalar int)
  10. %
  11. % exp_var_lim = percentage of explained variance to predict (scalar - double)
  12. %
  15. if nargin < 2
  16. n_lag = 10; % Number of future time-points to predict
  17. end
  18. if nargin < 3
  19. exp_var_lim = 99; % Variance explained
  20. end
  23. % Data dimensions
  24. [~,n_time,n_subjs] = size(data_ts);
  27. for subj = 1: n_subjs
  28. subj_ts = data_ts(:,:,subj);
  30. X = subj_ts(:,1:end-1); % X_t
  31. Y = subj_ts(:,2:end); % X_t+1
  33. % SVD
  34. [U, S, V]=svd(X,0); % X = U*S*V'
  36. % ---- Variance Explained
  37. exp_var = 100.*diag(S).^2./sum(diag(S).^2);
  38. accum_exp_var = cumsum(exp_var);
  39. n_pcs = find(accum_exp_var > exp_var_lim,1,'first');
  41. % Reduce rank
  42. U=U(:,1:n_pcs); % Space
  43. V=V(:,1:n_pcs); % Time
  44. S=S(1:n_pcs,1:n_pcs);
  46. % Projection timeseries
  47. X_svd = (S*V.').';
  49. % Estimate linear propagator A_tilde
  50. A_tilde=U'*Y*V/S; % Y = AX -> A = Y*inv(X)
  51. % X = U*S*V'
  54. % ----- Forecast Linear model
  55. % For each timepoint
  56. for ss = 1:n_time-n_lag
  57. X_plus = X_svd(ss,:); % Initialize current point
  58. % For each lag into the future
  59. for ll = 1 : n_lag
  60. % MSE linear model predictions
  61. X_plus(ll+1,:) = A_tilde*X_plus(ll,:).';
  62. lmse(ss,ll,subj) = mean((X_plus(ll,:) - X_svd(ss+ll-1,:)).^2);
  64. % MSD of autocorrelation
  65. msd(ss,ll,subj) = mean((X_svd(ss,:) - X_svd(ss+ll-1,:)).^2);
  66. end
  67. end
  68. %disp(subj)
  69. end
  70. end

run_LFA.m, under CC-BY-4.0 · at the source

Overview

Authors: Eli J. Müller1,2, Brandon R. Munn1,2, Giulia Baracchini1,2, Ben D. Fulcher3, Vicente Medel4,5, Michelle J. Redinbaugh6,7,8, Yuri B. Saalmann7,8, Jordan J. Wehrman9,10, Robert D. Sanders9,10, Bingni W. Brunton11, Steven L. Brunton12, James M. Shine1,2
ORCID iDs: Eli J. Müller, Brandon R. Munn, Giulia Baracchini, Ben D. Fulcher, Vicente Medel, Michelle J. Redinbaugh, Yuri B. Saalmann, Jordan J. Wehrman, Bingni W. Brunton, Steven L. Brunton, James M. Shine
  1. School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
  2. Centre for Complex Systems, The University of Sydney, Sydney, NSW, Australia
  3. School of Physics, The University of Sydney, Sydney, NSW, Australia
  4. Latin American Brain Health Institute, Universidad Adolfo Ibañez, Santiago, Chile
  5. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
  6. Department of Biology, Stanford University, Stanford, CA, USA
  7. Department of Psychology, University of Wisconsin–Madison, Madison, WI, USA
  8. Wisconsin National Primate Research Center, Madison, WI, USA
  9. Central Clinical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
  10. Department of Anaesthetics, Royal Prince Alfred Hospital, Sydney Local Health District, NSW, Australia
  11. Department of Biology, University of Washington, Seattle, WA, USA
  12. Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
Institutions: The University of Sydney (Australia); Pontificia Universidad Católica de Chile (Chile); Adolfo Ibáñez University (Chile); University of Wisconsin–Madison (United States); Stanford University (United States); Royal Prince Alfred Hospital (Australia); Sydney Local Health District (Australia); University of Washington (United States)
Journal: Science advances, volume 12, issue 38, article eaef5358
Dates: received 18 January 2026; accepted 7 August 2026; published online 18 September 2026; in print September 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1126/sciadv.aef5358 · PMID 42758834 · PMCID PMC13588182 · OpenAlex W7213562880
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism)
Methods: Spectral & time-frequency, Connectivity, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, fMRI & imaging, Physiology & signal measures
MeSH: Arousal*, Cerebral Cortex*, Thalamus*, Animals, Brain Mapping, Humans, Magnetic Resonance Imaging, Male (* major topic)
Journal subjects: Neuroscience, Systems Biology
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: NIH (R01MH110311, P51OD011106, 201732); Alzheimer’s Association (25-1490306); Australian Research Council (DE250100540, DE260101935); National Health and Medical Research Council (GNT2033162); ANID/FONDECYT de Iniciación (11251578); ANID/FONDECYT Exploración (13240170)
Citations: not cited yet (Europe PMC); 84 references in the paper

Abstract

The human brain must support both stable and flexible neural dynamics to adapt to changing contexts. The thalamus has been hypothesized to coordinate these opposing dynamical regimes in the cerebral cortex; however, this has not been directly tested at the systems level. Here, we apply a time-resolved measure of linearity to multimodal recordings in humans and macaques, demonstrating irregular fluctuations in both human functional magnetic resonance imaging and electrophysiological in the awake state. These fluctuations follow a key neuroanatomical axis of the thalamus, are diminished under pharmacological ablation of arousal, and recovered following arousal-inducing direct electrical stimulation of thalamus. Together, these findings identify a thalamic organizational axis that modulates cortical linearity across arousal states, linking thalamocortical architecture to the regulation of large-scale cortical dynamics.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

Zenodo 19905547

License: CC-BY-4.0
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Languages: MATLAB (2)
Size: 2 files, 2 scripts
Software Heritage: not checked
Found in: the text, “Linear forecast analysis”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers (HTTP 200)
  • 26 September 2026: the link answers (HTTP 200)
2 files
At the source: doi.org/10.5281/zenodo.19905547

The paper's code and data availability statement is in the Data section.

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;
  • 2 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • 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

Datasets cited

Data, code, and materials availability

All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials. This study did not generate new materials. The human EEG data can be provided by R. A. Pearce (University of Wisconsin) pending scientific review and a completed material transfer agreement through University of Wisconsin. Requests for the EEG data should be submitted to .

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

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, 12 authors, 8 MeSH terms, 6 funders, 75 references.

Cite

This paper

Müller, E. J., Munn, B. R., Baracchini, G., Fulcher, B. D., Medel, V., Redinbaugh, M. J., Saalmann, Y. B., Wehrman, J. J., Sanders, R. D., Brunton, B. W., Brunton, S. L., & Shine, J. M. (2026). Thalamic modulation of cortical linearity across arousal states. Science advances, 12(38), eaef5358. https://doi.org/10.1126/sciadv.aef5358

BibTeX

@article{muller2026thalamic,
author = {Müller, Eli J. and Munn, Brandon R. and Baracchini, Giulia and Fulcher, Ben D. and Medel, Vicente and Redinbaugh, Michelle J. and Saalmann, Yuri B. and Wehrman, Jordan J. and Sanders, Robert D. and Brunton, Bingni W. and Brunton, Steven L. and Shine, James M.},
title = {{Thalamic modulation of cortical linearity across arousal states}},
journal = {Science advances},
year = {2026},
month = sep,
volume = {12},
number = {38},
pages = {eaef5358},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
doi = {10.1126/sciadv.aef5358},
url = {https://doi.org/10.1126/sciadv.aef5358},
pmid = {42758834},
pmcid = {PMC13588182}
}

RIS

TY - JOUR
AU - Müller, Eli J.
AU - Munn, Brandon R.
AU - Baracchini, Giulia
AU - Fulcher, Ben D.
AU - Medel, Vicente
AU - Redinbaugh, Michelle J.
AU - Saalmann, Yuri B.
AU - Wehrman, Jordan J.
AU - Sanders, Robert D.
AU - Brunton, Bingni W.
AU - Brunton, Steven L.
AU - Shine, James M.
TI - Thalamic modulation of cortical linearity across arousal states
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/09/18
VL - 12
IS - 38
SP - eaef5358
SN - 2375-2548
PB - American Association for the Advancement of Science
DO - 10.1126/sciadv.aef5358
UR - https://doi.org/10.1126/sciadv.aef5358
LA - en
ER -

CSL-JSON

{
"id": "10.1126/sciadv.aef5358",
"type": "article-journal",
"title": "Thalamic modulation of cortical linearity across arousal states",
"container-title": "Science advances",
"author": [
{
"family": "Müller",
"given": "Eli J."
},
{
"family": "Munn",
"given": "Brandon R."
},
{
"family": "Baracchini",
"given": "Giulia"
},
{
"family": "Fulcher",
"given": "Ben D."
},
{
"family": "Medel",
"given": "Vicente"
},
{
"family": "Redinbaugh",
"given": "Michelle J."
},
{
"family": "Saalmann",
"given": "Yuri B."
},
{
"family": "Wehrman",
"given": "Jordan J."
},
{
"family": "Sanders",
"given": "Robert D."
},
{
"family": "Brunton",
"given": "Bingni W."
},
{
"family": "Brunton",
"given": "Steven L."
},
{
"family": "Shine",
"given": "James M."
}
],
"container-title-short": "Sci Adv",
"volume": "12",
"issue": "38",
"page": "eaef5358",
"DOI": "10.1126/sciadv.aef5358",
"PMID": "42758834",
"PMCID": "PMC13588182",
"ISSN": "2375-2548",
"publisher": "American Association for the Advancement of Science",
"URL": "https://doi.org/10.1126/sciadv.aef5358",
"language": "en",
"issued": {
"date-parts": [
[
2026,
9,
18
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1371/journal.pcbi.1014673 [code]
Modeling the influences of non-local connectomic projections on geometrically constrained cortical dynamics.
Journal: PLoS computational biology
In common: 6 references, author Ben D. Fulcher
[2] doi:10.1186/s41016-026-00441-x
Advances in local field potential research in prolonged disorders of consciousness: a narrative review.
Journal: Chinese neurosurgical journal
In common: 8 references
[3] doi:10.1093/braincomms/fcag151
Brain function in language and associated networks in non- or minimally verbal children.
Journal: Brain communications
In common: OpenNeuro 10.18112/openneuro.ds003171.v2.0.0, 5 references
[4] doi:10.1038/s41467-026-76011-7 [code]
Human cortex organizes dynamic co-fluctuations along the sensorimotor-association axis.
Journal: Nature communications
In common: 7 references
[5] doi:10.1038/s41467-026-75585-6 [code]
Brain network dynamics reflect psychiatric illness status and transdiagnostic symptom profiles across health and disease.
Journal: Nature communications
In common: 5 references
[6] doi:10.7554/elife.110294 [code]
Arousal modulates functional connectivity through structured and hemispherically asymmetric community architecture during wakefulness.
Journal: eLife
In common: 4 references
[7] doi:10.1038/s41467-026-72931-6 [code]
Three parsimonious spatiotemporal patterns in cerebellum reveal individual traits in function and behavior.
Journal: Nature communications
In common: 4 references
[8] doi:10.1371/journal.pbio.3003916 [code]
Arousal-driven critical roaming reproduces human functional connectivity dynamics.
Journal: PLoS biology
In common: 4 references
[9] doi:10.1212/wnl.0000000000218472 [code]
Lesion-Level Subtypes of White Matter Hyperintensity Evolution Beyond Spatial Location.
Journal: Neurology
In common: author Vicente Medel
[10] doi:10.1038/s41593-026-02205-3 [code]
Competitive interactions shape mammalian brain network dynamics and computation.
Journal: Nature neuroscience
In common: 4 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.