OSCR

Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates and Exposes Selective Neuronal Vulnerability.

Code ↔ Paper

3 matches 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 3 matches · 1 of them tie a paragraph to a whole file without given lines: a weak match, whose lines are not tinted
  1. [1] § Modelling › Mathematical Model for Ca2+ Oscillations ↔ model_run.m, lines 6 to 53 · score 0.76 · simplified model, SERCA pumping, ER lumen, clearance, IP3, activation · Report a mismatch
  2. [2] § Modelling › Model Parameters ↔ model_run.m, lines 6 to 53 · score 0.76 · half max, IP3R, strength, binding, cytoplasmic, WT · Report a mismatch
  3. [3] § Modelling › Mathematical Model for Ca2+ Oscillations ↔ calcium_ode_cyto_V.m, the whole file · a weak match · score 0.56 · SERCA pumping, IP3 receptors, SOCE, dynamics · Report a mismatch

Paper

Loaded from Europe PMC by your browser; OSCR does not store it: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

MATLAB · 85 lines · 2.6 KB · no license · 2 matches

  1. % This script simulates Ca2+ dynamics with hardcoded parameters for two cases:
  2. % - Wild Type (WT): set volchange = 1 and params.k_soce = 6.5227
  3. % - RTN3OE: set volchange = 4.3808 and params.k_soce = 3.9583
  4. % Ensure the matching k_soce value is uncommented when switching between cases
  6. %% Setup Ca2+ model parameters
  8. volchange = 1; % Set to 1 to run simulation with the ER volume of WT
  10. % Volume of ER and cytosol (μm^3)
  11. params.VER = 212;
  12. params.Vcyto = 4/3 * pi * (10^3 - 5^3) - params.VER; % Cell minus nucleus minus ER
  14. % IP3R Ca2+ release rate (μm^3/s)
  15. params.v1 = 69.075;
  17. % Passive leak rate (μm^3/s)
  18. params.v2 = 0.00;
  20. % SERCA pump rate (μM·μm^3/s)
  21. params.v3 = 496;
  23. % Cytoplasmic clearance rate (μM·μm^3/s)
  24. params.v4 = 368;
  26. % Half-max [Ca2+] for cytosolic clearance (μM)
  27. params.k_pl = 0.106;
  29. % SOCE entry rate (μm^3/s)
  30. params.k_soce = 6.5227; % for WT
  31. %params.k_soce = 3.9583; % for RTN3OE
  33. % Extracellular Ca2+ concentration (μM)
  34. params.c_cs = 200;
  36. % Half-max constants for IP3R gating (μM)
  37. params.k_er = 0.117; % SERCA half-max [Ca2+] (μM)
  38. params.d_ip3 = 0.1300; % IP3 binding (μM)
  39. params.d_act = 0.0823; % Activation by Ca2+ (μM)
  40. % inhibition by Ca, not using the simplified model, different IP3 binding
  41. % strength depending on whether Ca is present in other sites
  42. d2 = 1.049; d3 = 0.9434;
  43. params.d_inh = d2*(params.IP3 + params.d_ip3)/(params.IP3 + d3); % μM
  44. params.a = 0.5940; % h-gate kinetics (1/μM/s)
  46. % IP3 concentration (μM)
  47. params.IP3 = 0.4;
  49. % Buffer parameters in ER lumen
  50. params.k_D = 201.6; % Dissociation constant (μM)
  51. params.S = 2700 / volchange; % Total buffer site conc. (μM)
  53. params0 = params; % Save a copy
  55. %% Initial conditions
  56. c_cyto0 = 0.06; % Initial cytosolic free Ca2+ (μM)
  57. h0 = 0.8; % Initial h-inactivation variable
  58. u_er0 = 170; % Initial ER free Ca2+ (μM)
  59. c_er0 = u_er0 + u_er0 * params.S / (u_er0 + params.k_D); % Total ER Ca2+ (free + bound)
  61. % Initial state vector: [cytosol Ca2+, h, ER free Ca2+, ER total Ca2+]
  62. y0 = [c_cyto0; h0; u_er0; c_er0];
  64. % Time span (s)
  65. tspan = [0, 480];
  67. % Solve ODE system
  68. [t, y] = ode45(@(t, y) calcium_ode_cyto_V(t, y, params), tspan, y0);
  70. %% Plot cytosolic and ER free Ca2+ over time
  71. subplot(2,1,1);
  72. plot(t/60, y(:,1), 'LineWidth', 2);
  73. plot_cleanup(gca, 'FontSize', 16)
  74. ylabel('$c_\mathrm{cyto}\;\; \mu M$');
  75. xlabel('Time (min)');
  76. title('Cytosol Ca$^{2+}$');
  77. legend off
  79. subplot(2,1,2);
  80. plot(t/60, y(:,3), 'LineWidth', 2);
  81. plot_cleanup(gca, 'FontSize', 16)
  82. ylabel('$u_\mathrm{ER}\;\; \mu M$');
  83. xlabel('Time (min)');
  84. title('ER free Ca$^{2+}$');
  85. legend off

model_run.m at commit f577f4e, no license · at the source

Overview

Authors: Valentina Davi1, Pierre Parutto1, Yuyi Zhang2, Tasuku Konno1, Cecile Crapart1, Raquel Pereira3,4, John P. Franklin5,6, Mosab Ali Awadelkareem7, Daniel C Maddison1, Michael J. Devine5,8, Edgar R. Gomes3,4, Joseph Chambers9, Elena Koslover2, Edward Avezov1
ORCID iDs: Raquel Pereira, Michael J. Devine, Joseph Chambers, Edward Avezov
  1. Department of Clinical Neurosciences UK Dementia Research Institute at University of Cambridge Cambridge UK
  2. Department of Physics University of California San Diego, La Jolla California USA
  3. GIMM – Gulbenkian Institute for Molecular Medicine Avenida Prof. Egas Moniz Lisboa Portugal
  4. Faculdade de Medicina Universidade De Lisboa Av. Prof. Egas Moniz Lisboa Portugal
  5. Mitochondrial Neurobiology Laboratory The Francis Crick Institute London UK
  6. Department of Basic and Clinical Neuroscience Institute of Psychiatry Psychology and Neuroscience King's College London London UK
  7. Nuffield Department of Clinical Neurosciences University of Oxford Oxford UK
  8. Department of Clinical and Movement Neurosciences UCL Queen Square Institute of Neurology University College London London UK
  9. Cambridge Institute for Medical Research (CIMR) Department of Medicine University of Cambridge Cambridge UK
Institutions: University of Cambridge (United Kingdom); UK Dementia Research Institute (United Kingdom); University of California San Diego (United States); University of Lisbon (Portugal); Gulbenkian Institute for Molecular Medicine (Portugal); King's College London (United Kingdom); The Francis Crick Institute (United Kingdom); University of Oxford (United Kingdom); UCL Queen Square Institute of Neurology (United Kingdom); University College London (United Kingdom)
Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany), volume 13, issue 36, article e21101
Dates: received 27 October 2025; accepted 13 March 2026; published online 31 March 2026; in print June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1002/advs.202521101 · PMID 41915835 · PMCID PMC13317608 · OpenAlex W7147087334
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: human (organism), cellular / molecular (subfield)
Methods: Statistics, fMRI & imaging, Smoothing, state filtering, decompositions
Keywords: calcium oscillations, endoplasmic reticulum Ca2+ refill, endoplasmic reticulum morphology, human iPSC‐derived neurons, modelling, neurodegenerative diseases, neuronal firing
MeSH: Calcium*, Calcium Signaling*, Endoplasmic Reticulum*, Induced Pluripotent Stem Cells*, Neurons*, Humans (* major topic)
Topic: Cellular transport and secretion (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: UK Dementia Research Institute (UKDRI‐2203); Medical Research Council; National Science Foundation (2034482); Alzheimer Society of Canada (grant AS‐525 (AS‐PhD 19a‐015)); Evelyn Trust
Citations: cited by 1 paper (Europe PMC); 69 references in the paper
Research resources: HEK293T RRID:CVCL_0063, COS‐7 RRID:CVCL_0224, Human: NGN2 iPSCs RRID:CVCL_C7XJ, Fiji (ImageJ v2) RRID:SCR_002285, Leica Application Suite X RRID:SCR_013673, IncuCyte S3 Live Cell Analysis System RRID:SCR_023147

Abstract

The endoplasmic reticulum (ER)’s continuous morphology is tightly controlled by ER‐shaping proteins, whose genetic or expression defects drive a spectrum of neurodegenerative disorders from Hereditary Spastic Paraplegia to Alzheimer's disease. Why perturbations in ER morphology manifest specifically in neurons remains unknown. Here, by coupling visualisation of global sub‐Hz firing bursts to ER ultrastructural manipulations in human inducible Pluripotent Stem Cells (hiPSC)‐derived cortical neurons, alongside physical simulations, we establish a key ER structure‐function principle: neuronal ER architecture dictates Ca2+ replenishment speed. Altering ER structure hinders network ER luminal connectivity and Ca2+ propagation from refill points at plasma membrane contact sites, impairing the ER's capability to supply repetitive Ca2+ bursts. The ER morpho‐regulatory control of Ca2+ refill speed thus constitutes a switch on neuronal activity. Further, perturbed ER shape also abolishes Ca2+ firing and contraction in primary skeletal muscle cells. These results expose the selective vulnerability of Ca2+‐firing cells to ER structural disruptions, rationalizing ER dysfunction in neurodegeneration and unveiling a new role for the continuous ER morphology that could apply universally to Ca2+‐firing cells.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.

lenafabr/networkSpreadFVM

License: GPL-3.0
State: the link answers, verified on 31 October 2026
Evidence: files inventoried
Commit: 7a33595ded23d64e9ec2ef41c439528dae422c98, 22 January 2026
Languages: MATLAB (27), Fortran (20)
Size: 80 files, 47 scripts
Software Heritage: not archived
Found in: the text, “Simulations of Network Ca 2+ Refill”
Holds: README, license file, documentation
Not found: CITATION.cff, environment file, tests, continuous integration
Availability: 2 checks, the latest on 31 October 2026: the link answers
  • 31 October 2026: the link answers
  • 30 September 2026: the link answers
49 files
At the source: github.com/lenafabr/networkSpreadFVM

lenafabr/aspatialCaERrefill

License: none: the authors keep all their rights
State: the link answers, verified on 31 October 2026
Evidence: files inventoried
Commit: f577f4e0f280742c4c111cffdb0f76c622e352bc, 11 July 2025
Languages: MATLAB (2)
Size: 3 files, 2 scripts
Software Heritage: not archived
Found in: the text, “Implementation”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 2 checks, the latest on 31 October 2026: the link answers
  • 31 October 2026: the link answers
  • 30 September 2026: the link answers
3 files
At the source: github.com/lenafabr/aspatialCaERrefill

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 49 scripts, each with its path and the digest of its content;
  • 3 matches 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.

Data Availability Statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Reproduced under the paper's license (CC BY), 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, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 14 authors, 7 keywords, 6 MeSH terms, 5 funders, 68 references, 6 RRIDs.

Cite

This paper

Davi, V., Parutto, P., Zhang, Y., Konno, T., Crapart, C., Pereira, R., Franklin, J. P., Awadelkareem, M. A., Maddison, D. C., Devine, M. J., Gomes, E. R., Chambers, J., Koslover, E., & Avezov, E. (2026). Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates and Exposes Selective Neuronal Vulnerability. Advanced science (Weinheim, Baden-Wurttemberg, Germany), 13(36), e21101. https://doi.org/10.1002/advs.202521101

BibTeX

@article{davi2026endoplasmic,
author = {Davi, Valentina and Parutto, Pierre and Zhang, Yuyi and Konno, Tasuku and Crapart, Cecile and Pereira, Raquel and Franklin, John P. and Awadelkareem, Mosab Ali and Maddison, Daniel C and Devine, Michael J. and Gomes, Edgar R. and Chambers, Joseph and Koslover, Elena and Avezov, Edward},
title = {{Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates and Exposes Selective Neuronal Vulnerability}},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
year = {2026},
month = mar,
volume = {13},
number = {36},
pages = {e21101},
publisher = {Wiley},
issn = {2198-3844},
doi = {10.1002/advs.202521101},
url = {https://doi.org/10.1002/advs.202521101},
pmid = {41915835},
pmcid = {PMC13317608}
}

RIS

TY - JOUR
AU - Davi, Valentina
AU - Parutto, Pierre
AU - Zhang, Yuyi
AU - Konno, Tasuku
AU - Crapart, Cecile
AU - Pereira, Raquel
AU - Franklin, John P.
AU - Awadelkareem, Mosab Ali
AU - Maddison, Daniel C
AU - Devine, Michael J.
AU - Gomes, Edgar R.
AU - Chambers, Joseph
AU - Koslover, Elena
AU - Avezov, Edward
TI - Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates and Exposes Selective Neuronal Vulnerability
T2 - Advanced science (Weinheim, Baden-Wurttemberg, Germany)
J2 - Adv Sci (Weinh)
PY - 2026
DA - 2026/03/31
VL - 13
IS - 36
SP - e21101
SN - 2198-3844
PB - Wiley
DO - 10.1002/advs.202521101
UR - https://doi.org/10.1002/advs.202521101
LA - en
ER -

CSL-JSON

{
"id": "10.1002/advs.202521101",
"type": "article-journal",
"title": "Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates and Exposes Selective Neuronal Vulnerability",
"container-title": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)",
"author": [
{
"family": "Davi",
"given": "Valentina"
},
{
"family": "Parutto",
"given": "Pierre"
},
{
"family": "Zhang",
"given": "Yuyi"
},
{
"family": "Konno",
"given": "Tasuku"
},
{
"family": "Crapart",
"given": "Cecile"
},
{
"family": "Pereira",
"given": "Raquel"
},
{
"family": "Franklin",
"given": "John P."
},
{
"family": "Awadelkareem",
"given": "Mosab Ali"
},
{
"family": "Maddison",
"given": "Daniel C"
},
{
"family": "Devine",
"given": "Michael J."
},
{
"family": "Gomes",
"given": "Edgar R."
},
{
"family": "Chambers",
"given": "Joseph"
},
{
"family": "Koslover",
"given": "Elena"
},
{
"family": "Avezov",
"given": "Edward"
}
],
"container-title-short": "Adv Sci (Weinh)",
"volume": "13",
"issue": "36",
"page": "e21101",
"DOI": "10.1002/advs.202521101",
"PMID": "41915835",
"PMCID": "PMC13317608",
"ISSN": "2198-3844",
"publisher": "Wiley",
"URL": "https://doi.org/10.1002/advs.202521101",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
31
]
]
}
}

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:10.1016/j.celrep.2022.111943
Electrical signals in the ER are cell type and stimulus specific with extreme spatial compartmentalization in neurons.
Journal: Cell reports
In common: cellular / molecular, 6 references
[2] doi:10.1126/sciadv.aeb3209 [code]
The actomyosin cortex controls t-tubule remodeling in skeletal muscle.
Journal: Science advances
In common: cellular / molecular, 2 references, author Ana Raquel Pereira
[3] doi:10.1126/science.abn1366
Cytosolic antibody receptor TRIM21 is required for effective tau immunotherapy in mouse models.
Journal: Science (New York, N.Y.)
In common: cellular / molecular, 1 reference, author Edward Avezov
[4] doi:10.1038/s41467-024-53232-2 [code]
Deep-prior ODEs augment fluorescence imaging with chemical sensors.
Journal: Nature communications
In common: 5 references
[5] doi:10.1038/s41556-024-01356-4 [code]
Combinatorial selective ER-phagy remodels the ER during neurogenesis.
Journal: Nature cell biology
In common: 4 references
[6] doi:10.1016/j.cell.2023.08.034 [code]
Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells.
Journal: Cell
In common: cellular / molecular, author Joseph Chambers
[7] doi:10.1016/j.celrep.2023.112883
COPI-regulated mitochondria-ER contact site formation maintains axonal integrity.
Journal: Cell reports
In common: cellular / molecular, 3 references
[8] doi:10.1038/s42255-026-01451-w [code]
Mitochondrial Ca<sup>2+</sup> efflux controls neuronal metabolism and long-term memory across species.
Journal: Nature metabolism
In common: cellular / molecular, 4 references
[9] doi:10.1016/j.xpro.2026.104773 [code]
Protocol for fluorescent false neurotransmitter live imaging of dopamine release dynamics from individual synapses in acute brain slices.
Journal: STAR protocols
In common: cellular / molecular, author Michael J. Devine
[10] doi:10.1016/j.crmeth.2026.101338
MitoTracker transfers from astrocytes to neurons independently of mitochondria.
Journal: Cell reports methods
In common: cellular / molecular, author Michael J. Devine

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.

Add the badge to the code's README

OSCR: the badge of this paper

If you are an author or a maintainer of this paper's code, you can add this badge. It says what OSCR knows of the paper (its code, its validated tracing map) and links the code to this page. Paste one of these snippets under the README's title. Keep the two marks around it, so that the badge can be replaced in place and is never added twice. OSCR changes nothing in your repository.

Markdown
<!-- oscr-badge:start -->
[![OSCR](https://openscicode.org/badge/doi/10.1002/advs.202521101.svg)](https://openscicode.org/badge/doi/10.1002/advs.202521101)
<!-- oscr-badge:end -->
reStructuredText
.. oscr-badge:start

.. image:: https://openscicode.org/badge/doi/10.1002/advs.202521101.svg
   :target: https://openscicode.org/badge/doi/10.1002/advs.202521101
   :alt: OSCR

.. oscr-badge:end
HTML
<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/doi/10.1002/advs.202521101"><img src="https://openscicode.org/badge/doi/10.1002/advs.202521101.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->

On GitHub, open the README, choose Edit (the pencil), paste the snippet under the title, then "Commit changes".

If you choose to, you can have the badge kept up to date for you, with oscr badge --write from the command line or with the GitHub Action in your repository's workflows. Every other form and option (a card, AsciiDoc, LaTeX, shields.io) is on the badge 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: code errors and mismatches between the code and the paper about this paper and its code, from readers and its authors, beside the paper and its tracing map.

Report a mismatch between the code and the paper · Report a code error (signed in)

Reproductions: reports from readers who ran the authors' code and did not get the paper's result, what they ran, with which environment, commit and data.

Report a reproduction failure (signed in)

Versions of its code: the releases of its code tied to a version of this paper (the preprint, the accepted manuscript, the version of record…), each with the tracing map versioned with it.

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