OSCR

Calmodulin controls spatial and temporal specificity of calcium-induced calcium release.

Code ↔ Paper

2 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 2 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § Materials and methods › Analysis ↔ scripts/run_fig_9_a_b_c_d.py, lines 203–263 · score 0.57 · peak duration, peak frequency, spatial spread, Amplitude, Figure 9
  2. [2] § Materials and methods › Analysis ↔ scripts/reg_analysis_temporal_decay.py, the whole file · a weak match · score 0.57 · linear regression, temporal decay, RyR2, fits, buffers, ctrl

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

Python · 321 lines · 12 KB · CC-BY-4.0 · 1 match

The registry keeps no copy of this file: the license of its repository (CC-BY-4.0) is not one it has verified to allow it. Your browser shows it from its source, with JavaScript.

It can be read at the source: scripts/run_fig_9_a_b_c_d.py.

Overview

  1. Nencki Institute of Experimental Biology Polish Academy of Sciences, Warszawa, Poland
  2. Roy J. Carver Department of Biomedical Engineering and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
Journal: PLoS computational biology, volume 22, issue 9, article e1013752
Dates: received 14 November 2025; accepted 20 August 2026; published online 10 September 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pcbi.1013752 · PMID 42721222 · PMCID PMC13581220 · OpenAlex W7212192282
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), rat (organism), Alzheimer's / dementia (population), cellular / molecular (subfield)
Methods: Statistics, Spectral & time-frequency
MeSH: Calcium*, Calcium Signaling*, Calmodulin*, Aging, Alzheimer Disease, Animals, Computational Biology, Dendrites, Endoplasmic Reticulum, Humans, Neurons, Plasma Membrane Calcium-Transporting ATPases, Rats, Ryanodine Receptor Calcium Release Channel (* major topic)
Journal subjects: Biology and Life Sciences, Cell Biology, Cellular Types, Animal Cells, Neurons, Neuronal Dendrites, Neuroscience, Cellular Neuroscience, Cellular Structures and Organelles, Endoplasmic Reticulum, Cell Processes, Secretory Pathway, Medicine and Health Sciences, Mental Health and Psychiatry, Dementia, Alzheimer's Disease, Neurology, Medical Conditions, Neurodegenerative Diseases, Signal Transduction, Cell Signaling, Calcium Signaling, Biophysics, Ion Channels, Calcium Channels, Physical Sciences, Physics, Physiology, Electrophysiology, Neurophysiology, Biochemistry, Proteins, Developmental Biology, Organism Development, Aging, Physiological Processes, Cytosol, Research and Analysis Methods, Simulation and Modeling
Topic: Alzheimer's disease research and treatments (Physiology, Medicine), according to OpenAlex
Citations: not cited yet (Europe PMC); 119 references in the paper

Abstract

Calcium dynamics controls learning and memory, and abnormal calcium dynamics have been implicated in neurodegenerative disorders, such as Alzheimer’s disease (AD). Calcium dynamics are influenced by calcium-induced calcium release (CICR), which is mediated by ryanodine receptors (RyR) located on endoplasmic reticulum (ER) membrane. Calmodulin, one of the most abundant proteins in the brain, inhibits RyR2, expressed in the dendrites of hippocampal CA1 neurons, with several reported consequences: relief of this inhibition is responsible for heart failure, and enhancing calmodulin to RyR binding alleviates cell loss and AD-like neuronal hyperexcitability. To investigate the role of calmodulin in aging and AD, we built a sophisticated reaction-diffusion model of a dendritic branch with ER. We showed that relieving calmodulin inhibition of RyR2 increased spatial and temporal spread of calcium transients in the dendrite. This effect was also visible in a model of old age, where disinhibition of half of the RyR2 population increased spatial spread of calcium transients by a factor of 2, and disinhibition of RyR2 combined with increased concentration of calcium buffering molecules increased duration of calcium transients. Lower activation of plasma membrane calcium ATPase (PMCA), which is also activated by calmodulin and inhibited by β-Amyloid oligomers, and not RyR2 disinhibition, led to an increase in resting intracellular calcium concentration as observed in AD. Overall, our research demonstrates that changes in calmodulin that are associated with AD and aging, by regulation of RyR2 (in old age) and PMCA (in AD), underlie changes in calcium dynamics that might have consequences for learning and memory.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

asiaszmek/stochastic_ER

License: CC-BY-4.0
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 3367f34a82c441f107f2eb0ee47f4aab639e1bf7, 15 June 2026
Languages: Python (38)
Size: 884 files, 38 scripts
Software Heritage: not archived
Found in: “Data Availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Matplotlib (25 files), NumPy (20 files), h5py (13 files), SciPy (6 files), pandas (5 files), statsmodels (4 files), Pingouin (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
39 files, not copied: shown from their source

OSCR keeps no copy of these files: the license of this repository (CC-BY-4.0) is not one it has verified to allow it. The reader above shows each one from its source, fetched by your browser at commit 3367f34, when its fingerprint is the one OSCR verified. How this works.

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;
  • 38 scripts, each with its path and the digest of its content;
  • 2 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

Code is available at https://github.com/asiaszmek/stochastic_ER.

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, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 14 MeSH terms, 117 references.

Cite

This paper

Jędrzejewska-Szmek, J., & Blackwell, K. T. (2026). Calmodulin controls spatial and temporal specificity of calcium-induced calcium release. PLoS computational biology, 22(9), e1013752. https://doi.org/10.1371/journal.pcbi.1013752

BibTeX

@article{jedrzejewskaszmek2026calmodulin,
author = {Jędrzejewska-Szmek, Joanna and Blackwell, Kim T.},
title = {{Calmodulin controls spatial and temporal specificity of calcium-induced calcium release}},
journal = {PLoS computational biology},
year = {2026},
month = sep,
volume = {22},
number = {9},
pages = {e1013752},
publisher = {PLOS},
issn = {1553-734X},
doi = {10.1371/journal.pcbi.1013752},
url = {https://doi.org/10.1371/journal.pcbi.1013752},
pmid = {42721222},
pmcid = {PMC13581220}
}

RIS

TY - JOUR
AU - Jędrzejewska-Szmek, Joanna
AU - Blackwell, Kim T.
TI - Calmodulin controls spatial and temporal specificity of calcium-induced calcium release
T2 - PLoS computational biology
J2 - PLoS Comput Biol
PY - 2026
DA - 2026/09/10
VL - 22
IS - 9
SP - e1013752
SN - 1553-734X
PB - PLOS
DO - 10.1371/journal.pcbi.1013752
UR - https://doi.org/10.1371/journal.pcbi.1013752
LA - en
ER -

CSL-JSON

{
"id": "10.1371/journal.pcbi.1013752",
"type": "article-journal",
"title": "Calmodulin controls spatial and temporal specificity of calcium-induced calcium release",
"container-title": "PLoS computational biology",
"author": [
{
"family": "Jędrzejewska-Szmek",
"given": "Joanna"
},
{
"family": "Blackwell",
"given": "Kim T."
}
],
"container-title-short": "PLoS Comput Biol",
"volume": "22",
"issue": "9",
"page": "e1013752",
"DOI": "10.1371/journal.pcbi.1013752",
"PMID": "42721222",
"PMCID": "PMC13581220",
"ISSN": "1553-734X",
"publisher": "PLOS",
"URL": "https://doi.org/10.1371/journal.pcbi.1013752",
"language": "en",
"issued": {
"date-parts": [
[
2026,
9,
10
]
]
}
}

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.2026.117793 [code]
Clustered inputs engage dendritic nonlinearities and calcium signaling to support efficient place-field formation in CA1 pyramidal neurons.
Journal: Cell reports
In common: Pingouin, pandas, SciPy, 2 other tools, cellular / molecular, 3 references
[2] doi:10.1111/ejn.70480 [code]
Astrocyte Proximity Protects Synapses From Human Amyloid-Beta Induced Degeneration in a Mouse Ex Vivo Model of Early Alzheimer's Disease.
Journal: The European journal of neuroscience
In common: statsmodels, pandas, SciPy, 2 other tools, Alzheimer's / dementia, cellular / molecular, 2 references
[3] doi:10.1111/apha.70264 [code]
Clustering Properties of Neuronal Ryanodine Receptor 2 and Remodeling in the APP/PS1 Mouse Model of Alzheimer's Disease.
Journal: Acta physiologica (Oxford, England)
In common: Alzheimer's / dementia, cellular / molecular, 4 references
[4] doi:10.1038/s41467-026-74227-1 [code]
Age-related changes in behavioural and neural variability in a decision-making task.
Journal: Nature communications
In common: Pingouin, statsmodels, pandas, 3 other tools, 1 reference
[5] doi:10.1038/s41467-026-74823-1 [code]
Cerebellar activity is triggered by reach endpoint during learning of a complex locomotor task.
Journal: Nature communications
In common: Pingouin, h5py, statsmodels, 4 other tools, cellular / molecular
[6] doi:10.7554/elife.108408 [code]
Frequency and laminar profile of feature-specific visual activity revealed by interleaved EEG-fMRI.
Journal: eLife
In common: Pingouin, h5py, statsmodels, 4 other tools
[7] doi:10.1038/s41467-026-75705-2 [code]
Redundant prefrontal hemispheres adapt storage strategy to working memory demands.
Journal: Nature communications
In common: Pingouin, h5py, statsmodels, 4 other tools
[8] doi:10.1002/advs.202519479 [code]
Diminished Signal-to-Noise Ratio Disrupts Somatosensory Population Encoding and Drives Tactile Hyposensitivity in the Fmr1<sup>-/y</sup> Autism Model.
Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)
In common: Pingouin, h5py, statsmodels, 4 other tools
[9] doi:10.7554/elife.100605 [code]
Age-related changes in ‘cortical’ 1/f dynamics are linked to cardiac activity
Journal: —
In common: Pingouin, h5py, statsmodels, 4 other tools
[10] doi: [code]
Real-time closed-loop feedback system for mouse mesoscale cortical signal and movement control
Journal: eLife
In common: Pingouin, h5py, statsmodels, 4 other tools

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.