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Linking functional and structural dendritic spine remodeling during fear learning and extinction in vivo.

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. [1] § MATERIALS AND METHODS › Simulation of the biophysically detailed neural network model › Basic setting of the simulation ↔ orig/netParams.py, lines 872–937 · score 0.57 · NetPyNE, cell models, Python, cortical, PV, spike
  2. [2] § MATERIALS AND METHODS › Simulation of the biophysically detailed neural network model › Basic setting of the simulation ↔ seed_search/netParams.py, lines 868–933 · score 0.57 · NetPyNE, cell models, Python, cortical, PV, spike

Paper

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

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The authors' code

Python · 937 lines · 50 KB · no license · 1 match

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It can be read at the source: orig/netParams.py.

Overview

Authors: Xiaoyang Li1, Qiyu Zheng1,2, Kim Hoi Kin Wong1, Kenneth Kin Yip Wong2,3, Cora Sau Wan Lai1,2
ORCID iDs: Xiaoyang Li, Qiyu Zheng, Kim Hoi Kin Wong, Kenneth Kin Yip Wong, Cora Sau Wan Lai
  1. School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
  2. Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
  3. Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
Institutions: University of Hong Kong (Hong Kong SAR China); Hong Kong Science and Technology Parks Corporation (Hong Kong SAR China)
Journal: Science advances, volume 12, issue 29, article eaec3961
Dates: received 18 September 2025; accepted 2 June 2026; published online 17 July 2026; in print July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1126/sciadv.aec3961 · PMID 42467781 · PMCID PMC13378561 · OpenAlex W7169527484
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), mouse (organism), cognitive (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Connectivity, fMRI & imaging, Single-unit activity, calcium imaging
MeSH: Dendritic Spines*, Extinction, Psychological*, Fear*, Learning*, Neuronal Plasticity*, Animals, Male, Mice (* major topic)
Topic: Neuroscience and Neuropharmacology Research (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: National Natural Science Foundation of China (N_HKU735/21); Research Grants Council, University Grants Committee (C1024-22GF, C7074-21G, 17103922, C7011-24GF, 17108821, C7026-25G, 17102525); Innovation and Technology Commission; Health and Medical Research Fund (09200966); Li Ka Shing Faculty of Medicine, University of Hong Kong
Citations: not cited yet (Europe PMC); 84 references in the paper

Abstract

Structural plasticity of dendritic spines has been observed during different learning paradigms, but how the functional dynamics of dendritic spines changes with memory processing and how these patterns relate to structural plasticity and dendritic integration remain unclear. Here, we perform longitudinal functional and structural in vivo imaging of the frontal association cortex in mice subject to fear conditioning and extinction over several days. We show that fear learning induced responsive spines that are more likely to be synchronous and clustered, which are consolidated over the following days but attenuated by extinction. We develop a causal inference model demonstrating that the active spine calcium signals during fear learning prevent the spines from being eliminated while promoting the elimination of neighboring spines after memory consolidation. Furthermore, the dendritic responsive signal reveals a learning-dependent tone discrimination pattern that is correlated to spines’ structural remodeling. Our findings provide in vivo evidence consistent with functional-structural link of dendritic spines in a bidirectional learning paradigm.

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 2 matches between paragraphs and lines of code.

Zenodo 20301802

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data, code, and materials availability:”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source: doi.org/10.5281/zenodo.20301802

4768/reversible_spine_model

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 8edb39e800efb9af9fc2a80421d0de4267bdbab8, 2 September 2025
Languages: NEURON (455), Python (80), C/C++ (7)
Size: 794 files, 542 scripts
Software Heritage: not archived
Found in: “Data, code, and materials availability:”
Holds: README, environment (requirements.txt)
Not found: license file, CITATION.cff, tests, continuous integration, documentation
Tools: NEURON (511 files), NumPy (43 files), NetPyNE (37 files), Matplotlib (33 files), SciPy (24 files), Pillow (7 files), pandas (2 files)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
543 files, not copied: shown from their source

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At the source: github.com/4768/reversible_spine_model.git

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 542 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, code, and materials availability

This study did not generate new materials. All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplemental Materials. The raw data files and simulation model codes have been deposited to Zenodo under the following accession DOI: https://doi.org/10.5281/zenodo.20301802. The simulation model codes used in this paper are also available in the following repository: https://github.com/4768/reversible_spine_model.git.

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

Versions

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Version 2, 28 September 2026

  • Funding: added National Natural Science Foundation of China: N_HKU735/21; Research Grants Council, University Grants Committee: C1024-22GF, C7074-21G, 17103922, C7011-24GF, 17108821, C7026-25G, 17102525; Innovation and Technology Commission; Health and Medical Research Fund: 09200966; Li Ka Shing Faculty of Medicine, University of Hong Kong

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 8 MeSH terms, 84 references.

Cite

This paper

Li, X., Zheng, Q., Wong, K. H. K., Wong, K. K. Y., & Lai, C. S. W. (2026). Linking functional and structural dendritic spine remodeling during fear learning and extinction in vivo. Science advances, 12(29), eaec3961. https://doi.org/10.1126/sciadv.aec3961

BibTeX

@article{li2026linking,
author = {Li, Xiaoyang and Zheng, Qiyu and Wong, Kim Hoi Kin and Wong, Kenneth Kin Yip and Lai, Cora Sau Wan},
title = {{Linking functional and structural dendritic spine remodeling during fear learning and extinction in vivo}},
journal = {Science advances},
year = {2026},
month = jul,
volume = {12},
number = {29},
pages = {eaec3961},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
doi = {10.1126/sciadv.aec3961},
url = {https://doi.org/10.1126/sciadv.aec3961},
pmid = {42467781},
pmcid = {PMC13378561}
}

RIS

TY - JOUR
AU - Li, Xiaoyang
AU - Zheng, Qiyu
AU - Wong, Kim Hoi Kin
AU - Wong, Kenneth Kin Yip
AU - Lai, Cora Sau Wan
TI - Linking functional and structural dendritic spine remodeling during fear learning and extinction in vivo
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/07/17
VL - 12
IS - 29
SP - eaec3961
SN - 2375-2548
PB - American Association for the Advancement of Science
DO - 10.1126/sciadv.aec3961
UR - https://doi.org/10.1126/sciadv.aec3961
LA - en
ER -

CSL-JSON

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