OSCR

Generalization of fear learning is shaped by inhibitory sensory processing in mice.

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

Text · 50 lines · 2.9 KB · CC-BY-4.0

  1. This is the data and code depository for the paper "Generalization of fear learning is shaped by inhibitory sensory processing in mice", NCOMMS-25-57165.
  4. miasma.zip ; contains custom-written imaging analysis software used in this article.
  5. miasma_documentation.docx ; detailed description of files and analysis steps for miasma.
  6. xls.zip ; contains the numerical data used in the findings.
  7. rstats.zip ; contains the stats codes written in rstudio.
  9. Description of files in xls:
  11. - habituation.xls: dataset for habituation/dishabituation experiment.
  13. - mobility.xls: dataset for mobility and mean calcium increase after drug application, in imaging experiments.
  14. - all the animals are listed with their groups and mobility scores for each odor.
  15. - sheet O includes OSN animals, sheet G for PG cells, sheet M for mitral. "PRD" isolates paired animals. ALL and ALL_SHORT has all the animals, latter in short format.
  17. - openfield.xls: dataset for openfield experiments.
  18. - detection: accuracy of ethovision, mobility: active time of the animals. center-zone2: percentage of time animals spent in each zone.
  19. - dists: mean distance from each zone, all danger: areas adjacent to CS+., all safe: areas adjacent to no odor.
  20. - sheet "testing_rep" includes interactable representative graphs for each point made in the paper along with additional ones.
  21. - sheet "test_dist" isolated data of distances used to run stats.
  23. - percentages.xls: dataset for calcium findings, change in df/f ater drug application.
  24. - experimental specifics of all animals listed from B to E.
  25. - odor: presented odor, roi: ROI number, max: change in df/f of peak fluorescence, maxtime: time of peak, time1-5: peak within time section, offvol/area: offset metrics.
  26. - sheets are named according to cell type of animal. _rep includes interactable graphs for findings presented.
  28. - peaks.xls: same as percentage, but divided by peaks rather than just percentages.
  29. - block: 1, before application; 2, after application.
  31. - spatial: dataset for spatial analysis.
  32. - max_pre: peak before drug, max_post: peak after drug, perc: change in df/f
  33. - roi_x/y: centroid location of the ROI, ref_x/y: centroid location of the max responding CS+ glomerulus of specific animal.
  34. - eucl: euclidian distance between the ROI and peak CS+ ROI, micron: pixel converted to microns based on lens used.
  35. - overlap: 1 if this ROI is overlapping with any other, top50: 1 if this roi is a top 50 responding ROI.
  36. - m400: 1 if ROI is within 400 microns of peak CS+ ROI.
  38. Description of files in rstats:
  40. *all files include a comment for which excel file to run and what to change in order to get the specific subsection of the analysis.
  42. - calcium_mobility_correlation: Fig 2K.
  43. - compare_percentages: Fig 2 D-J.
  44. - mobility_across_odors: Fig 1C.
  45. - mobility_sex: Fig 1C, sex differences.
  46. - no_ceiling: Fig S2.
  47. - openf_distances: Fig 1D, Fig 4G-H.
  48. - overlap_glom: Fig 3C-D.
  49. - proximity_CS+: Fig 3E.
  50. - habituation: Fig 5C-D.

readme.txt, under CC-BY-4.0 · at the source

Overview

Authors: Alper K. Bakir1, Ankur A. Gaikwad1, Natalia Efimova1, Katharina L. L. Clark1, Michelle C. Rosenthal1, John P. McGann1,2,3
ORCID iDs: Alper K. Bakir, Ankur A. Gaikwad, Natalia Efimova, John P. McGann
  1. Behavioral and Systems Neuroscience, Psychology Department, Rutgers, The State University of New Jersey,Piscataway, NJ US
  2. Rutgers Center for Cognitive Science, Rutgers, The State University of New Jersey,Piscataway, NJ US
  3. Department of Otolaryngology-Head and Neck Surgery, Rutgers Robert Wood Johnson Medical School,New Brunswick, NJ US
Institutions: Rutgers, The State University of New Jersey (United States)
Journal: Nature communications, volume 17, issue 1, article 4825
Dates: received 22 July 2025; accepted 17 March 2026; published online 3 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41467-026-71356-5 · PMID 41932880 · PMCID PMC13223235 · OpenAlex W7148887781
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: behavior only (modality), mouse (organism), cellular / molecular (subfield)
Methods: fMRI & imaging, Single-unit activity, calcium imaging
Keywords: Olfactory bulb, Fear conditioning, Sensory processing
MeSH: Fear*, Generalization, Psychological*, Learning*, Animals, Avoidance Learning, Conditioning, Classical, Male, Mice, Mice, Inbred C57BL, Odorants, Olfactory Bulb, Receptors, GABA-B (* major topic)
Topic: Olfactory and Sensory Function Studies (Sensory Systems, Neuroscience), according to OpenAlex
Funding: NIH (R01MH101293)
Citations: cited by 1 paper (Europe PMC); 89 references in the paper

Abstract

When an organism learns that a sensory stimulus predicts a threat, the brain’s neural representation of the stimulus somehow incorporates that information into early sensory processing. That altered sensory processing may causally shape the organism’s response to the stimulus. We used contextual fear conditioning in mice to induce odor avoidance that generalized across odors in proportion to their similarity to the conditioning odor. Visualization of odor representations in vivo revealed they were being reshaped by reductions in GABAB receptor-mediated inhibitory signaling in the presynaptic terminals of the olfactory nerve and downstream neurons in proportion to the generalized fear of each odor. Locally blocking GABAB receptors in the olfactory bulb caused mice to switch from generalizing fear in proportion to similarity to instead overgeneralizing fear to all odors equally. Learning-induced sensory plasticity thus plays a causal role in shaping fear generalization.

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

Repositories

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

Zenodo 18809357

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 5 files
Software Heritage: not checked
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
1 file
At the source:

Zenodo 18809358

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 5 files
Software Heritage: not checked
Found in: the references
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
1 file
At the source:

Code availability

Code used for analyzing the data is deposited at Zenodo (10.5281/zenodo.18809357).

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

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;
  • 0 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

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

Data availability

Source data underlying the figures are provided with this paper. Processed datasets and analysis code are available at Zenodo (10.5281/zenodo.18809357). Raw imaging data are not publicly available due to their large file size and will be made available by the corresponding author upon request. Source data are provided with this paper.

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, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 3 keywords, 12 MeSH terms, 1 funder, 89 references.

Cite

This paper

Bakir, A. K., Gaikwad, A. A., Efimova, N., Clark, K. L. L., Rosenthal, M. C., & McGann, J. P. (2026). Generalization of fear learning is shaped by inhibitory sensory processing in mice. Nature communications, 17(1), 4825. https://doi.org/10.1038/s41467-026-71356-5

BibTeX

@article{bakir2026generalization,
author = {Bakir, Alper K. and Gaikwad, Ankur A. and Efimova, Natalia and Clark, Katharina L. L. and Rosenthal, Michelle C. and McGann, John P.},
title = {{Generalization of fear learning is shaped by inhibitory sensory processing in mice}},
journal = {Nature communications},
year = {2026},
month = apr,
volume = {17},
number = {1},
pages = {4825},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-71356-5},
url = {https://doi.org/10.1038/s41467-026-71356-5},
pmid = {41932880},
pmcid = {PMC13223235}
}

RIS

TY - JOUR
AU - Bakir, Alper K.
AU - Gaikwad, Ankur A.
AU - Efimova, Natalia
AU - Clark, Katharina L. L.
AU - Rosenthal, Michelle C.
AU - McGann, John P.
TI - Generalization of fear learning is shaped by inhibitory sensory processing in mice
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/04/03
VL - 17
IS - 1
SP - 4825
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-71356-5
UR - https://doi.org/10.1038/s41467-026-71356-5
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41467-026-71356-5",
"type": "article-journal",
"title": "Generalization of fear learning is shaped by inhibitory sensory processing in mice",
"container-title": "Nature communications",
"author": [
{
"family": "Bakir",
"given": "Alper K."
},
{
"family": "Gaikwad",
"given": "Ankur A."
},
{
"family": "Efimova",
"given": "Natalia"
},
{
"family": "Clark",
"given": "Katharina L. L."
},
{
"family": "Rosenthal",
"given": "Michelle C."
},
{
"family": "McGann",
"given": "John P."
}
],
"container-title-short": "Nat Commun",
"volume": "17",
"issue": "1",
"page": "4825",
"DOI": "10.1038/s41467-026-71356-5",
"PMID": "41932880",
"PMCID": "PMC13223235",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41467-026-71356-5",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
3
]
]
}
}

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.isci.2026.115897 [code]
Experience and behavior modulate piriform cortex odor representation in freely moving mice.
Journal: iScience
In common: mouse, 5 references
[2] doi:10.1038/s41598-026-51082-0
Non-uniform endogenous regeneration of olfactory sensory neuron axons across the mouse olfactory bulb.
Journal: Scientific reports
In common: mouse, 3 references
[3] doi:10.3758/s13415-026-01450-0 [code]
Attentional processing in individual anxiety: Electrocortical correlates of threat- and safety-related declarative memory formation.
Journal: Cognitive, affective & behavioral neuroscience
In common: 3 references
[4] doi:10.7554/elife.92882 [code]
Fear conditioning biases olfactory sensory neuron frequencies across generations.
Journal: eLife
In common: mouse, cellular / molecular, 2 references
[5] doi:10.1016/j.isci.2026.115373 [code]
Conserved post-odor dynamics in the olfactory systems of mice and locusts.
Journal: iScience
In common: mouse, 2 references
[6] doi:10.1038/s41598-026-51854-8 [code]
Sound-evoked auditory neurophysiological signals are a window into prodromal functional differences in a preclinical model of Alzheimer's disease.
Journal: Scientific reports
In common: 2 references
[7] doi:10.1155/da/2699511
Fear Generalization in Adolescent Anxiety Disorders: A MEG Study.
Journal: Depression and anxiety
In common: 2 references
[8] doi:10.1038/s41592-026-03065-2 [code]
PinkyCaMP: an mScarlet-based calcium sensor with enhanced brightness, photostability and multiplexing capabilities.
Journal: Nature methods
In common: mouse, cellular / molecular, 2 references
[9] doi:10.1016/j.isci.2026.116836
Layer 1 NDNF interneurons modulate thalamocortical input to the auditory cortex.
Journal: iScience
In common: 2 references
[10] doi:10.7554/elife.107939 [code]
Resolving synaptic events using subsynaptically targeted GCaMP8 variants.
Journal: eLife
In common: cellular / molecular, 2 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.