OSCR

PLX5622 did not alter anxiety-like behaviour and showed limited microglial depletion efficacy in a spinal cord injury model in female rats.

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

Shell · 93 lines · 1.7 KB · MIT

  2. #
  3. # distribute.sh
  4. #
  5. # prepares rat-apps for distribution such that they can be copied
  6. # to a new computer without an existing Python installation.
  7. #
  9. # To overide defalt parameters, set the folling variables:
  10. # PY: Command to run python3 with
  11. PY=""
  12. # PYINSTALL_OPTS: Arguments to pass th pyinstaller.
  13. PYINSTALL_OPTS="--onefile"
  15. VENVACTIVATE="build/venv/bin/activate"
  17. if [[ -z "$PY" ]]; then
  18. # PY not configured. Auto-detect.
  19. if [[ "$OSTYPE" == "darwin"* ]]; then
  20. echo "Mac OSX detected"
  21. PY="python3"
  22. PYINSTALL_OPTS="--windowed --onefile"
  23. elif [[ "$OSTYPE" == "msys"* ]]; then
  24. PY="py -3"
  25. PYINSTALL_OPTS="--onefile"
  26. VENVACTIVATE="build/venv/scripts/activate"
  27. else
  28. echo "Unknown OS detected. Please manually set PY variable in this script."
  29. exit 0
  30. fi
  31. sleep 1
  32. fi
  35. echo
  36. echo Installing Python virtualenv
  37. echo
  39. $PY -m pip install --user virtualenv
  40. rm -rf dist build
  41. mkdir build
  43. echo
  44. echo Creating new Python virtual environment
  45. echo
  46. sleep 1
  48. $PY -m virtualenv build/venv
  49. source $VENVACTIVATE
  51. echo
  52. echo Installing requirements
  53. echo
  54. sleep 1
  56. # bug in setuptools 45.0.0
  57. # https://github.com/pypa/setuptools/issues/1963
  58. $PY -m pip install --upgrade 'setuptools<45.0.0'
  60. $PY -m pip install . pyinstaller
  62. echo
  63. echo Distributing Xmaze
  64. echo
  65. sleep 1
  66. pyinstaller ratapps/xmaze.py -n Xmaze $PYINSTALL_OPTS
  68. echo
  69. echo Distributing SPGanalysis
  70. echo
  71. sleep 1
  72. pyinstaller ratapps/spganalysis.py -n SPGAnalysis $PYINSTALL_OPTS
  74. echo
  75. echo Distributing Whitebox
  76. echo
  77. sleep 1
  78. pyinstaller ratapps/whitebox.py -n Whitebox $PYINSTALL_OPTS
  80. echo
  81. echo Distributing Openfield
  82. echo
  83. sleep 1
  84. pyinstaller ratapps/openfield.py -n Openfield $PYINSTALL_OPTS
  86. echo
  87. echo Cleaning up
  88. echo
  89. sleep 1
  91. rm -rf build
  93. echo Done

distribute.sh at commit 236360e, under MIT · at the source

Overview

Authors: Jaison Cucarian1, Ram Rakheja1, Kale R Scatterty1, Edward Armstrong2, Sydney Storvold2, Antoinette T Nguyen2, Keith Fenrich1,2,3, Philippe Monnier4,5, Karim Fouad1,2
  1. Faculty of Medicine and Dentistry, Neuroscience and Mental Health Institute, University of Alberta, 8205 114 St NW, Edmonton, AB T6G 2E1 Canada
  2. Department of Physical Therapy, Faculty of Rehabilitation Medicine, University of Alberta, Edmonton, T6G 2G4 Canada
  3. Institute of Smart Augmentative and Restorative Technologies and Health Innovations (iSMART), University of Alberta, Edmonton, T6G 1G7 Canada
  4. Krembil Research Institute, University Health Network, Toronto, M5T 0S8 Canada
  5. Department of Ophthalmology and Vision Science, Faculty of Medicine, University of Toronto, Toronto, M5T 3A9 Canada
Institutions: University of Alberta (Canada); Neuroscience and Mental Health Institute (Canada); University Health Network (Canada); University of Toronto (Canada); Krembil Research Institute
Journal: Scientific reports, volume 16, issue 1, article 18749
Dates: received 15 December 2025; accepted 10 April 2026; published online 22 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41598-026-48842-3 · PMID 42020492 · PMCID PMC13272775 · OpenAlex W7155161770
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: rat (organism), other condition (population), cellular / molecular (subfield)
Methods: Statistics, fMRI & imaging
Keywords: Spinal cord injury (SCI), Microglia depletion, Colony-stimulating factor-1 (CSF1R), Plexxikon (PLX) 5622, Inflammation, Functional recovery, Neurology, Neuroscience
MeSH: Anxiety*, Behavior, Animal*, Microglia*, Spinal Cord Injuries*, Animals, Disease Models, Animal, Female, Organic Chemicals, Rats, Rats, Inbred Lew, Recovery of Function, Spinal Cord (* major topic)
Topic: Spinal Cord Injury Research (Pathology and Forensic Medicine, Medicine), according to OpenAlex
Funding: Canadian Institute of Health Research (CIHR) (CIHR PS 175048 Fouad)
Citations: not cited yet (Europe PMC); 73 references in the paper

Abstract

We previously reported that inflammation, when coupled with motor training following spinal cord injury (SCI) in female rats, promotes neuroplasticity as evidenced by enhanced performance in the trained task. However, this beneficial effect was accompanied by exacerbated anxiety-like behaviours, which are also a recognized consequence of SCI itself. Given that microglia are central mediators of the inflammatory response, their pharmacological ablation may help to clarify their specific role in enhanced motor recovery and their contribution to anxiety exacerbation. To this end, we first aimed to determine the efficacy and impact of the microglia-depleting compound PLX5622 in rats after SCI, as its effects in this traumatic injury model remain poorly characterized. The present study investigated how a four-week PLX5622 diet, started one week post-cervical SCI, influences anxiety-related behaviours, microglial depletion in the central nervous system (CNS), and SCI lesion pathology in adult female Lewis rats. Following the PLX5622 diet, no impact on anxiety-like behaviour was observed. The treatment achieved partial microglial depletion in all CNS regions examined, though to a lesser extent than reported in mice; no microglia morphological changes were detected in the brain or spinal cord. As expected due to delayed treatment, SCI lesion sizes were comparable across groups, but PLX5622-treated rats exhibited a less compact and thinner astrocytic scar at the lesion core. Importantly, our data revealed that PLX5622 also reduces resident macrophage populations in the liver, highlighting that its effects extend beyond the CNS. The limited impact of PLX5622 in our rat model of SCI, together with its lack of microglia specificity, raises concerns about its suitability for isolating microglial contributions to neuroplasticity, particularly regarding anxiety-like behaviour and post-injury motor recovery.

Supplementary Information: The online version contains supplementary material available at 10.1038/s41598-026-48842-3.

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

Repository

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

cdoolin/rat-apps

License: MIT
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 236360e42016abb38211c0bb69e6cabd70d07db0, 13 March 2023
Languages: Python (7), Shell (1)
Size: 13 files, 8 scripts
Software Heritage: archived
Found in: the text, “Behavioural testing”
Holds: README, license file, environment (setup.py)
Not found: CITATION.cff, tests, continuous integration, documentation
Tools: NumPy (5 files), OpenCV (5 files)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
10 files
At the source: github.com/cdoolin/rat-apps

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;
  • 8 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

All data obtained from this study is available from the Spinal Cord Injury Open Data Commons (10.34945/F5MS4M).

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, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 8 keywords, 12 MeSH terms, 1 funder, 73 references.

Cite

This paper

Cucarian, J., Rakheja, R., Scatterty, K. R., Armstrong, E., Storvold, S., Nguyen, A. T., Fenrich, K., Monnier, P., & Fouad, K. (2026). PLX5622 did not alter anxiety-like behaviour and showed limited microglial depletion efficacy in a spinal cord injury model in female rats. Scientific reports, 16(1), 18749. https://doi.org/10.1038/s41598-026-48842-3

BibTeX

@article{cucarian2026plx5622,
author = {Cucarian, Jaison and Rakheja, Ram and Scatterty, Kale R and Armstrong, Edward and Storvold, Sydney and Nguyen, Antoinette T and Fenrich, Keith and Monnier, Philippe and Fouad, Karim},
title = {{PLX5622 did not alter anxiety-like behaviour and showed limited microglial depletion efficacy in a spinal cord injury model in female rats}},
journal = {Scientific reports},
year = {2026},
month = apr,
volume = {16},
number = {1},
pages = {18749},
publisher = {Nature Publishing Group},
issn = {2045-2322},
doi = {10.1038/s41598-026-48842-3},
url = {https://doi.org/10.1038/s41598-026-48842-3},
pmid = {42020492},
pmcid = {PMC13272775}
}

RIS

TY - JOUR
AU - Cucarian, Jaison
AU - Rakheja, Ram
AU - Scatterty, Kale R
AU - Armstrong, Edward
AU - Storvold, Sydney
AU - Nguyen, Antoinette T
AU - Fenrich, Keith
AU - Monnier, Philippe
AU - Fouad, Karim
TI - PLX5622 did not alter anxiety-like behaviour and showed limited microglial depletion efficacy in a spinal cord injury model in female rats
T2 - Scientific reports
J2 - Sci Rep
PY - 2026
DA - 2026/04/22
VL - 16
IS - 1
SP - 18749
SN - 2045-2322
PB - Nature Publishing Group
DO - 10.1038/s41598-026-48842-3
UR - https://doi.org/10.1038/s41598-026-48842-3
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41598-026-48842-3",
"type": "article-journal",
"title": "PLX5622 did not alter anxiety-like behaviour and showed limited microglial depletion efficacy in a spinal cord injury model in female rats",
"container-title": "Scientific reports",
"author": [
{
"family": "Cucarian",
"given": "Jaison"
},
{
"family": "Rakheja",
"given": "Ram"
},
{
"family": "Scatterty",
"given": "Kale R"
},
{
"family": "Armstrong",
"given": "Edward"
},
{
"family": "Storvold",
"given": "Sydney"
},
{
"family": "Nguyen",
"given": "Antoinette T"
},
{
"family": "Fenrich",
"given": "Keith"
},
{
"family": "Monnier",
"given": "Philippe"
},
{
"family": "Fouad",
"given": "Karim"
}
],
"container-title-short": "Sci Rep",
"volume": "16",
"issue": "1",
"page": "18749",
"DOI": "10.1038/s41598-026-48842-3",
"PMID": "42020492",
"PMCID": "PMC13272775",
"ISSN": "2045-2322",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41598-026-48842-3",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
22
]
]
}
}

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:10.1186/s12974-026-03852-w
Microglial Ccl4-Ccr5 signaling links systemic inflammation to synaptic loss and memory deficits in chronic kidney disease.
Journal: Journal of neuroinflammation
In common: rat, cellular / molecular, 4 references
[2] doi:10.1016/j.celrep.2026.117418 [code]
Astrocyte-microglia crosstalk via CSF1 and IFN-β promotes central nervous system repair.
Journal: Cell reports
In common: other condition, cellular / molecular, 4 references
[3] doi:10.1002/ctm2.70683 [code]
Niacin promotes motor function recovery after spinal cord injury via Hcar2-dependent microglia immunometabolic regulation.
Journal: Clinical and translational medicine
In common: other condition, cellular / molecular, 4 references
[4] doi:10.1126/sciadv.adz6517 [code]
Corticosterone-linked microglial activity underpins sexually dimorphic neuroplasticity after ketamine anesthesia.
Journal: Science advances
In common: NumPy, cellular / molecular, 3 references
[5] doi:10.1038/s41536-026-00475-w
The SHEDs-derived apoptotic bodies for inflammatory regulation in spinal cord repair.
Journal: NPJ Regenerative medicine
In common: other condition, cellular / molecular, 3 references
[6] doi:10.1007/s12035-026-05792-1
Identification and Experimental Validation of Biomarkers Associated with PI3K/AKT Signaling Pathway in Spinal Cord Injury.
Journal: Molecular neurobiology
In common: other condition, 3 references
[7] doi:10.1038/s41467-026-72639-7
Neuregulin-1 facilitates myelin regeneration through microglia-mediated mechanisms in a mouse model of chronic demyelination.
Journal: Nature communications
In common: cellular / molecular, 3 references
[8] doi:10.1073/pnas.2532488123 [code]
Control of microglial dynamics by the Arp2/3 complex and the autism- and schizophrenia-associated protein CYFIP1.
Journal: Proceedings of the National Academy of Sciences of the United States of America
In common: cellular / molecular, 3 references
[9] doi:10.1002/cns.70834
Wnt5a-Induced Exosomes From Bone Marrow Mesenchymal Stem Cells Promote Spinal Cord Injury Repair by Modulating Immune Cell Phenotypes and Alleviating Neuroinflammation via the NF-κB Pathway.
Journal: CNS neuroscience & therapeutics
In common: rat, other condition, cellular / molecular, 2 references
[10] doi:10.1016/j.celrep.2026.117411
Enhancing the specificity of microglia genetic targeting using a CSF1R inhibitor.
Journal: Cell reports
In common: cellular / molecular, 3 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.