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Alpha-synuclein overexpression reduces neural activity within a basal ganglia vocal nucleus in a zebra finch model.

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. [1] § 3. Results › 3.2. Extracellular identification of neuronal subtypes in anesthetized finches ↔ ZEB_Classify_Neurons.m, lines 1–73 · score 0.91 · low threshold spiking, awake finches, MSN neurons, low firing rates, waveform features, wide waveforms
  2. [2] § 3. Results › 3.2. Extracellular identification of neuronal subtypes in anesthetized finches ↔ ZEB_Classify_Neurons.m, lines 1–73 · score 0.74 · PAL neurons, high firing rates, Waveform features, wide waveforms, awake, tonic
  3. [3] § 3. Results › 3.2. Extracellular identification of neuronal subtypes in anesthetized finches ↔ ZEB_Classify_Neurons.m, lines 416–442 · score 0.52 · clear bimodality, spike width, trough width, Hz, firing rate, classification

Paper

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

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The authors' code

MATLAB · 453 lines · 20 KB · no license · 3 matches

This file is not shown here: its repository has no license, so its authors keep all their rights to it. Your browser cannot show it from its source either: PubMed Central's collection of supplementary files does not let the page of another site read them.

It can be read in its repository, supp:PMC13374917/pone.0333158.s010.zip.

Overview

Authors: Brian R Dominguez1, Gabriel Holguin2, Madeleine S Daly1, Reed T Bjork1, Stephen L Cowen2,3, Julie E Miller1,4
ORCID iDs: Julie E Miller
  1. Department of Neuroscience, University of Arizona, Tucson, Arizona, United States of America
  2. Department of Psychology, University of Arizona, Tucson, Arizona, United States of America
  3. Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, Arizona, United States of America
  4. Departments of Speech, Language and Hearing Sciences, Neurology, Graduate Interdisciplinary Program in Neuroscience, and the BIO5 Institute, Tucson, Arizona, United States of America
Institutions: University of Arizona (United States); BIO5 Institute
Journal: PloS one, volume 21, issue 7, article e0333158
Dates: received 26 September 2025; accepted 22 June 2026; published online 16 July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pone.0333158 · PMID 42461894 · PMCID PMC13374917 · OpenAlex W4414258321
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.09.11.675693
Status: code verified
Categories: human (organism), other (organism), Parkinson's (population), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Evoked potentials, Single-unit activity, calcium imaging, Physiology & signal measures
MeSH: alpha-Synuclein*, Basal Ganglia*, Finches*, Neurons*, Vocalization, Animal*, Animals, Dependovirus, Humans, Male (* major topic)
Topic: Animal Vocal Communication and Behavior (Developmental Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: NINDS NIH HHS (R21 NS123512)
Citations: not cited yet (Europe PMC); 111 references in the paper
Research resources: RRID:AB_2192672, RRID:AB_2535813, RRID:SCR_023355

Abstract

Changes in vocal pitch, loudness, and timing are prevalent in Parkinson’s Disease (PD) and a target for early intervention and treatment. The neural mechanisms underlying these impairments are not understood, motivating work in animal models. The adult male zebra finch songbird is uniquely poised for these studies given vocally-dedicated brain nuclei and a quantifiable output (birdsong). Our prior publication revealed that injection of an adeno-associated virus (AAV5) expressing the human (h) alpha-synuclein (hSNCA, a-syn) gene into basal ganglia vocal nucleus Area X results in elevated insoluble a-syn protein and parkinsonian-like changes including softer, shorter, and reduced vocalizations compared to controls. Here, we test the hypothesis that AAV-hSNCA overexpression reduces the firing rate of specific neuronal sub-types in Area X using in vivo recordings in anesthetized finches. Five classes of neurons were differentiated in AAV-treated finches based on waveform width (narrow vs. wide) and firing rates (low vs. high). We found that neurons in the AAV-hSNCA group with wide waveforms exhibited reduced firing rates and enhanced post-peak rebound compared to AAV controls. No differences in firing rate nor waveform shape were detected for the narrow waveform neurons. Our findings provide the first characterization of early a-syn-driven neural activity changes in vocal control neurocircuitry.

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 3 matches between paragraphs and lines of code.

supp:PMC13374917/pone.0333158.s010.zip

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Languages: MATLAB (7)
Size: 8 files, 7 scripts
Software Heritage: not checked
Found in: the supplementary material
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Statistics and Machine Learning Toolbox (3 files), Signal Processing Toolbox (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
8 files, to read at the source

This repository has no license: its authors keep all rights. Read it at the source.

At the source: pmc-oa-opendata.s3.amazonaws.com/PMC13374917.1/pone.0333158.s010.zip

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;
  • 7 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

The raw electrophysiological data, birdsong data, and microscopy images (Fig 2) used in this study will be available at the time of publication through the University of Arizona figshare ReData Repository, under a CC-BY license. https://doi.org/10.25422/azu.data.27868266 All other data including the Matlab code used for the electrophysiological analyses can be found in the Supporting Information.

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, 6 authors, 9 MeSH terms, 1 funder, 109 references, 3 RRIDs.

Cite

This paper

Dominguez, B. R., Holguin, G., Daly, M. S., Bjork, R. T., Cowen, S. L., & Miller, J. E. (2026). Alpha-synuclein overexpression reduces neural activity within a basal ganglia vocal nucleus in a zebra finch model. PloS one, 21(7), e0333158. https://doi.org/10.1371/journal.pone.0333158

BibTeX

@article{dominguez2026alpha,
author = {Dominguez, Brian R and Holguin, Gabriel and Daly, Madeleine S and Bjork, Reed T and Cowen, Stephen L and Miller, Julie E},
title = {{Alpha-synuclein overexpression reduces neural activity within a basal ganglia vocal nucleus in a zebra finch model}},
journal = {PloS one},
year = {2026},
month = jul,
volume = {21},
number = {7},
pages = {e0333158},
publisher = {PLOS},
issn = {1932-6203},
doi = {10.1371/journal.pone.0333158},
url = {https://doi.org/10.1371/journal.pone.0333158},
pmid = {42461894},
pmcid = {PMC13374917}
}

RIS

TY - JOUR
AU - Dominguez, Brian R
AU - Holguin, Gabriel
AU - Daly, Madeleine S
AU - Bjork, Reed T
AU - Cowen, Stephen L
AU - Miller, Julie E
TI - Alpha-synuclein overexpression reduces neural activity within a basal ganglia vocal nucleus in a zebra finch model
T2 - PloS one
J2 - PLoS One
PY - 2026
DA - 2026/07/16
VL - 21
IS - 7
SP - e0333158
SN - 1932-6203
PB - PLOS
DO - 10.1371/journal.pone.0333158
UR - https://doi.org/10.1371/journal.pone.0333158
LA - en
ER -

CSL-JSON

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The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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