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Sensory nerve-derived signaling coordinates oropharyngeal structural organization that supports suckling and vocalization in neonatal mice.

Code ↔ Paper

5 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 5 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Artificial nipple assay › Spectral analysis ↔ getSuckFreqfromSpectra.m, the whole file · a weak match · score 0.81 · peak amplitude, peak frequency, spectral, power, signal
  2. [2] § Methods › Mice ↔ Seurat Integration.R, lines 41–81 · score 0.70 · E15.5, E18.5, E14.5, E13.5
  3. [3] § Results › AvCreERT2;Gdf11fl/fl mice with soft palatal muscle defects exhibit impaired suckling function and reduced nutritional intake efficiency ↔ getSuckFreqfromSpectra.m, the whole file · a weak match · score 0.67 · power spectrum, peak amplitude, peak frequency, suckling frequency
  4. [4] § Methods › Single-cell RNA sequencing (scRNA-seq) ↔ Seurat.rmd, lines 37–43 · score 0.61 · LogNormalize, ScaleData, variable, Seurat, RNA, gene
  5. [5] § Results › Trigeminal nerve-derived GDF11 signaling is essential for soft palatal muscle morphogenesis ↔ Seurat Integration.R, lines 41–81 · score 0.56 · E18.5, E14.5, E13.5

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

MATLAB · 29 lines · 1.1 KB · CC-BY-4.0 · 2 matches

  1. function [peakFreq peakAmp suckPower] = sacha_getSuckFreqfromSpectra(f,S,suckParams)
  2. % inputs:
  3. % signals - matrix
  4. % % S- power spectrum
  5. % f - frequencies for values of Sof signals to process (samples x trials)
  6. % suckParams - signal processing parameters for experiment
  7. % outputs%
  8. % peakFreq - peak frequency in spectrum
  9. % peakAmp - S amplitude at peak frequency
  10. % suckPower - avg power in suckling frequency band
  13. % estimate midpoint of spectral peak as the center of mass of the spectrum that comprises the peak above half the difference between
  14. % baseline (mean) power and peak power
  15. fpeak = f(S>(max(S)-mean(S))/2+mean(S));
  16. Speak = S(S>(max(S)-mean(S))/2+mean(S));
  17. peakFreq = sum((fpeak .* Speak'))/sum(Speak);
  18. %peakAmp = mean(S(find(S==max(S))));
  19. %peakAmp = mean(Speak);
  20. %peakFreq = median(fpeak);
  21. peakAmp = interp1(fpeak,Speak,peakFreq);
  23. % get avg power in suckling band
  24. fband_inds = find(f>=suckParams.powerBand(1) & f<=suckParams.powerBand(2));
  25. Sband = S(fband_inds);
  26. df = mean(diff(f));
  27. suckPower = sum(Sband)*df/(suckParams.powerBand(2)-suckParams.powerBand(1));

getSuckFreqfromSpectra.m, under CC-BY-4.0 · at the source

Overview

Authors: Sa Cha1, Jifan Feng1, Tingwei Guo1, Lin Meng1, Peng Chen1, Calista Ly1, Thach-Vu Ho1, Pedro A. Sanchez-Lara2, Lauren E. McElvain3, Jeffrey D. Moore3, Yang Chai1
ORCID iDs: Sa Cha, Lin Meng, Lauren E. McElvain, Yang Chai
  1. Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California,Los Angeles, CA USA
  2. Section of Medical Genetics, Department of Pediatrics, Guerin Children’s at Cedars-Sinai Medical Center,Los Angeles, CA USA
  3. Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California,Los Angeles, CA USA
Institutions: University of Southern California (United States); Cedars-Sinai Medical Center (United States)
Journal: Nature communications, volume 17, issue 1, article 9970
Dates: received 5 September 2025; accepted 16 June 2026; published online 14 July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-74959-0 · PMID 42449098 · PMCID PMC13588789 · OpenAlex W7168268863
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), developmental (subfield)
Methods: Spectral & time-frequency, Connectivity, Statistics, Smoothing, state filtering, decompositions, Evoked potentials
Keywords: Morphogenesis, Experimental models of disease
MeSH: Oropharynx*, Sensory Receptor Cells*, Vocalization, Animal*, Animals, Animals, Newborn, Animals, Suckling, Bone Morphogenetic Proteins, Female, Growth Differentiation Factors, Male, Mice, Mice, Knockout, Neural Crest, Palate, Soft, Proto-Oncogene Proteins c-akt, Signal Transduction, Trigeminal Nerve (* major topic)
Topic: Cleft Lip and Palate Research (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR) (R01 DE012711, U01 DE028729)
Citations: not cited yet (Europe PMC); 80 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repositories

Its files are read in the Code ↔ Paper reader above, with 5 matches between paragraphs and lines of code.

Zenodo 20251696

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Languages: MATLAB (5)
Size: 6 files, 5 scripts
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Chronux (1 file), 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)
5 files
At the source:

Zenodo 15085996

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: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (2 files), Matplotlib (2 files), NumPy (2 files), pandas (2 files), patchwork (2 files), Scanpy (2 files), SciPy (2 files), Seurat (2 files), tidyverse (2 files), anndata (1 file), cowplot (1 file), PyTorch (1 file), seaborn (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
4 files
At the source:

chailabusc/code

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 2fa624671c8217e7a590cf9b5c33aebcc9589e56, 16 April 2025
Languages: Jupyter (2), R (2)
Size: 6 files, 4 scripts
Software Heritage: not archived
Found in: the Zenodo archive record
Holds: README, 3 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (2 files), Matplotlib (2 files), NumPy (2 files), pandas (2 files), patchwork (2 files), Scanpy (2 files), SciPy (2 files), Seurat (2 files), tidyverse (2 files), anndata (1 file), cowplot (1 file), PyTorch (1 file), seaborn (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
5 files
At the source: github.com/ChaiLabUSC/code/tree/V1.0.0

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it points to the authors' code: Zenodo 15085996, Zenodo 20251696

Read it in the paper: doi.org/10.1038/s41467-026-74959-0.

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:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 13 scripts, each with its path and the digest of its content;
  • 5 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.

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it points to the authors' code: Zenodo 15085996, Zenodo 20251696

Read it in the paper: doi.org/10.1038/s41467-026-74959-0.

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, 11 authors, 2 keywords, 17 MeSH terms, 1 funder, 75 references.

Cite

This paper

Cha, S., Feng, J., Guo, T., Meng, L., Chen, P., Ly, C., Ho, T.-V., Sanchez-Lara, P. A., McElvain, L. E., Moore, J. D., & Chai, Y. (2026). Sensory nerve-derived signaling coordinates oropharyngeal structural organization that supports suckling and vocalization in neonatal mice. Nature communications, 17(1), 9970. https://doi.org/10.1038/s41467-026-74959-0

BibTeX

@article{cha2026sensory,
author = {Cha, Sa and Feng, Jifan and Guo, Tingwei and Meng, Lin and Chen, Peng and Ly, Calista and Ho, Thach-Vu and Sanchez-Lara, Pedro A. and McElvain, Lauren E. and Moore, Jeffrey D. and Chai, Yang},
title = {{Sensory nerve-derived signaling coordinates oropharyngeal structural organization that supports suckling and vocalization in neonatal mice}},
journal = {Nature communications},
year = {2026},
month = jul,
volume = {17},
number = {1},
pages = {9970},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-74959-0},
url = {https://doi.org/10.1038/s41467-026-74959-0},
pmid = {42449098},
pmcid = {PMC13588789}
}

RIS

TY - JOUR
AU - Cha, Sa
AU - Feng, Jifan
AU - Guo, Tingwei
AU - Meng, Lin
AU - Chen, Peng
AU - Ly, Calista
AU - Ho, Thach-Vu
AU - Sanchez-Lara, Pedro A.
AU - McElvain, Lauren E.
AU - Moore, Jeffrey D.
AU - Chai, Yang
TI - Sensory nerve-derived signaling coordinates oropharyngeal structural organization that supports suckling and vocalization in neonatal mice
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/07/14
VL - 17
IS - 1
SP - 9970
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-74959-0
UR - https://doi.org/10.1038/s41467-026-74959-0
LA - en
ER -

CSL-JSON

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"id": "10.1038/s41467-026-74959-0",
"type": "article-journal",
"title": "Sensory nerve-derived signaling coordinates oropharyngeal structural organization that supports suckling and vocalization in neonatal mice",
"container-title": "Nature communications",
"author": [
{
"family": "Cha",
"given": "Sa"
},
{
"family": "Feng",
"given": "Jifan"
},
{
"family": "Guo",
"given": "Tingwei"
},
{
"family": "Meng",
"given": "Lin"
},
{
"family": "Chen",
"given": "Peng"
},
{
"family": "Ly",
"given": "Calista"
},
{
"family": "Ho",
"given": "Thach-Vu"
},
{
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"given": "Pedro A."
},
{
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"given": "Lauren E."
},
{
"family": "Moore",
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}
],
"container-title-short": "Nat Commun",
"volume": "17",
"issue": "1",
"page": "9970",
"DOI": "10.1038/s41467-026-74959-0",
"PMID": "42449098",
"PMCID": "PMC13588789",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41467-026-74959-0",
"language": "en",
"issued": {
"date-parts": [
[
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7,
14
]
]
}
}

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

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