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Thalamic reticular neurons provide cell type-specific modulation of sound processing in the auditory thalamus.

Code ↔ Paper

6 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 6 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and methods › Computational modeling ↔ TRN_MGB_celltypespecific-main.zip/simulations/GJ_PV_SOM/PV_SOM_inh/TRN_div/simParams.m, lines 1–67 · score 0.86 · Electrical synapses, Capacitance, cm2, leak, rise, AR
  2. [2] § Materials and methods › Computational modeling ↔ TRN_MGB_celltypespecific-main.zip/simulations/GJ_PV_SOM/PV_SOM_inh/TRN_div/dsim.m, lines 52–86 · score 0.57 · rectifier, AR, K2, Kd, Kt, NaT
  3. [3] § Materials and methods › Acute electrophysiological recordings ↔ Rolon_Martinez_2024-main.zip/Jupyter notebooks/previous_code/SpikeAnalysis_All_Mice_PaperCode_Final2.ipynb, lines 815–885 · score 0.53 · OpenEphys, spike sorted, viral, probe, Mice, Stimuli
  4. [4] § Materials and methods › Acute electrophysiological recordings ↔ Rolon_Martinez_2024-main.zip/Jupyter notebooks/previous_code/SpikeAnalysis_All_Mice_PaperCode_Final2_MUA.ipynb, lines 917–993 · score 0.53 · OpenEphys, spike sorted, viral, probe, Mice, Stimuli
  5. [5] § Results › Specifics of connectivity between MGB-TRN circuits determine the sign of MGB responses during TRN cell-type inactivation ↔ TRN_MGB_celltypespecific-main.zip/simulations/GJ_PV_SOM/recip_div_TRN_inh/extractData.m, the whole file · a weak match · score 0.51 · Divergence ratio, Reciprocal ratio, TRN MGB, silencing, HO, peak
  6. [6] § Results › Specifics of connectivity between MGB-TRN circuits determine the sign of MGB responses during TRN cell-type inactivation ↔ TRN_MGB_celltypespecific-main.zip/simulations/recip_div_TRN_wSOMlat_inh/extractData.m, the whole file · a weak match · score 0.51 · Divergence ratio, Reciprocal ratio, TRN MGB, silencing, HO, peak

Paper

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

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The authors' code

MATLAB · 95 lines · 2.6 KB · MIT · 1 match

  1. classdef simParams
  2. % Parameters passed to a dsim function
  3. % 'default' values:
  4. properties
  5. g_ca_lts = 0.75; %gca of .75 with leak of .1 is good;
  6. g_nat = 60.5;
  7. g_kd = 60;
  8. g_nap = 0;
  9. g_kt = 5;
  10. g_k2 = .5;
  11. g_ar = 0.025;
  12. g_L = 0.1;
  13. g_GtACR = 10;
  14. E_na = 50;
  15. E_k = -100;
  16. E_ca = 125;
  17. E_ar = -40;
  18. E_L = -75;
  19. E_GtACR = -70;
  20. E_AMPA = 0;
  21. E_GABA = -100;
  22. C = 1; % membrance capacitance uF/cm^2
  23. Ti1 = 5; %Inh rise time constant %1e-4/5e-4 is good for b-let.
  24. Ti2 = 35; %fall time constant %5e-3 / 20e-3 ?? ~50 ms rise.
  25. Te1 = 5; %Exc
  26. Te2 = 35;
  27. GtACR_on = {};
  28. GtACR_off = {};
  30. n
  31. names
  32. per_neuron
  33. s0
  34. Rin
  35. vm_rest
  37. %DC pulses
  38. bias
  39. iDC % uA/cm2; DC .25 is ~TR for burst
  40. istart={};
  41. %istop={};
  43. %Alpha/Beta Synapses
  44. A %amplitude of AMPAergic input to cell 1. (0.2)
  45. tA={}; %arrival time of AMPAergic input to cell 1.
  47. AI %amplitude of GABAergic input to cell 1.
  48. tAI={}; %arrival time of GABAergic input to cell 1.
  50. A_TC_MGB =0; %amplitude of AMPAergic TC synapses
  51. A_TC_HO =0;
  52. A_TCx_MGB =0; %TC cross-exc MGB->SOM
  53. A_TCx_HO =0; % HO->PV
  54. AI_TRN_PV =0; %amplitude of GABAergic TRN synapses
  55. AI_TRN_SOM =0;
  56. AI_TRNx_PV =0; %TRN cross-inh PV-|HO
  57. AI_TRNx_SOM=0; % SOM-|MGB
  58. AI_TRNi_PV =0; %intra-TRN inh PV-|SOM
  59. AI_TRNi_SOM=0; % SOM-|PV
  61. %Electrical Synapses
  62. Gc_total
  63. gj
  64. cc
  65. end
  67. methods
  68. function sp = simParams(namesOfNeurons,per_neuron,s0)
  69. if nargin > 0
  70. sp.names = namesOfNeurons;
  71. sp.n = length(namesOfNeurons);
  72. sp.per_neuron = per_neuron;
  73. sp.s0 = s0;
  75. sp.g_L(1:sp.n) = 0.1;
  77. sp.bias(1:sp.n) = 0;
  79. sp.iDC(1:sp.n) = 0;
  80. sp.istart(1:sp.n) = {0};
  82. sp.A(1:sp.n) = 0;
  83. sp.tA(1:sp.n) = {0};
  85. sp.AI(1:sp.n) = 0;
  86. sp.tAI(1:sp.n) = {0};
  88. sp.GtACR_on(1:sp.n) = {0};
  89. sp.GtACR_off(1:sp.n) = {0};
  91. sp.gj=zeros(sum(startsWith(namesOfNeurons,'TRN')));
  92. end
  93. end
  94. end
  95. end

simParams.m, under MIT · at the source

Overview

Authors: Solymar Rolón-Martínez1, Austin J Mendoza2, Christopher F Angeloni1, Nathan W Vogler1, Audrey C Drotos1, Mark Aizenberg1, Ruoyi Chen1, Kaylie Vu2, Julie S Haas2, Maria N Geffen1,3
ORCID iDs: Maria N Geffen
  1. Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
  2. Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
  3. Departments of Neuroscience and Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
Institutions: University of Pennsylvania (United States); Lehigh University (United States)
Journal: PLoS biology, volume 24, issue 3, article e3003693
Dates: received 27 March 2025; accepted 23 February 2026; published online 12 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pbio.3003693 · PMID 41818303 · PMCID PMC12998953 · OpenAlex W7135042092
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), systems (subfield)
Methods: Statistics, Preprocessing, Evoked potentials, fMRI & imaging, Single-unit activity, calcium imaging
MeSH: Auditory Pathways*, Auditory Perception*, Geniculate Bodies*, Neurons*, Thalamus*, Acoustic Stimulation, Animals, Auditory Cortex, Female, Male, Mice, Parvalbumins, Somatostatin, Thalamic Nuclei (* major topic)
Topic: Hearing, Cochlea, Tinnitus, Genetics (Sensory Systems, Neuroscience), according to OpenAlex
Funding: National Institute on Deafness and Other Communication Disorders (R01DC15527, R01DC014479, R03DC013660, F31DC016524, F31DC018473); NINDS NIH HHS (R01 NS128713); National Institutes of Health (R01NS113241); Foundation for the National Institutes of Health (R01 NS128713)
Citations: cited by 3 papers (Europe PMC); 87 references in the paper
Research resources: RRID:AB_10000343, RRID:AB_2633275, RRID:AB_2633280, RRID:AB_2721226, RRID:AB_2896330, 20067 RRID:AB_572264, RRID:IMSR_JAX:002756, SST-Cre mice RRID:IMSR_JAX:013044, RRID:IMSR_JAX:017320

Abstract

Inhibition plays an important role in controlling the flow and processing of auditory information throughout the central auditory pathway, yet how inhibitory circuits shape auditory processing in the medial geniculate body (MGB), the key region in the auditory thalamus, is poorly understood. The MGB gates the flow of auditory information to the auditory cortex, and it is inhibited largely by the thalamic reticular nucleus (TRN). The TRN contains two major classes of inhibitory neurons: parvalbumin (PVTRN)-positive and somatostatin (SSTTRN)-positive neurons. PV and SST neurons have been shown to play differential roles in controlling sound responses in auditory cortex. In the somatosensory and visual subregions of the TRN, PVTRN and SSTTRN neurons exhibit anatomical and functional differences. However, it remains unknown whether and how PVTRN and SSTTRN neurons differ in their anatomical projections from the TRN to the auditory thalamus, and whether and how they differentially modulate activity in the MGB. Here, we investigated virally labeled projections of PVTRN or SSTTRN neurons, and recorded neuronal responses in the MGB of awake, head-fixed mice while presenting sound stimuli and selectivity suppressing PVTRN or SSTTRN neurons on a subset of trials. We find that PVTRN and SSTTRN neurons exhibit differential projection patterns within the auditory thalamus: PVTRN neurons predominantly project to ventral MGB, whereas SSTTRN neurons project to the dorso-medial regions of MGB. Optogenetic inactivation of PVTRN neurons bidirectionally modulated sound-evoked activity in MGB, increasing firing in 29% of MGB neurons, while suppressing firing in 41%. In contrast, inactivating SSTTRN neurons largely suppressed tone-evoked activity in MGB neurons. Cell type-specific computational models identified candidate circuit mechanisms for generating the differential effects of TRN inactivation on MGB sound responses. These distinct inhibitory pathways within the auditory thalamus reveal cell type-specific organization of thalamic inhibition in auditory computation.

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 6 matches between paragraphs and lines of code.

Zenodo 18601673

License: MIT
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Size: 2 files
Software Heritage: not checked
Found in: “Data Availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (17 files), pandas (17 files), SciPy (17 files), Matplotlib (15 files), seaborn (15 files), Parallel Computing Toolbox (11 files), Signal Processing Toolbox (11 files), statsmodels (8 files), scikit-learn (7 files)
Availability: 2 checks, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
80 files
At the source: doi.org/10.5281/zenodo.18601673

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;
  • 78 scripts, each with its path and the digest of its content;
  • 6 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

Datasets cited

Data Availability

Source data has been deposited in Dryad: https://doi.org/10.5061/dryad.f7m0cfzb1 [86]. Data analysis code is available on Zenodo: https://doi.org/10.5281/zenodo.18601673 [87]. Numerical data underlying the figures are available in the Supporting information files.

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, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 14 MeSH terms, 4 funders, 87 references, 9 RRIDs.

Cite

This paper

Rolón-Martínez, S., Mendoza, A. J., Angeloni, C. F., Vogler, N. W., Drotos, A. C., Aizenberg, M., Chen, R., Vu, K., Haas, J. S., & Geffen, M. N. (2026). Thalamic reticular neurons provide cell type-specific modulation of sound processing in the auditory thalamus. PLoS biology, 24(3), e3003693. https://doi.org/10.1371/journal.pbio.3003693

BibTeX

@article{rolonmartinez2026thalamic,
author = {Rolón-Martínez, Solymar and Mendoza, Austin J and Angeloni, Christopher F and Vogler, Nathan W and Drotos, Audrey C and Aizenberg, Mark and Chen, Ruoyi and Vu, Kaylie and Haas, Julie S and Geffen, Maria N},
title = {{Thalamic reticular neurons provide cell type-specific modulation of sound processing in the auditory thalamus}},
journal = {PLoS biology},
year = {2026},
month = mar,
volume = {24},
number = {3},
pages = {e3003693},
publisher = {PLOS},
issn = {1544-9173},
doi = {10.1371/journal.pbio.3003693},
url = {https://doi.org/10.1371/journal.pbio.3003693},
pmid = {41818303},
pmcid = {PMC12998953}
}

RIS

TY - JOUR
AU - Rolón-Martínez, Solymar
AU - Mendoza, Austin J
AU - Angeloni, Christopher F
AU - Vogler, Nathan W
AU - Drotos, Audrey C
AU - Aizenberg, Mark
AU - Chen, Ruoyi
AU - Vu, Kaylie
AU - Haas, Julie S
AU - Geffen, Maria N
TI - Thalamic reticular neurons provide cell type-specific modulation of sound processing in the auditory thalamus
T2 - PLoS biology
J2 - PLoS Biol
PY - 2026
DA - 2026/03/12
VL - 24
IS - 3
SP - e3003693
SN - 1544-9173
PB - PLOS
DO - 10.1371/journal.pbio.3003693
UR - https://doi.org/10.1371/journal.pbio.3003693
LA - en
ER -

CSL-JSON

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