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Temporal dynamics of neuroplasticity and neurodegeneration in the central auditory system following noise-induced hearing loss: a multimodal imaging and histological study.

Code ↔ Paper

2 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 2 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § Material and methods › Diffusion MRI (dMRI) ↔ mouse_singleShell_dtiConnectomics/mouse_connectome_7texpmri.sh, the whole file · a weak match · score 0.72 · connectivity matrices, Connectome reconstruction, optimization, SIFT2, sum, weighted
  2. [2] § Material and methods › Diffusion MRI (dMRI) ↔ rat_multishell_dtiConnectomics/rat_exvivo_prepro_7texpmri.sh, lines 43–85 · score 0.64 · bias field correction, sum, echo, maps, EPI, eddy

Paper

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The authors' code

Shell · 40 lines · 2.4 KB · no license · 1 match

  1. #!/bin/bash
  2. # connectome reconstruction
  3. # Script reconstructs connectome, does filtering, writes connectivity matrix
  4. # requires ANO.nii atlas and ANO.txt containing all structures and label IDs of the atlas
  7. for_each * : tckgen IN/mrtrix/wm.mif IN/mrtrix/100m.tck -seed_dynamic IN/mrtrix/wm.mif -select 100M -maxlength 30 -cutoff 0.06
  8. for_each * : tckgen IN/mrtrix/wm.mif IN/mrtrix/100k.tck -seed_dynamic IN/mrtrix/wm.mif -select 100K -maxlength 30 -cutoff 0.06
  10. # cutoff optimisation, define CCROI (corpus callosum)
  11. #for_each * : tckgen IN/mrtrix/wm.mif IN/mrtrix/5K_cutoff_XX.tck -seed_image IN/mrtrix/CCROI.mif -select 5K -maxlength 30 -cutoff XX
  13. # maxlength optimisation, define CCROI (corpus callosum)
  14. #for_each * : tckgen IN/mrtrix/wm.mif IN/mrtrix/5K_maxlength_XX.tck -seed_image IN/mrtrix/CCROI.mif -select 5K -maxlength XX -cutoff OPTIMIZEDVALUE
  16. # debugging with 10000 seeds
  17. #for_each * : tckgen IN/mrtrix/wm.mif IN/mrtrix/10M.tck -seed_dynamic IN/mrtrix/wm.mif -select 10000 -maxlength 250 -cutoff 0.06
  20. # sift_2
  21. for_each * : tcksift2 IN/mrtrix/100m.tck IN/mrtrix/wm.mif IN/mrtrix/tck_weights.txt -out_mu IN/mrtrix/SIFT2_mu.txt -out_coeffs IN/mrtrix/tck_coeffs.txt
  23. # upscale atlas and convert to mif with ascending label ids, probably not needed if original atlas has no missing values in between, check later
  24. #for_each * : mrresize IN/rc_ix_ANO.nii -vox 0.1 -interp IN/mrtrix/ANO_up.mif
  25. for_each * : cp IN/ANO_DTI.txt IN/mrtrix/atlas_lut.txt
  26. for_each * : labelconvert IN/ANO_DTI.nii IN/ANO_DTI.txt IN/mrtrix/atlas_lut.txt IN/mrtrix/atlas.mif
  28. # inpect AAL brain pacellations
  29. #mrview ../t1.nii.gz -plane 2 \ -overlay.load parc_aal.mif -overlay.opacity 0.2 -overlay.colourmap 3 -overlay.interpolation 0 &
  30. #head -n 50 aal.txt
  32. # connectome edge: sum of SIFT1 tractogram
  33. for_each * : tck2connectome IN/mrtrix/100m.tck IN/mrtrix/atlas.mif IN/mrtrix/connectome_di_sy.csv -tck_weights_in IN/mrtrix/tck_weights.txt -out_assignments IN/mrtrix/assignments_di_sy.txt -zero_diagonal -symmetric
  35. # generate exemplar streamlines for edges visualisation
  36. for_each * : connectome2tck IN/mrtrix/100m.tck IN/mrtrix/assignments_di_sy.txt IN/mrtrix/exemplars.tck -tck_weights_in IN/mrtrix/tck_weights.txt -exemplars IN/mrtrix/atlas.mif -files single
  38. # generate a smooth surface representation of each parcellation
  39. for_each * : label2mesh IN/mrtrix/atlas.mif IN/mrtrix/mesh.obj;
  40. for_each * : meshfilter IN/mrtrix/mesh.obj smooth IN/mrtrix/smoothed_atlas.obj

mouse_connectome_7texpmri.sh at commit 7f6ac19, no license · at the source

Overview

Authors: Víctor Giménez-Esbrí1,2,3, Susanne Schwitzer2, Susanne Mueller1,3,4, Stefan Koch1,3,4, Marco Foddis1,3,4, Stefan Donat5, Jan Schmoranzer5, Niclas Gimber5, Janina Zeqiraj2, Dietmar Basta2, Philipp Boehm-Sturm1,3,4, Moritz Gröschel6
ORCID iDs: Víctor Giménez-Esbrí, Susanne Mueller, Stefan Koch, Marco Foddis, Stefan Donat, Jan Schmoranzer, Niclas Gimber, Janina Zeqiraj, Dietmar Basta, Philipp Boehm-Sturm, Moritz Gröschel
  1. Charité Core Facility Experimental MRIs (RRID:SCR_017810), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
  2. HNO-Klinik, Zentrum für angewandte Medizintechnologie, Unfallkrankenhaus Berlin, Charité Medical School, Warener Str. 7, 12683 Berlin, Germany
  3. Department of Experimental Neurology and Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
  4. Charité 3R – Replace | Reduce | Refine, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
  5. Advanced Medical Bioimaging Core Facility (AMBIO), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
  6. Klinik für Hals-, Nasen-, Ohrenheilkunde, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
Institutions: Charité - Universitätsmedizin Berlin (Germany); Unfallkrankenhaus Berlin (Germany); Center for Stroke Research Berlin (Germany)
Journal: Acta neuropathologica communications, volume 14, issue 1, article 119
Dates: received 24 November 2025; accepted 5 February 2026; published online 2 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1186/s40478-026-02252-8 · PMID 42231490 · PMCID PMC13227874 · OpenAlex W4414194354
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.09.10.675281
Status: code verified
Categories: structural MRI / diffusion (modality), histology / microscopy (modality), mouse (organism), other condition (population)
Methods: Spectral & time-frequency, Statistics, Evoked potentials, Connectivity, fMRI & imaging, Physiology & signal measures, Preprocessing
Keywords: Noise-induced hearing loss, Neurodegeneration, Neuroplasticity, Central inferior colliculus, Ventral medial geniculate body of the thalamus
MeSH: Hearing Loss, Noise-Induced*, Nerve Degeneration*, Neuronal Plasticity*, Noise*, Animals, Anisotropy, Disease Models, Animal, Female, Geniculate Bodies, Inferior Colliculi, Male, Mice, Multimodal Imaging (* major topic)
Topic: Noise Effects and Management (Speech and Hearing, Health Professions), according to OpenAlex
Funding: Charité – Universitätsmedizin Berlin
Citations: not cited yet (Europe PMC); 90 references in the paper
Research resources: RRID:SCR_017810

Abstract

Noise-induced hearing loss (NIHL) is a sensorineural disorder that provokes complex neuroplastic and neurodegenerative changes within the central nervous system (CNS). This study investigated the temporal dynamics of neuronal density, axonal integrity and glutamatergic and GABAergic neurotransmission in the central inferior colliculus (CIC) and the ventral medial geniculate body of the thalamus (MGV) after NIHL. To achieve this, a correlative multimodal approach combining audiometric, magnetic resonance imaging (MRI) and histological biomarkers was performed. Adult mice were noise-exposed to broadband white noise (5–20 kHz) for 3 h at either high (115 dB SPL) or moderate (90 dB SPL) intensity, while unexposed mice served as controls. Separate cohorts of mice were investigated 1, 7, 56 and 84 days post-exposure using in vivo magnetic resonance imaging (MRI) techniques: Voxel-based morphometry (VBM) of gray matter density (GMD), diffusion MRI (dMRI) of microstructural connectivity, and proton magnetic resonance spectroscopy (1H-MRS) for glutamate and GABA quantification. Frequency-specific auditory brainstem responses (ABR) were recorded at 4, 8, 16 and 32 kHz before and after exposure to examine hearing threshold (HT) shifts. Brains were subsequently processed for fluorescence immunohistochemistry (FIHC) targeting NeuN, DAPI, NF, VGAT, VGLUT1 and VGLUT2. Mice exposed to 115 dB exhibited sustained HT elevations up to 84 days, suggesting a NIHL phenotype. Neurofilament (NF) expression significantly increased in the CIC and MGV 1d after 115 dB noise exposure, suggesting early axonal stress followed by normalization. dMRI alterations were observed 7d after 90 dB noise exposure. Glutamate and GABA decreases 84d after 90 dB exposure were also detected by 1H-MRS. No consistent changes in GMD or neuronal density were observed. Correlation analyses revealed weak relationships across audiometric, MRI and histological parameters. Overall, these findings reveal rapid neuroplastic adaptations following NIHL, and underscore the need for more sensitive biomarkers to detect early CNS consequences of NIHL.

Supplementary Information: The online version contains supplementary material available at 10.1186/s40478-026-02252-8.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

ChariteExpMri/rodentDtiConnectomics

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 7f6ac1998855219073a41ba5a839869683d2dbc8, 13 May 2022
Languages: Shell (10)
Size: 11 files, 10 scripts
Software Heritage: not archived
Found in: the text, “Diffusion MRI (dMRI)”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: MRtrix3 (8 files), FSL (2 files)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
11 files
At the source: github.com/ChariteExpMri/rodentDtiConnectomics

doi:10.12751/g-node.yx9wb4

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source: doi.org/10.12751/g-node.yx9wb4

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 10 scripts, each with its path and the digest of its content;
  • 2 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

All data, data analysis and scripts presented in the current manuscript will be openly available in the following open access repository: 10.12751/g-node.yx9wb4.

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 2, 28 September 2026

  • Authors: added Stefan Donat (0000-0003-3901-3733); Jan Schmoranzer (0000-0002-4482-7080); Dietmar Basta (0000-0002-8861-8459); removed Stefan Donat; Jan Schmoranzer; Dietmar Basta
  • Funding: added Charité – Universitätsmedizin Berlin

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 12 authors, 5 keywords, 13 MeSH terms, 87 references, 1 RRID.

Cite

This paper

Giménez-Esbrí, V., Schwitzer, S., Mueller, S., Koch, S., Foddis, M., Donat, S., Schmoranzer, J., Gimber, N., Zeqiraj, J., Basta, D., Boehm-Sturm, P., & Gröschel, M. (2026). Temporal dynamics of neuroplasticity and neurodegeneration in the central auditory system following noise-induced hearing loss: a multimodal imaging and histological study. Acta neuropathologica communications, 14(1), 119. https://doi.org/10.1186/s40478-026-02252-8

BibTeX

@article{gimenezesbri2026temporal,
author = {Giménez-Esbrí, Víctor and Schwitzer, Susanne and Mueller, Susanne and Koch, Stefan and Foddis, Marco and Donat, Stefan and Schmoranzer, Jan and Gimber, Niclas and Zeqiraj, Janina and Basta, Dietmar and Boehm-Sturm, Philipp and Gröschel, Moritz},
title = {{Temporal dynamics of neuroplasticity and neurodegeneration in the central auditory system following noise-induced hearing loss: a multimodal imaging and histological study}},
journal = {Acta neuropathologica communications},
year = {2026},
month = jun,
volume = {14},
number = {1},
pages = {119},
publisher = {BMC},
issn = {2051-5960},
doi = {10.1186/s40478-026-02252-8},
url = {https://doi.org/10.1186/s40478-026-02252-8},
pmid = {42231490},
pmcid = {PMC13227874}
}

RIS

TY - JOUR
AU - Giménez-Esbrí, Víctor
AU - Schwitzer, Susanne
AU - Mueller, Susanne
AU - Koch, Stefan
AU - Foddis, Marco
AU - Donat, Stefan
AU - Schmoranzer, Jan
AU - Gimber, Niclas
AU - Zeqiraj, Janina
AU - Basta, Dietmar
AU - Boehm-Sturm, Philipp
AU - Gröschel, Moritz
TI - Temporal dynamics of neuroplasticity and neurodegeneration in the central auditory system following noise-induced hearing loss: a multimodal imaging and histological study
T2 - Acta neuropathologica communications
J2 - Acta Neuropathol Commun
PY - 2026
DA - 2026/06/02
VL - 14
IS - 1
SP - 119
SN - 2051-5960
PB - BMC
DO - 10.1186/s40478-026-02252-8
UR - https://doi.org/10.1186/s40478-026-02252-8
LA - en
ER -

CSL-JSON

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