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HIV-Associated Microstructural Abnormalities in Default Mode, Executive Control, and Salience Networks: Insights from Tensor-Valued Diffusion Encoding.

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Paper

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The authors' code

MATLAB · 67 lines · 1.6 KB · BSD-3-Clause

  1. function xps = mdm_xps_ge_xm1(sys, prot)
  2. % function xps = mdm_xps_ge_xm1(sys, prot)
  3. % Creates experimental parameter structure (xps) that is compatible with the
  4. % myltidimensional dMRI framework (https://github.com/markus-nilsson/md-dmri).
  5. % The xps is valid for the first (xm 1) GE implementation of free waveform
  6. % encoding. More info can be found at:
  7. % https://github.com/filip-szczepankiewicz/fwf_seq_resources
  8. %
  9. % If sys is only input we assume that it is the path to the .mat file that
  10. % contains the xps.
  11. % If both inputs are used, the file path is constructed and points to the
  12. % same folder as this function.
  14. if nargin == 1
  16. fnp = sys;
  18. else
  20. switch sys
  21. case 'XRMB'
  22. % Discovery MR450 1.5T
  23. % Discovery MR750 3.0T
  24. prefix = 'XRMB';
  26. case 'XRMW'
  27. % Optima MR450w 1.5T
  28. % Discovery MR750w 3.0T
  29. % SIGNA Artist
  30. % SIGNA Architect
  31. prefix = 'XRMW';
  33. case 'HRMW'
  34. % SIGNA Premier
  35. prefix = 'HRMW';
  37. otherwise
  38. error('System not recognised!')
  39. end
  42. switch prot
  43. case {1, 'short'}
  44. num = '001';
  46. case {2, 'intermediate', 'inter', 'med'}
  47. num = '002';
  49. case {3, 'long'}
  50. num = '003';
  52. otherwise
  53. error('Protocol not recognised!')
  54. end
  56. fn = [prefix num '.mat'];
  57. fnp = [fileparts(mfilename('fullpath')) filesep fn];
  59. end
  61. load(fnp);
  63. xps.gwf = permute(waveforms, [3 2 1]);

mdm_xps_ge_xm1.m at commit e23397c, under BSD-3-Clause · at the source

Overview

Authors: Md Nasir Uddin1,2,3, Abrar Faiyaz1, Chase R Figley4, Xing Qiu5, Miriam T Weber1, Giovanni Schifitto1,3,6
ORCID iDs: Md Nasir Uddin, Abrar Faiyaz, Chase R Figley, Miriam T Weber
  1. Department of Neurology, University of Rochester, Rochester, NY 14642, USA; (A.F.); (M.T.W.); (G.S.)
  2. Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
  3. Department of Electrical and Computer Engineering, University of Rochester, Rochester, NY 14627, USA
  4. Department of Radiology, University of Manitoba, Winnipeg, MB R3A 1R9, Canada
  5. Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14642, USA
  6. Department of Imaging Sciences, University of Rochester, Rochester, NY 14642, USA
Institutions: University of Rochester Medicine (United States); University of Rochester (United States); University of Manitoba (Canada)
Journal: Bioengineering (Basel, Switzerland), volume 13, issue 4, article 413
Dates: received 18 February 2026; accepted 28 March 2026; published online 1 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.3390/bioengineering13040413 · PMID 42072207 · PMCID PMC13113118 · OpenAlex W7147097408
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: structural MRI / diffusion (modality), other condition (population), cognitive (subfield)
Methods: Statistics, Preprocessing, Connectivity, fMRI & imaging
Keywords: tensor-valued diffusion MRI, HIV, brain, neuroimaging, default mode network, executive control network, salience network, cognition
Topic: HIV Research and Treatment (Virology, Immunology and Microbiology), according to OpenAlex
Funding: Foundation for the National Institutes of Health (R01MH118020, R01AG054328); University of Rochester (UR CABIN Pilot)
Citations: cited by 1 paper (Europe PMC); 67 references in the paper

Abstract

Cognitive impairment persists in people with HIV (PWH) despite effective combination antiretroviral therapy, possibly as a result of persistent alterations in white matter microstructural abnormalities in the brain. Noninvasive tensor-valued diffusion MRI (dMRI) is sensitive to microstructural integrity; thus, it may contribute to the understanding of HIV-associated cognitive impairment. In this exploratory cross-sectional study, 31 healthy controls (HCs) and 24 PWH underwent 3T MRI and neurocognitive assessment. Tensor-valued dMRI metrics, including microscopic fractional anisotropy (µFA) and isotropic, anisotropic, and total mean kurtosis (MKi, MKa, MKt), and conventional DTI and DKI metrics (FA, MD, and MK) were evaluated across six functionally defined brain networks. Compared with HCs, PWH exhibited reduced FA, µFA, and MKa in the dorsal default mode and anterior salience networks, along with increased MKi in the salience network and decreased MKi in the executive control network, with moderate effect sizes. Compared with HCs, PWH performed significantly worse on measures of learning, memory, and language, but showed no differences in executive function, attention, or processing speed. Additionally, significant associations and interactions between dMRI metrics and HIV status were observed, particularly for MKi and attention, executive function, and processing speed across the default mode, salience, and executive control networks. These preliminary findings underscore tensor-valued dMRI as a sensitive biomarker of network-specific neurocognitive vulnerability in HIV.

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

Repository

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

filip-szczepankiewicz/fwf_seq_resources

License: BSD-3-Clause
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: e23397c97e4b6f06476573b363aa16b6a3eb4583, 23 September 2026
Languages: MATLAB (10)
Size: 159 files, 10 scripts
Software Heritage: archived
Found in: the text, “2. Materials and Methods”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
12 files
At the source: github.com/filip-szczepankiewicz/fwf_seq_resources

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;
  • 10 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
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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 Statement

Anonymized data will be made available upon reasonable request, pending approval from the appropriate institutional review board.

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

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 8 keywords, 2 funders, 65 references.

Cite

This paper

Uddin, M. N., Faiyaz, A., Figley, C. R., Qiu, X., Weber, M. T., & Schifitto, G. (2026). HIV-Associated Microstructural Abnormalities in Default Mode, Executive Control, and Salience Networks: Insights from Tensor-Valued Diffusion Encoding. Bioengineering (Basel, Switzerland), 13(4), 413. https://doi.org/10.3390/bioengineering13040413

BibTeX

@article{uddin2026hiv,
author = {Uddin, Md Nasir and Faiyaz, Abrar and Figley, Chase R and Qiu, Xing and Weber, Miriam T and Schifitto, Giovanni},
title = {{HIV-Associated Microstructural Abnormalities in Default Mode, Executive Control, and Salience Networks: Insights from Tensor-Valued Diffusion Encoding}},
journal = {Bioengineering (Basel, Switzerland)},
year = {2026},
month = apr,
volume = {13},
number = {4},
pages = {413},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
issn = {2306-5354},
doi = {10.3390/bioengineering13040413},
url = {https://doi.org/10.3390/bioengineering13040413},
pmid = {42072207},
pmcid = {PMC13113118}
}

RIS

TY - JOUR
AU - Uddin, Md Nasir
AU - Faiyaz, Abrar
AU - Figley, Chase R
AU - Qiu, Xing
AU - Weber, Miriam T
AU - Schifitto, Giovanni
TI - HIV-Associated Microstructural Abnormalities in Default Mode, Executive Control, and Salience Networks: Insights from Tensor-Valued Diffusion Encoding
T2 - Bioengineering (Basel, Switzerland)
J2 - Bioengineering (Basel)
PY - 2026
DA - 2026/04/01
VL - 13
IS - 4
SP - 413
SN - 2306-5354
PB - Multidisciplinary Digital Publishing Institute (MDPI)
DO - 10.3390/bioengineering13040413
UR - https://doi.org/10.3390/bioengineering13040413
LA - en
ER -

CSL-JSON

{
"id": "10.3390/bioengineering13040413",
"type": "article-journal",
"title": "HIV-Associated Microstructural Abnormalities in Default Mode, Executive Control, and Salience Networks: Insights from Tensor-Valued Diffusion Encoding",
"container-title": "Bioengineering (Basel, Switzerland)",
"author": [
{
"family": "Uddin",
"given": "Md Nasir"
},
{
"family": "Faiyaz",
"given": "Abrar"
},
{
"family": "Figley",
"given": "Chase R"
},
{
"family": "Qiu",
"given": "Xing"
},
{
"family": "Weber",
"given": "Miriam T"
},
{
"family": "Schifitto",
"given": "Giovanni"
}
],
"container-title-short": "Bioengineering (Basel)",
"volume": "13",
"issue": "4",
"page": "413",
"DOI": "10.3390/bioengineering13040413",
"PMID": "42072207",
"PMCID": "PMC13113118",
"ISSN": "2306-5354",
"publisher": "Multidisciplinary Digital Publishing Institute (MDPI)",
"URL": "https://doi.org/10.3390/bioengineering13040413",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
1
]
]
}
}

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