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Intracellular fluid accumulation underlies brain volume increases in early Alzheimer's disease.

Code ↔ Paper

4 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 4 matches
  1. [1] § Materials and methods › Statistical analysis ↔ Create_Table_demographics.m, lines 80–158 · score 0.76 · AD signature, S100B, hippocampal volume, sTREM2, CL, IL6
  2. [2] § Results › Association of GM volume with amyloid-PET positivity, CSF Aβ42/40, IVIM parameters, and MD ↔ Scatterplots_DWI_metrics_vs_GMvolumes_PET_CL_cluster.m, lines 2–21 · score 0.61 · slow signal portion, fast DC, perfusion fraction, slow DC, PET, SSP
  3. [3] § Materials and methods › DWI quantifications ↔ Scatterplots_DWI_metrics_vs_GMvolumes_PET_CL_cluster.m, lines 2–21 · score 0.60 · slow signal portion, fast DC, slow DC, tissue, DWI, SSP
  4. [4] § Materials and methods › Statistical analysis ↔ Scatterplots_DWI_metrics_vs_GMvolumes_PET_CL_cluster.m, lines 32–86 · score 0.50 · stat maps, GM volume, Clusters, status, PET, variables

Paper

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The authors' code

MATLAB · 86 lines · 3.3 KB · MIT · 3 matches

  1. %% Load data
  2. clear, clc, close all
  3. addpath('..')
  4. path_DWI = 'D:\Projects\2023_multib\MK_multi_b\Stats_group_level_297_subjs\Mediation_analysis\';
  5. list_phys_variables = {'slow_ADC'; 'fast_ADC'; 'slow_signal_portion'; 'tissueFraction'; 'meanDiffusivity'};
  6. list_phys_variables_long_name = { ...
  7. 'Slow DC (a.u.)'; ...
  8. 'Fast DC (a.u.)'; ...
  9. 'SSP (a.u.)'; ...
  10. 'Perfusion fraction (a.u.)'; ...
  11. 'Mean diffusivity (10^{-3} mm²/s)'};
  12. list_stat_maps = {'PET_CLs_group_p0.005.nii'; 'Ab4240_elecsys_continuous_p0.005.nii'};
  13. n_stat_maps = length(list_stat_maps);
  14. sample = 'all_subjs'; % 'A-T-' or 'all_subjs'
  15. load('Table_297_subjs_demographics_biomarkers_2024_05_03.mat')
  16. n_subjects = size(T_subjects,1);
  17. %% Load fluid biomarkers and attach missing fields
  18. path_fluid_biomarkers = '..\..\Biomarkers\f_bmk_long_09_05_23.xlsx';
  19. T_fluid_biomarkers = readtable(path_fluid_biomarkers);
  20. list_subject_IDs = str2double(T_subjects.Subject_ID);
  21. list_B = T_fluid_biomarkers.IdParticipante;
  22. [found, idx] = ismember(list_subject_IDs, list_B, 'rows');
  23. T_subjects.Ab42_elecsys = T_fluid_biomarkers.Ab42_CSFNC_RocheElecsys_BL(idx);
  24. %% Scatterplots (GM volume vs diffusion metrics)
  25. close all, clc
  26. id_stat_map = 4; % 1: Ab PET (group), 4: Ab CSF continuous (elecsys)
  27. disp(list_stat_maps{id_stat_map})
  28. path_DWI_stat = [path_DWI, 'DWI_pars_signif_ROIs_all_subjs_', list_stat_maps{id_stat_map}, '.mat'];
  29. load(path_DWI_stat) % loads T_DWI_pars
  30. % Group indices
  31. ind_AmTm = find(strcmp(T_subjects.AT_status,'A-T-'));
  32. ind_ApTm = find(strcmp(T_subjects.AT_status,'A+T-'));
  33. ind_ApTp = find(strcmp(T_subjects.AT_status,'A+T+'));
  34. T_Stats = nan(5,2); % [r, p] per parameter
  35. for i_phys = 1:5
  36. phys_variable = list_phys_variables{i_phys};
  37. fprintf('------------------------- \n')
  38. disp(phys_variable)
  39. % x: DWI parameter within significant clusters; y: GM volume
  40. eval(sprintf('x = T_DWI_pars.DWI_%s;', phys_variable))
  41. y = T_DWI_pars.GMvol;
  42. if i_phys == 5, x = x*1000; end % scale MD to 10^{-3} mm²/s
  43. % Remove outliers in x only (as in original)
  44. ind_outliers = isoutlier(x);
  45. x(ind_outliers) = nan;
  46. n_samples_test = length(x) - sum(isnan(x));
  47. fprintf('Sample size N: %d \n', n_samples_test)
  48. % Scatter + LS fit (overall)
  49. figure('Position',[652 692 328 283])
  50. scatter(x, y, 5, 'filled', 'k'); hold on
  51. xlabel(list_phys_variables_long_name{i_phys}, 'Interpreter','tex');
  52. ylabel('GM volume (a.u.)')
  53. h = lsline; h.LineWidth = 2; h.Color = [0.5 0.5 0.5];
  54. grid on
  55. [corr_r, corr_p] = corr(x, y, 'rows','complete');
  56. fprintf('Corr: %3.2f, p-value: %3.3f \n', corr_r, corr_p)
  57. T_Stats(i_phys,1) = corr_r;
  58. T_Stats(i_phys,2) = corr_p;
  59. % Overlay groups with shapes/colors
  60. par_size = 20; par_linewidth = 0.1; par_edge_colour = [0.2 0.2 0.2];
  61. scatter(x(ind_AmTm), y(ind_AmTm), par_size, [0.4660 0.6740 0.1880], 'filled', ...
  62. 'MarkerEdgeColor', par_edge_colour, 'LineWidth', par_linewidth);
  63. scatter(x(ind_ApTm), y(ind_ApTm), par_size, [0 0.4470 0.7410], 's', 'filled', ...
  64. 'MarkerEdgeColor', par_edge_colour, 'LineWidth', par_linewidth);
  65. scatter(x(ind_ApTp), y(ind_ApTp), par_size, [1 0 1], 'd', 'filled', ...
  66. 'MarkerEdgeColor', par_edge_colour, 'LineWidth', par_linewidth);
  67. end

Scatterplots_DWI_metrics_vs_GMvolumes_PET_CL_cluster.m at commit b40e71a, under MIT · at the source

Overview

Authors: Michalis Kassinopoulos1, Paula Montesinos2, Carles Falcon1,3,4, Jordi Huguet1, Carolina Minguillon1,4, Karine Fauria1,4,5, Gwendlyn Kollmorgen6, Clara Quijano-Rubio7, José Luis Molinuevo1, Oriol Grau-Rivera1,4,5,8, Henrik Zetterberg9,10,11,12,13,14, Kaj Blennow9,10,15,16, Marc Suárez-Calvet1,4,5,8, Javier Sanchez-Gonzalez2, Juan Domingo Gispert1,3,4, ALFA study
16 affiliations
  1. Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona 08005, Spain
  2. Philips Healthcare Iberia, Madrid 28050, Spain
  3. Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid 28029, Spain
  4. Hospital del Mar Research Institute, Barcelona 08003, Spain
  5. Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid 28029, Spain
  6. Roche Diagnostics GmbH, Penzberg 82377, Germany
  7. Roche Diagnostics International Ltd, Rotkreuz 6343, Switzerland
  8. Servei de Neurologia, Hospital del Mar, Barcelona 08003, Spain
  9. Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 431 80, Sweden
  10. Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal 431 80, Sweden
  11. UK Dementia Research Institute at University College London (UCL), London WC1N 3BG, UK
  12. Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1M 3BG, UK
  13. Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
  14. Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison 53705, WI, USA
  15. Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris 75013, France
  16. Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, and Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei 230001, P.R. China
Journal: Brain communications, volume 8, issue 2, article fcag075
Dates: received 3 June 2025; accepted 9 March 2026; published online 10 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/braincomms/fcag075 · PMID 41884594 · PMCID PMC13009408 · OpenAlex W7134922349
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), PET / SPECT (modality), Alzheimer's / dementia (population), cellular / molecular (subfield)
Methods: Statistics, Connectivity, fMRI & imaging, Preprocessing
Keywords: neuroinflammation, brain volume, early AD, multi-shell DWI, amyloid PET
Topic: Advanced Neuroimaging Techniques and Applications (Radiology, Nuclear Medicine and Imaging, Medicine), according to OpenAlex
Funding: Swedish Research Council (#2019-02397, #FO2017-0243, 948677, PI22/00456, #ALFGBG-71320, #ALZ2022-0006, 101053962, #2022-00732, #ADSF-21-831377-C, PI19/00155, #2017-00915, #22HLT07, #ADSF-21-831381-C, #AF-930351, #AF-968270, #2023-00356, 860197, JPND2019-466-236, SG-23-1038904 QC, #2022-01018, #201809-2016862, #AF-939721, #AF-994551, JPND2021-00694, #ADSF-21-831376-C, #ADSF-24-1284328-C, #ALFGBG-715986, #ALFGBG-965240, #FO2022-0270, ZEN-21-848495); "la Caixa" Foundation (TriBEKa-17-519007, ID 100010434, LCF/BQ/PR21/11840004, LCF/PR/GN17/50300004, 847648, SLT002/16/00201); UK Dementia Research Institute (2019-AARF-644568, UKDRI-1003); Spanish Ministry of Science, Innovation and Universities (IJC2020-043417-I); Ministry of Business and Knowledge of the Catalan Government (2021 SGR 00913); Universities and Research Secretariat; National Institute for Health and Care Research University College London Hospitals Biomedical Research Centre
Citations: cited by 1 paper (Europe PMC); 40 references in the paper

Abstract

In the preclinical stages of Alzheimer’s disease, increased brain volume has been associated with amyloid-beta pathology, particularly in regions that undergo volume reductions as the disease progresses. Glial reactivity and water diffusion alterations have been linked to such macroscopic volumetric changes. Brain volume reductions have also been reported following amyloid-beta removal with anti-amyloid therapies with beneficial clinical effects, but it remains unclear whether these changes result from resolving amyloid-triggered neuroinflammation or neurodegeneration. Intravoxel incoherent motion modelling based on multi-shell diffusion-weighted imaging may provide a better understanding of the processes underlying these paradoxical changes. This study used intravoxel incoherent motion diffusion MRI to examine how alterations in cerebral water pools contribute to increased brain volume linked to amyloid-beta deposition and neuroinflammation in cognitively unimpaired individuals. We developed a three-compartment diffusion MRI model with four parameters of cerebral water diffusion: slow diffusion coefficient, fast diffusion coefficient, slow signal portion, and perfusion fraction. We computed these diffusion parameters in 297 cognitively unimpaired late middle-aged adults, 35% of whom showed evidence of amyloid deposition. We examined their correlation with demographic factors (age, sex, apolipoprotein E status), markers of Alzheimer’s disease pathology, neurodegeneration, neuroinflammation, and mean diffusivity. Then, we identified regions showing grey matter volume increases related to amyloid burden and examined the association between grey matter volume and diffusion parameters within these regions. We did not find evidence of associations between diffusion parameters and amyloid-related biomarkers, whether assessed by PET or cerebrospinal fluid measures. In contrast, the four diffusion parameters showed strong and widespread associations with biomarkers of neuroinflammation and neurodegeneration, particularly in frontoparietal and cingulate regions. Additionally, in grey matter regions where volume increases were related to amyloid levels, volumes were negatively correlated with the slow diffusion coefficient (P = 0.001), perfusion fraction (P = 0.036) and mean diffusivity (P = 0.047). These findings indicate that diffusion-derived measures are more sensitive to neuroinflammatory and neurodegenerative processes than to amyloid pathology in cognitively unimpaired individuals. Furthermore, the observed negative association between grey matter volume and slow diffusion coefficient in amyloid-related regions may reflect increased cellular complexity rather than intracellular water accumulation. This interpretation suggests that glial remodelling or microstructural changes could underlie brain volume increases in amyloid-positive individuals without overt neurodegeneration. These results underscore the value of intravoxel incoherent motion-derived metrics for gaining deeper insights into the pathophysiological mechanisms of Alzheimer’s disease, influencing brain volume changes as well as those resulting from the response to anti-amyloid therapies.

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 4 matches between paragraphs and lines of code.

mkassinopoulos/2026_multib_paper_AlfaPLUS

License: MIT
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: b40e71aedb3fdaccfdea2985c8d6b11689cbd16c, 22 January 2026
Languages: MATLAB (15)
Size: 17 files, 15 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
17 files

The paper's code and data availability statement is in the Data section.

Tracing map

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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;
  • 15 scripts, each with its path and the digest of its content;
  • 4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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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

The data supporting the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions. Code used for the analyses is available at the following GitHub repository: https://github.com/mkassinopoulos/2026_multib_paper_AlfaPLUS.

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

Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 16 authors, 5 keywords, 7 funders, 40 references.

Cite

This paper

Kassinopoulos, M., Montesinos, P., Falcon, C., Huguet, J., Minguillon, C., Fauria, K., Kollmorgen, G., Quijano-Rubio, C., Molinuevo, J. L., Grau-Rivera, O., Zetterberg, H., Blennow, K., Suárez-Calvet, M., Sanchez-Gonzalez, J., Gispert, J. D., & ALFA study. (2026). Intracellular fluid accumulation underlies brain volume increases in early Alzheimer's disease. Brain communications, 8(2), fcag075. https://doi.org/10.1093/braincomms/fcag075

BibTeX

@article{kassinopoulos2026intracellular,
author = {Kassinopoulos, Michalis and Montesinos, Paula and Falcon, Carles and Huguet, Jordi and Minguillon, Carolina and Fauria, Karine and Kollmorgen, Gwendlyn and Quijano-Rubio, Clara and Molinuevo, José Luis and Grau-Rivera, Oriol and Zetterberg, Henrik and Blennow, Kaj and Suárez-Calvet, Marc and Sanchez-Gonzalez, Javier and Gispert, Juan Domingo and {ALFA study}},
title = {{Intracellular fluid accumulation underlies brain volume increases in early Alzheimer's disease}},
journal = {Brain communications},
year = {2026},
month = mar,
volume = {8},
number = {2},
pages = {fcag075},
publisher = {Oxford University Press},
issn = {2632-1297},
doi = {10.1093/braincomms/fcag075},
url = {https://doi.org/10.1093/braincomms/fcag075},
pmid = {41884594},
pmcid = {PMC13009408}
}

RIS

TY - JOUR
AU - Kassinopoulos, Michalis
AU - Montesinos, Paula
AU - Falcon, Carles
AU - Huguet, Jordi
AU - Minguillon, Carolina
AU - Fauria, Karine
AU - Kollmorgen, Gwendlyn
AU - Quijano-Rubio, Clara
AU - Molinuevo, José Luis
AU - Grau-Rivera, Oriol
AU - Zetterberg, Henrik
AU - Blennow, Kaj
AU - Suárez-Calvet, Marc
AU - Sanchez-Gonzalez, Javier
AU - Gispert, Juan Domingo
AU - ALFA study
TI - Intracellular fluid accumulation underlies brain volume increases in early Alzheimer's disease
T2 - Brain communications
J2 - Brain Commun
PY - 2026
DA - 2026/03/10
VL - 8
IS - 2
SP - fcag075
SN - 2632-1297
PB - Oxford University Press
DO - 10.1093/braincomms/fcag075
UR - https://doi.org/10.1093/braincomms/fcag075
LA - en
ER -

CSL-JSON

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"id": "10.1093/braincomms/fcag075",
"type": "article-journal",
"title": "Intracellular fluid accumulation underlies brain volume increases in early Alzheimer's disease",
"container-title": "Brain communications",
"author": [
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"family": "Kassinopoulos",
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{
"family": "Kollmorgen",
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{
"family": "Quijano-Rubio",
"given": "Clara"
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{
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{
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"PMID": "41884594",
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