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Dysfunction of the episodic memory network in the Alzheimer's disease cascade.

Code ↔ Paper

3 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 3 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Results › Investigating third variables to disease-related brain activation ↔ Parallel_Mediation.R, the whole file · a weak match · score 0.87 · parallel mediation, white matter hyperintensities, Effective connectivity, hippocampal volume, Entorhinal volume, indirect
  2. [2] § Methods › White matter hyperintensities and effective connectivity ↔ Parallel_Mediation.R, the whole file · a weak match · score 0.51 · white matter hyperintensity, WMH, connectivity, volumes
  3. [3] § Methods › Statistical analyses ↔ SandwichEstimation.m, the whole file · a weak match · score 0.51 · quadratic, scans, intercept, interaction, Sandwich, sex

Paper

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The authors' code

R · 51 lines · 1.5 KB · no license · 2 matches

  1. ###################################################################
  2. ##################### Lavaan Model syntax for #####################
  3. ####### Dysfunction of the episodic memory network in the #######
  4. ################### Alzheimer's disease cascade ###################
  5. ###################################################################
  7. # packages
  8. library(lavaan)
  9. library(tidySEM)
  12. ##### Parallel Mediation models #####
  14. # Please find the pseudocode for the parallel mediation models generated
  15. # in Lattmann et al. below. All variables were corrected for age, sex, and
  16. # years of education before entering the model. Afterwards, the variables were z-transformed.
  17. # White Matter Hyperintensities were Log10 transformed.
  18. #
  19. # - René Lattmann (last updated 23.02.2026)
  22. model <- '
  23. # Direct effect
  24. Cognition ~ c_prime*Deactivation
  26. # Mediation paths
  27. Hippocampal_Volume ~ a1*Deactivation
  28. Entorhinal_Volume ~ a2*Deactivation
  30. WhiteMatterHyperintensities ~ a3*Deactivation
  31. Effective_Connectivity ~ a4*Deactivation
  33. Cognition ~ b1*Hippocampal_Volume + b2*Entorhinal_Volume + b3*WhiteMatterHyperintensities + b4*Effective_Connectivity
  35. # Indirect effects
  36. indirect_HC := a1 * b1
  37. indirect_EC := a2 * b2
  38. indirect_WMH := a3 * b3
  39. indirect_EffConn := a4 * b4
  40. total_indirect := indirect_HC + indirect_EC + indirect_WMH + indirect_EffConn
  42. # Direct effect
  43. direct := c_prime
  45. # Total effect
  46. total := c_prime + total_indirect
  48. # Covariances
  49. Entorhinal_Volume ~~ Hippocampal_Volume
  51. '

Parallel_Mediation.R at commit 44d7ef2, no license · at the source

Overview

Authors: René Lattmann1,2, Niklas Vockert1, Jose Bernal1,2,3,4, Judith Wesenberg2, Yanin Suksangkharn1,2, Renat Yakupov1,2, Hartmut Schütze1,2, Wenzel Glanz1, Enise Incesoy1,2,5, Michaela Butryn1, Falk Lüsebrink1, Matthias Schmid6,7, Melina Stark6,8, Luca Kleineidam6,8, Annika Spottke6,9, Marie Coenjaerts6, Frederic Brosseron6, Klaus Fliessbach6,8, Anja Schneider6,8, Peter Dechent10
and 24 other authorsKlaus Scheffler11, Stefan Hetzer12, Alfredo Ramirez6,8,13,14,15, Christoph Laske16,17, Sebastian Sodenkamp16,18, Slawek Altenstein19,20, Luisa-Sophie Schneider21, Daria Gref21, Eike Jakob Spruth19,20, Andrea Lohse20, Björn H. Schott22,23,24, Jens Wiltfang22,23,25, Ingo Kilimann26,27, Doreen Goerss26,27, Ayda Rostamzadeh28, Josef Priller19,29,30, Oliver Peters19,20, Julian Hellmann-Regen19,31,32, Stefan Teipel26,27, Michael Wagner6,8, Frank Jessen6,13,28, Anne Maass1,33, Gabriel Ziegler1,2, Emrah Düzel1,2,34
ORCID iDs: René Lattmann, Niklas Vockert, Renat Yakupov, Matthias Schmid, Melina Stark, Frederic Brosseron, Anja Schneider, Stefan Hetzer, Alfredo Ramirez, Slawek Altenstein, Luisa-Sophie Schneider, Daria Gref, Jens Wiltfang, Josef Priller, Oliver Peters, Michael Wagner, Anne Maass, Gabriel Ziegler, Emrah Düzel
34 affiliations
  1. German Center for Neurodegenerative Diseases (DZNE),Magdeburg, Germany
  2. Institute of Cognitive Neurology and Dementia Research, Otto von Guericke University Magdeburg,Magdeburg, Germany
  3. Department of Neuroimaging Sciences, Institute for Neuroscience and Cardiovascular Research, Row Fogo Centre for Research into Ageing and the Brain, University of Edinburgh,Edinburgh, UK
  4. Department of Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU),Erlangen, Germany
  5. Department for Psychiatry and Psychotherapy, University Clinic Magdeburg, Magdeburg, Germany
  6. German Center for Neurodegenerative Diseases (DZNE),Bonn, Germany
  7. Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, University of Bonn,Bonn, Germany
  8. Department for Old Age Psychiatry and Cognitive Disorders, University Hospital Bonn,Bonn, Germany
  9. Department of Neurology, University Hospital Bonn,Bonn, Germany
  10. MR-Research in Neurosciences, Department of Cognitive Neurology, University Medical Center Göttingen,Göttingen, Germany
  11. Department for Biomedical Magnetic Resonance, University of Tübingen,Tübingen, Germany
  12. Charité – Universitätsmedizin Berlin, Berlin Center for Advanced Neuroimaging,Berlin, Germany
  13. Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne,Cologne, Germany
  14. Department of Psychiatry and Psychotherapy, Division of Neurogenetics and Molecular Psychiatry, Faculty of Medicine and University Hospital Cologne, University of Cologne,Cologne, Germany
  15. Department of Psychiatry & Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX USA
  16. German Center for Neurodegenerative Diseases (DZNE),Tübingen, Germany
  17. Section for Dementia Research, Hertie Institute for Clinical Brain Research and Department of Psychiatry and Psychotherapy, University of Tübingen,Tübingen, Germany
  18. Department of Psychiatry and Psychotherapy, University of Tübingen,Tübingen, Germany
  19. German Center for Neurodegenerative Diseases (DZNE),Berlin, Germany
  20. Department of Psychiatry and Psychotherapy, Charité – University Medical Center Berlin,Berlin, Germany
  21. Institute of Psychiatry and Psychotherapy, Charité – University Medical Center Berlin,Berlin, Germany
  22. German Center for Neurodegenerative Diseases (DZNE),Göttingen, Germany
  23. Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, University of Göttingen,Göttingen, Germany
  24. Leibniz Institute for Neurobiology,Magdeburg, Germany
  25. Department of Medical Sciences, Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), University of Aveiro,Aveiro, Portugal
  26. German Center for Neurodegenerative Diseases (DZNE),Rostock, Germany
  27. Department of Psychosomatic Medicine, Rostock University Medical Center,Rostock, Germany
  28. Department of Psychiatry, Medical Faculty, University of Cologne,Cologne, Germany
  29. Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich,Munich, Germany
  30. University of Edinburgh and UK DRI,Edinburgh, UK
  31. Department of Psychiatry and Neurosciences, Charité – University Medical Center Berlin,Berlin, Germany
  32. ECRC Experimental and Clinical Research Center, Charité – University Medical Center Berlin,Berlin, Germany
  33. Institute for Biology, Otto von Guericke University Magdeburg,Magdeburg, Germany
  34. Institute of Cognitive Neuroscience, University College London,London, UK
Institutions: German Center for Neurodegenerative Diseases (Germany); Otto-von-Guericke-Universität Magdeburg (Germany); University of Edinburgh (United Kingdom); Friedrich-Alexander-Universität Erlangen-Nürnberg (Germany); University Hospital Bonn (Germany); Universitätsmedizin Göttingen (Germany); University of Tübingen (Germany); Charité - Universitätsmedizin Berlin (Germany); University of Cologne (Germany); University of Göttingen (Germany); Leibniz Institute for Neurobiology (Germany); University of Aveiro (Portugal); University of Rostock (Germany); Technical University of Munich (Germany); University College London (United Kingdom)
Journal: Nature communications, volume 17, issue 1, article 3578
Dates: received 17 February 2025; accepted 30 March 2026; published online 17 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41467-026-71831-z · PMID 41997924 · PMCID PMC13090369 · OpenAlex W7154687356
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: fMRI (modality), human (organism), Alzheimer's / dementia (population), cognitive (subfield)
Methods: Statistics, Connectivity, Complexity, fMRI & imaging, Smoothing, state filtering, decompositions, Machine learning
Keywords: Alzheimer's disease, Computational models, Functional magnetic resonance imaging
MeSH: Alzheimer Disease*, Memory, Episodic*, Nerve Net*, Aged, Brain, Cognitive Dysfunction, Disease Progression, Female, Humans, Longitudinal Studies, Magnetic Resonance Imaging, Male, tau Proteins (* major topic)
Topic: Dementia and Cognitive Impairment Research (Psychiatry and Mental health, Medicine), according to OpenAlex
Funding: Deutsches Zentrum für Neurodegenerative Erkrankungen (German Center for Neurodegenerative Diseases) (BN012)
Citations: cited by 1 paper (Europe PMC); 86 references in the paper

Abstract

Alzheimer’s disease (AD) is a major cause of dementia and cognitive decline. Here, we assessed how episodic memory (EM) network dysfunction, a hallmark of AD, is related to the longitudinal progression of AD biomarkers, neurodegeneration and cognition using data from the DZNE DELCODE study. This data set includes over 1000 longitudinal functional magnetic resonance imaging measurements of EM network function. We related activation and deactivation of EM to individual disease progression scores from a disease progression model. Voxel-wise analyses revealed widespread loss of deactivation and activation with disease progression. Trajectories for the loss of deactivation were nonlinear, associated with amyloid- and tau-positivity and visually preceded trajectories of cognitive decline. The relationship between deactivation and cognitive decline was partly independent of neurodegeneration. Our results provide evidence that synaptic dysfunction and neurodegeneration are independent drivers of cognitive decline, providing a rationale for targeting synaptic dysfunction along the AD cascade.

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 3 matches between paragraphs and lines of code.

gitlab.inria.fr/epione/gp_progression_model_v2

License: other
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 829889f3a4162694ae0ba46d9421abfda1711006, 10 April 2021
Languages: Python (6), Shell (3), Jupyter (1)
Size: 53 files, 10 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, license file, environment (setup.py, conda/environment.yaml), 1 notebook
Not found: CITATION.cff, tests, continuous integration, documentation
Tools: Matplotlib (5 files), NumPy (5 files), pandas (4 files), PyTorch (4 files), scikit-learn (1 file), seaborn (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
12 files
At the source: gitlab.inria.fr/epione/GP_progression_model_V2

renelattmann/EMN_dysfunction

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 44d7ef2840c5464435a0f61d2e72fc57bb95fe44, 17 April 2026
Languages: MATLAB (3), R (1)
Size: 6 files, 4 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: GIfTI library for MATLAB (2 files), CAT12 (1 file), lavaan (1 file), Statistics and Machine Learning Toolbox (1 file), SPM (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
5 files
At the source: github.com/renelattmann/EMN_dysfunction

Code availability

Code to the DPM utilized in this study and for the visualization of Figs. 1a and 1b can be found under https://gitlab.inria.fr/epione/GP_progression_model_V2. Code for the second-level GLM and the parallel mediation model, and the surface renderings can be found on GitHub at https://github.com/renelattmann/EMN_dysfunction86.

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

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;
  • 14 scripts, each with its path and the digest of its content;
  • 3 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

The raw data collected in the study “DELCODE—DZNE-Longitudinal Cognitive Impairment and Dementia Study (BN012)” cannot be made openly available without violation of the data protection concept of the DZNE. The same applies to the processed individual (f)MRI images. Access to the relevant study data can be obtained by submitting an application to the Clinical Research Platform of the DZNE. The template for the application for the submission of data and biomaterial samples is available on the DZNE homepage (https://www.dzne.de/en/research/research-areas/clinical-research/databases-of-the-clinical-research/). The expected timeframe for response to access requests is 1 month. Access will be granted for 10 years. Source data are provided with this paper.

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, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 44 authors, 3 keywords, 13 MeSH terms, 1 funder, 85 references.

Cite

This paper

Lattmann, R., Vockert, N., Bernal, J., Wesenberg, J., Suksangkharn, Y., Yakupov, R., Schütze, H., Glanz, W., Incesoy, E., Butryn, M., Lüsebrink, F., Schmid, M., Stark, M., Kleineidam, L., Spottke, A., Coenjaerts, M., Brosseron, F., Fliessbach, K., Schneider, A., . . . Düzel, E. (2026). Dysfunction of the episodic memory network in the Alzheimer's disease cascade. Nature communications, 17(1), 3578. https://doi.org/10.1038/s41467-026-71831-z

BibTeX

@article{lattmann2026dysfunction,
author = {Lattmann, René and Vockert, Niklas and Bernal, Jose and Wesenberg, Judith and Suksangkharn, Yanin and Yakupov, Renat and Schütze, Hartmut and Glanz, Wenzel and Incesoy, Enise and Butryn, Michaela and Lüsebrink, Falk and Schmid, Matthias and Stark, Melina and Kleineidam, Luca and Spottke, Annika and Coenjaerts, Marie and Brosseron, Frederic and Fliessbach, Klaus and Schneider, Anja and Dechent, Peter and Scheffler, Klaus and Hetzer, Stefan and Ramirez, Alfredo and Laske, Christoph and Sodenkamp, Sebastian and Altenstein, Slawek and Schneider, Luisa-Sophie and Gref, Daria and Spruth, Eike Jakob and Lohse, Andrea and Schott, Björn H. and Wiltfang, Jens and Kilimann, Ingo and Goerss, Doreen and Rostamzadeh, Ayda and Priller, Josef and Peters, Oliver and Hellmann-Regen, Julian and Teipel, Stefan and Wagner, Michael and Jessen, Frank and Maass, Anne and Ziegler, Gabriel and Düzel, Emrah},
title = {{Dysfunction of the episodic memory network in the Alzheimer's disease cascade}},
journal = {Nature communications},
year = {2026},
month = apr,
volume = {17},
number = {1},
pages = {3578},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-71831-z},
url = {https://doi.org/10.1038/s41467-026-71831-z},
pmid = {41997924},
pmcid = {PMC13090369}
}

RIS

TY - JOUR
AU - Lattmann, René
AU - Vockert, Niklas
AU - Bernal, Jose
AU - Wesenberg, Judith
AU - Suksangkharn, Yanin
AU - Yakupov, Renat
AU - Schütze, Hartmut
AU - Glanz, Wenzel
AU - Incesoy, Enise
AU - Butryn, Michaela
AU - Lüsebrink, Falk
AU - Schmid, Matthias
AU - Stark, Melina
AU - Kleineidam, Luca
AU - Spottke, Annika
AU - Coenjaerts, Marie
AU - Brosseron, Frederic
AU - Fliessbach, Klaus
AU - Schneider, Anja
AU - Dechent, Peter
AU - Scheffler, Klaus
AU - Hetzer, Stefan
AU - Ramirez, Alfredo
AU - Laske, Christoph
AU - Sodenkamp, Sebastian
AU - Altenstein, Slawek
AU - Schneider, Luisa-Sophie
AU - Gref, Daria
AU - Spruth, Eike Jakob
AU - Lohse, Andrea
AU - Schott, Björn H.
AU - Wiltfang, Jens
AU - Kilimann, Ingo
AU - Goerss, Doreen
AU - Rostamzadeh, Ayda
AU - Priller, Josef
AU - Peters, Oliver
AU - Hellmann-Regen, Julian
AU - Teipel, Stefan
AU - Wagner, Michael
AU - Jessen, Frank
AU - Maass, Anne
AU - Ziegler, Gabriel
AU - Düzel, Emrah
TI - Dysfunction of the episodic memory network in the Alzheimer's disease cascade
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/04/17
VL - 17
IS - 1
SP - 3578
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-71831-z
UR - https://doi.org/10.1038/s41467-026-71831-z
LA - en
ER -

CSL-JSON

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