Personalized Recommendations for Neurodegenerative Disease

Deliverables

Interim source-space, multiresolution MEG time series in BIDS share. Initial MEG and SEEG brain dynamics measures at the disposal of other WPs

Full-cohort individual MEG brain dynamics measures at the disposal of other WPs, harmonized with Task 3.3 M36 deliverable

Fullcohort individual MEG brain dynamics measures at the disposal of other WPs harmonized with Task 33 M36 deliverable

Integrated, open source terminology versioning and management tool CTS2 compliant application shared with project partners

Stakeholder Conference: Specific issues of neurodegenerative diseases: The patients’ perspective

Stakeholder Conference Specific issues of neurodegenerative diseases The patients perspective

Framework for multi-modal integrated annotations established and in use

Framework for multimodal integrated annotations established and in use

Group level SEEG brain dynamics measures and analysis pipeline for SEEG

Short list of candidate mechanisms to be used in personalized simulations. The short list will be explained and motivated in a dedicated Webinar that will be made publicly available

Short list of candidate mechanisms to be used in personalized simulations The short list will be explained and motivated in a dedicated Webinar that will be made publicly available

Digital atlas that maps signaling pathways on corresponding brain regions for different neurodegenerative states in humans

Initial version of full-scope containerized pipeline developed

Initial version of fullscope containerized pipeline developed

Stakeholder conference on GDPR-impact

Stakeholder conference on GDPRimpact

Evaluation and optimization of pipeline for practical use concluded

Workshop with policy-makers

Workshop with policymakers

Full-cohort MEG time series in BIDS share and analysis pipeline ready

Fullcohort MEG time series in BIDS share and analysis pipeline ready

Most appropriate RS-processing pipelines for TVB modelling finished

Most appropriate RSprocessing pipelines for TVB modelling finished

Establishment of contact with relevant external stakeholders

Gateway to PRACE documentation and guidelines

Report on VBC operation report and published services on EOSC/EGI Marketplace

Report on VBC operation report and published services on EOSCEGI Marketplace

Publication of a study on deconfounding for inference

Complete, updated semantic framework for neurodegeneration research documented

Evaluation of cross-modal atlas-based compression for machine-learning

Evaluation of crossmodal atlasbased compression for machinelearning

Report on cloud implementation strategy applying “trusted cloud” principles

Paper manuscript describing the initial characterization of the studies, the equivalence of their variables and the summary statistics (mean, standard deviation etc.) submitted to relevant journal

Data catalogue with harmonized annotations at project

Text mining workflow to use ontologies and terminologies in OLS for information extraction of “cause-and-effect” statements. The demonstration will be delivered as a “Webinar”

Text mining workflow to use ontologies and terminologies in OLS for information extraction of causeandeffect statements The demonstration will be delivered as a Webinar

A functionally integrated version of VBC is evaluated for therapeutical targets

Short title: Semantically enhanced multi-viewer that embeds a newly developed TVB 3D viewer

Full title A semantically enhanced multiviewer that embeds a newly developed TVB 3D viewer that allows for integration of personalized 3D coordinates with knowledge about pathways and mechanisms in situ The deliverable for this task is a joint highranking journal publication of the teams building this environment

Publications

Differences in cohort study data affect external validation of artificial intelligence models for predictive diagnostics of dementia - lessons for translation into clinical practice.

Author(s): Colin Birkenbihl; Colin Birkenbihl; Mohammad Asif Emon; Mohammad Asif Emon; Henri A. Vrooman; Sarah Westwood; Simon Lovestone; Martin Hofmann-Apitius; Martin Hofmann-Apitius; Holger Fröhlich; Holger Fröhlich
Published in: The E P M A Journal, 1, 2020, ISSN 1878-5077
Publisher: BioMed Central
DOI: 10.1007/s13167-020-00216-z

Understanding the Variability in Graph Data Sets through Statistical Modeling on the Stiefel Manifold

Author(s): Clément Mantoux; Baptiste Couvy-Duchesne; Federica Cacciamani; Stéphane Epelbaum; Stanley Durrleman; Stéphanie Allassonnière
Published in: Entropy, 2, 2021, ISSN 1099-4300
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e23040490

Parcellation-induced variation of empirical and simulated brain connectomes at group and subject levels

Author(s): Justin W. M. Domhof; Kyesam Jung; Simon B. Eickhoff; Oleksandr V. Popovych
Published in: Network neuroscience, 5(3), 2021, Page(s) 798–830, ISSN 2472-1751
Publisher: MIT Press Journals
DOI: 10.1162/netn_a_00202

On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread

Author(s): Hashemi, M., Vattikonda, A.N., Sip, V., Diaz-Pier, S., Peyser, A., Wang, H., Guye, M., Bartolomei, F., Woodman, M.M. and Jirsa, V.K.
Published in: PLoS computational biology, 2021, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1009129

Inter-subject and inter-parcellation variability of resting-state whole-brain dynamical modeling

Author(s): Oleksandr V. Popovych, Kyesam Jung, Thanos Manos, Sandra Diaz-Pier, Felix Hoffstaedter, Jan Schreiber, B.T. Thomas Yeo, Simon B. Eickhoff
Published in: NeuroImage, 236, 2021, Page(s) 118201, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2021.118201

AD Course Map charts Alzheimer’s disease progression

Author(s): Koval, Igor; Bône, Alexandre; Louis, Maxime; Lartigue, Thomas; Bottani, Simona; Marcoux, Arnaud; Samper-Gonzalez, Jorge; Burgos, Ninon; Charlier, Benjamin; Bertrand, Anne; Epelbaum, Stéphane; Colliot, Olivier; Allassonnière, Stéphanie; Durrleman, Stanley
Published in: EISSN: 2045-2322, 2, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-87434-1

Learning the spatiotemporal variability in longitudinal shape data sets

Author(s): Bône, Alexandre; Colliot, Olivier; Durrleman, Stanley
Published in: International Journal of Computer Vision, 2, 2020, ISSN 0920-5691
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11263-020-01343-w

Unraveling the heterogeneity in Alzheimer's disease progression across multiple cohorts and the implications for data-driven disease modeling

Author(s): Birkenbihl, Colin; Salimi, Yasamin; Fröhlich, Holger
Published in: Fraunhofer SCAI, 2, 2021, ISSN 1552-5279
Publisher: Wiley
DOI: 10.1002/alz.12387

Tractography density affects whole-brain structural architecture and resting-state dynamical modeling

Author(s): Kyesam Jung; Simon B. Eickhoff; Oleksandr V. Popovych
Published in: NeuroImage, 237, 2021, Page(s) 118176, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2021.118176

Dynamic Functional Connectivity between order and randomness and its evolution across the human adult lifespan.

Author(s): Demian Battaglia; Thomas Boudou; Thomas Boudou; Enrique C. A. Hansen; Enrique C. A. Hansen; Diego Lombardo; Sabrina Chettouf; Sabrina Chettouf; Andreas Daffertshofer; Anthony R. McIntosh; Joelle Zimmermann; Petra Ritter; Viktor K. Jirsa
Published in: "NeuroImage, Elsevier, 2020, 222, pp.117156. ⟨10.1016/j.neuroimage.2020.117156⟩", 2, 2020, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2020.117156

In defense of decentralized research data management

Author(s): Michael Hanke; Franco Pestilli; Adina Wagner; Christopher J. Markiewicz; Jean-Baptiste Poline; Yaroslav O. Halchenko
Published in: Neuroforum, 2021, ISSN 2363-7013
Publisher: Walter de Gruyter GmbH
DOI: 10.1515/nf-2020-0037

DataLad: distributed system for joint management of code, data, and their relationship

Author(s): Yaroslav O. Halchenko, Kyle Meyer, Benjamin Poldrack, Debanjum Singh Solanky, Adina S. Wagner, Jason Gors, Dave MacFarlane,Dorian Pustina, Vanessa Sochat, Satrajit S. Ghosh, Christian Mönch, Christopher J. Markiewicz, Laura Waite, Ilya Shlyakhter,Alejandro de la Vega, Soichi Hayashi, Christian Olaf Häusler, Jean-Baptiste Poline, Tobias Kadelka, Kusti Skytén, DorotaJ arecka, David Kennedy, Ted S
Published in: The Journal of Open Source Software, 2021, ISSN 2475-9066
Publisher: IGI Global Publishing
DOI: 10.21105/joss.03262

Phase and amplitude electroencephalography correlations change with disease progression in people with idiopathic rapid eye-movement sleep behavior disorder

Author(s): Monica Roascio, Andrea Canessa, Rosella Trò, Pietro Mattioli, Francesco Famà, Laura Giorgetti, Nicola Girtler, Beatrice Orso, Silvia Morbelli, Flavio Nobili, Dario Arnaldi, Gabriele Arnulfo
Published in: Sleep, 2021, ISSN 0161-8105
Publisher: The American Academy of Sleep Medicine
DOI: 10.1093/sleep/zsab232

Entorhinal mismatch: A model of self-supervised learning in the hippocampus

Author(s): Diogo Santos-Pata; Adrián F. Amil; Ivan Georgiev Raikov; César Rennó-Costa; Anna Mura; Ivan Soltesz; Paul F.M.J. Verschure
Published in: iScience, Vol 24, Iss 5, Pp 102501- (2021), 2, 2021, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2021.102501

NeuroQuery: comprehensive meta-analysis of human brain mapping

Author(s): Jérôme Dockès; Russell A. Poldrack; Romain Primet; Hande Gözükan; Tal Yarkoni; Fabian M. Suchanek; Bertrand Thirion; Gaël Varoquaux
Published in: 2020, 2, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.53385

Movement disorders after hypoxic brain injury following cardiac arrest in adults.

Author(s): Franziska Scheibe; Franziska Scheibe; Wolf-Julian Neumann; Catharina Lange; Michael Scheel; Christian Furth; Martin Köhnlein; Philipp Mergenthaler; Jörg Schultze‐Amberger; Paul Triebkorn; Petra Ritter; Andrea A. Kühn; Andreas Meisel
Published in: European Journal of Neurology, 2, 2021, ISSN 1468-1331
Publisher: Wiley
DOI: 10.1111/ene.14326

Advanced brain aging in Parkinson’s disease is related to disease duration and individual impairment

Author(s): Eickhoff, Claudia R; Hoffstaedter, Felix; Caspers, Julian; Reetz, Kathrin; Mathys, Christian; Dogan, Imis; Amunts, Katrin; Schnitzler, Alfons; Eickhoff, Simon B
Published in: Brain communications, 2021, ISSN 2632-1297
Publisher: Oxford University Press on behalf of the Guarantors of Brain
DOI: 10.1093/braincomms/fcab191

Gaussian Graphical Model exploration and selection in high dimension low sample size setting.

Author(s): Thomas Lartigue; Simona Bottani; Stephanie Baron; Olivier Colliot; Stanley Durrleman; Stéphanie Allassonnière
Published in: "IEEE Transactions on Pattern Analysis and Machine Intelligence, Institute of Electrical and Electronics Engineers, 2021, 43 (9), pp.3196-3213. ⟨10.1109/TPAMI.2020.2980542⟩", 2, 2021, ISSN 0162-8828
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tpami.2020.2980542

Movement disorders after hypoxic brain injury following cardiac arrest in adults

Author(s): F. Scheibe, W. J. Neumann, C. Lange, M. Scheel, C. Furth, M. Köhnlein, P. Mergenthaler, J. Schultze‐Amberger, P. Triebkorn, P. Ritter, A. A. Kühn, A. Meisel
Published in: European Journal of Neurology, 2020, ISSN 1351-5101
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/ene.14326

Are unimanual movements bilateral?

Author(s): Sabrina Chettouf, Laura M. Rueda-Delgado, Ralph de Vries, Petra Ritter, Andreas Daffertshofer
Published in: Neuroscience & Biobehavioral Reviews, 113, 2020, Page(s) 39-50, ISSN 0149-7634
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.neubiorev.2020.03.002

A macaque connectome for large-scale network simulations in TheVirtualBrain

Author(s): Kelly Shen, Gleb Bezgin, Michael Schirner, Petra Ritter, Stefan Everling, Anthony R. McIntosh
Published in: Scientific Data, 6/1, 2019, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1038/s41597-019-0129-z

Linking Molecular Pathways and Large-Scale Computational Modeling to Assess Candidate Disease Mechanisms and Pharmacodynamics in Alzheimer's Disease

Author(s): Leon Stefanovski, Paul Triebkorn, Andreas Spiegler, Margarita-Arimatea Diaz-Cortes, Ana Solodkin, Viktor Jirsa, Anthony Randal McIntosh, Petra Ritter
Published in: Frontiers in Computational Neuroscience, 13, 2019, ISSN 1662-5188
Publisher: Frontiers Research Foundation
DOI: 10.3389/fncom.2019.00054

Modeling brain dynamics after tumor resection using The Virtual Brain

Author(s): Hannelore Aerts, Michael Schirner, Thijs Dhollander, Ben Jeurissen, Eric Achten, Dirk Van Roost, Petra Ritter, Daniele Marinazzo
Published in: NeuroImage, 213, 2020, Page(s) 116738, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2020.116738

The Importance of Standards for Sharing of Computational Models and Data

Author(s): Russell A Poldrack, Franklin Feingold, Michael J Frank, Padraig Gleeson, Gilles de Hollander, Quentin J. M. Huys, Bradley C. Love, Christopher J. Markiewicz, Rosalyn Moran, Petra Ritter, Timothy T. Rogers, Brandon M. Turner, Tal Yarkoni, Ming Zhan, Jonathan D. Cohen
Published in: Computational Brain & Behavior, 2/3-4, 2019, Page(s) 229-232, ISSN 2522-0861
Publisher: Springer Nature
DOI: 10.1007/s42113-019-00062-x

Frequency cluster formation and slow oscillations in neural populations with plasticity

Author(s): Vera Röhr, Rico Berner, Ewandson L. Lameu, Oleksandr V. Popovych, Serhiy Yanchuk
Published in: PLOS ONE, 14/11, 2019, Page(s) e0225094, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0225094

The Bayesian Virtual Epileptic Patient: A probabilistic framework designed to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread

Author(s): M. Hashemi, A.N. Vattikonda, V. Sip, M. Guye, F. Bartolomei, M.M. Woodman, V.K. Jirsa
Published in: NeuroImage, 217, 2020, Page(s) 116839, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2020.116839

Modulating grid cell scale and intrinsic frequencies via slow high-threshold conductances: A simplified model

Author(s): Diogo Santos-Pata, Riccardo Zucca, Héctor López-Carral, Paul F.M.J. Verschure
Published in: Neural Networks, 119, 2019, Page(s) 66-73, ISSN 0893-6080
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.neunet.2019.06.011

Switching Operation Modes in the Neocortex via Cholinergic Neuromodulation

Author(s): J.-Y. Puigbò, X. D. Arsiwalla, M. A. González-Ballester, P. F. M. J. Verschure
Published in: Molecular Neurobiology, 57/1, 2020, Page(s) 139-149, ISSN 0893-7648
Publisher: Humana Press, Inc.
DOI: 10.1007/s12035-019-01764-w

Identification d’une signature moléculaire d’hypercortisolisme par analyse du methylome du sang total

Author(s): Roberta Armignacco; T. Lartigue; Anne Jouinot; Amandine Septier; Mario Neou; C. Gaspar; Karine Perlemoine; Lucas Bouys; Leah T. Braun; Anna Riester; S. Allassonnière; Maria-Christina Zennaro; Martin Reincke; Jérôme Bertherat; F Beuschlein; Guillaume Assié
Published in: https://hal.archives-ouvertes.fr/hal-03035962, 2, 2020, ISSN 0003-4266
Publisher: Elsevier Masson
DOI: 10.1016/j.ando.2020.07.117

Evaluating the Alzheimer's disease data landscape

Author(s): Colin Birkenbihl; Colin Birkenbihl; Yasamin Salimi; Yasamin Salimi; Daniel Domingo-Fernández; Daniel Domingo-Fernández; Simon Lovestone; Holger Fröhlich; Holger Fröhlich; Martin Hofmann-Apitius; Martin Hofmann-Apitius; Japanese Alzheimer's Disease Neuroimaging Initiative
Published in: Alzheimer's & Dementia : Translational Research & Clinical Interventions, 1, 2020, ISSN 1552-5279
Publisher: Wiley
DOI: 10.1002/trc2.12102

The Importance of Cerebellar Connectivity on Simulated Brain Dynamics.

Author(s): Fulvia Palesi; Fulvia Palesi; Roberta Maria Lorenzi; Claudia Casellato; Petra Ritter; Petra Ritter; Viktor Jirsa; Claudia A.M. Gandini Wheeler-Kingshott; Claudia A.M. Gandini Wheeler-Kingshott; Claudia A.M. Gandini Wheeler-Kingshott; Egidio D’Angelo; Egidio D’Angelo
Published in: Frontiers in Cellular Neuroscience, Vol 14 (2020), 2, 2020, ISSN 1662-5102
Publisher: Frontiers Research Foundation
DOI: 10.3389/fncel.2020.00240

Linking molecular pathways and large-scale computational modeling to assess candidate disease mechanisms and pharmacodynamics in Alzheimer\'s disease

Author(s): Leon Stefanovski; Leon Stefanovski; Paul Triebkorn; Paul Triebkorn; Andreas Spiegler; Andreas Spiegler; Margarita-Arimatea Diaz-Cortes; Margarita-Arimatea Diaz-Cortes; Margarita-Arimatea Diaz-Cortes; Ana Solodkin; Viktor Jirsa; Anthony Randal McIntosh; Petra Ritter; Petra Ritter; Petra Ritter; for the Alzheimer's Disease Neuroimaging Initiative
Published in: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700386/, 2, 2020, ISSN 1662-5188
Publisher: Frontiers Research Foundation
DOI: 10.17169/refubium-25500

Genetic factors influencing a neurobiological substrate for psychiatric disorders

Author(s): Till F. M. Andlauer; Thomas W. Mühleisen; Felix Hoffstaedter; Alexander Teumer; Katharina Wittfeld; Anja Teuber; Céline S. Reinbold; Dominik Grotegerd; Robin Bülow; Svenja Caspers; Udo Dannlowski; Stefan Herms; Per Hoffmann; Tilo Kircher; Heike Minnerup; Susanne Moebus; Igor Nenadić; Henning Teismann; Uwe Völker; Amit Etkin; Klaus Berger; Hans J. Grabe; Markus M. Nöthen; Katrin Amunts; Simon
Published in: Translational Psychiatry, Vol 11, Iss 1, Pp 1-13 (2021), 2, 2021, ISSN 2158-3188
Publisher: Nature Publishing Group
DOI: 10.1038/s41398-021-01317-7

FNS allows efficient event-driven spiking neural network simulations based on a neuron model supporting spike latency

Author(s): Gianluca Susi; Pilar Garcés; Emanuele Paracone; Alessandro Cristini; Mario Salerno; Fernando Maestú; Ernesto Pereda
Published in: Scientific Reports, Vol 11, Iss 1, Pp 1-17 (2021), 1, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-91513-8

Fine-grain atlases of functional modes for fMRI analysis.

Author(s): Kamalaker Dadi; Gaël Varoquaux; Antonia Machlouzarides-Shalit; Krzysztof J. Gorgolewski; Demian Wassermann; Bertrand Thirion; Arthur Mensch
Published in: 2020, 2, 2020, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2020.117126

Mixture of Conditional Gaussian Graphical Models for unlabelled heterogeneous populations in the presence of co-factors

Author(s): Thomas Lartigue; Stanley Durrleman; Stéphanie Allassonnière
Published in: 2020, 2, 2020, ISSN 2331-8422
Publisher: Cornell University
DOI: 10.1007/s42979-021-00865-5

Brain Modelling as a Service: The Virtual Brain on EBRAINS

Author(s): Schirner, Michael; Domide, Lia; Perdikis, Dionysios; Triebkorn, Paul; Stefanovski, Leon; Pai, Roopa; Popa, Paula; Valean, Bogdan; Palmer, Jessica; Langford, Chloê; Blickensdörfer, André; van der Vlag, Michiel; Diaz-Pier, Sandra; Peyser, Alexander; Klijn, Wouter; Pleiter, Dirk; Nahm, Anne; Schmid, Oliver; Woodman, Marmaduke; Zehl, Lyuba; Fousek, Jan; Petkoski, Spase; Kusch, Lionel; Hashemi, Meys
Published in: ArXiv, 2021
Publisher: Cornell University

Identifying optimal working points of individual Virtual Brains: A large-scale brain network modelling study

Author(s): Paul Triebkorn; Joelle Zimmermann; Leon Stefanovski; Dipanjan Roy; Ana Solodkin; Viktor K. Jirsa; Gustavo Deco; Michael Breakspear; Anthony R. McIntosh; Petra Ritter
Published in: 2, 2020, ISBN 978-0-879699-41-3
Publisher: Cold Spring Habor Laboratory
DOI: 10.1101/2020.03.26.009795

Basal forebrain rhythmicity is modulated by the exploration phase of novel environments

Author(s): Paul F. M. J. Verschure; Diogo Santos-Pata
Published in: bioRxiv, 7, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.01.11.902742

Deterministic Approximate EM Algorithm; Application to the Riemann Approximation EM and the Tempered EM

Author(s): Lartigue, Thomas; Durrleman, Stanley; Allassonnière, Stéphanie
Published in: 2020, 2, 2021, ISSN 2331-8422
Publisher: Cornell University

Human CA1 and subiculum activity forecast stroke chronicity

Author(s): Diogo Santos-Pata, Belen Rubio Ballester, Riccardo Zucca, Carlos Stefano Filho, Sara Regina Almeida, Li Li Min, Gabriela Castellano, Paul FMJ Verschure
Published in: medRxiv, 2020
Publisher: CSHL
DOI: 10.1101/2020.01.19.20017996

Simulating Alzheimer's disease progression with personalised digital brain models

Author(s): Koval, Igor; Bône, Alexandre; Louis, Maxime; Bottani, Simona; Marcoux, Arnaud; Samper-Gonzalez, Jorge; Burgos, Ninon; CHARLIER, Benjamin; Bertrand, Anne; Epelbaum, Stéphane; Colliot, Olivier; Allassonnière, Stéphanie; Durrleman, Stanley
Published in: 2018, 2, 2018
Publisher: INRIA

Proposal of an Architecture for Terminology Management in a Research Project

Author(s): Sara, Mora; Sumit, Madan; Stephan, Gebel; Mauro, Giacomini
Published in: Fraunhofer SCAI, 1, 2020
Publisher: IOS Press

Multivariate analysis is sufficient for lesion-behaviour mapping

Author(s): Martin, Lucas; Josse, Julie; Thirion, Bertrand
Published in: MICCAI BrainLes 2020 workshop, Oct 2020, Lima, Peru, 1, 2021
Publisher: Springer
DOI: 10.1007/978-3-030-72084-1_9

Deliverables

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