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  1. Article ; Online: Ten simple rules for aspiring graduate students.

    Andrea I Luppi / Charlotte Coco Newton / Lynde Folsom / Elisa Galliano / Rafael Romero-Garcia

    PLoS Computational Biology, Vol 17, Iss 8, p e

    2021  Volume 1009276

    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Interventional neurorehabilitation for promoting functional recovery post-craniotomy

    Anujan Poologaindran / Christos Profyris / Isabella M. Young / Nicholas B. Dadario / Syed A. Ahsan / Kassem Chendeb / Robert G. Briggs / Charles Teo / Rafael Romero-Garcia / John Suckling / Michael E. Sughrue

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    a proof-of-concept

    2022  Volume 11

    Abstract: Abstract The human brain is a highly plastic ‘complex’ network—it is highly resilient to damage and capable of self-reorganisation after a large perturbation. Clinically, neurological deficits secondary to iatrogenic injury have very few active ... ...

    Abstract Abstract The human brain is a highly plastic ‘complex’ network—it is highly resilient to damage and capable of self-reorganisation after a large perturbation. Clinically, neurological deficits secondary to iatrogenic injury have very few active treatments. New imaging and stimulation technologies, though, offer promising therapeutic avenues to accelerate post-operative recovery trajectories. In this study, we sought to establish the safety profile for ‘interventional neurorehabilitation’: connectome-based therapeutic brain stimulation to drive cortical reorganisation and promote functional recovery post-craniotomy. In n = 34 glioma patients who experienced post-operative motor or language deficits, we used connectomics to construct single-subject cortical networks. Based on their clinical and connectivity deficit, patients underwent network-specific transcranial magnetic stimulation (TMS) sessions daily over five consecutive days. Patients were then assessed for TMS-related side effects and improvements. 31/34 (91%) patients were successfully recruited and enrolled for TMS treatment within two weeks of glioma surgery. No seizures or serious complications occurred during TMS rehabilitation and 1-week post-stimulation. Transient headaches were reported in 4/31 patients but improved after a single session. No neurological worsening was observed while a clinically and statistically significant benefit was noted in 28/31 patients post-TMS. We present two clinical vignettes and a video demonstration of interventional neurorehabilitation. For the first time, we demonstrate the safety profile and ability to recruit, enroll, and complete TMS acutely post-craniotomy in a high seizure risk population. Given the lack of randomisation and controls in this study, prospective randomised sham-controlled stimulation trials are now warranted to establish the efficacy of interventional neurorehabilitation following craniotomy.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610 ; 616
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: A normative modelling approach reveals age-atypical cortical thickness in a subgroup of males with autism spectrum disorder

    Richard A. I. Bethlehem / Jakob Seidlitz / Rafael Romero-Garcia / Stavros Trakoshis / Guillaume Dumas / Michael V. Lombardo

    Communications Biology, Vol 3, Iss 1, Pp 1-

    2020  Volume 10

    Abstract: Richard Bethlehem et al. identify a subgroup of autism spectrum disorders (ASD) individuals with highly age-atypical cortical thickness using a normative modelling approach across a large cohort. This work highlights the importance of individualized ... ...

    Abstract Richard Bethlehem et al. identify a subgroup of autism spectrum disorders (ASD) individuals with highly age-atypical cortical thickness using a normative modelling approach across a large cohort. This work highlights the importance of individualized approaches to gain insight into ASD heterogeneity.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Versatility of nodal affiliation to communities

    Maxwell Shinn / Rafael Romero-Garcia / Jakob Seidlitz / František Váša / Petra E. Vértes / Edward Bullmore

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Volume 10

    Abstract: Abstract Graph theoretical analysis of the community structure of networks attempts to identify the communities (or modules) to which each node affiliates. However, this is in most cases an ill-posed problem, as the affiliation of a node to a single ... ...

    Abstract Abstract Graph theoretical analysis of the community structure of networks attempts to identify the communities (or modules) to which each node affiliates. However, this is in most cases an ill-posed problem, as the affiliation of a node to a single community is often ambiguous. Previous solutions have attempted to identify all of the communities to which each node affiliates. Instead of taking this approach, we introduce versatility, V, as a novel metric of nodal affiliation: V ≈ 0 means that a node is consistently assigned to a specific community; V >> 0 means it is inconsistently assigned to different communities. Versatility works in conjunction with existing community detection algorithms, and it satisfies many theoretically desirable properties in idealised networks designed to maximise ambiguity of modular decomposition. The local minima of global mean versatility identified the resolution parameters of a hierarchical community detection algorithm that least ambiguously decomposed the community structure of a social (karate club) network and the mouse brain connectome. Our results suggest that nodal versatility is useful in quantifying the inherent ambiguity of modular decomposition.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006
    Language English
    Publishing date 2017-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Shifts in myeloarchitecture characterise adolescent development of cortical gradients

    Casey Paquola / Richard AI Bethlehem / Jakob Seidlitz / Konrad Wagstyl / Rafael Romero-Garcia / Kirstie J Whitaker / Reinder Vos de Wael / Guy B Williams / NSPN Consortium / Petra E Vértes / Daniel S Margulies / Boris Bernhardt / Edward T Bullmore

    eLife, Vol

    2019  Volume 8

    Abstract: We studied an accelerated longitudinal cohort of adolescents and young adults (n = 234, two time points) to investigate dynamic reconfigurations in myeloarchitecture. Intracortical profiles were generated using magnetization transfer (MT) data, a myelin- ... ...

    Abstract We studied an accelerated longitudinal cohort of adolescents and young adults (n = 234, two time points) to investigate dynamic reconfigurations in myeloarchitecture. Intracortical profiles were generated using magnetization transfer (MT) data, a myelin-sensitive magnetic resonance imaging contrast. Mixed-effect models of depth specific intracortical profiles demonstrated two separate processes i) overall increases in MT, and ii) flattening of the MT profile related to enhanced signal in mid-to-deeper layers, especially in heteromodal and unimodal association cortices. This development was independent of morphological changes. Enhanced MT in mid-to-deeper layers was found to spatially co-localise specifically with gene expression markers of oligodendrocytes. Interregional covariance analysis revealed that these intracortical changes contributed to a gradual differentiation of higher-order from lower-order systems. Depth-dependent trajectories of intracortical myeloarchitectural development contribute to the maturation of structural hierarchies in the human neocortex, providing a model for adolescent development that bridges microstructural and macroscopic scales of brain organisation.
    Keywords adolescence ; MRI ; microstructure ; hierarchy ; gradients ; transcriptomics ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-11-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Brain-behaviour modes of covariation in healthy and clinically depressed young people

    Agoston Mihalik / Fabio S. Ferreira / Maria J. Rosa / Michael Moutoussis / Gabriel Ziegler / Joao M. Monteiro / Liana Portugal / Rick A. Adams / Rafael Romero-Garcia / Petra E. Vértes / Manfred G. Kitzbichler / František Váša / Matilde M. Vaghi / Edward T. Bullmore / Peter Fonagy / Ian M. Goodyer / Peter B. Jones / NSPN Consortium / Raymond Dolan /
    Janaina Mourão-Miranda

    Scientific Reports, Vol 9, Iss 1, Pp 1-

    2019  Volume 11

    Abstract: Abstract Understanding how variations in dimensions of psychometrics, IQ and demographics relate to changes in brain connectivity during the critical developmental period of adolescence and early adulthood is a major challenge. This has particular ... ...

    Abstract Abstract Understanding how variations in dimensions of psychometrics, IQ and demographics relate to changes in brain connectivity during the critical developmental period of adolescence and early adulthood is a major challenge. This has particular relevance for mental health disorders where a failure to understand these links might hinder the development of better diagnostic approaches and therapeutics. Here, we investigated this question in 306 adolescents and young adults (14–24 y, 25 clinically depressed) using a multivariate statistical framework, based on canonical correlation analysis (CCA). By linking individual functional brain connectivity profiles to self-report questionnaires, IQ and demographic data we identified two distinct modes of covariation. The first mode mapped onto an externalization/internalization axis and showed a strong association with sex. The second mode mapped onto a well-being/distress axis independent of sex. Interestingly, both modes showed an association with age. Crucially, the changes in functional brain connectivity associated with changes in these phenotypes showed marked developmental effects. The findings point to a role for the default mode, frontoparietal and limbic networks in psychopathology and depression.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2019-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Multi-scale semi-supervised clustering of brain images: Deriving disease subtypes.

    Wen, Junhao / Varol, Erdem / Sotiras, Aristeidis / Yang, Zhijian / Chand, Ganesh B / Erus, Guray / Shou, Haochang / Abdulkadir, Ahmed / Hwang, Gyujoon / Dwyer, Dominic B / Pigoni, Alessandro / Dazzan, Paola / Kahn, Rene S / Schnack, Hugo G / Zanetti, Marcus V / Meisenzahl, Eva / Busatto, Geraldo F / Crespo-Facorro, Benedicto / Rafael, Romero-Garcia /
    Pantelis, Christos / Wood, Stephen J / Zhuo, Chuanjun / Shinohara, Russell T / Fan, Yong / Gur, Ruben C / Gur, Raquel E / Satterthwaite, Theodore D / Koutsouleris, Nikolaos / Wolf, Daniel H / Davatzikos, Christos

    Medical image analysis

    2021  Volume 75, Page(s) 102304

    Abstract: Disease heterogeneity is a significant obstacle to understanding pathological processes and delivering precision diagnostics and treatment. Clustering methods have gained popularity for stratifying patients into subpopulations (i.e., subtypes) of brain ... ...

    Abstract Disease heterogeneity is a significant obstacle to understanding pathological processes and delivering precision diagnostics and treatment. Clustering methods have gained popularity for stratifying patients into subpopulations (i.e., subtypes) of brain diseases using imaging data. However, unsupervised clustering approaches are often confounded by anatomical and functional variations not related to a disease or pathology of interest. Semi-supervised clustering techniques have been proposed to overcome this and, therefore, capture disease-specific patterns more effectively. An additional limitation of both unsupervised and semi-supervised conventional machine learning methods is that they typically model, learn and infer from data using a basis of feature sets pre-defined at a fixed anatomical or functional scale (e.g., atlas-based regions of interest). Herein we propose a novel method, "Multi-scAle heteroGeneity analysIs and Clustering" (MAGIC), to depict the multi-scale presentation of disease heterogeneity, which builds on a previously proposed semi-supervised clustering method, HYDRA. It derives multi-scale and clinically interpretable feature representations and exploits a double-cyclic optimization procedure to effectively drive identification of inter-scale-consistent disease subtypes. More importantly, to understand the conditions under which the clustering model can estimate true heterogeneity related to diseases, we conducted extensive and systematic semi-simulated experiments to evaluate the proposed method on a sizeable healthy control sample from the UK Biobank (N = 4403). We then applied MAGIC to imaging data from Alzheimer's disease (ADNI, N = 1728) and schizophrenia (PHENOM, N = 1166) patients to demonstrate its potential and challenges in dissecting the neuroanatomical heterogeneity of common brain diseases. Taken together, we aim to provide guidance regarding when such analyses can succeed or should be taken with caution. The code of the proposed method is publicly available at https://github.com/anbai106/MAGIC.
    MeSH term(s) Alzheimer Disease/diagnostic imaging ; Brain/diagnostic imaging ; Cluster Analysis ; Humans ; Supervised Machine Learning
    Language English
    Publishing date 2021-11-11
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2021.102304
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Transcriptomic and cellular decoding of regional brain vulnerability to neurogenetic disorders

    Jakob Seidlitz / Ajay Nadig / Siyuan Liu / Richard A. I. Bethlehem / Petra E. Vértes / Sarah E. Morgan / František Váša / Rafael Romero-Garcia / François M. Lalonde / Liv S. Clasen / Jonathan D. Blumenthal / Casey Paquola / Boris Bernhardt / Konrad Wagstyl / Damon Polioudakis / Luis de la Torre-Ubieta / Daniel H. Geschwind / Joan C. Han / Nancy R. Lee /
    Declan G. Murphy / Edward T. Bullmore / Armin Raznahan

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 14

    Abstract: How neurodevelopmental disorder-associated risk genes are translated into spatially patterned brain vulnerabilities is unclear. Here, the authors show that disorder-specific patterns of neuroanatomical changes are aligned to brain expression maps of ... ...

    Abstract How neurodevelopmental disorder-associated risk genes are translated into spatially patterned brain vulnerabilities is unclear. Here, the authors show that disorder-specific patterns of neuroanatomical changes are aligned to brain expression maps of disease risk genes in healthy subjects.
    Keywords Science ; Q
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Author Correction

    Jakob Seidlitz / Ajay Nadig / Siyuan Liu / Richard A. I. Bethlehem / Petra E. Vértes / Sarah E. Morgan / František Váša / Rafael Romero-Garcia / François M. Lalonde / Liv S. Clasen / Jonathan D. Blumenthal / Casey Paquola / Boris Bernhardt / Konrad Wagstyl / Damon Polioudakis / Luis de la Torre-Ubieta / Daniel H. Geschwind / Joan C. Han / Nancy R. Lee /
    Declan G. Murphy / Edward T. Bullmore / Armin Raznahan

    Nature Communications, Vol 11, Iss 1, Pp 1-

    Transcriptomic and cellular decoding of regional brain vulnerability to neurogenetic disorders

    2020  Volume 6

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Transcriptomic and cellular decoding of regional brain vulnerability to neurogenetic disorders

    Jakob Seidlitz / Ajay Nadig / Siyuan Liu / Richard A. I. Bethlehem / Petra E. Vértes / Sarah E. Morgan / František Váša / Rafael Romero-Garcia / François M. Lalonde / Liv S. Clasen / Jonathan D. Blumenthal / Casey Paquola / Boris Bernhardt / Konrad Wagstyl / Damon Polioudakis / Luis de la Torre-Ubieta / Daniel H. Geschwind / Joan C. Han / Nancy R. Lee /
    Declan G. Murphy / Edward T. Bullmore / Armin Raznahan

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 14

    Abstract: How neurodevelopmental disorder-associated risk genes are translated into spatially patterned brain vulnerabilities is unclear. Here, the authors show that disorder-specific patterns of neuroanatomical changes are aligned to brain expression maps of ... ...

    Abstract How neurodevelopmental disorder-associated risk genes are translated into spatially patterned brain vulnerabilities is unclear. Here, the authors show that disorder-specific patterns of neuroanatomical changes are aligned to brain expression maps of disease risk genes in healthy subjects.
    Keywords Science ; Q
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
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