1
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Lei T, Liao X, Liang X, Sun L, Xia M, Xia Y, Zhao T, Chen X, Men W, Wang Y, Ma L, Liu N, Lu J, Zhao G, Ding Y, Deng Y, Wang J, Chen R, Zhang H, Tan S, Gao JH, Qin S, Tao S, Dong Q, He Y. Functional network modules overlap and are linked to interindividual connectome differences during human brain development. PLoS Biol 2024; 22:e3002653. [PMID: 39292711 DOI: 10.1371/journal.pbio.3002653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 08/29/2024] [Indexed: 09/20/2024] Open
Abstract
The modular structure of functional connectomes in the human brain undergoes substantial reorganization during development. However, previous studies have implicitly assumed that each region participates in one single module, ignoring the potential spatial overlap between modules. How the overlapping functional modules develop and whether this development is related to gray and white matter features remain unknown. Using longitudinal multimodal structural, functional, and diffusion MRI data from 305 children (aged 6 to 14 years), we investigated the maturation of overlapping modules of functional networks and further revealed their structural associations. An edge-centric network model was used to identify the overlapping modules, and the nodal overlap in module affiliations was quantified using the entropy measure. We showed a regionally heterogeneous spatial topography of the overlapping extent of brain nodes in module affiliations in children, with higher entropy (i.e., more module involvement) in the ventral attention, somatomotor, and subcortical regions and lower entropy (i.e., less module involvement) in the visual and default-mode regions. The overlapping modules developed in a linear, spatially dissociable manner, with decreased entropy (i.e., decreased module involvement) in the dorsomedial prefrontal cortex, ventral prefrontal cortex, and putamen and increased entropy (i.e., increased module involvement) in the parietal lobules and lateral prefrontal cortex. The overlapping modular patterns captured individual brain maturity as characterized by chronological age and were predicted by integrating gray matter morphology and white matter microstructural properties. Our findings highlight the maturation of overlapping functional modules and their structural substrates, thereby advancing our understanding of the principles of connectome development.
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Affiliation(s)
- Tianyuan Lei
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Xuhong Liao
- School of Systems Science, Beijing Normal University, Beijing, China
| | - Xinyuan Liang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Lianglong Sun
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Mingrui Xia
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Yunman Xia
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Tengda Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Xiaodan Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Weiwei Men
- Center for MRI Research, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing City Key Laboratory for Medical Physics and Engineering, Institute of Heavy Ion Physics, School of Physics, Peking University, Beijing, China
| | - Yanpei Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Leilei Ma
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Ningyu Liu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Jing Lu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Gai Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Yuyin Ding
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Yao Deng
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Jiali Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Rui Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Haibo Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Shuping Tan
- Psychiatry Research Center, Beijing Huilongguan Hospital, Peking University Huilongguan Clinical College, Beijing, China
| | - Jia-Hong Gao
- Center for MRI Research, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing City Key Laboratory for Medical Physics and Engineering, Institute of Heavy Ion Physics, School of Physics, Peking University, Beijing, China
- IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Shaozheng Qin
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
| | - Sha Tao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Qi Dong
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Yong He
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
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2
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Betzel R, Puxeddu MG, Seguin C. Hierarchical communities in the larval Drosophila connectome: Links to cellular annotations and network topology. Proc Natl Acad Sci U S A 2024; 121:e2320177121. [PMID: 39269775 DOI: 10.1073/pnas.2320177121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/28/2024] [Indexed: 09/15/2024] Open
Abstract
One of the longstanding aims of network neuroscience is to link a connectome's topological properties-i.e., features defined from connectivity alone-with an organism's neurobiology. One approach for doing so is to compare connectome properties with annotational maps. This type of analysis is popular at the meso-/macroscale, but is less common at the nano-scale, owing to a paucity of neuron-level connectome data. However, recent methodological advances have made possible the reconstruction of whole-brain connectomes at single-neuron resolution for a select set of organisms. These include the fruit fly, Drosophila melanogaster, and its developing larvae. In addition to fine-scale descriptions of connectivity, these datasets are accompanied by rich annotations. Here, we use a variant of the stochastic blockmodel to detect multilevel communities in the larval Drosophila connectome. We find that communities partition neurons based on function and cell type and that most interact assortatively, reflecting the principle of functional segregation. However, a small number of communities interact nonassortatively, forming form a "rich-club" of interneurons that receive sensory/ascending inputs and deliver outputs along descending pathways. Next, we investigate the role of community structure in shaping communication patterns. We find that polysynaptic signaling follows specific trajectories across modular hierarchies, with interneurons playing a key role in mediating communication routes between modules and hierarchical scales. Our work suggests a relationship between system-level architecture and the biological function and classification of individual neurons. We envision our study as an important step toward bridging the gap between complex systems and neurobiological lines of investigation in brain sciences.
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Affiliation(s)
- Richard Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47401
- Cognitive Science Program, Indiana University, Bloomington, IN 47401
- Program in Neuroscience, Indiana University, Bloomington, IN 47401
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455
| | - Maria Grazia Puxeddu
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47401
| | - Caio Seguin
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47401
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3
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Farahani FV, Nebel MB, Wager TD, Lindquist MA. Effects of connectivity hyperalignment (CHA) on estimated brain network properties: from coarse-scale to fine-scale. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609817. [PMID: 39253413 PMCID: PMC11383013 DOI: 10.1101/2024.08.27.609817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Recent gains in functional magnetic resonance imaging (fMRI) studies have been driven by increasingly sophisticated statistical and computational techniques and the ability to capture brain data at finer spatial and temporal resolution. These advances allow researchers to develop population-level models of the functional brain representations underlying behavior, performance, clinical status, and prognosis. However, even following conventional preprocessing pipelines, considerable inter-individual disparities in functional localization persist, posing a hurdle to performing compelling population-level inference. Persistent misalignment in functional topography after registration and spatial normalization will reduce power in developing predictive models and biomarkers, reduce the specificity of estimated brain responses and patterns, and provide misleading results on local neural representations and individual differences. This study aims to determine how connectivity hyperalignment (CHA)-an analytic approach for handling functional misalignment-can change estimated functional brain network topologies at various spatial scales from the coarsest set of parcels down to the vertex-level scale. The findings highlight the role of CHA in improving inter-subject similarities, while retaining individual-specific information and idiosyncrasies at finer spatial granularities. This highlights the potential for fine-grained connectivity analysis using this approach to reveal previously unexplored facets of brain structure and function.
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Affiliation(s)
- Farzad V Farahani
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Mary Beth Nebel
- Center for Neurodevelopmental and Imaging Research, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tor D Wager
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Martin A Lindquist
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
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4
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Massimini M, Corbetta M, Sanchez-Vives MV, Andrillon T, Deco G, Rosanova M, Sarasso S. Sleep-like cortical dynamics during wakefulness and their network effects following brain injury. Nat Commun 2024; 15:7207. [PMID: 39174560 PMCID: PMC11341729 DOI: 10.1038/s41467-024-51586-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 08/07/2024] [Indexed: 08/24/2024] Open
Abstract
By connecting old and recent notions, different spatial scales, and research domains, we introduce a novel framework on the consequences of brain injury focusing on a key role of slow waves. We argue that the long-standing finding of EEG slow waves after brain injury reflects the intrusion of sleep-like cortical dynamics during wakefulness; we illustrate how these dynamics are generated and how they can lead to functional network disruption and behavioral impairment. Finally, we outline a scenario whereby post-injury slow waves can be modulated to reawaken parts of the brain that have fallen asleep to optimize rehabilitation strategies and promote recovery.
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Grants
- The authors thank Dr Ezequiel Mikulan, Dr Silvia Casarotto, Dr Andrea Pigorini, Dr Simone Russo, and Dr Pilleriin Sikka for their help and comments on the manuscript draft and illustrations. This work was financially supported by the following entities: ERC-2022-SYG Grant number 101071900 Neurological Mechanisms of Injury and Sleep-like Cellular Dynamics (NEMESIS); Italian National Recovery and Resilience Plan (NRRP), M4C2, funded by the European Union - NextGenerationEU (Project IR0000011, CUP B51E22000150006, “EBRAINS-Italy”); European Union’s Horizon 2020 Framework Program for Research and Innovation under the Specific Grant Agreement No.945539 (Human Brain Project SGA3); Tiny Blue Dot Foundation; Canadian Institute for Advanced Research (CIFAR), Canada; Italian Ministry for Universities and Research (PRIN 2022); Fondazione Regionale per la Ricerca Biomedica (Regione Lombardia), Project ERAPERMED2019–101, GA 779282; CORTICOMOD PID2020-112947RB-I00 financed by MCIN/ AEI /10.13039/501100011033; Fondazione Cassa di Risparmio di Padova e Rovigo (CARIPARO) Grant Agreement number 55403; Ministry of Health, Italy (RF-2008 -12366899) Brain connectivity measured with high-density electroencephalography: a novel neurodiagnostic tool for stroke- NEUROCONN; BIAL foundation grant (Grant Agreement number 361/18); H2020 European School of Network Neuroscience (euSNN); H2020 Visionary Nature Based Actions For Heath, Wellbeing & Resilience in Cities (VARCITIES); Ministry of Health Italy (RF-2019-12369300): Eye-movement dynamics during free viewing as biomarker for assessment of visuospatial functions and for closed-loop rehabilitation in stroke (EYEMOVINSTROKE).
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Affiliation(s)
- Marcello Massimini
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, Milan, Italy.
| | - Maurizio Corbetta
- Department of Neuroscience and Padova Neuroscience Center (PNC), University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Maria V Sanchez-Vives
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Thomas Andrillon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Mov'it team, Inserm, CNRS, Paris, France
- Monash Centre for Consciousness and Contemplative Studies, Faculty of Arts, Monash University, Melbourne, VIC, Australia
| | - Gustavo Deco
- Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Center for Brain and Cognition, Computational Neuroscience Group, Barcelona, Spain
| | - Mario Rosanova
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Simone Sarasso
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
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5
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Neşe H, Harı E, Ay U, Demiralp T, Ademoğlu A. Integrative role of attention networks in frequency-dependent modular organization of human brain. Brain Struct Funct 2024:10.1007/s00429-024-02847-8. [PMID: 39155311 DOI: 10.1007/s00429-024-02847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/31/2024] [Indexed: 08/20/2024]
Abstract
Despite converging evidence of hierarchical organization in the cerebral cortex, with sensory-motor and association regions at opposite ends, the mechanism of such hierarchical interactions remains elusive. This organization was primarily investigated regarding the spatiotemporal dynamics of intrinsic connectivity networks (ICNs). However, more effort is needed to investigate network dynamics in the frequency domain. We aimed to examine the integrative role of brain regions in the frequency domain with graph metrics. Phase-based connectivity estimation was performed in three frequency bands (0.011-0.038, 0.043-0.071, and 0.076-0.103 Hz) in the BOLD signal during rest. We applied modularity analysis to connectivity matrices and investigated those areas, which we called integrative regions, that showed frequency-domain flexibility. Integrative regions, mostly belonging to attention networks, were densely connected to higher-order cognitive ICNs in lower frequency bands but to sensory-motor ICNs in higher frequency bands. We compared the normalized participation coefficient (Pnorm) values of integrative and core regions with respect to their relation to higher-order cognition using a permutation-based t-test for multiple linear regression. Regression parameters of integrative regions in relation to three cognitive scores in executive functions, and working memory were significantly larger than those of core regions (Pfdr < 0.05) for salience ventral attention network. Parameters of integrative regions in relation to intelligence scores were significantly larger than those with core regions (Pfdr < 0.05) in dorsal attention network. Larger parameters of neuropsychological test scores in relation to these flexible parcels further indicate their essential role at an intermediate level in behavior. Results emphasize the importance of frequency-band analysis of brain networks.
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Affiliation(s)
- Hüden Neşe
- Institute of Biomedical Engineering, Boğaziçi University, 34684, Istanbul, Turkey.
| | - Emre Harı
- Department of Physiology, Istanbul Faculty of Medicine, Istanbul University, 34093, Istanbul, Turkey
- Hulusi Behcet Life Sciences Research Laboratory, Neuroimaging Unit, Istanbul University, 34093, Istanbul, Turkey
| | - Ulaş Ay
- Department of Physiology, Istanbul Faculty of Medicine, Istanbul University, 34093, Istanbul, Turkey
- Hulusi Behcet Life Sciences Research Laboratory, Neuroimaging Unit, Istanbul University, 34093, Istanbul, Turkey
| | - Tamer Demiralp
- Department of Physiology, Istanbul Faculty of Medicine, Istanbul University, 34093, Istanbul, Turkey
- Hulusi Behcet Life Sciences Research Laboratory, Neuroimaging Unit, Istanbul University, 34093, Istanbul, Turkey
| | - Ahmet Ademoğlu
- Institute of Biomedical Engineering, Boğaziçi University, 34684, Istanbul, Turkey
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6
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Tu D, Wrobel J, Satterthwaite TD, Goldsmith J, Gur RC, Gur RE, Gertheiss J, Bassett DS, Shinohara RT. Regression and alignment for functional data and network topology. Biostatistics 2024:kxae026. [PMID: 39140988 DOI: 10.1093/biostatistics/kxae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
Abstract
In the brain, functional connections form a network whose topological organization can be described by graph-theoretic network diagnostics. These include characterizations of the community structure, such as modularity and participation coefficient, which have been shown to change over the course of childhood and adolescence. To investigate if such changes in the functional network are associated with changes in cognitive performance during development, network studies often rely on an arbitrary choice of preprocessing parameters, in particular the proportional threshold of network edges. Because the choice of parameter can impact the value of the network diagnostic, and therefore downstream conclusions, we propose to circumvent that choice by conceptualizing the network diagnostic as a function of the parameter. As opposed to a single value, a network diagnostic curve describes the connectome topology at multiple scales-from the sparsest group of the strongest edges to the entire edge set. To relate these curves to executive function and other covariates, we use scalar-on-function regression, which is more flexible than previous functional data-based models used in network neuroscience. We then consider how systematic differences between networks can manifest in misalignment of diagnostic curves, and consequently propose a supervised curve alignment method that incorporates auxiliary information from other variables. Our algorithm performs both functional regression and alignment via an iterative, penalized, and nonlinear likelihood optimization. The illustrated method has the potential to improve the interpretability and generalizability of neuroscience studies where the goal is to study heterogeneity among a mixture of function- and scalar-valued measures.
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Affiliation(s)
- Danni Tu
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Julia Wrobel
- Department of Biostatistics and Bioinformatics, 1518 Clifton Rd. NE, Emory University, Atlanta, GA, 30322, United States
| | - Theodore D Satterthwaite
- Department of Psychiatry, 3700 Hamilton Walk, Perelman School of Medicine, Philadelphia, PA, 19104, United States
- Penn Lifespan Informatics and Neuroimaging Center, 3700 Hamilton Walk, Philadelphia, PA, 19104, United States
| | - Jeff Goldsmith
- Department of Biostatistics, 722 W. 168th St, Columbia University, New York, NY, 10032, United States
| | - Ruben C Gur
- Department of Psychiatry, 3700 Hamilton Walk, Perelman School of Medicine, Philadelphia, PA, 19104, United States
- The Penn Medicine-CHOP Lifespan Brain Institute, 3700 Hamilton Walk, Philadelphia, PA, 19104, United States
| | - Raquel E Gur
- Department of Psychiatry, 3700 Hamilton Walk, Perelman School of Medicine, Philadelphia, PA, 19104, United States
- The Penn Medicine-CHOP Lifespan Brain Institute, 3700 Hamilton Walk, Philadelphia, PA, 19104, United States
| | - Jan Gertheiss
- Department of Mathematics and Statistics, School of Economics and Social Sciences, Holstenhofweg 85, Helmut Schmidt University, 22043 Hamburg, Germany
| | - Dani S Bassett
- Department of Bioengineering, 210 S 33rd St, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Department of Physics and Astronomy, 209 S 33rd St, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Department of Electrical and Systems Engineering, 200 S 33rd St, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Department of Neurology, 3400 Spruce St, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Russell T Shinohara
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA, 19104, United States
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7
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Alavash M, Obleser J. Brain Network Interconnectivity Dynamics Explain Metacognitive Differences in Listening Behavior. J Neurosci 2024; 44:e2322232024. [PMID: 38839303 PMCID: PMC11293451 DOI: 10.1523/jneurosci.2322-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024] Open
Abstract
Complex auditory scenes pose a challenge to attentive listening, rendering listeners slower and more uncertain in their perceptual decisions. How can we explain such behaviors from the dynamics of cortical networks that pertain to the control of listening behavior? We here follow up on the hypothesis that human adaptive perception in challenging listening situations is supported by modular reconfiguration of auditory-control networks in a sample of N = 40 participants (13 males) who underwent resting-state and task functional magnetic resonance imaging (fMRI). Individual titration of a spatial selective auditory attention task maintained an average accuracy of ∼70% but yielded considerable interindividual differences in listeners' response speed and reported confidence in their own perceptual decisions. Whole-brain network modularity increased from rest to task by reconfiguring auditory, cinguloopercular, and dorsal attention networks. Specifically, interconnectivity between the auditory network and cinguloopercular network decreased during the task relative to the resting state. Additionally, interconnectivity between the dorsal attention network and cinguloopercular network increased. These interconnectivity dynamics were predictive of individual differences in response confidence, the degree of which was more pronounced after incorrect judgments. Our findings uncover the behavioral relevance of functional cross talk between auditory and attentional-control networks during metacognitive assessment of one's own perception in challenging listening situations and suggest two functionally dissociable cortical networked systems that shape the considerable metacognitive differences between individuals in adaptive listening behavior.
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Affiliation(s)
- Mohsen Alavash
- Department of Psychology, University of Lübeck, Lübeck 23562, Germany
- Center for Brain, Behavior, and Metabolism, University of Lübeck, Lübeck 23562, Germany
| | - Jonas Obleser
- Department of Psychology, University of Lübeck, Lübeck 23562, Germany
- Center for Brain, Behavior, and Metabolism, University of Lübeck, Lübeck 23562, Germany
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8
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Parkes L, Kim JZ, Stiso J, Brynildsen JK, Cieslak M, Covitz S, Gur RE, Gur RC, Pasqualetti F, Shinohara RT, Zhou D, Satterthwaite TD, Bassett DS. A network control theory pipeline for studying the dynamics of the structural connectome. Nat Protoc 2024:10.1038/s41596-024-01023-w. [PMID: 39075309 DOI: 10.1038/s41596-024-01023-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/16/2024] [Indexed: 07/31/2024]
Abstract
Network control theory (NCT) is a simple and powerful tool for studying how network topology informs and constrains the dynamics of a system. Compared to other structure-function coupling approaches, the strength of NCT lies in its capacity to predict the patterns of external control signals that may alter the dynamics of a system in a desired way. An interesting development for NCT in the neuroscience field is its application to study behavior and mental health symptoms. To date, NCT has been validated to study different aspects of the human structural connectome. NCT outputs can be monitored throughout developmental stages to study the effects of connectome topology on neural dynamics and, separately, to test the coherence of empirical datasets with brain function and stimulation. Here, we provide a comprehensive pipeline for applying NCT to structural connectomes by following two procedures. The main procedure focuses on computing the control energy associated with the transitions between specific neural activity states. The second procedure focuses on computing average controllability, which indexes nodes' general capacity to control the dynamics of the system. We provide recommendations for comparing NCT outputs against null network models, and we further support this approach with a Python-based software package called 'network control theory for python'. The procedures in this protocol are appropriate for users with a background in network neuroscience and experience in dynamical systems theory.
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Affiliation(s)
- Linden Parkes
- Department of Psychiatry, Rutgers University, Piscataway, NJ, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jason Z Kim
- Department of Physics, Cornell University, Ithaca, NY, USA
| | - Jennifer Stiso
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia K Brynildsen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Raquel E Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabio Pasqualetti
- Department of Mechanical Engineering, University of California, Riverside, Riverside, CA, USA
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, PA, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dale Zhou
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Theodore D Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
- Santa Fe Institute, Santa Fe, NM, USA
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9
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Lohia K, Soans RS, Saxena R, Mahajan K, Gandhi TK. Distinct rich and diverse clubs regulate coarse and fine binocular disparity processing: Evidence from stereoscopic task-based fMRI. iScience 2024; 27:109831. [PMID: 38784010 PMCID: PMC11111836 DOI: 10.1016/j.isci.2024.109831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/07/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
While cortical regions involved in processing binocular disparities have been studied extensively, little is known on how the human visual system adapts to changing disparity magnitudes. In this paper, we investigate causal mechanisms of coarse and fine binocular disparity processing using fMRI with a clinically validated, custom anaglyph-based stimulus. We make use of Granger causality and graph measures to reveal the existence of distinct rich and diverse clubs across different disparity magnitudes. We demonstrate that Middle Temporal area (MT) plays a specialized role with overlapping rich and diverse characteristics. Next, we show that subtle interhemispheric differences exist across various brain regions, despite an overall right hemisphere dominance. Finally, we pass the graph measures through the decision tree and found that the diverse clubs outperform rich clubs in decoding disparity magnitudes. Our study sets the stage for conducting further investigations on binocular disparity processing, particularly in the context of neuro-ophthalmic disorders with binocular impairments.
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Affiliation(s)
- Kritika Lohia
- Department of Electrical Engineering, Indian Institute of Technology – Delhi, New Delhi, India
| | - Rijul Saurabh Soans
- Department of Electrical Engineering, Indian Institute of Technology – Delhi, New Delhi, India
- Laboratory of Experimental Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Herbert Wertheim School of Optometry and Vision Science, University of California, Berkeley, Berkeley, CA, USA
| | - Rohit Saxena
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | | | - Tapan K. Gandhi
- Department of Electrical Engineering, Indian Institute of Technology – Delhi, New Delhi, India
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10
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Nenning KH, Xu T, Tambini A, Franco AR, Margulies DS, Colcombe SJ, Milham MP. Fast connectivity gradient approximation: maintaining spatially fine-grained connectivity gradients while reducing computational costs. Commun Biol 2024; 7:697. [PMID: 38844612 PMCID: PMC11156950 DOI: 10.1038/s42003-024-06401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
Brain connectome analysis suffers from the high dimensionality of connectivity data, often forcing a reduced representation of the brain at a lower spatial resolution or parcellation. This is particularly true for graph-based representations, which are increasingly used to characterize connectivity gradients, capturing patterns of systematic spatial variation in the functional connectivity structure. However, maintaining a high spatial resolution is crucial for enabling fine-grained topographical analysis and preserving subtle individual differences that might otherwise be lost. Here we introduce a computationally efficient approach to establish spatially fine-grained connectivity gradients. At its core, it leverages a set of landmarks to approximate the underlying connectivity structure at the full spatial resolution without requiring a full-scale vertex-by-vertex connectivity matrix. We show that this approach reduces computational time and memory usage while preserving informative individual features and demonstrate its application in improving brain-behavior predictions. Overall, its efficiency can remove computational barriers and enable the widespread application of connectivity gradients to capture spatial signatures of the connectome. Importantly, maintaining a spatially fine-grained resolution facilitates to characterize the spatial transitions inherent in the core concept of gradients of brain organization.
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Affiliation(s)
- Karl-Heinz Nenning
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA.
| | - Ting Xu
- Child Mind Institute, New York, NY, USA
| | - Arielle Tambini
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- New York University, New York, NY, USA
| | - Alexandre R Franco
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Child Mind Institute, New York, NY, USA
- New York University, New York, NY, USA
| | | | - Stanley J Colcombe
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Child Mind Institute, New York, NY, USA
- New York University, New York, NY, USA
| | - Michael P Milham
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Child Mind Institute, New York, NY, USA
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11
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Tang H, Bartolo-Orozco R, Averbeck BB. Ventral frontostriatal circuitry mediates the computation of reinforcement from symbolic gains and losses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587097. [PMID: 38617219 PMCID: PMC11014508 DOI: 10.1101/2024.04.03.587097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Reinforcement learning (RL), particularly in primates, is often driven by symbolic outcomes. However, it is usually studied with primary reinforcers. To examine the neural mechanisms underlying learning from symbolic outcomes, we trained monkeys on a task in which they learned to choose options that led to gains of tokens and avoid choosing options that led to losses of tokens. We then recorded simultaneously from the orbitofrontal cortex (OFC), ventral striatum (VS), amygdala (AMY), and the mediodorsal thalamus (MDt). We found that the OFC played a dominant role in coding token outcomes and token prediction errors. The other areas contributed complementary functions with the VS coding appetitive outcomes and the AMY coding the salience of outcomes. The MDt coded actions and relayed information about tokens between the OFC and VS. Thus, OFC leads the process of symbolic reinforcement learning in the ventral frontostriatal circuitry.
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12
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Vohryzek J, Cabral J, Timmermann C, Atasoy S, Roseman L, Nutt DJ, Carhart-Harris RL, Deco G, Kringelbach ML. The flattening of spacetime hierarchy of the N,N-dimethyltryptamine brain state is characterized by harmonic decomposition of spacetime (HADES) framework. Natl Sci Rev 2024; 11:nwae124. [PMID: 38778818 PMCID: PMC11110867 DOI: 10.1093/nsr/nwae124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 05/25/2024] Open
Abstract
The human brain is a complex system, whose activity exhibits flexible and continuous reorganization across space and time. The decomposition of whole-brain recordings into harmonic modes has revealed a repertoire of gradient-like activity patterns associated with distinct brain functions. However, the way these activity patterns are expressed over time with their changes in various brain states remains unclear. Here, we investigate healthy participants taking the serotonergic psychedelic N,N-dimethyltryptamine (DMT) with the Harmonic Decomposition of Spacetime (HADES) framework that can characterize how different harmonic modes defined in space are expressed over time. HADES demonstrates significant decreases in contributions across most low-frequency harmonic modes in the DMT-induced brain state. When normalizing the contributions by condition (DMT and non-DMT), we detect a decrease specifically in the second functional harmonic, which represents the uni- to transmodal functional hierarchy of the brain, supporting the leading hypothesis that functional hierarchy is changed in psychedelics. Moreover, HADES' dynamic spacetime measures of fractional occupancy, life time and latent space provide a precise description of the significant changes of the spacetime hierarchical organization of brain activity in the psychedelic state.
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Affiliation(s)
- Jakub Vohryzek
- Centre for Eudaimonia and Human Flourishing, Linacre College, Department of Psychiatry, University of Oxford, Oxford OX3 9BX, UK
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
- Center for Music in the Brain, Aarhus University, Aarhus 8000, Denmark
- Center for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona 08005, Spain
| | - Joana Cabral
- Centre for Eudaimonia and Human Flourishing, Linacre College, Department of Psychiatry, University of Oxford, Oxford OX3 9BX, UK
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães 4710-057, Portugal
| | - Christopher Timmermann
- Centre for Psychedelic Research, Department of Brain Sciences, Imperial College London, London SW7 2AZ, UK
| | - Selen Atasoy
- Centre for Eudaimonia and Human Flourishing, Linacre College, Department of Psychiatry, University of Oxford, Oxford OX3 9BX, UK
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Leor Roseman
- Centre for Psychedelic Research, Department of Brain Sciences, Imperial College London, London SW7 2AZ, UK
| | - David J Nutt
- Centre for Psychedelic Research, Department of Brain Sciences, Imperial College London, London SW7 2AZ, UK
| | - Robin L Carhart-Harris
- Centre for Psychedelic Research, Department of Brain Sciences, Imperial College London, London SW7 2AZ, UK
- Departments of Neurology and Psychiatry, University of California San Francisco, San Francisco 94143, USA
| | - Gustavo Deco
- Center for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona 08005, Spain
- Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- School of Psychological Sciences, Monash University, Melbourne, Australia
| | - Morten L Kringelbach
- Centre for Eudaimonia and Human Flourishing, Linacre College, Department of Psychiatry, University of Oxford, Oxford OX3 9BX, UK
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
- Center for Music in the Brain, Aarhus University, Aarhus 8000, Denmark
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13
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Yadav A, Fialkowski J, Berner R, Chandrasekar VK, Senthilkumar DV. Disparity-driven heterogeneous nucleation in finite-size adaptive networks. Phys Rev E 2024; 109:L052301. [PMID: 38907508 DOI: 10.1103/physreve.109.l052301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/16/2024] [Indexed: 06/24/2024]
Abstract
Phase transitions are crucial in shaping the collective dynamics of a broad spectrum of natural systems across disciplines. Here, we report two distinct heterogeneous nucleation facilitating single step and multistep phase transitions to global synchronization in a finite-size adaptive network due to the trade off between time scale adaptation and coupling strength disparities. Specifically, small intracluster nucleations coalesce either at the population interface or within the populations resulting in the two distinct phase transitions depending on the degree of the disparities. We find that the coupling strength disparity largely controls the nature of phase transition in the phase diagram irrespective of the adaptation disparity. We provide a mesoscopic description for the cluster dynamics using the collective coordinates approach that brilliantly captures the multicluster dynamics among the populations leading to distinct phase transitions. Further, we also deduce the upper bound for the coupling strength for the existence of two intraclusters explicitly in terms of adaptation and coupling strength disparities. These insights may have implications across domains ranging from neurological disorders to segregation dynamics in social networks.
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Affiliation(s)
- Akash Yadav
- School of Physics, Indian Institute of Science Education and Research, Thiruvananthapuram-695551, Kerala, India
| | - Jan Fialkowski
- Complexity Science Hub Vienna, Josefstädter Straße 39, 1080 Vienna, Austria
- Center for Medical Data Science, Medical University Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Rico Berner
- Department of Physics, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - V K Chandrasekar
- Centre for Nonlinear Science & Engineering, School of Electrical & Electronics Engineering, SASTRA Deemed University, Thanjavur-613401, Tamil Nadu, India
| | - D V Senthilkumar
- School of Physics, Indian Institute of Science Education and Research, Thiruvananthapuram-695551, Kerala, India
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14
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Pugliese CE, Handsman R, You X, Anthony LG, Vaidya C, Kenworthy L. Probing heterogeneity to identify individualized treatment approaches in autism: Specific clusters of executive function challenges link to distinct co-occurring mental health problems. AUTISM : THE INTERNATIONAL JOURNAL OF RESEARCH AND PRACTICE 2024:13623613241246091. [PMID: 38642028 DOI: 10.1177/13623613241246091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2024]
Abstract
LAY ABSTRACT Many autistic people struggle with mental health problems like anxiety, depression, inattention, and aggression, which can be challenging to treat. Executive function challenges, which impact many autistic individuals, may serve as a risk factor for mental health problems or make treating mental health conditions more difficult. While some people respond well to medication or therapy, others do not. This study tried to understand if there are different subgroups of autistic young people who may have similar patterns of executive function strengths and challenges-like flexibility, planning, self-monitoring, and emotion regulation. Then, we investigated whether executive function subgroups were related to mental health problems in autistic youth. We found three different types of executive function subgroups in autistic youth, each with different patterns of mental health problems. This helps us identify specific profiles of executive function strengths and challenges that may be helpful with identifying personalized supports, services, and treatment strategies for mental health conditions.
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15
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Wylie KP, Vu T, Legget KT, Tregellas JR. Hierarchical Principal Components for Data-Driven Multiresolution fMRI Analyses. Brain Sci 2024; 14:325. [PMID: 38671978 PMCID: PMC11048444 DOI: 10.3390/brainsci14040325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Understanding the organization of neural processing is a fundamental goal of neuroscience. Recent work suggests that these systems are organized as a multiscale hierarchy, with increasingly specialized subsystems nested inside general processing systems. Current neuroimaging methods, such as independent component analysis (ICA), cannot fully capture this hierarchy since they are limited to a single spatial scale. In this manuscript, we introduce multiresolution hierarchical principal components analysis (hPCA) and compare it to ICA using simulated fMRI datasets. Furthermore, we describe a parametric statistical filtering method developed to focus analyses on biologically relevant features. Lastly, we apply hPCA to the Human Connectome Project (HCP) to demonstrate its ability to estimate a hierarchy from real fMRI data. hPCA accurately estimated spatial maps and time series from networks with diverse hierarchical structures. Simulated hierarchies varied in the degree of branching, such as two-way or three-way subdivisions, and the total number of levels, with varying equal or unequal subdivision sizes at each branch. In each case, as well as in the HCP, hPCA was able to reconstruct a known hierarchy of networks. Our results suggest that hPCA can facilitate more detailed and comprehensive analyses of the brain's network of networks and the multiscale regional specializations underlying neural processing and cognition.
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Affiliation(s)
- Korey P. Wylie
- Department of Psychiatry, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (K.T.L.); (J.R.T.)
| | - Thao Vu
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristina T. Legget
- Department of Psychiatry, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (K.T.L.); (J.R.T.)
- Research Service, Rocky Mountain Regional VA Medical Center, Aurora, CO 80045, USA
| | - Jason R. Tregellas
- Department of Psychiatry, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (K.T.L.); (J.R.T.)
- Research Service, Rocky Mountain Regional VA Medical Center, Aurora, CO 80045, USA
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16
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Chinichian N, Lindner M, Yanchuk S, Schwalger T, Schöll E, Berner R. Modeling brain network flexibility in networks of coupled oscillators: a feasibility study. Sci Rep 2024; 14:5713. [PMID: 38459077 PMCID: PMC10923875 DOI: 10.1038/s41598-024-55753-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Modeling the functionality of the human brain is a major goal in neuroscience for which many powerful methodologies have been developed over the last decade. The impact of working memory and the associated brain regions on the brain dynamics is of particular interest due to their connection with many functions and malfunctions in the brain. In this context, the concept of brain flexibility has been developed for the characterization of brain functionality. We discuss emergence of brain flexibility that is commonly measured by the identification of changes in the cluster structure of co-active brain regions. We provide evidence that brain flexibility can be modeled by a system of coupled FitzHugh-Nagumo oscillators where the network structure is obtained from human brain Diffusion Tensor Imaging (DTI). Additionally, we propose a straightforward and computationally efficient alternative macroscopic measure, which is derived from the Pearson distance of functional brain matrices. This metric exhibits similarities to the established patterns of brain template flexibility that have been observed in prior investigations. Furthermore, we explore the significance of the brain's network structure and the strength of connections between network nodes or brain regions associated with working memory in the observation of patterns in networks flexibility. This work enriches our understanding of the interplay between the structure and function of dynamic brain networks and proposes a modeling strategy to study brain flexibility.
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Affiliation(s)
- Narges Chinichian
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany.
- Psychiatry Department, Charité-Universitätsmedizin, Berlin, Germany.
- Bernstein Center for Computational Neuroscience, Berlin, Germany.
| | - Michael Lindner
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | - Serhiy Yanchuk
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
- Institute of Mathematics, Humboldt Universität zu Berlin, Berlin, Germany
- School of Mathematical Sciences, University College Cork, Cork, Ireland
| | - Tilo Schwalger
- Bernstein Center for Computational Neuroscience, Berlin, Germany
- Institute of Mathematics, Technische Universität Berlin, Berlin, Germany
| | - Eckehard Schöll
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
- Bernstein Center for Computational Neuroscience, Berlin, Germany
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | - Rico Berner
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
- Department of Physics, Humboldt Universität zu Berlin, Berlin, Germany
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17
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Stella M, Citraro S, Rossetti G, Marinazzo D, Kenett YN, Vitevitch MS. Cognitive modelling of concepts in the mental lexicon with multilayer networks: Insights, advancements, and future challenges. Psychon Bull Rev 2024:10.3758/s13423-024-02473-9. [PMID: 38438713 DOI: 10.3758/s13423-024-02473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2024] [Indexed: 03/06/2024]
Abstract
The mental lexicon is a complex cognitive system representing information about the words/concepts that one knows. Over decades psychological experiments have shown that conceptual associations across multiple, interactive cognitive levels can greatly influence word acquisition, storage, and processing. How can semantic, phonological, syntactic, and other types of conceptual associations be mapped within a coherent mathematical framework to study how the mental lexicon works? Here we review cognitive multilayer networks as a promising quantitative and interpretative framework for investigating the mental lexicon. Cognitive multilayer networks can map multiple types of information at once, thus capturing how different layers of associations might co-exist within the mental lexicon and influence cognitive processing. This review starts with a gentle introduction to the structure and formalism of multilayer networks. We then discuss quantitative mechanisms of psychological phenomena that could not be observed in single-layer networks and were only unveiled by combining multiple layers of the lexicon: (i) multiplex viability highlights language kernels and facilitative effects of knowledge processing in healthy and clinical populations; (ii) multilayer community detection enables contextual meaning reconstruction depending on psycholinguistic features; (iii) layer analysis can mediate latent interactions of mediation, suppression, and facilitation for lexical access. By outlining novel quantitative perspectives where multilayer networks can shed light on cognitive knowledge representations, including in next-generation brain/mind models, we discuss key limitations and promising directions for cutting-edge future research.
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Affiliation(s)
- Massimo Stella
- CogNosco Lab, Department of Psychology and Cognitive Science, University of Trento, Trento, Italy.
| | - Salvatore Citraro
- Institute of Information Science and Technologies, National Research Council, Pisa, Italy
| | - Giulio Rossetti
- Institute of Information Science and Technologies, National Research Council, Pisa, Italy
| | - Daniele Marinazzo
- Faculty of Psychology and Educational Sciences, Department of Data Analysis, University of Ghent, Ghent, Belgium
| | - Yoed N Kenett
- Faculty of Data and Decision Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| | - Michael S Vitevitch
- Department of Speech Language Hearing, University of Kansas, Lawrence, KS, USA
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18
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Jimenez-Marin A, Diez I, Erramuzpe A, Stramaglia S, Bonifazi P, Cortes JM. Open datasets and code for multi-scale relations on structure, function and neuro-genetics in the human brain. Sci Data 2024; 11:256. [PMID: 38424112 PMCID: PMC10904384 DOI: 10.1038/s41597-024-03060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
The human brain is an extremely complex network of structural and functional connections that operate at multiple spatial and temporal scales. Investigating the relationship between these multi-scale connections is critical to advancing our comprehension of brain function and disorders. However, accurately predicting structural connectivity from its functional counterpart remains a challenging pursuit. One of the major impediments is the lack of public repositories that integrate structural and functional networks at diverse resolutions, in conjunction with modular transcriptomic profiles, which are essential for comprehensive biological interpretation. To mitigate this limitation, our contribution encompasses the provision of an open-access dataset consisting of derivative matrices of functional and structural connectivity across multiple scales, accompanied by code that facilitates the investigation of their interrelations. We also provide additional resources focused on neuro-genetic associations of module-level network metrics, which present promising opportunities to further advance research in the field of network neuroscience, particularly concerning brain disorders.
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Affiliation(s)
- Antonio Jimenez-Marin
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain
- Biomedical Research Doctorate Program, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ibai Diez
- Department of Radiology, Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, United States of America
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, United States of America
| | - Asier Erramuzpe
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Sebastiano Stramaglia
- Dipartamento Interateneo di Fisica, Universita Degli Studi di Bari Aldo Moro, INFN, Bari, Italy
| | - Paolo Bonifazi
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Jesus M Cortes
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain.
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain.
- Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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19
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Tu D, Wrobel J, Satterthwaite TD, Goldsmith J, Gur RC, Gur RE, Gertheiss J, Bassett DS, Shinohara RT. Regression and Alignment for Functional Data and Network Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.13.548836. [PMID: 37503017 PMCID: PMC10370026 DOI: 10.1101/2023.07.13.548836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In the brain, functional connections form a network whose topological organization can be described by graph-theoretic network diagnostics. These include characterizations of the community structure, such as modularity and participation coefficient, which have been shown to change over the course of childhood and adolescence. To investigate if such changes in the functional network are associated with changes in cognitive performance during development, network studies often rely on an arbitrary choice of pre-processing parameters, in particular the proportional threshold of network edges. Because the choice of parameter can impact the value of the network diagnostic, and therefore downstream conclusions, we propose to circumvent that choice by conceptualizing the network diagnostic as a function of the parameter. As opposed to a single value, a network diagnostic curve describes the connectome topology at multiple scales-from the sparsest group of the strongest edges to the entire edge set. To relate these curves to executive function and other covariates, we use scalar-on-function regression, which is more flexible than previous functional data-based models used in network neuroscience. We then consider how systematic differences between networks can manifest in misalignment of diagnostic curves, and consequently propose a supervised curve alignment method that incorporates auxiliary information from other variables. Our algorithm performs both functional regression and alignment via an iterative, penalized, and nonlinear likelihood optimization. The illustrated method has the potential to improve the interpretability and generalizability of neuroscience studies where the goal is to study heterogeneity among a mixture of function- and scalar-valued measures.
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Affiliation(s)
- Danni Tu
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Wrobel
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Theodore D. Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA USA
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, PA, USA
| | - Jeff Goldsmith
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Ruben C. Gur
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA USA
- The Penn Medicine-CHOP Lifespan Brain Institute, Philadelphia, PA, USA
| | - Raquel E. Gur
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA USA
- The Penn Medicine-CHOP Lifespan Brain Institute, Philadelphia, PA, USA
| | - Jan Gertheiss
- Department of Mathematics and Statistics, School of Economics and Social Sciences, Helmut Schmidt University, Hamburg, Germany
| | - Dani S. Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T. Shinohara
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
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20
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Irastorza-Valera L, Benítez JM, Montáns FJ, Saucedo-Mora L. An Agent-Based Model to Reproduce the Boolean Logic Behaviour of Neuronal Self-Organised Communities through Pulse Delay Modulation and Generation of Logic Gates. Biomimetics (Basel) 2024; 9:101. [PMID: 38392147 PMCID: PMC10886514 DOI: 10.3390/biomimetics9020101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/16/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
The human brain is arguably the most complex "machine" to ever exist. Its detailed functioning is yet to be fully understood, let alone modelled. Neurological processes have logical signal-processing and biophysical aspects, and both affect the brain's structure, functioning and adaptation. Mathematical approaches based on both information and graph theory have been extensively used in an attempt to approximate its biological functioning, along with Artificial Intelligence frameworks inspired by its logical functioning. In this article, an approach to model some aspects of the brain learning and signal processing is presented, mimicking the metastability and backpropagation found in the real brain while also accounting for neuroplasticity. Several simulations are carried out with this model to demonstrate how dynamic neuroplasticity, neural inhibition and neuron migration can reshape the brain's logical connectivity to synchronise signal processing and obtain certain target latencies. This work showcases the importance of dynamic logical and biophysical remodelling in brain plasticity. Combining mathematical (agents, graph theory, topology and backpropagation) and biomedical ingredients (metastability, neuroplasticity and migration), these preliminary results prove complex brain phenomena can be reproduced-under pertinent simplifications-via affordable computations, which can be construed as a starting point for more ambitiously accurate simulations.
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Affiliation(s)
- Luis Irastorza-Valera
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain
- PIMM Laboratory, Arts et Métiers Institute of Technology, 151 Bd de l'Hôpital, 75013 Paris, France
| | - José María Benítez
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain
| | - Francisco J Montáns
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Luis Saucedo-Mora
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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21
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Lurie DJ, Pappas I, D'Esposito M. Cortical timescales and the modular organization of structural and functional brain networks. Hum Brain Mapp 2024; 45:e26587. [PMID: 38339903 PMCID: PMC10823764 DOI: 10.1002/hbm.26587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/01/2023] [Accepted: 12/21/2023] [Indexed: 02/12/2024] Open
Abstract
Recent years have seen growing interest in characterizing the properties of regional brain dynamics and their relationship to other features of brain structure and function. In particular, multiple studies have observed regional differences in the "timescale" over which activity fluctuates during periods of quiet rest. In the cerebral cortex, these timescales have been associated with both local circuit properties as well as patterns of inter-regional connectivity, including the extent to which each region exhibits widespread connectivity to other brain areas. In the current study, we build on prior observations of an association between connectivity and dynamics in the cerebral cortex by investigating the relationship between BOLD fMRI timescales and the modular organization of structural and functional brain networks. We characterize network community structure across multiple scales and find that longer timescales are associated with greater within-community functional connectivity and diverse structural connectivity. We also replicate prior observations of a positive correlation between timescales and structural connectivity degree. Finally, we find evidence for preferential functional connectivity between cortical areas with similar timescales. We replicate these findings in an independent dataset. These results contribute to our understanding of functional brain organization and structure-function relationships in the human brain, and support the notion that regional differences in cortical dynamics may in part reflect the topological role of each region within macroscale brain networks.
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Affiliation(s)
- Daniel J. Lurie
- Department of PsychologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPennsylvaniaUSA
| | - Ioannis Pappas
- Department of Neurology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Mark D'Esposito
- Department of Psychology and Helen Wills Neuroscience InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
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22
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Li D, Hou D, Zhang Y, Zhao Y, Cui X, Niu Y, Xiang J, Wang B. Aberrant Functional Connectivity in Core-Periphery Structure Based on WSBM in ADHD. J Atten Disord 2024; 28:415-430. [PMID: 38102929 DOI: 10.1177/10870547231214985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
OBJECTIVE Brain network studies have revealed that the community structure of ADHD is altered. However, these studies have only focused on modular community structure, ignoring the core-periphery community structure. METHOD This paper employed the weighted stochastic block model to divide the functional connectivity (FC) into 10 communities. And we adopted core score to define the core-periphery structure of FC. Finally, connectivity strength (CS) and disruption index (DI) were used to evaluate the changes of core-periphery structure in ADHD. RESULTS The core community of visual network showed reduced CS and a positive value of DI, while the CS of periphery community was enhanced. In addition, the interaction between core communities (involving the sensorimotor and visual network) and periphery community of attention network showed increased CS and a negative valve of DI. CONCLUSION Anomalies in core-periphery community structure provide a new perspective for understanding the community structure of ADHD.
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Affiliation(s)
- Dandan Li
- Taiyuan University of Technology, Shanxi, China
| | - Dianni Hou
- Taiyuan University of Technology, Shanxi, China
| | | | - Yao Zhao
- Taiyuan University of Technology, Shanxi, China
| | | | - Yan Niu
- Taiyuan University of Technology, Shanxi, China
| | - Jie Xiang
- Taiyuan University of Technology, Shanxi, China
| | - Bin Wang
- Taiyuan University of Technology, Shanxi, China
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23
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Liu M, Huang Q, Huang L, Ren S, Cui L, Zhang H, Guan Y, Guo Q, Xie F, Shen D. Dysfunctions of multiscale dynamic brain functional networks in subjective cognitive decline. Brain Commun 2024; 6:fcae010. [PMID: 38304005 PMCID: PMC10833653 DOI: 10.1093/braincomms/fcae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/22/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Subjective cognitive decline is potentially the earliest symptom of Alzheimer's disease, whose objective neurological basis remains elusive. To explore the potential biomarkers for subjective cognitive decline, we developed a novel deep learning method based on multiscale dynamical brain functional networks to identify subjective cognitive declines. We retrospectively constructed an internal data set (with 112 subjective cognitive decline and 64 healthy control subjects) to develop and internally validate the deep learning model. Conventional deep learning methods based on static and dynamic brain functional networks are compared. After the model is established, we prospectively collect an external data set (26 subjective cognitive decline and 12 healthy control subjects) for testing. Meanwhile, our method provides monitoring of the transitions between normal and abnormal (subjective cognitive decline-related) dynamical functional network states. The features of abnormal dynamical functional network states are quantified by network and variability metrics and associated with individual cognitions. Our method achieves an area under the receiver operating characteristic curve of 0.807 ± 0.046 in the internal validation data set and of 0.707 (P = 0.007) in the external testing data set, which shows improvements compared to conventional methods. The method further suggests that, at the local level, the abnormal dynamical functional network states are characterized by decreased connectivity strength and increased connectivity variability at different spatial scales. At the network level, the abnormal states are featured by scale-specifically altered modularity and all-scale decreased efficiency. Low tendencies to stay in abnormal states and high state transition variabilities are significantly associated with high general, language and executive functions. Overall, our work supports the deficits in multiscale brain dynamical functional networks detected by the deep learning method as reliable and meaningful neural alternation underpinning subjective cognitive decline.
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Affiliation(s)
- Mianxin Liu
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Qi Huang
- Department of Nuclear Medicine & PET Center, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lin Huang
- Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Shuhua Ren
- Department of Nuclear Medicine & PET Center, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Liang Cui
- Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Han Zhang
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Yihui Guan
- Department of Nuclear Medicine & PET Center, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Qihao Guo
- Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Fang Xie
- Department of Nuclear Medicine & PET Center, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Dinggang Shen
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai United Imaging Intelligence Co., Ltd., Shanghai 200230, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
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24
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Bonosi L, Torrente A, Brighina F, Tito Petralia CC, Merlino P, Avallone C, Gulino V, Costanzo R, Brunasso L, Iacopino DG, Maugeri R. Corticocortical Evoked Potentials in Eloquent Brain Tumor Surgery. A Systematic Review. World Neurosurg 2024; 181:38-51. [PMID: 37832637 DOI: 10.1016/j.wneu.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Eloquent brain tumor surgery involves the delicate task of resecting tumors located in regions of the brain responsible for critical functions, such as language, motor control, and sensory perception. Preserving these functions is of paramount importance to maintain the patient's quality of life. Corticocortical evoked potentials (CCEPs) have emerged as a valuable intraoperative monitoring technique that aids in identifying and preserving eloquent cortical areas during surgery. This systematic review aimed to assess the utility of CCEPs in eloquent brain tumor surgery and determine their effectiveness in improving patient outcomes. A comprehensive literature search was conducted using electronic databases, including PubMed/Medline and Scopus. The search strategy identified 11 relevant articles for detailed analysis. The findings of the included studies consistently demonstrated the potential of CCEPs in guiding surgical decision making, minimizing the risk of postoperative neurological deficits, and mapping functional connectivity during surgery. However, further research and standardization are needed to fully establish the clinical benefits and refine the implementation of CCEPs in routine neurosurgical practice.
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Affiliation(s)
- Lapo Bonosi
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy.
| | - Angelo Torrente
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, Palermo, Italy
| | - Filippo Brighina
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, Palermo, Italy
| | - Cateno Concetto Tito Petralia
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Pietro Merlino
- Department of Neuroscience, Psychology, Pharmacology and Child Health, Neurosurgery Clinic, Careggi University Hospital and University of Florence, Florence, Italy
| | - Chiara Avallone
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Vincenzo Gulino
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Roberta Costanzo
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Lara Brunasso
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Domenico Gerardo Iacopino
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Rosario Maugeri
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
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25
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Wen J, Nasrallah IM, Abdulkadir A, Satterthwaite TD, Yang Z, Erus G, Robert-Fitzgerald T, Singh A, Sotiras A, Boquet-Pujadas A, Mamourian E, Doshi J, Cui Y, Srinivasan D, Skampardoni I, Chen J, Hwang G, Bergman M, Bao J, Veturi Y, Zhou Z, Yang S, Dazzan P, Kahn RS, Schnack HG, Zanetti MV, Meisenzahl E, Busatto GF, Crespo-Facorro B, Pantelis C, Wood SJ, Zhuo C, Shinohara RT, Gur RC, Gur RE, Koutsouleris N, Wolf DH, Saykin AJ, Ritchie MD, Shen L, Thompson PM, Colliot O, Wittfeld K, Grabe HJ, Tosun D, Bilgel M, An Y, Marcus DS, LaMontagne P, Heckbert SR, Austin TR, Launer LJ, Espeland M, Masters CL, Maruff P, Fripp J, Johnson SC, Morris JC, Albert MS, Bryan RN, Resnick SM, Fan Y, Habes M, Wolk D, Shou H, Davatzikos C. Genomic loci influence patterns of structural covariance in the human brain. Proc Natl Acad Sci U S A 2023; 120:e2300842120. [PMID: 38127979 PMCID: PMC10756284 DOI: 10.1073/pnas.2300842120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023] Open
Abstract
Normal and pathologic neurobiological processes influence brain morphology in coordinated ways that give rise to patterns of structural covariance (PSC) across brain regions and individuals during brain aging and diseases. The genetic underpinnings of these patterns remain largely unknown. We apply a stochastic multivariate factorization method to a diverse population of 50,699 individuals (12 studies and 130 sites) and derive data-driven, multi-scale PSCs of regional brain size. PSCs were significantly correlated with 915 genomic loci in the discovery set, 617 of which are newly identified, and 72% were independently replicated. Key pathways influencing PSCs involve reelin signaling, apoptosis, neurogenesis, and appendage development, while pathways of breast cancer indicate potential interplays between brain metastasis and PSCs associated with neurodegeneration and dementia. Using support vector machines, multi-scale PSCs effectively derive imaging signatures of several brain diseases. Our results elucidate genetic and biological underpinnings that influence structural covariance patterns in the human brain.
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Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science, Department of Neurology, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ilya M. Nasrallah
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Ahmed Abdulkadir
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Theodore D. Satterthwaite
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Zhijian Yang
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Guray Erus
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Timothy Robert-Fitzgerald
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ashish Singh
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Aristeidis Sotiras
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Aleix Boquet-Pujadas
- Biomedical Imaging Group, Department of Biomedical Engineering, École Polytechnique Fédérale de Lausanne, Lausanne1015, Switzerland
| | - Elizabeth Mamourian
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jimit Doshi
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Yuhan Cui
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Dhivya Srinivasan
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ioanna Skampardoni
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jiong Chen
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Gyujoon Hwang
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Mark Bergman
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Yogasudha Veturi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Zhen Zhou
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Shu Yang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Paola Dazzan
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, LondonWC2R 2LS, United Kingdom
| | - Rene S. Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Hugo G. Schnack
- Department of Psychiatry, University Medical Center Utrecht, Utrecht 3584 CX Ut, Netherlands
| | - Marcus V. Zanetti
- Institute of Psychiatry, Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo05508-070, Brazil
| | - Eva Meisenzahl
- Department of Psychiatry and Psychotherapy, Heinrich Heine University, Düsseldorf40204, Germany
| | - Geraldo F. Busatto
- Institute of Psychiatry, Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo05508-070, Brazil
| | - Benedicto Crespo-Facorro
- Hospital Universitario Virgen del Rocio, School of Medicine, University of Sevilla,Sevilla41004, Spain
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Stephen J. Wood
- Orygen and the Centre for Youth Mental Health, Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Chuanjun Zhuo
- Key Laboratory of Real Tine Tracing of Brain Circuits in Psychiatry and Neurology, Department of Psychiatry, Tianjin Medical University, Tianjin300070, China
| | - Russell T. Shinohara
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ruben C. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Raquel E. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich 80539, Germany
| | - Daniel H. Wolf
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Andrew J. Saykin
- Indiana Alzheimer’s Disease Research Center, Department of Radiology, Indiana University School of Medicine, Indianapolis, IN46202-3082
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Paul M. Thompson
- Imaging Genetics Center, Department of Neurology, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
| | - Olivier Colliot
- Institut du Cerveau, Sorbonne Université, Paris75013, France
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, German Center for Neurodegenerative Diseases, University Medicine Greifswald, Greifswald17475, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, German Center for Neurodegenerative Diseases, University Medicine Greifswald, Greifswald17475, Germany
| | - Duygu Tosun
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Daniel S. Marcus
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Pamela LaMontagne
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA98195
| | - Thomas R. Austin
- Department of Epidemiology, University of Washington, Seattle, WA98195
| | - Lenore J. Launer
- Neuroepidemiology Section, Intramural Research Program, National Institute on Aging, Washington, MD20817
| | - Mark Espeland
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Divisions of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC27101
| | - Colin L. Masters
- Florey Institute of Neuroscience and Mental Health, Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC3010, Australia
| | - Paul Maruff
- Florey Institute of Neuroscience and Mental Health, Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC3010, Australia
| | - Jurgen Fripp
- Health and Biosecurity, Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD4029, Australia
| | - Sterling C. Johnson
- Wisconsin Alzheimer's Institute, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI53792
| | - John C. Morris
- Knight Alzheimer Disease Research Center, Department of Neurology, Washington University in St. Louis, St. Louis, MO63110
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - R. Nick Bryan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Yong Fan
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Mohamad Habes
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, Department of Radiology, University of Texas Health Science Center at San Antonio, San Antonio, TX78229
| | - David Wolk
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Neurology, University of Pennsylvania, Philadelphia, PA19104
| | - Haochang Shou
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Christos Davatzikos
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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26
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Kotlarz P, Lankinen K, Hakonen M, Turpin T, Polimeni JR, Ahveninen J. Multilayer Network Analysis across Cortical Depths in Resting-State 7T fMRI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.23.573208. [PMID: 38187540 PMCID: PMC10769454 DOI: 10.1101/2023.12.23.573208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In graph theory, "multilayer networks" represent systems involving several interconnected topological levels. A neuroscience example is the hierarchy of connections between different cortical depths or "lamina". This hierarchy is becoming non-invasively accessible in humans using ultra-high-resolution functional MRI (fMRI). Here, we applied multilayer graph theory to examine functional connectivity across different cortical depths in humans, using 7T fMRI (1-mm3 voxels; 30 participants). Blood oxygenation level dependent (BOLD) signals were derived from five depths between the white matter and pial surface. We then compared networks where the inter-regional connections were limited to a single cortical depth only ("layer-by-layer matrices") to those considering all possible connections between regions and cortical depths ("multilayer matrix"). We utilized global and local graph theory features that quantitatively characterize network attributes such as network composition, nodal centrality, path-based measures, and hub segregation. Detecting functional differences between cortical depths was improved using multilayer connectomics compared to the layer-by-layer versions. Superficial aspects of the cortex dominated information transfer and deeper aspects clustering. These differences were largest in frontotemporal and limbic brain regions. fMRI functional connectivity across different cortical depths may contain neurophysiologically relevant information. Multilayer connectomics could provide a methodological framework for studies on how information flows across this hierarchy.
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Affiliation(s)
- Parker Kotlarz
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kaisu Lankinen
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Maria Hakonen
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | | | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jyrki Ahveninen
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
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27
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Gajwani M, Oldham S, Pang JC, Arnatkevičiūtė A, Tiego J, Bellgrove MA, Fornito A. Can hubs of the human connectome be identified consistently with diffusion MRI? Netw Neurosci 2023; 7:1326-1350. [PMID: 38144690 PMCID: PMC10631793 DOI: 10.1162/netn_a_00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/17/2023] [Indexed: 12/26/2023] Open
Abstract
Recent years have seen a surge in the use of diffusion MRI to map connectomes in humans, paralleled by a similar increase in processing and analysis choices. Yet these different steps and their effects are rarely compared systematically. Here, in a healthy young adult population (n = 294), we characterized the impact of a range of analysis pipelines on one widely studied property of the human connectome: its degree distribution. We evaluated the effects of 40 pipelines (comparing common choices of parcellation, streamline seeding, tractography algorithm, and streamline propagation constraint) and 44 group-representative connectome reconstruction schemes on highly connected hub regions. We found that hub location is highly variable between pipelines. The choice of parcellation has a major influence on hub architecture, and hub connectivity is highly correlated with regional surface area in most of the assessed pipelines (ρ > 0.70 in 69% of the pipelines), particularly when using weighted networks. Overall, our results demonstrate the need for prudent decision-making when processing diffusion MRI data, and for carefully considering how different processing choices can influence connectome organization.
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Affiliation(s)
- Mehul Gajwani
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
| | - Stuart Oldham
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
- Developmental Imaging, Murdoch Children’s Research Institute, The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - James C. Pang
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
| | - Aurina Arnatkevičiūtė
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
| | - Jeggan Tiego
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
| | - Mark A. Bellgrove
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
| | - Alex Fornito
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
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28
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Langensee L, Spotorno N, Mårtensson J. Beyond the language network: Associations between reading, receptive vocabulary, and grey matter volume in 10-year-olds. Neuropsychologia 2023; 191:108719. [PMID: 37939873 DOI: 10.1016/j.neuropsychologia.2023.108719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
Most research on the neurostructural basis of language abilities in children stems from small samples and surface-based measures. To complement and expand the existent knowledge, we investigated associations between grey matter volume and language performance in a large sample of 9-to-11-year-old children, using data from the Adolescent Brain Cognitive Development (ABCD) Study (N = 1865) and an alternative measure of grey matter morphology. We estimated whole-brain grey matter volume for one half of the sample (N = 939) and tested for correlations with scores on a picture vocabulary and a letter and word reading test, with and without factoring in general intelligence and total grey matter volume as additional covariates. The initial analyses yielded correlations between grey matter in the right occipital fusiform gyrus, the right lingual gyrus, and the cerebellum for both vocabulary and reading. Employing the significant clusters from the first analyses as regions of interest in the second half of the cohort (N = 926) in correlational and multiple regression analyses suggests the cluster in the right occipital fusiform and lingual gyri to be most robust. Overall, the amount of variance explained by grey matter volume is limited and factoring in additional covariates paints an inconsistent picture. The present findings reinforce existent doubt with respect to explaining individual differences in reading and vocabulary performance based on unique contributions of macrostructural brain features.
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Affiliation(s)
- Lara Langensee
- Department of Clinical Sciences, Lund University, Lund, Sweden.
| | - Nicola Spotorno
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
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29
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Guo Z, Zhao X, Yao L, Long Z. Improved brain community structure detection by two-step weighted modularity maximization. PLoS One 2023; 18:e0295428. [PMID: 38064462 PMCID: PMC10707683 DOI: 10.1371/journal.pone.0295428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The human brain can be regarded as a complex network with interacting connections between brain regions. Complex brain network analyses have been widely applied to functional magnetic resonance imaging (fMRI) data and have revealed the existence of community structures in brain networks. The identification of communities may provide insight into understanding the topological functions of brain networks. Among various community detection methods, the modularity maximization (MM) method has the advantages of model conciseness, fast convergence and strong adaptability to large-scale networks and has been extended from single-layer networks to multilayer networks to investigate the community structure changes of brain networks. However, the problems of MM, suffering from instability and failing to detect hierarchical community structure in networks, largely limit the application of MM in the community detection of brain networks. In this study, we proposed the weighted modularity maximization (WMM) method by using the weight matrix to weight the adjacency matrix and improve the performance of MM. Moreover, we further proposed the two-step WMM method to detect the hierarchical community structures of networks by utilizing node attributes. The results of the synthetic networks without node attributes demonstrated that WMM showed better partition accuracy than both MM and robust MM and better stability than MM. The two-step WMM method showed better accuracy of community partitioning than WMM for synthetic networks with node attributes. Moreover, the results of resting state fMRI (rs-fMRI) data showed that two-step WMM had the advantage of detecting the hierarchical communities over WMM and was more insensitive to the density of the rs-fMRI networks than WMM.
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Affiliation(s)
- Zhitao Guo
- School of Artificial Intelligence, Beijing Normal University, Beijing, China
| | - Xiaojie Zhao
- School of Artificial Intelligence, Beijing Normal University, Beijing, China
| | - Li Yao
- School of Artificial Intelligence, Beijing Normal University, Beijing, China
| | - Zhiying Long
- School of Artificial Intelligence, Beijing Normal University, Beijing, China
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30
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Li Z, Li J, Wang N, Lv Y, Zou Q, Wang J. Single-subject cortical morphological brain networks: Phenotypic associations and neurobiological substrates. Neuroimage 2023; 283:120434. [PMID: 37907157 DOI: 10.1016/j.neuroimage.2023.120434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/28/2023] [Accepted: 10/28/2023] [Indexed: 11/02/2023] Open
Abstract
Although single-subject morphological brain networks provide an important way for human connectome studies, their roles and origins are poorly understood. Combining cross-sectional and repeated structural magnetic resonance imaging scans from adults, children and twins with behavioral and cognitive measures and brain-wide transcriptomic, cytoarchitectonic and chemoarchitectonic data, this study examined phenotypic associations and neurobiological substrates of single-subject morphological brain networks. We found that single-subject morphological brain networks explained inter-individual variance and predicted individual outcomes in Motor and Cognition domains, and distinguished individuals from each other. The performance can be further improved by integrating different morphological indices for network construction. Low-moderate heritability was observed for single-subject morphological brain networks with the highest heritability for sulcal depth-derived networks and higher heritability for inter-module connections. Furthermore, differential roles of genetic, cytoarchitectonic and chemoarchitectonic factors were observed for single-subject morphological brain networks. Cortical thickness-derived networks were related to the three factors with contributions from genes enriched in membrane and transport related functions, genes preferentially located in supragranular and granular layers, overall thickness in the molecular layer and thickness of wall in the infragranular layers, and metabotropic glutamate receptor 5 and dopamine transporter; fractal dimension-, gyrification index- and sulcal depth-derived networks were only associated with the chemoarchitectonic factor with contributions from different sets of neurotransmitter receptors. Most results were reproducible across different parcellation schemes and datasets. Altogether, this study demonstrates phenotypic associations and neurobiological substrates of single-subject morphological brain networks, which provide intermediate endophenotypes to link molecular and cellular architecture and behavior and cognition.
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Affiliation(s)
- Zhen Li
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Junle Li
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Ningkai Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Yating Lv
- Institute of Psychological Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Qihong Zou
- Center for MRI Research, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jinhui Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China; Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Center for Studies of Psychological Application, South China Normal University, Guangzhou, China; Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China.
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31
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Xu X, Lin L, Wu S, Sun S. Exploring Successful Cognitive Aging: Insights Regarding Brain Structure, Function, and Demographics. Brain Sci 2023; 13:1651. [PMID: 38137099 PMCID: PMC10741933 DOI: 10.3390/brainsci13121651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
In the realm of cognitive science, the phenomenon of "successful cognitive aging" stands as a hallmark of individuals who exhibit cognitive abilities surpassing those of their age-matched counterparts. However, it is paramount to underscore a significant gap in the current research, which is marked by a paucity of comprehensive inquiries that deploy substantial sample sizes to methodically investigate the cerebral biomarkers and contributory elements underpinning this cognitive success. It is within this context that our present study emerges, harnessing data derived from the UK Biobank. In this study, a highly selective cohort of 1060 individuals aged 65 and above was meticulously curated from a larger pool of 17,072 subjects. The selection process was guided by their striking cognitive resilience, ascertained via rigorous evaluation encompassing both generic and specific cognitive assessments, compared to their peers within the same age stratum. Notably, the cognitive abilities of the chosen participants closely aligned with the cognitive acumen commonly observed in middle-aged individuals. Our study leveraged a comprehensive array of neuroimaging-derived metrics, obtained from three Tesla MRI scans (T1-weighted images, dMRI, and resting-state fMRI). The metrics included image-derived phenotypes (IDPs) that addressed grey matter morphology, the strength of brain network connectivity, and the microstructural attributes of white matter. Statistical analyses were performed employing ANOVA, Mann-Whitney U tests, and chi-square tests to evaluate the distinctive aspects of IDPs pertinent to the domain of successful cognitive aging. Furthermore, these analyses aimed to elucidate lifestyle practices that potentially underpin the maintenance of cognitive acumen throughout the aging process. Our findings unveiled a robust and compelling association between heightened cognitive aptitude and the integrity of white matter structures within the brain. Furthermore, individuals who exhibited successful cognitive aging demonstrated markedly enhanced activity in the cerebral regions responsible for auditory perception, voluntary motor control, memory retention, and emotional regulation. These advantageous cognitive attributes were mirrored in the health-related lifestyle choices of the surveyed cohort, characterized by elevated educational attainment, a lower incidence of smoking, and a penchant for moderate alcohol consumption. Moreover, they displayed superior grip strength and enhanced walking speeds. Collectively, these findings furnish valuable insights into the multifaceted determinants of successful cognitive aging, encompassing both neurobiological constituents and lifestyle practices. Such comprehensive comprehension significantly contributes to the broader discourse on aging, thereby establishing a solid foundation for the formulation of targeted interventions aimed at fostering cognitive well-being among aging populations.
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Affiliation(s)
- Xinze Xu
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (X.X.); (S.W.); (S.S.)
| | - Lan Lin
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (X.X.); (S.W.); (S.S.)
- Intelligent Physiological Measurement and Clinical Translation, Beijing International Base for Scientific and Technological Cooperation, Beijing University of Technology, Beijing 100124, China
| | - Shuicai Wu
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (X.X.); (S.W.); (S.S.)
- Intelligent Physiological Measurement and Clinical Translation, Beijing International Base for Scientific and Technological Cooperation, Beijing University of Technology, Beijing 100124, China
| | - Shen Sun
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (X.X.); (S.W.); (S.S.)
- Intelligent Physiological Measurement and Clinical Translation, Beijing International Base for Scientific and Technological Cooperation, Beijing University of Technology, Beijing 100124, China
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32
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Jordão S, Stergiou N, Brandão R, Pezarat-Correia P, Oliveira R, Cortes N, Vaz JR. Muscle activity variability patterns and stride to stride fluctuations of older adults are positively correlated during walking. Sci Rep 2023; 13:20721. [PMID: 38007498 PMCID: PMC10676363 DOI: 10.1038/s41598-023-47828-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023] Open
Abstract
It has been found that fractal-like patterns are present in the temporal structure of the variability of healthy biological rhythms, while pathology and disease lead to their deterioration. Interestingly, it has recently been suggested that these patterns in biological rhythms are related with each other, reflecting overall health or lack of it, due to their interaction. However, the underlying neurophysiological mechanisms responsible for such dependency remain unknown. In addition, this relationship between different elements needs to be first verified before we even pursue understanding their interaction. This study aimed to investigate the relationship between two elements of the neuromuscular system, gait and muscle activity variability patterns in older adults. Twenty-one older adults walked at their preferred walking speed on a treadmill. Inter-stride intervals were obtained through an accelerometer placed on the lateral malleoli to assess the temporal structure of variability of stride-to-stride fluctuations. Inter muscle peak intervals were obtained through the electromyographic signal of the gastrocnemius to assess the temporal structure of the variability of the simultaneous muscle activity. The temporal structure of variability from both signals was evaluated through the detrended fluctuation analysis, while their magnitude of variability was evaluated using the coefficient of variation. The Pearson's Correlation coefficient was used to identify the relationship between the two dependent variables. A significant strong positive correlation was found between the temporal structure of gait and muscle activity patterns. This result suggests that there is an interdependency between biological rhythms that compose the human neuromuscular system.
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Affiliation(s)
- Sofia Jordão
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Campus Universitário, Quinta da Granja, Monte da Caparica, 2829 - 511, Caparica, Portugal
- Hospital da Ordem Terceira Chiado, Lisbon, Portugal
| | - Nick Stergiou
- Department of Biomechanics, University of Nebraska at Omaha, Omaha, NE, USA
- Department of Physical Education and Sport Science, Aristotle University, Thessaloniki, Greece
| | - Rita Brandão
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
| | - Pedro Pezarat-Correia
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
| | - Raúl Oliveira
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
| | - Nelson Cortes
- School of Sport, Rehabilitation and Exercise Sciences, University of Essex, Colchester, UK
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | - João R Vaz
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal.
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Campus Universitário, Quinta da Granja, Monte da Caparica, 2829 - 511, Caparica, Portugal.
- Department of Biomechanics, University of Nebraska at Omaha, Omaha, NE, USA.
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33
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Liu M, Zhang J, Wang Y, Zhou Y, Xie F, Guo Q, Shi F, Zhang H, Wang Q, Shen D. A common spectrum underlying brain disorders across lifespan revealed by deep learning on brain networks. iScience 2023; 26:108244. [PMID: 38026184 PMCID: PMC10651682 DOI: 10.1016/j.isci.2023.108244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Brain disorders in the early and late life of humans potentially share pathological alterations in brain functions. However, the key neuroimaging evidence remains unrevealed for elucidating such commonness and the relationships among these disorders. To explore this puzzle, we build a restricted single-branch deep learning model, using multi-site functional magnetic resonance imaging data (N = 4,410, 6 sites), for classifying 5 different early- and late-life brain disorders from healthy controls (cognitively unimpaired). Our model achieves 62.6 ± 1.9% overall classification accuracy and thus supports us in detecting a set of commonly affected functional subnetworks, including default mode, executive control, visual, and limbic networks. In the deep-layer representation of data, we observe young and aging patients with disorders are continuously distributed, which is in line with the clinical concept of the "spectrum of disorders." The relationships among brain disorders from the revealed spectrum promote the understanding of disorder comorbidities and time associations in the lifespan.
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Affiliation(s)
- Mianxin Liu
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - Jingyang Zhang
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Yao Wang
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| | - Yan Zhou
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| | - Fang Xie
- PET Center, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Qihao Guo
- Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Feng Shi
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd, Shanghai 200232, China
| | - Han Zhang
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Qian Wang
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
| | - Dinggang Shen
- School of Biomedical Engineering, State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd, Shanghai 200232, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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34
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Wang Y, Yin J, Desai RH. Topological inference on brain networks across subtypes of post-stroke aphasia. ARXIV 2023:arXiv:2311.01625v1. [PMID: 37961747 PMCID: PMC10635302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Persistent homology (PH) characterizes the shape of brain networks through the persistence features. Group comparison of persistence features from brain networks can be challenging as they are inherently heterogeneous. A recent scale-space representation of persistence diagram (PD) through heat diffusion reparameterizes using the finite number of Fourier coefficients with respect to the Laplace-Beltrami (LB) eigenfunction expansion of the domain, which provides a powerful vectorized algebraic representation for group comparisons of PDs. In this study, we advance a transposition-based permutation test for comparing multiple groups of PDs through the heat-diffusion estimates of the PDs. We evaluate the empirical performance of the spectral transposition test in capturing within- and between-group similarity and dissimilarity with respect to statistical variation of topological noise and hole location. We also illustrate how the method extends naturally into a clustering scheme by subtyping individuals with post-stroke aphasia through the PDs of their resting-state functional brain networks.
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Affiliation(s)
- Yuan Wang
- Department of Epidemiology and Biostatistics University of South Carolina U.S.A
| | - Jian Yin
- Department of Biostatistics Nanjing Medical University China
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35
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Finn ES, Poldrack RA, Shine JM. Functional neuroimaging as a catalyst for integrated neuroscience. Nature 2023; 623:263-273. [PMID: 37938706 DOI: 10.1038/s41586-023-06670-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/22/2023] [Indexed: 11/09/2023]
Abstract
Functional magnetic resonance imaging (fMRI) enables non-invasive access to the awake, behaving human brain. By tracking whole-brain signals across a diverse range of cognitive and behavioural states or mapping differences associated with specific traits or clinical conditions, fMRI has advanced our understanding of brain function and its links to both normal and atypical behaviour. Despite this headway, progress in human cognitive neuroscience that uses fMRI has been relatively isolated from rapid advances in other subdomains of neuroscience, which themselves are also somewhat siloed from one another. In this Perspective, we argue that fMRI is well-placed to integrate the diverse subfields of systems, cognitive, computational and clinical neuroscience. We first summarize the strengths and weaknesses of fMRI as an imaging tool, then highlight examples of studies that have successfully used fMRI in each subdomain of neuroscience. We then provide a roadmap for the future advances that will be needed to realize this integrative vision. In this way, we hope to demonstrate how fMRI can help usher in a new era of interdisciplinary coherence in neuroscience.
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Affiliation(s)
- Emily S Finn
- Department of Psychological and Brain Sciences, Dartmouth College, Dartmouth, NH, USA.
| | | | - James M Shine
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia.
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36
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Li D, Nguyen P, Zhang Z, Dunson D. Tree representations of brain structural connectivity via persistent homology. Front Neurosci 2023; 17:1200373. [PMID: 37901431 PMCID: PMC10603366 DOI: 10.3389/fnins.2023.1200373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/05/2023] [Indexed: 10/31/2023] Open
Abstract
The brain structural connectome is generated by a collection of white matter fiber bundles constructed from diffusion weighted MRI (dMRI), acting as highways for neural activity. There has been abundant interest in studying how the structural connectome varies across individuals in relation to their traits, ranging from age and gender to neuropsychiatric outcomes. After applying tractography to dMRI to get white matter fiber bundles, a key question is how to represent the brain connectome to facilitate statistical analyses relating connectomes to traits. The current standard divides the brain into regions of interest (ROIs), and then relies on an adjacency matrix (AM) representation. Each cell in the AM is a measure of connectivity, e.g., number of fiber curves, between a pair of ROIs. Although the AM representation is intuitive, a disadvantage is the high-dimensionality due to the large number of cells in the matrix. This article proposes a simpler tree representation of the brain connectome, which is motivated by ideas in computational topology and takes topological and biological information on the cortical surface into consideration. We demonstrate that our tree representation preserves useful information and interpretability, while reducing dimensionality to improve statistical and computational efficiency. Applications to data from the Human Connectome Project (HCP) are considered and code is provided for reproducing our analyses.
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Affiliation(s)
- Didong Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Phuc Nguyen
- Department of Statistical Science, Duke University, Durham, NC, United States
| | - Zhengwu Zhang
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David Dunson
- Department of Statistical Science, Duke University, Durham, NC, United States
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37
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Gaiteri C, Connell DR, Sultan FA, Iatrou A, Ng B, Szymanski BK, Zhang A, Tasaki S. Robust, scalable, and informative clustering for diverse biological networks. Genome Biol 2023; 24:228. [PMID: 37828545 PMCID: PMC10571258 DOI: 10.1186/s13059-023-03062-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data. However, due to foundational issues in how they are defined and detected, such clusters are not always reliable, leading to unstable conclusions. We compare popular clustering algorithms across thousands of synthetic and real biological datasets, including a new consensus clustering algorithm-SpeakEasy2: Champagne. These tests identify trends in performance, show no single method is universally optimal, and allow us to examine factors behind variation in performance. Multiple metrics indicate SpeakEasy2 generally provides robust, scalable, and informative clusters for a range of applications.
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Affiliation(s)
- Chris Gaiteri
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA.
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - David R Connell
- Rush University Graduate College, Rush University Medical Center, Chicago, IL, USA
| | - Faraz A Sultan
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Harvard University, Belmont, MA, USA
| | - Bernard Ng
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Boleslaw K Szymanski
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, USA
- Network Science and Technology Center, Rensselaer Polytechnic Institute, Troy, NY, USA
- Academy of Social Sciences, Łódź, Poland
| | - Ada Zhang
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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38
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D'Andrea CB, Laumann TO, Newbold DJ, Nelson SM, Nielsen AN, Chauvin R, Marek S, Greene DJ, Dosenbach NUF, Gordon EM. Substructure of the brain's Cingulo-Opercular network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561772. [PMID: 37873065 PMCID: PMC10592749 DOI: 10.1101/2023.10.10.561772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The Cingulo-Opercular network (CON) is an executive network of the human brain that regulates actions. CON is composed of many widely distributed cortical regions that are involved in top-down control over both lower-level (i.e., motor) and higher-level (i.e., cognitive) functions, as well as in processing of painful stimuli. Given the topographical and functional heterogeneity of the CON, we investigated whether subnetworks within the CON support separable aspects of action control. Using precision functional mapping (PFM) in 15 participants with > 5 hours of resting state functional connectivity (RSFC) and task data, we identified three anatomically and functionally distinct CON subnetworks within each individual. These three distinct subnetworks were linked to Decisions, Actions, and Feedback (including pain processing), respectively, in convergence with a meta-analytic task database. These Decision, Action and Feedback subnetworks represent pathways by which the brain establishes top-down goals, transforms those goals into actions, implemented as movements, and processes critical action feedback such as pain.
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Affiliation(s)
- Carolina Badke D'Andrea
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Cognitive Science, University of California San Diego, La Jolla, California 92093, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63310, USA
| | - Timothy O Laumann
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Dillan J Newbold
- Department of Neurology, New York University Medical Center, New York, New York 10016, USA
| | - Steven M Nelson
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Ashley N Nielsen
- Department of Neurology, New York University Medical Center, New York, New York 10016, USA
| | - Roselyne Chauvin
- Department of Neurology, New York University Medical Center, New York, New York 10016, USA
| | - Scott Marek
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Deanna J Greene
- Department of Cognitive Science, University of California San Diego, La Jolla, California 92093, USA
| | - Nico U F Dosenbach
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Evan M Gordon
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Uddin LQ, Betzel RF, Cohen JR, Damoiseaux JS, De Brigard F, Eickhoff SB, Fornito A, Gratton C, Gordon EM, Laird AR, Larson-Prior L, McIntosh AR, Nickerson LD, Pessoa L, Pinho AL, Poldrack RA, Razi A, Sadaghiani S, Shine JM, Yendiki A, Yeo BTT, Spreng RN. Controversies and progress on standardization of large-scale brain network nomenclature. Netw Neurosci 2023; 7:864-905. [PMID: 37781138 PMCID: PMC10473266 DOI: 10.1162/netn_a_00323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/10/2023] [Indexed: 10/03/2023] Open
Abstract
Progress in scientific disciplines is accompanied by standardization of terminology. Network neuroscience, at the level of macroscale organization of the brain, is beginning to confront the challenges associated with developing a taxonomy of its fundamental explanatory constructs. The Workgroup for HArmonized Taxonomy of NETworks (WHATNET) was formed in 2020 as an Organization for Human Brain Mapping (OHBM)-endorsed best practices committee to provide recommendations on points of consensus, identify open questions, and highlight areas of ongoing debate in the service of moving the field toward standardized reporting of network neuroscience results. The committee conducted a survey to catalog current practices in large-scale brain network nomenclature. A few well-known network names (e.g., default mode network) dominated responses to the survey, and a number of illuminating points of disagreement emerged. We summarize survey results and provide initial considerations and recommendations from the workgroup. This perspective piece includes a selective review of challenges to this enterprise, including (1) network scale, resolution, and hierarchies; (2) interindividual variability of networks; (3) dynamics and nonstationarity of networks; (4) consideration of network affiliations of subcortical structures; and (5) consideration of multimodal information. We close with minimal reporting guidelines for the cognitive and network neuroscience communities to adopt.
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Affiliation(s)
- Lucina Q. Uddin
- Department of Psychiatry and Biobehavioral Sciences and Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard F. Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Jessica R. Cohen
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
| | - Jessica S. Damoiseaux
- Institute of Gerontology and Department of Psychology, Wayne State University, Detroit, MI, USA
| | | | - Simon B. Eickhoff
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alex Fornito
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
| | - Caterina Gratton
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Evan M. Gordon
- Mallinckrodt Institute of Radiology, Washington University, St. Louis, MO, USA
| | - Angela R. Laird
- Department of Physics, Florida International University, Miami, FL, USA
| | - Linda Larson-Prior
- Deptartment of Psychiatry and Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A. Randal McIntosh
- Institute for Neuroscience and Neurotechnology, Simon Fraser University, Vancouver, BC, Canada
| | | | - Luiz Pessoa
- Department of Psychology, University of Maryland, College Park, MD, USA
| | - Ana Luísa Pinho
- Brain and Mind Institute, Western University, London, Ontario, Canada
| | | | - Adeel Razi
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, Australia
| | - Sepideh Sadaghiani
- Department of Psychology, University of Illinois, Urbana Champaign, IL, USA
| | - James M. Shine
- Brain and Mind Center, University of Sydney, Sydney, Australia
| | - Anastasia Yendiki
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - B. T. Thomas Yeo
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore
| | - R. Nathan Spreng
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
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40
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Betzel RF, Cutts SA, Tanner J, Greenwell SA, Varley T, Faskowitz J, Sporns O. Hierarchical organization of spontaneous co-fluctuations in densely sampled individuals using fMRI. Netw Neurosci 2023; 7:926-949. [PMID: 37781150 PMCID: PMC10473297 DOI: 10.1162/netn_a_00321] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/03/2023] [Indexed: 10/03/2023] Open
Abstract
Edge time series decompose functional connectivity into its framewise contributions. Previous studies have focused on characterizing the properties of high-amplitude frames (time points when the global co-fluctuation amplitude takes on its largest value), including their cluster structure. Less is known about middle- and low-amplitude co-fluctuations (peaks in co-fluctuation time series but of lower amplitude). Here, we directly address those questions, using data from two dense-sampling studies: the MyConnectome project and Midnight Scan Club. We develop a hierarchical clustering algorithm to group peak co-fluctuations of all magnitudes into nested and multiscale clusters based on their pairwise concordance. At a coarse scale, we find evidence of three large clusters that, collectively, engage virtually all canonical brain systems. At finer scales, however, each cluster is dissolved, giving way to increasingly refined patterns of co-fluctuations involving specific sets of brain systems. We also find an increase in global co-fluctuation magnitude with hierarchical scale. Finally, we comment on the amount of data needed to estimate co-fluctuation pattern clusters and implications for brain-behavior studies. Collectively, the findings reported here fill several gaps in current knowledge concerning the heterogeneity and richness of co-fluctuation patterns as estimated with edge time series while providing some practical guidance for future studies.
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Affiliation(s)
- Richard F. Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
- Program in Neuroscience, Indiana University, Bloomington, IN, USA
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
- Network Science Institute, Indiana University, Bloomington, IN, USA
| | - Sarah A. Cutts
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
- Program in Neuroscience, Indiana University, Bloomington, IN, USA
| | - Jacob Tanner
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Sarah A. Greenwell
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Thomas Varley
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Joshua Faskowitz
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
- Program in Neuroscience, Indiana University, Bloomington, IN, USA
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
- Network Science Institute, Indiana University, Bloomington, IN, USA
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41
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Milano G, Cultrera A, Boarino L, Callegaro L, Ricciardi C. Tomography of memory engrams in self-organizing nanowire connectomes. Nat Commun 2023; 14:5723. [PMID: 37758693 PMCID: PMC10533552 DOI: 10.1038/s41467-023-40939-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
Self-organizing memristive nanowire connectomes have been exploited for physical (in materia) implementation of brain-inspired computing paradigms. Despite having been shown that the emergent behavior relies on weight plasticity at single junction/synapse level and on wiring plasticity involving topological changes, a shift to multiterminal paradigms is needed to unveil dynamics at the network level. Here, we report on tomographical evidence of memory engrams (or memory traces) in nanowire connectomes, i.e., physicochemical changes in biological neural substrates supposed to endow the representation of experience stored in the brain. An experimental/modeling approach shows that spatially correlated short-term plasticity effects can turn into long-lasting engram memory patterns inherently related to network topology inhomogeneities. The ability to exploit both encoding and consolidation of information on the same physical substrate would open radically new perspectives for in materia computing, while offering to neuroscientists an alternative platform to understand the role of memory in learning and knowledge.
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Affiliation(s)
- Gianluca Milano
- Advanced Materials Metrology and Life Sciences Division, INRiM (Istituto Nazionale di Ricerca Metrologica), Strada delle Cacce 91, 10135, Torino, Italy.
| | - Alessandro Cultrera
- Quantum Metrology and Nanotechnologies Division, INRiM (Istituto Nazionale di Ricerca Metrologica), Strada delle Cacce 91, 10135, Torino, Italy
| | - Luca Boarino
- Advanced Materials Metrology and Life Sciences Division, INRiM (Istituto Nazionale di Ricerca Metrologica), Strada delle Cacce 91, 10135, Torino, Italy
| | - Luca Callegaro
- Quantum Metrology and Nanotechnologies Division, INRiM (Istituto Nazionale di Ricerca Metrologica), Strada delle Cacce 91, 10135, Torino, Italy
| | - Carlo Ricciardi
- Department of Applied Science and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129, Torino, Italy.
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42
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Lagasse E, Levin M. Future medicine: from molecular pathways to the collective intelligence of the body. Trends Mol Med 2023; 29:687-710. [PMID: 37481382 PMCID: PMC10527237 DOI: 10.1016/j.molmed.2023.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
The remarkable anatomical homeostasis exhibited by complex living organisms suggests that they are inherently reprogrammable information-processing systems that offer numerous interfaces to their physiological and anatomical problem-solving capacities. We briefly review data suggesting that the multiscale competency of living forms affords a new path for biomedicine that exploits the innate collective intelligence of tissues and organs. The concept of tissue-level allostatic goal-directedness is already bearing fruit in clinical practice. We sketch a roadmap towards 'somatic psychiatry' by using advances in bioelectricity and behavioral neuroscience to design methods that induce self-repair of structure and function. Relaxing the assumption that cellular control mechanisms are static, exploiting powerful concepts from cybernetics, behavioral science, and developmental biology may spark definitive solutions to current biomedical challenges.
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Affiliation(s)
- Eric Lagasse
- McGowan Institute for Regenerative Medicine and Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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43
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Royer J, Larivière S, Rodriguez-Cruces R, Cabalo DG, Tavakol S, Auer H, Ngo A, Park BY, Paquola C, Smallwood J, Jefferies E, Caciagli L, Bernasconi A, Bernasconi N, Frauscher B, Bernhardt BC. Cortical microstructural gradients capture memory network reorganization in temporal lobe epilepsy. Brain 2023; 146:3923-3937. [PMID: 37082950 PMCID: PMC10473569 DOI: 10.1093/brain/awad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/21/2023] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
Temporal lobe epilepsy (TLE), one of the most common pharmaco-resistant epilepsies, is associated with pathology of paralimbic brain regions, particularly in the mesiotemporal lobe. Cognitive dysfunction in TLE is frequent, and particularly affects episodic memory. Crucially, these difficulties challenge the quality of life of patients, sometimes more than seizures, underscoring the need to assess neural processes of cognitive dysfunction in TLE to improve patient management. Our work harnessed a novel conceptual and analytical approach to assess spatial gradients of microstructural differentiation between cortical areas based on high-resolution MRI analysis. Gradients track region-to-region variations in intracortical lamination and myeloarchitecture, serving as a system-level measure of structural and functional reorganization. Comparing cortex-wide microstructural gradients between 21 patients and 35 healthy controls, we observed a reorganization of this gradient in TLE driven by reduced microstructural differentiation between paralimbic cortices and the remaining cortex with marked abnormalities in ipsilateral temporopolar and dorsolateral prefrontal regions. Findings were replicated in an independent cohort. Using an independent post-mortem dataset, we observed that in vivo findings reflected topographical variations in cortical cytoarchitecture. We indeed found that macroscale changes in microstructural differentiation in TLE reflected increased similarity of paralimbic and primary sensory/motor regions. Disease-related transcriptomics could furthermore show specificity of our findings to TLE over other common epilepsy syndromes. Finally, microstructural dedifferentiation was associated with cognitive network reorganization seen during an episodic memory functional MRI paradigm and correlated with interindividual differences in task accuracy. Collectively, our findings showing a pattern of reduced microarchitectural differentiation between paralimbic regions and the remaining cortex provide a structurally-grounded explanation for large-scale functional network reorganization and cognitive dysfunction characteristic of TLE.
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Affiliation(s)
- Jessica Royer
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Raul Rodriguez-Cruces
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Donna Gift Cabalo
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Shahin Tavakol
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Hans Auer
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexander Ngo
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Bo-yong Park
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- Department of Data Science, Inha University, Incheon 22212, Republic of Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon 34126, Republic of Korea
| | - Casey Paquola
- Multiscale Neuroanatomy Lab, INM-1, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jonathan Smallwood
- Department of Psychology, Queen’s University, Kingston, ON, K7L 3N6, Canada
| | | | - Lorenzo Caciagli
- Department of Bioengineering, University of Pennsylvania, Philadelphia, MA 19104, USA
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Birgit Frauscher
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
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44
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Brynildsen JK, Rajan K, Henderson MX, Bassett DS. Network models to enhance the translational impact of cross-species studies. Nat Rev Neurosci 2023; 24:575-588. [PMID: 37524935 PMCID: PMC10634203 DOI: 10.1038/s41583-023-00720-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2023] [Indexed: 08/02/2023]
Abstract
Neuroscience studies are often carried out in animal models for the purpose of understanding specific aspects of the human condition. However, the translation of findings across species remains a substantial challenge. Network science approaches can enhance the translational impact of cross-species studies by providing a means of mapping small-scale cellular processes identified in animal model studies to larger-scale inter-regional circuits observed in humans. In this Review, we highlight the contributions of network science approaches to the development of cross-species translational research in neuroscience. We lay the foundation for our discussion by exploring the objectives of cross-species translational models. We then discuss how the development of new tools that enable the acquisition of whole-brain data in animal models with cellular resolution provides unprecedented opportunity for cross-species applications of network science approaches for understanding large-scale brain networks. We describe how these tools may support the translation of findings across species and imaging modalities and highlight future opportunities. Our overarching goal is to illustrate how the application of network science tools across human and animal model studies could deepen insight into the neurobiology that underlies phenomena observed with non-invasive neuroimaging methods and could simultaneously further our ability to translate findings across species.
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Affiliation(s)
- Julia K Brynildsen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Kanaka Rajan
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael X Henderson
- Parkinson's Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Electrical & Systems Engineering, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA.
- Santa Fe Institute, Santa Fe, NM, USA.
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45
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Parkes L, Kim JZ, Stiso J, Brynildsen JK, Cieslak M, Covitz S, Gur RE, Gur RC, Pasqualetti F, Shinohara RT, Zhou D, Satterthwaite TD, Bassett DS. Using network control theory to study the dynamics of the structural connectome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554519. [PMID: 37662395 PMCID: PMC10473719 DOI: 10.1101/2023.08.23.554519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Network control theory (NCT) is a simple and powerful tool for studying how network topology informs and constrains dynamics. Compared to other structure-function coupling approaches, the strength of NCT lies in its capacity to predict the patterns of external control signals that may alter dynamics in a desired way. We have extensively developed and validated the application of NCT to the human structural connectome. Through these efforts, we have studied (i) how different aspects of connectome topology affect neural dynamics, (ii) whether NCT outputs cohere with empirical data on brain function and stimulation, and (iii) how NCT outputs vary across development and correlate with behavior and mental health symptoms. In this protocol, we introduce a framework for applying NCT to structural connectomes following two main pathways. Our primary pathway focuses on computing the control energy associated with transitioning between specific neural activity states. Our second pathway focuses on computing average controllability, which indexes nodes' general capacity to control dynamics. We also provide recommendations for comparing NCT outputs against null network models. Finally, we support this protocol with a Python-based software package called network control theory for python (nctpy).
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Affiliation(s)
- Linden Parkes
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Rutgers University, Piscataway, NJ 08854, USA
| | - Jason Z Kim
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer Stiso
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
| | | | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raquel E Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruben C Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fabio Pasqualetti
- Department of Mechanical Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dale Zhou
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
| | - Theodore D Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, PA 19104, USA
- Department of Physics and Astronomy, University of Pennsylvania, PA 19104, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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46
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Barabási DL, Bianconi G, Bullmore E, Burgess M, Chung S, Eliassi-Rad T, George D, Kovács IA, Makse H, Nichols TE, Papadimitriou C, Sporns O, Stachenfeld K, Toroczkai Z, Towlson EK, Zador AM, Zeng H, Barabási AL, Bernard A, Buzsáki G. Neuroscience Needs Network Science. J Neurosci 2023; 43:5989-5995. [PMID: 37612141 PMCID: PMC10451115 DOI: 10.1523/jneurosci.1014-23.2023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023] Open
Abstract
The brain is a complex system comprising a myriad of interacting neurons, posing significant challenges in understanding its structure, function, and dynamics. Network science has emerged as a powerful tool for studying such interconnected systems, offering a framework for integrating multiscale data and complexity. To date, network methods have significantly advanced functional imaging studies of the human brain and have facilitated the development of control theory-based applications for directing brain activity. Here, we discuss emerging frontiers for network neuroscience in the brain atlas era, addressing the challenges and opportunities in integrating multiple data streams for understanding the neural transitions from development to healthy function to disease. We underscore the importance of fostering interdisciplinary opportunities through workshops, conferences, and funding initiatives, such as supporting students and postdoctoral fellows with interests in both disciplines. By bringing together the network science and neuroscience communities, we can develop novel network-based methods tailored to neural circuits, paving the way toward a deeper understanding of the brain and its functions, as well as offering new challenges for network science.
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Affiliation(s)
- Dániel L Barabási
- Biophysics Program, Harvard University, Cambridge, 02138, Massachusetts
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, 02138, Massachusetts
| | - Ginestra Bianconi
- School of Mathematical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
- Alan Turing Institute, The British Library, London, NW1 2DB, United Kingdom
| | - Ed Bullmore
- Department of Psychiatry and Wolfson Brain Imaging Centre, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | | | - SueYeon Chung
- Center for Neural Science, New York University, New York, New York 10003
- Center for Computational Neuroscience, Flatiron Institute, Simons Foundation, New York, New York 10010
| | - Tina Eliassi-Rad
- Network Science Institute, Northeastern University, Boston, 02115, Massachusetts
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, Massachusetts
- Santa Fe Institute, Santa Fe, New Mexico 87501
| | | | - István A Kovács
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois 60208
| | - Hernán Makse
- Levich Institute and Physics Department, City College of New York, New York, New York 10031
| | - Thomas E Nichols
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, United Kingdom
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | | | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana 47405
| | - Kim Stachenfeld
- DeepMind, London, EC4A 3TW, United Kingdom
- Columbia University, New York, New York 10027
| | - Zoltán Toroczkai
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556
| | - Emma K Towlson
- Department of Computer Science, University of Calgary, Calgary, Alberta, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, AB T2N 1N4, Canada
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, AB T2N 1N4, Canada
| | - Anthony M Zador
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, 98109, Washington
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, 02115, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
- Department of Network and Data Science, Central European University, Budapest, H-1051, Hungary
| | - Amy Bernard
- The Kavli Foundation, Los Angeles, 90230, California
| | - György Buzsáki
- Center for Neural Science, New York University, New York, New York 10003
- Neuroscience Institute and Department of Neurology, NYU Grossman School of Medicine, New York University, New York, New York 10016
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47
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Dichio V, De Vico Fallani F. Statistical models of complex brain networks: a maximum entropy approach. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023; 86:102601. [PMID: 37437559 DOI: 10.1088/1361-6633/ace6bc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 07/12/2023] [Indexed: 07/14/2023]
Abstract
The brain is a highly complex system. Most of such complexity stems from the intermingled connections between its parts, which give rise to rich dynamics and to the emergence of high-level cognitive functions. Disentangling the underlying network structure is crucial to understand the brain functioning under both healthy and pathological conditions. Yet, analyzing brain networks is challenging, in part because their structure represents only one possible realization of a generative stochastic process which is in general unknown. Having a formal way to cope with such intrinsic variability is therefore central for the characterization of brain network properties. Addressing this issue entails the development of appropriate tools mostly adapted from network science and statistics. Here, we focus on a particular class of maximum entropy models for networks, i.e. exponential random graph models, as a parsimonious approach to identify the local connection mechanisms behind observed global network structure. Efforts are reviewed on the quest for basic organizational properties of human brain networks, as well as on the identification of predictive biomarkers of neurological diseases such as stroke. We conclude with a discussion on how emerging results and tools from statistical graph modeling, associated with forthcoming improvements in experimental data acquisition, could lead to a finer probabilistic description of complex systems in network neuroscience.
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Affiliation(s)
- Vito Dichio
- Sorbonne Universite, Paris Brain Institute-ICM, CNRS, Inria, Inserm, AP-HP, Hopital de la Pitie Salpêtriere, F-75013 Paris, France
| | - Fabrizio De Vico Fallani
- Sorbonne Universite, Paris Brain Institute-ICM, CNRS, Inria, Inserm, AP-HP, Hopital de la Pitie Salpêtriere, F-75013 Paris, France
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48
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Simonovic M, Nedovic B, Radisavljevic M, Stojanovic N. The Co-Occurrence of Post-Traumatic Stress Disorder and Depression in Individuals with and without Traumatic Brain Injury: A Comprehensive Investigation. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1467. [PMID: 37629756 PMCID: PMC10456657 DOI: 10.3390/medicina59081467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023]
Abstract
Post-traumatic stress disorder (PTSD) is a prevalent psychiatric disorder that often occurs following war trauma. Despite its high prevalence, there is still a lack of comprehensive understanding regarding the mechanisms underlying its progression and treatment resistance. Recent research has shed light on the biological basis of PTSD, with neuroimaging studies revealing altered brain connectivity patterns in affected individuals. In war contexts, traumatic brain injury (TBI) is a common occurrence and is associated with a high prevalence of PTSD. This study aimed to compare the severity of PTSD and depression in patients with and without a history of TBI to shed light on the impact of comorbid TBI on the presentation of PTSD symptoms. To achieve this goal, a cross-sectional study was conducted involving a sample of 60 outpatients who were diagnosed with both PTSD and Depressive Disorder. The inclusion criteria required participants to meet the diagnostic criteria for both disorders using validated tools. The severities of PTSD and depressive symptoms were assessed using scales that have been widely used and validated in previous research. By utilizing these standardized assessment tools, this study aimed to ensure the reliability and validity of the obtained data. The results of this study revealed that patients with comorbid PTSD and TBI exhibited a significantly higher severity of PTSD symptoms compared to those with PTSD only. Specifically, the comorbid group demonstrated higher ratings of symptom intensity across all symptom clusters. These findings are consistent with previous research that has highlighted the impact of comorbid TBI on the intensity and persistence of PTSD symptoms. When controlling for PTSD severity, no significant differences were observed in the severity of depressive symptoms between the two groups. This suggests that the increased depressive symptoms observed in the comorbid group may be primarily driven by the presence of more intense PTSD symptoms rather than TBI per se. The findings highlight the need for an accurate diagnosis of TBI in individuals with PTSD to guide appropriate treatment interventions. Further research is warranted to delve into the underlying mechanisms that contribute to the interaction between TBI and PTSD and to develop targeted interventions for individuals with comorbid PTSD and TBI.
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Affiliation(s)
- Maja Simonovic
- Faculty of Medicine, University of Nis, Nis 18000, Serbia; (B.N.)
- Center for Mental Health, University Clinical Center, Nis 18000, Serbia
| | - Bojan Nedovic
- Faculty of Medicine, University of Nis, Nis 18000, Serbia; (B.N.)
| | - Misa Radisavljevic
- Faculty of Medicine, University of Nis, Nis 18000, Serbia; (B.N.)
- Clinic for Neurosurgery, University Clinical Center, Nis 18000, Serbia
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49
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Astle DE, Johnson MH, Akarca D. Toward computational neuroconstructivism: a framework for developmental systems neuroscience. Trends Cogn Sci 2023; 27:726-744. [PMID: 37263856 DOI: 10.1016/j.tics.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/05/2023] [Accepted: 04/19/2023] [Indexed: 06/03/2023]
Abstract
Brain development is underpinned by complex interactions between neural assemblies, driving structural and functional change. This neuroconstructivism (the notion that neural functions are shaped by these interactions) is core to some developmental theories. However, due to their complexity, understanding underlying developmental mechanisms is challenging. Elsewhere in neurobiology, a computational revolution has shown that mathematical models of hidden biological mechanisms can bridge observations with theory building. Can we build a similar computational framework yielding mechanistic insights for brain development? Here, we outline the conceptual and technical challenges of addressing this theory gap, and demonstrate that there is great potential in specifying brain development as mathematically defined processes operating within physical constraints. We provide examples, alongside broader ingredients needed, as the field explores computational explanations of system-wide development.
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Affiliation(s)
- Duncan E Astle
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 2QQ, UK; MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, CB2 7EF, UK.
| | - Mark H Johnson
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK; Centre for Brain and Cognitive Development, Birkbeck, University of London, London, WC1E 7JL, UK
| | - Danyal Akarca
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, CB2 7EF, UK
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50
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Cabrera-Álvarez J, Doorn N, Maestú F, Susi G. Modeling the role of the thalamus in resting-state functional connectivity: Nature or structure. PLoS Comput Biol 2023; 19:e1011007. [PMID: 37535694 PMCID: PMC10426958 DOI: 10.1371/journal.pcbi.1011007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/15/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023] Open
Abstract
The thalamus is a central brain structure that serves as a relay station for sensory inputs from the periphery to the cortex and regulates cortical arousal. Traditionally, it has been regarded as a passive relay that transmits information between brain regions. However, recent studies have suggested that the thalamus may also play a role in shaping functional connectivity (FC) in a task-based context. Based on this idea, we hypothesized that due to its centrality in the network and its involvement in cortical activation, the thalamus may also contribute to resting-state FC, a key neurological biomarker widely used to characterize brain function in health and disease. To investigate this hypothesis, we constructed ten in-silico brain network models based on neuroimaging data (MEG, MRI, and dwMRI), and simulated them including and excluding the thalamus, and raising the noise into thalamus to represent the afferences related to the reticular activating system (RAS) and the relay of peripheral sensory inputs. We simulated brain activity and compared the resulting FC to their empirical MEG counterparts to evaluate model's performance. Results showed that a parceled version of the thalamus with higher noise, able to drive damped cortical oscillators, enhanced the match to empirical FC. However, with an already active self-oscillatory cortex, no impact on the dynamics was observed when introducing the thalamus. We also demonstrated that the enhanced performance was not related to the structural connectivity of the thalamus, but to its higher noisy inputs. Additionally, we highlighted the relevance of a balanced signal-to-noise ratio in thalamus to allow it to propagate its own dynamics. In conclusion, our study sheds light on the role of the thalamus in shaping brain dynamics and FC in resting-state and allowed us to discuss the general role of criticality in the brain at the mesoscale level.
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Affiliation(s)
- Jesús Cabrera-Álvarez
- Department of Experimental Psychology, Complutense University of Madrid, Madrid, Spain
- Centre for Cognitive and Computational Neuroscience, Madrid, Spain
| | - Nina Doorn
- Department of Clinical Neurophysiology, University of Twente, Enschede, The Netherlands
| | - Fernando Maestú
- Department of Experimental Psychology, Complutense University of Madrid, Madrid, Spain
- Centre for Cognitive and Computational Neuroscience, Madrid, Spain
| | - Gianluca Susi
- Centre for Cognitive and Computational Neuroscience, Madrid, Spain
- Department of Structure of Matter, Thermal Physics and Electronics, Complutense University of Madrid, Madrid, Spain
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