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Coactivated Clique Based Multisource Overlapping Brain Subnetwork Extraction [article]

Chendi Wang, Rafeef Abugharbieh
2018 arXiv   pre-print
Subnetwork extraction using community detection methods is commonly used to study the brain's modular structure.  ...  In this paper, we present an approach for overlapping brain subnetwork extraction using cliques, which we defined as co-activated node groups performing multiple tasks.  ...  Dynamics ROI region of interest RW Random Walker SORD Stable Overlapping Replicator Dynamics  ... 
arXiv:1801.09589v1 fatcat:hcrdghhhcvh6ncwl5lxe3iq2ee

Contextual connectivity: A framework for understanding the intrinsic dynamic architecture of large-scale functional brain networks

Rastko Ciric, Jason S. Nomi, Lucina Q. Uddin, Ajay B. Satpute
2017 Scientific Reports  
By nesting localized dynamic connectivity states within their whole-brain contexts, we demonstrate the relative temporal independence of brain networks.  ...  Our assay for functional autonomy of coordinated neural systems is broadly applicable, and our findings provide evidence of structure in temporal state dynamics that complements the well-described static  ...  For each subject, we used Louvain-like multilayer community detection to compute each node's community membership at every point in time 45 .  ... 
doi:10.1038/s41598-017-06866-w pmid:28747717 pmcid:PMC5529582 fatcat:nnvi22vcbrajtf3adkmhupnztu

Contextual connectivity: A framework for understanding the intrinsic dynamic architecture of large-scale functional brain networks [article]

Rastko Ciric, Jason Nomi, Lucina Uddin, Ajay Satpute
2016 bioRxiv   pre-print
Our assay for functional autonomy of coordinated neural systems is broadly applicable across populations, and our findings provide evidence of structure in temporal dynamics that complements the well-described  ...  spatial organization of the brain.  ...  We used multilayer community detection 37 to obtain an allegiance matrix 40 representing each NC-state's WBCC.  ... 
doi:10.1101/068320 fatcat:fyla5hhz4faidl7td4ksydyqmu

Coupled Stable Overlapping Replicator Dynamics for Multimodal Brain Subnetwork Identification [chapter]

Burak Yoldemir, Bernard Ng, Rafeef Abugharbieh
2015 Lecture Notes in Computer Science  
We thus refer to our technique as coupled stable overlapping replicator dynamics (CSORD).  ...  We propose a multimodal integration technique based on a sex-differentiated formulation of replicator dynamics for identifying subnetworks of brain regions that exhibit high inter-connectivity both functionally  ...  Coupled Stable Overlapping Replicator Dynamics Since CRD is deterministic, reapplying it with the same initialization will converge to the same local maximum.  ... 
doi:10.1007/978-3-319-19992-4_61 fatcat:qcbcy67ksrcf3e65twombeez7y

Network attributes for segregation and integration in the human brain

Olaf Sporns
2013 Current Opinion in Neurobiology  
Network studies of large-scale brain connectivity have begun to reveal attributes that promote the segregation and integration of neural information: communities and hubs.  ...  Network hubs link communities to one another and ensure efficient communication and information integration.  ...  A detection algorithm was used to identify network communities, and nodes are colored according to their community membership.  ... 
doi:10.1016/j.conb.2012.11.015 pmid:23294553 fatcat:a54naz5o3jbuznysx6thc6d5q4

Mapping the human brain's cortical-subcortical functional network organization

Jie Lisa Ji, Marjolein Spronk, Kaustubh Kulkarni, Grega Repovš, Alan Anticevic, Michael W. Cole
2019 NeuroImage  
This whole-brain network atlas - released as an open resource for the neuroscience community - places all brain structures across both cortex and subcortex into a single large-scale functional framework  ...  We developed a highly principled approach to identify cortical network communities at the level of functional systems, calibrating our community detection algorithm using extremely well-established sensory  ...  Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.  ... 
doi:10.1016/j.neuroimage.2018.10.006 pmid:30291974 pmcid:PMC6289683 fatcat:j5xld4yp5nd6dd3j6nilemxhia

Functional Network Dynamics of the Language System

Lucy R. Chai, Marcelo G. Mattar, Idan Asher Blank, Evelina Fedorenko, Danielle S. Bassett
2016 Cerebral Cortex  
We observe the presence of a stable core of brain regions, predominantly located in the left hemisphere, that consistently coactivate with one another.  ...  Yet, how different regions within this system might be recruited dynamically during task performance is not well understood.  ...  Martinos Imaging Center at the McGovern Institute for Brain Research at MIT, and the support team (Steven Shannon, Atsushi Takahashi, and Sheeba Arnold). Conflict of Interest: None declared.  ... 
doi:10.1093/cercor/bhw238 pmid:27550868 pmcid:PMC5066829 fatcat:wy6hplwmdjhbdjj5mfaanme6su

Resting State fMRI Based Multilayer Network Configuration in Patients with Schizophrenia

George Gifford, Nicolas Crossley, Matthew J Kempton, Sarah Morgan, Paola Dazzan, Jonathan Young, Philip McGuire
2020 NeuroImage: Clinical  
Novel methods for measuring large-scale dynamic brain organisation are needed to provide new biomarkers of schizophrenia.  ...  This study suggests less stable community structure in a schizophrenia group at an RSN and node level and provides novel methods of exploring dynamic community structure.  ...  brain organisation and dynamics.  ... 
doi:10.1016/j.nicl.2020.102169 pmid:32032819 pmcid:PMC7005505 fatcat:vgylgpy4jjblnhfgdaz4oasffi

5-Formylcytosine can be a stable DNA modification in mammals

Martin Bachman, Santiago Uribe-Lewis, Xiaoping Yang, Heather E Burgess, Mario Iurlaro, Wolf Reik, Adele Murrell, Shankar Balasubramanian
2015 Nature Chemical Biology  
Here, we show that developmental dynamics of 5fC levels in mouse DNA differ from those of 5-hydroxymethylcytosine (5hmC), and using stable isotope labeling in vivo, we show that 5fC can be a stable DNA  ...  On the other hand, we recently demonstrated that 5hmC is a predominantly stable modification in mammalian DNA, especially in the adult mouse brain where 5hmC is most abundant 6 .  ...  Therefore, the lack of 5fC labeling in the adult brain means that this modified base must be stable in the genome as opposed to generally acting as a dynamic intermediate of active DNA demethylation.  ... 
doi:10.1038/nchembio.1848 pmid:26098680 pmcid:PMC5486442 fatcat:qtw3hio6yvgndnd32utr4ihl5q

Dynamic functional network connectivity reveals unique and overlapping profiles of insula subdivisions

Jason S. Nomi, Kristafor Farrant, Eswar Damaraju, Srinivas Rachakonda, Vince D. Calhoun, Lucina Q. Uddin
2016 Human Brain Mapping  
showing overlapping and unique subdivision connectivity profiles.  ...  The multiplicity of functions subserved by insular subdivisions calls for a nuanced investigation of their functional connectivity profiles.  ...  Acknowledgments This work was supported by the National Institute of Mental Health [K01MH092288 and R01MH107549], a Slifka/ Ritvo Innovation in Autism Research Award from the International Society for  ... 
doi:10.1002/hbm.23135 pmid:26880689 pmcid:PMC4837017 fatcat:r6eosr5wnfeyzarush4ss7i6ni

Mapping the human brain's cortical-subcortical functional network organization [article]

Marjolein Spronk, Jie Lisa Ji, Kaustubh Kulkarni, Grega Repovs, Alan Anticevic, Michael W. Cole
2017 bioRxiv   pre-print
This whole-brain network atlas - released as an open resource for the neuroscience community - places all brain structures across both cortex and subcortex in a single large-scale functional framework,  ...  We leveraged the Human Connectome Project dataset to identify network communities across cortical regions, replicating well-known networks and revealing several novel but robust networks, including a left-lateralized  ...  The dashed line indicates at which gamma-value the community detection gave the most stable and (neurobiologically) plausible results. C) Split-half validation results for the cortical partition.  ... 
doi:10.1101/206292 fatcat:6gevtwvzbvbj5ezbqptgq4jiey

Functional MRI applications for psychiatric disease subtyping: a review

Lucas Miranda, Riya Paul, Benno Pütz, Bertram Müller-Myhsok
2020 Zenodo  
With the advent of new technologies that allowed researchers to investigate brain mechanisms in a more direct manner, interest in not only the mechanistic rationale behind defined pathologies but also  ...  This is particularly appealing for the field of personalised medicine, which searches for data-driven approaches to improve diagnosis, prognosis and treatment selection on an individual basis.  ...  Yes Bootstrap No 5 2014 Brain network informed subject community detection in early-onset schizophrenia Schizophrenia 52 rs fMRI Functional connectivity (gRACIAR) Newmann's Graph-based  ... 
doi:10.5281/zenodo.3923918 fatcat:y33tncjqtbfpphlmkceg3hnd7y

Neurogenetic profiles delineate large-scale connectivity dynamics of the human brain

Ibai Diez, Jorge Sepulcre
2018 Nature Communications  
Importantly, we find that distinctive dynamic connectivity patterns are spatially associated with Allen Human Brain Atlas genetic transcription levels of synaptic long-term potentiation and long-term depression-related  ...  Here, we applied dynamic graph theory-based analyses to evaluate the dynamic streams of wholebrain functional connectivity over time across cognitive states.  ...  Data availability All neuroimaging and genetic data that support the findings of this study are available from the Human Connectome Project (https://www.humanconnectomeproject.org) and the Allen Human Brain  ... 
doi:10.1038/s41467-018-06346-3 pmid:30250030 pmcid:PMC6155203 fatcat:cxj7znhzsjdb3ea7ksnjg3zxf4

The Neural Dynamics of Individual Differences in Episodic Autobiographical Memory

Raluca Petrican, Daniela J. Palombo, Signy Sheldon, Brian Levine
2020 eNeuro  
Complementarily, we postulate that impoverished subjective E-AM and visual EM are linked to dynamic brain organization patterns implying a predisposition towards semanticizing novel perceptual information  ...  Interindividual differences in subjective E-AM were linked to the same neural mechanisms underlying visual, but not verbal, EM, in general agreement with the hypothesized static and dynamic brain organization  ...  Network Community Toolbox. 361 community detection algorithm implemented in the BCT.  ... 
doi:10.1523/eneuro.0531-19.2020 pmid:32060035 pmcid:PMC7171291 fatcat:magw2drdgzdxln2exsafxskmfm

A Functional Cartography of Cognitive Systems

Marcelo G. Mattar, Michael W. Cole, Sharon L. Thompson-Schill, Danielle S. Bassett, Christopher J Honey
2015 PLoS Computational Biology  
By applying dynamic community detection algorithms, we identify groups of brain regions that form putative functional communities, and we uncover changes in these groups across the 64-task battery.  ...  Novel and non-routine tasks, for example, are implemented faster than structural connections can be formed. The neural underpinnings of these dynamics are far from understood.  ...  Muldoon for her helpful comments on the manuscript. Author Contributions  ... 
doi:10.1371/journal.pcbi.1004533 pmid:26629847 pmcid:PMC4668064 fatcat:ddydtmbiarbjlon7ai23m5wsvy
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