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The UCLA multimodal connectivity database: a web-based platform for brain connectivity matrix sharing and analysis

Jesse A. Brown, Jeffrey D. Rudie, Anita Bandrowski, John D. Van Horn, Susan Y. Bookheimer
2012 Frontiers in Neuroinformatics  
Here we introduce the UCLA Multimodal Connectivity Database (http://umcd.humanconnectomeproject.org), an openly available website for brain network analysis and data sharing.  ...  Brain connectomics research has rapidly expanded using functional MRI (fMRI) and diffusion-weighted MRI (dwMRI). A common product of these varied analyses is a connectivity matrix (CM).  ...  The work was supported by NIH NRSA F31AG035438-01 to Jesse A. Brown and NIH Neuroscience Blueprint HHSN271200800035C via NIDA.  ... 
doi:10.3389/fninf.2012.00028 pmid:23226127 pmcid:PMC3508475 fatcat:uxm7gstvpjd6xb7twsjk53s6ju

Connected brains and minds—The UMCD repository for brain connectivity matrices

Jesse A. Brown, John D. Van Horn
2016 NeuroImage  
We describe the USC Multimodal Connectivity Database (http:// umcd.humanconnectomeproject.org ), an interactive web-based platform for brain connectivity matrix sharing and analysis.  ...  The site enables users to download connectivity matrices shared by other users, upload matrices from their own published studies, or select a specific matrix and perform a realtime graph theory-based analysis  ...  The USC Multimodal Connectivity Database (http://umcd.humanconnectomeproject.org; formerly the UCLA Multimodal Connectivity Database; (Brown et al., 2012) ) is an open repository for CMs.  ... 
doi:10.1016/j.neuroimage.2015.08.043 pmid:26311606 pmcid:PMC4972184 fatcat:krpyusi4ezaqjj6qtbkp6e6apa

Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox

Andre Santos Ribeiro, Luis Miguel Lacerda, Hugo Alexandre Ferreira
2015 PeerJ  
Brown JA, Rudie JD, Bandrowski A, Van Horn JD, Bookheimer SY. 2012. The ucla multimodal connectivity database: a web-based platform for brain connectivity matrix sharing and analysis.  ...  Thus, we have developed the Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox with the goal of diminishing time waste in data processing and to allow an innovative and comprehensive approach  ...  The UCLA Multimodal Connectivity Database (UMCD) (Brown et al., 2012) : The UMCD is a web platform for connectivity matrix data repository, sharing and analysis.  ... 
doi:10.7717/peerj.1078 pmid:26207191 pmcid:PMC4511822 fatcat:dtsbgeegqvc4ze244jcvrwcqpy

The Digital Fish Library: Using MRI to Digitize, Database, and Document the Morphological Diversity of Fish

Rachel M. Berquist, Kristen M. Gledhill, Matthew W. Peterson, Allyson H. Doan, Gregory T. Baxter, Kara E. Yopak, Ning Kang, H. J. Walker, Philip A. Hastings, Lawrence R. Frank, Andrew Iwaniuk
2012 PLoS ONE  
We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these  ...  an efficient method for online storage and sharing of this imaging data.  ...  Acknowledgments We are grateful to the CFMRI for providing access to their high-field MRI scanners and Cameron Perry, Miriam Scadeng (UCSD), Dexter Walpole The Digital Fish Library PLoS ONE | www.plosone.org  ... 
doi:10.1371/journal.pone.0034499 pmid:22493695 pmcid:PMC3321017 fatcat:syy2qimqnral7gvovozvfnex6y

Integration and segregation in Autism Spectrum Disorders modulated by age, disease, and interaction: A graph-theoretic study of intrinsic functional connectivity [article]

Vatika Harlalka, Shruti Naik, Raju S. Bapi, P.K. Vinod, Dipanjan Roy
2018 bioRxiv   pre-print
We have analyzed the resting-state functional magnetic resonance imaging (rs-fMRI) and diffusion tensor imaging (DTI) data from the University of California Los Angeles (UCLA) multimodal connectivity database  ...  Further, the graph-theoretic analysis showed that there is a significant effect of age and disease on modularity, clustering coefficient, and local efficiency.  ...  ., Bandrowski, A., Van Horn, J. D. & Bookheimer, S. Y. The UCLA multimodal connectivity database: a web-based platform for brain connectivity matrix sharing and analysis.  ... 
doi:10.1101/278846 fatcat:hzdk5tdjsjcbhktrlxvbcbq35i

Big data sharing and analysis to advance research in post-traumatic epilepsy

Dominique Duncan, Paul Vespa, Asla Pitkänen, Adebayo Braimah, Niina Lapinlampi, Arthur W. Toga
2018 Neurobiology of Disease  
We describe the infrastructure and functionality for a centralized preclinical and clinical data repository and analytic platform to support importing heterogeneous multi-modal data, automatically and  ...  Highlights:  We have created the infrastructure for a centralized data repository for multi-modal data  Innovative image and electrophysiology processing methods have been applied  Novel analytic tools  ...  Diffusion tractography is used to determine connectivity properties (WM bundle length, connectivity density, and FA) and each subject's weighted connectivity matrix.  ... 
doi:10.1016/j.nbd.2018.05.026 pmid:29864492 pmcid:PMC6274619 fatcat:hgn4qtkzhjag7oseeeqhz72pl4

The Human Connectome Project's neuroimaging approach

Matthew F Glasser, Stephen M Smith, Daniel S Marcus, Jesper L R Andersson, Edward J Auerbach, Timothy E J Behrens, Timothy S Coalson, Michael P Harms, Mark Jenkinson, Steen Moeller, Emma C Robinson, Stamatios N Sotiropoulos (+4 others)
2016 Nature Neuroscience  
analyze data using neurobiologically accurate brain parcellations; and (7) share published data via user-friendly databases.  ...  This paper presents an integrated approach to data acquisition, analysis, and sharing that builds upon recent advances, particularly from the Human Connectome Project (HCP).  ...  We thank the other investigators and staff members of the Human Connectome Project consortium for invaluable contributions to data acquisition, analysis, and sharing.  ... 
doi:10.1038/nn.4361 pmid:27571196 fatcat:wwg4h7gmw5eshc5bc3zsmt6zmy

iCAVE: an open source tool for immersive 3D visualization of complex biomolecular interaction networks [article]

Vaja Liluashvili, Selim Kalayci, Eugene Flouder, Manda Wilson, Aaron Gabow, Zeynep H. Gümüş
2016 bioRxiv   pre-print
We present an open-source software platform, interactome-CAVE, (iCAVE), that leverages stereoscopic (3D) immersive display technologies for visualizing complex biomolecular interaction networks.  ...  in addition to extensions of known 2D network layout, clustering and edge-bundling algorithms to the 3D space, to assist in understanding the underlying structures in large, dense, layered or clustered  ...  Shared nearest neighbors: A similarity metric based on the sharing of nearest neighbors between any two nodes.  ... 
doi:10.1101/061374 fatcat:wu5bs6lrwfb4nczmi2iqha3rbq

Network modeling of single-cell omics data: challenges, opportunities, and progresses

Montgomery Blencowe, Douglas Arneson, Jessica Ding, Yen-Wei Chen, Zara Saleem, Xia Yang
2019 Emerging Topics in Life Sciences  
Gene regulatory network modeling has been used as a powerful approach to elucidate the complex molecular interactions underlying biological processes and systems, yet its application in single-cell omics  ...  Finally, we outline the remaining gaps in single-cell gene network modeling and the outlooks of the field moving forward.  ...  Has a web UI.  ... 
doi:10.1042/etls20180176 pmid:32270049 pmcid:PMC7141415 fatcat:x47pn56f6fbhxkzb3vcze3cuuq

Topics and trends in artificial intelligence assisted human brain research

Xieling Chen, Juan Chen, Gary Cheng, Tao Gong, Zhaoqing Pan
2020 PLoS ONE  
This paper combines the structural topic modeling (STM) with the bibliometric analysis to automatically identify prominent research topics from the large-scale, unstructured text of AI-assisted human brain  ...  Artificial intelligence (AI) assisted human brain research is a dynamic interdisciplinary field with great interest, rich literature, and huge diversity.  ...  Many online, interactive platforms have become available for brain network analysis, e.g., the UCLA Multimodal Connectivity Database [90] .  ... 
doi:10.1371/journal.pone.0231192 pmid:32251489 fatcat:fopwroopq5germh5khwevx3uhq

Monitoring the Application [chapter]

Adam Shackelford
2015 Beginning Amazon Web Services with Node.js  
During the next few months we are doing field trials that will help us test if these ideas are practically feasible in adapting communication protocols to improve communication between gliders and shore  ...  We are currently working on using our classifier to make communication decisions on when to transmit files based upon wave-parameters.  ...  An Adobe Flash user interface connects to Python-based support components for socket-based access to the database and the tablet!s GPS.  ... 
doi:10.1007/978-1-4842-0653-9_7 fatcat:b6s3wv3jcvf6xiniouokdhwtba

Modeling & Analysis

2003 NeuroImage  
maps of CSF, PVL and SCL were computed for the categories (i) whole database; (ii) gender; (iii) age-intervals for the whole data base and (iv) age-intervals for each gender.  ...  Abstract Constrained Principal Component Analysis (CPCA) is introduced as a correlation-based method of identifying (a) connectivity between neuronal structures and (b) functional interactions between  ...  We use a wavelet basis function set (e.g. Daubechies 4, (2)) to generate the design matrix for the observation level.  ... 
doi:10.1016/s1053-8119(05)70006-9 fatcat:zff2suxcofbxvetfrwfwcxi3zm

A New Approach to Network Decomposition Problems [chapter]

Alexander Rubchinsky
2017 Springer Proceedings in Mathematics & Statistics  
In addition to an overall evaluation of the interest, scientific quality, and timeliness of each proposal at the hands of the publisher, individual contributions are all refereed to the high quality standards  ...  Thus, this series provides the research community with well-edited, authoritative reports on developments in the most exciting areas of mathematical and statistical research today.  ...  Communication is based on demonstrations and personal engagement that make the buying process highly tangible and multisensory for consumers [7].  ... 
doi:10.1007/978-3-319-56829-4_10 fatcat:oll4dy6vcjhlta2j65qpf4tnra

Poster Session I

2013 Neuropsychopharmacology  
KYNA-based animal model of SZ; and (3) the relative roles of a7nAChRs vs NMDA receptors in performance in the DNMTP task.To this end, we determined, in a separate group of intact animals, the effects  ...  A significant contributor to cognitive impairments seen in SZ may be the elevated levels of kynurenic acid (KYNA), observed in the brains of patients with SZ.  ...  Slifstein, A. Abi-Dargham, and S. Kapur, Arch Gen Psychiatry 69, 776 (2012). 2  ... 
doi:10.1038/npp.2013.279 fatcat:54ipecxjarcvljrvn5fgtgif5u

XI Convegno Nazionale: Firenze, 17–19 marzo 2016, Palazzo dei Congressi – Villa Vittoria

M. Musicco, P. Caffarra, M. Bozzali, A.C. Bruni, B. Nacmias, L. Pantoni, G. Sorrentino, A. Venneri
2016 Journal of Alzheimer's Disease  
Furthermore, in PD-ICD, the lack of increased functional connectivity within the sensorimotor-network together with their cortical thinning in the same regions, suggest a greater disconnection among these  ...  Conclusions: Relative to PD no-ICD, PD-ICD patients are characterized by a more severe involvement of frontal, meso-limbic and motor circuits.  ...  Conclusions: The role of genomic SNPs still represented a challenge for the genetics of SAD, having an effects in increasing the risk for SAD, if any, much smaller than those of APOE.  ... 
doi:10.3233/jad-169001 pmid:27232541 fatcat:ld4yvhhabbdrzeok5ghvddevze
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