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https://www.readbyqxmd.com/read/28926154/brain-functional-connectome-abnormalities-in-als-are-associated-with-disability-and-cortical-hyperexcitability
#1
Nimeshan Geevasinga, Mayuresh S Korgaonkar, Parvathi Menon, Mehdi Van den Bos, Lavier Gomes, Sheryl Foster, Matthew C Kiernan, Steve Vucic
OBJECTIVE: The present study utilized a multimodality approach encompassing connectome network combined with brain volume analysis, and assessment of cortical excitability to provide novel insights into amyotrophic lateral sclerosis (ALS) pathogenesis. METHODS: Magnetic resonance images (MRI) were acquired using a 3.0 Tesla GE Signa HDx scanner, using an 8-channel head coil. MR images for the resting state scan were acquired using echo planar imaging MR sequence, acquiring 40 contiguous axial/oblique slices...
September 19, 2017: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/28924302/robust-transport-over-networks
#2
Yongxin Chen, Tryphon Georgiou, Michele Pavon, Allen Tannenbaum
We consider transportation over a strongly connected, directed graph. The scheduling amounts to selecting transition probabilities for a discrete-time Markov evolution which is designed to be consistent with initial and final marginal constraints on mass transport. We address the situation where initially the mass is concentrated on certain nodes and needs to be transported in a certain time period to another set of nodes, possibly disjoint from the first. The random evolution is selected to be closest to a prior measure on paths in the relative entropy sense-such a construction is known as a Schrödinger bridge between the two given marginals...
September 2017: IEEE Transactions on Automatic Control
https://www.readbyqxmd.com/read/28924171/a-network-integration-approach-for-drug-target-interaction-prediction-and-computational-drug-repositioning-from-heterogeneous-information
#3
Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinglin Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen, Jianyang Zeng
The emergence of large-scale genomic, chemical and pharmacological data provides new opportunities for drug discovery and repositioning. In this work, we develop a computational pipeline, called DTINet, to predict novel drug-target interactions from a constructed heterogeneous network, which integrates diverse drug-related information. DTINet focuses on learning a low-dimensional vector representation of features, which accurately explains the topological properties of individual nodes in the heterogeneous network, and then makes prediction based on these representations via a vector space projection scheme...
September 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28923973/flow-induced-gelation-of-microfiber-suspensions
#4
Antonio Perazzo, Janine K Nunes, Stefano Guido, Howard A Stone
The flow behavior of fiber suspensions has been studied extensively, especially in the limit of dilute concentrations and rigid fibers; at the other extreme, however, where the suspensions are concentrated and the fibers are highly flexible, much less is understood about the flow properties. We use a microfluidic method to produce uniform concentrated suspensions of high aspect ratio, flexible microfibers, and we demonstrate the shear thickening and gelling behavior of such microfiber suspensions, which, to the best of our knowledge, has not been reported previously...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28918259/disrupted-structural-and-functional-connectivity-networks-in-ischemic-stroke-patients
#5
Jingna Zhang, Ye Zhang, Li Wang, Linqiong Sang, Jun Yang, Rubing Yan, Pengyue Li, Jian Wang, Mingguo Qiu
Local lesions caused by stroke may result in extensive structural and functional reorganization in the brain. Previous studies of this phenomenon have focused on specific brain networks. Here, we aimed to discover abnormalities in whole-brain networks and to explore the decoupling between structural and functional connectivity in patients with stroke. Fifteen ischemic stroke patients and 23 normal controls (NCs) were recruited in this study. A graph theoretical analysis was employed to investigate the abnormal topological properties of structural and functional brain networks in patients with stroke...
September 13, 2017: Neuroscience
https://www.readbyqxmd.com/read/28917952/identification-of-potential-allosteric-communication-pathways-between-functional-sites-of-the-bacterial-ribosome-by-graph-and-elastic-network-models
#6
Pelin Guzel, Ozge Kurkcuoglu
BACKGROUND: Accumulated evidence indicates that bacterial ribosome employs allostery throughout its structure for protein synthesis. The nature of the allosteric communication between remote functional sites remains unclear, but the contact topology and dynamics of residues may play role in transmission of a perturbation to distant sites. METHODS/RESULTS: We employ two computationally efficient approaches - graph and elastic network modeling to gain insights about the allosteric communication in ribosome...
September 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28916772/limits-of-predictability-of-cascading-overload-failures-in-spatially-embedded-networks-with-distributed-flows
#7
A Moussawi, N Derzsy, X Lin, B K Szymanski, G Korniss
Cascading failures are a critical vulnerability of complex information or infrastructure networks. Here we investigate the properties of load-based cascading failures in real and synthetic spatially-embedded network structures, and propose mitigation strategies to reduce the severity of damages caused by such failures. We introduce a stochastic method for optimal heterogeneous distribution of resources (node capacities) subject to a fixed total cost. Additionally, we design and compare the performance of networks with N-stable and (N-1)-stable network-capacity allocations by triggering cascades using various real-world node-attack and node-failure scenarios...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28915563/niaoduqing-granules-relieve-chronic-kidney-disease-symptoms-by-decreasing-renal-fibrosis-and-anemia
#8
Xu Wang, Suyun Yu, Qi Jia, Lichuan Chen, Jinqiu Zhong, Yanhong Pan, Peiliang Shen, Yin Shen, Siliang Wang, Zhonghong Wei, Yuzhu Cao, Yin Lu
NiaoDuQing (NDQ) granules, a traditional Chinese medicine, has been clinically used in China for over fourteen years to treat chronic kidney disease (CKD). To elucidate the mechanisms underlying the therapeutic benefits of NDQ, we designed an approach incorporating chemoinformatics, bioinformatics, network biology methods, and cellular and molecular biology experiments. A total of 182 active compounds were identified in NDQ granules, and 397 putative targets associated with different diseases were derived through ADME modelling and target prediction tools...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28913535/stepwise-microhydration-of-aromatic-amide-cations-water-solvation-networks-revealed-by-the-infrared-spectra-of-acetanilide-h2o-n-clusters-n-%C3%A2-3
#9
Johanna Klyne, Matthias Schmies, Mitsuhiko Miyazaki, Masaaki Fujii, Otto Dopfer
The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA(+), N-phenylacetamide), AA(+)-(H2O)n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (νOH, νNH, νCH, amide A, 2800-3800 cm(-1)) and fingerprint (amide I-II, 1000-1900 cm(-1)) ranges to probe the preferred hydration motifs and the cluster growth...
September 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28912698/altered-rich-club-and-frequency-dependent-subnetwork-organization-in-mild-traumatic-brain-injury-a-meg-resting-state-study
#10
Marios Antonakakis, Stavros I Dimitriadis, Michalis Zervakis, Andrew C Papanicolaou, George Zouridakis
Functional brain connectivity networks exhibit "small-world" characteristics and some of these networks follow a "rich-club" organization, whereby a few nodes of high connectivity (hubs) tend to connect more densely among themselves than to nodes of lower connectivity. The Current study followed an "attack strategy" to compare the rich-club and small-world network organization models using Magnetoencephalographic (MEG) recordings from mild traumatic brain injury (mTBI) patients and neurologically healthy controls to identify the topology that describes the underlying intrinsic brain network organization...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28910120/a-universal-pattern-in-the-percolation-and-dissipation-of-protein-structural-perturbations
#11
Nandakumar Rajasekaran, Ashok Sekhar, Athi N Naganathan
Understanding the extent to which information is transmitted through the intra-molecular interaction network of proteins upon a perturbation, i.e. an allosteric effect, has long remained an unsolved problem. Through an analysis of high-resolution NMR data from the literature on 28 different proteins and 49 structural perturbations, we show that the extent of induced structural changes through mutations, and molecular events including protein-protein, protein-peptide, protein-ligand binding and post-translational modifications exhibit a near-universal exponential functional form...
September 14, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28906364/altered-default-mode-network-configuration-in-posttraumatic-stress-disorder-after-earthquake-a-resting-stage-functional-magnetic-resonance-imaging-study
#12
Xiao-Dong Zhang, Yan Yin, Xiao-Lei Hu, Lian Duan, Rongfeng Qi, Qiang Xu, Guang-Ming Lu, Ling-Jiang Li
The neural substrates of posttraumatic stress disorder (PTSD) are still not fully elucidated. Hence, this study is to explore topological alterations of the default mode network (DMN) in victims with PTSD after a magnitude of 8.0 earthquake using resting-state functional magnetic resonance imaging (rs-fMRI).This study was approved by the local ethical review board, and all participants signed written informed consent. Sixty-two PTSD victims from the 2008 Sichuan earthquake and 62 matched exposed controls underwent rs-fMRI...
September 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28904392/emergent-spectral-properties-of-river-network-topology-an-optimal-channel-network-approach
#13
Armaghan Abed-Elmdoust, Arvind Singh, Zong-Liang Yang
Characterization of river drainage networks has been a subject of research for many years. However, most previous studies have been limited to quantities which are loosely connected to the topological properties of these networks. In this work, through a graph-theoretic formulation of drainage river networks, we investigate the eigenvalue spectra of their adjacency matrix. First, we introduce a graph theory model for river networks and explore the properties of the network through its adjacency matrix. Next, we show that the eigenvalue spectra of such complex networks follow distinct patterns and exhibit striking features including a spectral gap in which no eigenvalue exists as well as a finite number of zero eigenvalues...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28902906/users-participation-and-social-influence-during-information-spreading-on-twitter
#14
Xin Zhang, Ding-Ding Han, Ruiqi Yang, Ziqiao Zhang
Online Social Networks generate a prodigious wealth of real-time information at an incessant rate. In this paper we study the empirical data that crawled from Twitter to describe the topology and information spreading dynamics of Online Social Networks. We propose a measurement with three measures to state the efforts of users on Twitter to get their information spreading, based on the unique mechanisms for information retransmission on Twitter. It is noticed that small fraction of users with special performance on participation can gain great influence, while most other users play a role as middleware during the information propagation...
2017: PloS One
https://www.readbyqxmd.com/read/28902834/alternative-evolutionary-histories-in-the-sequence-space-of-an-ancient-protein
#15
Tyler N Starr, Lora K Picton, Joseph W Thornton
To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents an optimal state driven by natural selection or the contingent product of historical chance events; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28902399/using-the-contextual-hub-analysis-tool-chat-in-cytoscape-to-identify-contextually-relevant-network-hubs
#16
Tanja Muetze, David J Lynn
Highly connected nodes in biological networks are called network hubs. Hubs are topologically important to the structure of the network and have been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we provide a step-by-step protocol for using the Contextual Hub Analysis Tool (CHAT), an application within Cytoscape 3, which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene or protein expression data, and identify hub nodes that are more highly connected to contextual nodes than expected by chance...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28900176/network-attributes-underlying-intellectual-giftedness-in-the-developing-brain
#17
Jiyoung Ma, Hee Jin Kang, Jung Yoon Kim, Hyeonseok S Jeong, Jooyeon Jamie Im, Eun Namgung, Myeong Ju Kim, Suji Lee, Tammy D Kim, Jin Kyoung Oh, Yong-An Chung, In Kyoon Lyoo, Soo Mee Lim, Sujung Yoon
Brain network is organized to maximize the efficiency of both segregated and integrated information processing that may be related to human intelligence. However, there have been surprisingly few studies that focus on the topological characteristics of brain network underlying extremely high intelligence that is intellectual giftedness, particularly in adolescents. Here, we examined the network topology in 25 adolescents with superior intelligence (SI-Adol), 25 adolescents with average intelligence (AI-Adol), and 27 young adults with AI (AI-Adult)...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28900013/optimal-deployment-of-resources-for-maximizing-impact-in-spreading-processes
#18
Andrey Y Lokhov, David Saad
The effective use of limited resources for controlling spreading processes on networks is of prime significance in diverse contexts, ranging from the identification of "influential spreaders" for maximizing information dissemination and targeted interventions in regulatory networks, to the development of mitigation policies for infectious diseases and financial contagion in economic systems. Solutions for these optimization tasks that are based purely on topological arguments are not fully satisfactory; in realistic settings, the problem is often characterized by heterogeneous interactions and requires interventions in a dynamic fashion over a finite time window via a restricted set of controllable nodes...
September 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28899007/the-spectrum-of-structural-and-functional-network-alterations-in-malformations-of-cortical-development
#19
Seok-Jun Hong, Boris C Bernhardt, Ravnoor S Gill, Neda Bernasconi, Andrea Bernasconi
Neuroimaging studies of malformations of cortical development have mainly focused on the characterization of the primary lesional substrate, while whole-brain investigations remain scarce. Our purpose was to assess large-scale brain organization in prevalent cortical malformations. Based on experimental evidence suggesting that distributed effects of focal insults are modulated by stages of brain development, we postulated differential patterns of network anomalies across subtypes of malformations. We studied a cohort of patients with focal cortical dysplasia type II (n = 63), subcortical nodular heterotopia (n = 44), and polymicrogyria (n = 34), and compared them to 82 age- and sex-matched controls...
August 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28898869/disrupted-brain-network-hubs-in-subtype-specific-parkinson-s-disease
#20
Ling-Yan Ma, Xiao-Dan Chen, Yong He, Hui-Zi Ma, Tao Feng
BACKGROUND/AIMS: The topological organization of brain functional networks is impaired in Parkinson's disease (PD). However, the altered patterns of functional network hubs in different subtypes of PD are not completely understood. METHODS: 3T resting-state functional MRI and voxel-based graph-theory analysis were employed to systematically investigate the intrinsic functional connectivity patterns of whole-brain networks. We enrolled 31 patients with PD (12 tremor dominant [TD] and 19 with postural instability/gait difficulty [PIGD]) and 22 matched healthy controls...
August 25, 2017: European Neurology
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