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Graph Theory

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https://www.readbyqxmd.com/read/28804930/gaussian-covariance-graph-models-accounting-for-correlated-marker-effects-in-genome-wide-prediction
#1
C A Martínez, K Khare, S Rahman, M A Elzo
Several statistical models used in genome-wide prediction assume uncorrelated marker allele substitution effects, but it is known that these effects may be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high-dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G...
August 13, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28804744/reduced-rich-club-connectivity-is-related-to-disability-in-primary-progressive-ms
#2
Jan-Patrick Stellmann, Sibylle Hodecker, Bastian Cheng, Nadine Wanke, Kim Lea Young, Claus Hilgetag, Christian Gerloff, Christoph Heesen, Götz Thomalla, Susanne Siemonsen
OBJECTIVE: To investigate whether the structural connectivity of the brain's rich-club organization is altered in patients with primary progressive MS and whether such changes to this fundamental network feature are associated with disability measures. METHODS: We recruited 37 patients with primary progressive MS and 21 healthy controls for an observational cohort study. Structural connectomes were reconstructed based on diffusion-weighted imaging data using probabilistic tractography and analyzed with graph theory...
September 2017: Neurology® Neuroimmunology & Neuroinflammation
https://www.readbyqxmd.com/read/28799862/disrupted-topologic-efficiency-of-white-matter-structural-connectome-in-individuals-with-subjective-cognitive-decline
#3
Ni Shu, Xiaoni Wang, Qiuhui Bi, Tengda Zhao, Ying Han
Purpose To determine whether individuals with subjective cognitive decline (SCD), which is defined by memory complaints with normal performance at objective neuropsychologic examinations, exhibit disruptions of white matter (WM) connectivity and topologic alterations of the brain structural connectome. Materials and Methods Diffusion-tensor magnetic resonance imaging and graph theory approaches were used to investigate the topologic organization of the brain structural connectome in 36 participants with SCD (21 women: mean age, 62...
August 11, 2017: Radiology
https://www.readbyqxmd.com/read/28799540/corrigendum-understanding-cancer-complexome-using-networks-spectral-graph-theory-and-multilayer-framework
#4
Aparna Rai, Priodyuti Pradhan, Jyothi Nagraj, K Lohitesh, Rajdeep Chowdhury, Sarika Jalan
No abstract text is available yet for this article.
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28795465/a-molecular-breadboard-removal-and-replacement-of-subunits-in-an-hepatitis-b-virus-capsid
#5
Lye Siang Lee, Nicholas Brunk, Daniel G Haywood, David Keifer, Elizabeth Pierson, Panagiotis Kondylis, Joseph Che-Yen Wang, Stephen C Jacobson, Martin F Jarrold, Adam Zlotnick
Hepatitis B virus (HBV) core protein is a model system for studying assembly and disassembly of icosahedral structures. Controlling disassembly will allow re-engineering the 120 subunit HBV capsid, making it a molecular breadboard. We examined removal of subunits from partially crosslinked capsids to form stable incomplete particles. To characterize incomplete capsids, we used two single molecule techniques, resistive-pulse sensing and charge detection mass spectrometry. We expected to find a binomial distribution of capsid fragments...
August 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28795168/changes-in-brain-behavior-relationships-following-a-3-month-pilot-cognitive-intervention-program-for-adults-with-traumatic-brain-injury
#6
S Porter, I J Torres, W Panenka, Z Rajwani, D Fawcett, A Hyder, N Virji-Babul
Facilitating functional recovery following brain injury is a key goal of neurorehabilitation. Direct, objective measures of changes in the brain are critical to understanding how and when meaningful changes occur, however, assessing neuroplasticity using brain based results remains a significant challenge. Little is known about the underlying changes in functional brain networks that correlate with cognitive outcomes in traumatic brain injury (TBI). The purpose of this pilot study was to assess the feasibility of an intensive three month cognitive intervention program in individuals with chronic TBI and to evaluate the effects of this intervention on brain-behavioral relationships...
August 2017: Heliyon
https://www.readbyqxmd.com/read/28794979/identification-of-the-epileptogenic-zone-of-temporal-lobe-epilepsy-from-stereo-electroencephalography-signals-a-phase-transfer-entropy-and-graph-theory-approach
#7
Meng-Yang Wang, Jing Wang, Jian Zhou, Yu-Guang Guan, Feng Zhai, Chang-Qing Liu, Fei-Fei Xu, Yi-Xian Han, Zhao-Fen Yan, Guo-Ming Luan
The aim of this research is to apply an approach based on phase transfer entropy (PTE) and graph theory to study the interactions between the stereo-electroencephalography (SEEG) activities recorded in multilobar origin, in order to evaluate their ability to detect the epileptogenic zone (EZ) of temporal lobe epilepsies (TLE). Forty-three patients were included in this retrospective study. Five to sixteen (median = 12) multilead electrodes were implanted per patient, and, for each patient, a sub-set of between 10 and 32 (median = 22) bipolar derivations was selected for analysis...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28790907/a-neuroelectrical-brain-imaging-study-on-the-perception-of-figurative-paintings-against-only-their-color-or-shape-contents
#8
Anton G Maglione, Ambra Brizi, Giovanni Vecchiato, Dario Rossi, Arianna Trettel, Enrica Modica, Fabio Babiloni
In this study, the cortical activity correlated with the perception and appreciation of different set of pictures was estimated by using neuroelectric brain activity and graph theory methodologies in a group of artistic educated persons. The pictures shown to the subjects consisted of original pictures of Titian's and a contemporary artist's paintings (Orig dataset) plus two sets of additional pictures. These additional datasets were obtained from the previous paintings by removing all but the colors or the shapes employed (Color and Style dataset, respectively)...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28789772/mean-square-consensus-of-leader-following-multi-agent-systems-with-measurement-noises-and-time-delays
#9
Hongwei Ren, Feiqi Deng
This paper investigates the mean square consensus problem of dynamical networks of leader-following multi-agent systems with measurement noises and time-varying delays. We consider that the fixed undirected communication topologies are connected. A neighbor-based tracking algorithm together with distributed estimators are presented. Using tools of algebraic graph theory and the Gronwall-Bellman-Halanay type inequality, we establish sufficient conditions to reach consensus in mean square sense via the proposed consensus protocols...
August 5, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28772628/characterizing-adsorption-performance-of-granular-activated-carbon-with-permittivity
#10
Yang Yang, Chao Shi, Yi Zhang, Jinghua Ye, Huacheng Zhu, Kama Huang
A number of studies have achieved the consensus that microwave thermal technology can regenerate the granular activated carbon (GAC) more efficiently and energy-conservatively than other technologies. In particular, in the microwave heating industry, permittivity is a crucial parameter. This paper developed two equivalent models to establish the relationship between effective complex permittivity and pore volume of the GAC. It is generally based on Maxwell-Garnett approximation (MGA) theory. With two different assumptions in the model, two quantificational expressions were derived, respectively...
March 7, 2017: Materials
https://www.readbyqxmd.com/read/28772596/the-stability-analysis-method-of-the-cohesive-granular-slope-on-the-basis-of-graph-theory
#11
Yanpeng Guan, Xiaoli Liu, Enzhi Wang, Sijing Wang
This paper attempted to provide a method to calculate progressive failure of the cohesivefrictional granular geomaterial and the spatial distribution of the stability of the cohesive granular slope. The methodology can be divided into two parts: the characterization method of macro-contact and the analysis of the slope stability. Based on the graph theory, the vertexes, the edges and the edge sequences are abstracted out to characterize the voids, the particle contact and the macro-contact, respectively, bridging the gap between the mesoscopic and macro scales of granular materials...
February 27, 2017: Materials
https://www.readbyqxmd.com/read/28771208/the-quantified-characterization-method-of-the-micro-macro-contacts-of-three-dimensional-granular-materials-on-the-basis-of-graph-theory
#12
Yanpeng Guan, Enzhi Wang, Xiaoli Liu, Sijing Wang, Hebing Luan
We have attempted a multiscale and quantified characterization method of the contact in three-dimensional granular material made of spherical particles, particularly in cemented granular material. Particle contact is defined as a type of surface contact with voids in its surroundings, rather than a point contact. Macro contact is a particle contact set satisfying the restrictive condition of a two-dimensional manifold with a boundary. On the basis of graph theory, two dual geometrical systems are abstracted from the granular pack...
August 3, 2017: Materials
https://www.readbyqxmd.com/read/28771182/new-targets-for-schizophrenia-treatment-beyond-the-dopamine-hypothesis
#13
REVIEW
Albert C Yang, Shih-Jen Tsai
Schizophrenia has been primarily associated with dopamine dysfunction, and treatments have been developed that target the dopamine pathway in the central nervous system. However, accumulating evidence has shown that the core pathophysiology of schizophrenia might involve dysfunction in dopaminergic, glutamatergic, serotonergic, and gamma-aminobutyric acid (GABA) signaling, which may lead to aberrant functioning of interneurons that manifest as cognitive, behavioral, and social dysfunction through altered functioning of a broad range of macro- and microcircuits...
August 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28769858/dedifferentiation-does-not-account-for-hyperconnectivity-after-traumatic-brain-injury
#14
Rachel Anne Bernier, Arnab Roy, Umesh Meyyappan Venkatesan, Emily C Grossner, Einat K Brenner, Frank Gerard Hillary
OBJECTIVE: Changes in functional network connectivity following traumatic brain injury (TBI) have received increasing attention in recent neuroimaging literature. This study sought to understand how disrupted systems adapt to injury during resting and goal-directed brain states. Hyperconnectivity has been a common finding, and dedifferentiation (or loss of segregation of networks) is one possible explanation for this finding. We hypothesized that individuals with TBI would show dedifferentiation of networks (as noted in other clinical populations) and these effects would be associated with cognitive dysfunction...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28763447/braph-a-graph-theory-software-for-the-analysis-of-brain-connectivity
#15
Mite Mijalkov, Ehsan Kakaei, Joana B Pereira, Eric Westman, Giovanni Volpe
The brain is a large-scale complex network whose workings rely on the interaction between its various regions. In the past few years, the organization of the human brain network has been studied extensively using concepts from graph theory, where the brain is represented as a set of nodes connected by edges. This representation of the brain as a connectome can be used to assess important measures that reflect its topological architecture. We have developed a freeware MatLab-based software (BRAPH-BRain Analysis using graPH theory) for connectivity analysis of brain networks derived from structural magnetic resonance imaging (MRI), functional MRI (fMRI), positron emission tomography (PET) and electroencephalogram (EEG) data...
2017: PloS One
https://www.readbyqxmd.com/read/28760438/elucidating-functional-differences-between-cortical-gyri-and-sulci-via-sparse-representation-hcp-grayordinate-fmri-data
#16
Huan Liu, Xi Jiang, Tuo Zhang, Yudan Ren, Xintao Hu, Lei Guo, Junwei Han, Tianming Liu
The highly convoluted cerebral cortex is characterized by two different topographic structures: convex gyri and concave sulci. Increasing studies have demonstrated that cortical gyri and sulci exhibit different structural connectivity patterns. Inspired by the intrinsic structural differences between gyri and sulci, in this paper, we present a data-driven framework based on sparse representation of fMRI data for functional network inferences, then examine the interactions within and across gyral and sulcal functional networks and finally elucidate possible functional differences using graph theory based properties...
July 28, 2017: Brain Research
https://www.readbyqxmd.com/read/28757680/parallel-algorithms-for-switching-edges-in-heterogeneous-graphs
#17
Hasanuzzaman Bhuiyan, Maleq Khan, Jiangzhuo Chen, Madhav Marathe
An edge switch is an operation on a graph (or network) where two edges are selected randomly and one of their end vertices are swapped with each other. Edge switch operations have important applications in graph theory and network analysis, such as in generating random networks with a given degree sequence, modeling and analyzing dynamic networks, and in studying various dynamic phenomena over a network. The recent growth of real-world networks motivates the need for efficient parallel algorithms. The dependencies among successive edge switch operations and the requirement to keep the graph simple (i...
June 2017: Journal of Parallel and Distributed Computing
https://www.readbyqxmd.com/read/28756523/the-combinatorics-of-discrete-time-trees-theory-and-open-problems
#18
Alex Gavryushkin, Chris Whidden, Frederick A Matsen
A time-tree is a rooted phylogenetic tree such that all internal nodes are equipped with absolute divergence dates and all leaf nodes are equipped with sampling dates. Such time-trees have become a central object of study in phylogenetics but little is known about the parameter space of such objects. Here we introduce and study a hierarchy of discrete approximations of the space of time-trees from the graph-theoretic and algorithmic point of view. One of the basic and widely used phylogenetic graphs, the [Formula: see text] graph, is the roughest approximation and bottom level of our hierarchy...
July 29, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28751865/breakdown-of-modularity-in-complex-networks
#19
Sergi Valverde
The presence of modular organization is a common property of a wide range of complex systems, from cellular or brain networks to technological graphs. Modularity allows some degree of segregation between different parts of the network and has been suggested to be a prerequisite for the evolvability of biological systems. In technology, modularity defines a clear division of tasks and it is an explicit design target. However, many natural and artificial systems experience a breakdown in their modular pattern of connections, which has been associated with failures in hub nodes or the activation of global stress responses...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28750285/modelling-food-web-mediated-effects-of-hydrological-variability-and-environmental-flows
#20
REVIEW
Barbara J Robson, Rebecca E Lester, Darren S Baldwin, Nicholas R Bond, Romain Drouart, Robert J Rolls, Darren S Ryder, Ross M Thompson
Environmental flows are designed to enhance aquatic ecosystems through a variety of mechanisms; however, to date most attention has been paid to the effects on habitat quality and life-history triggers, especially for fish and vegetation. The effects of environmental flows on food webs have so far received little attention, despite food-web thinking being fundamental to understanding of river ecosystems. Understanding environmental flows in a food-web context can help scientists and policy-makers better understand and manage outcomes of flow alteration and restoration...
July 17, 2017: Water Research
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