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https://www.readbyqxmd.com/read/29344935/progressive-topological-disorganization-of-brain-network-in-focal-epilepsy
#1
K M Park, B I Lee, K J Shin, S Y Ha, J Park, T H Kim, C W Mun, S E Kim
OBJECTIVE: Increasing evidence has suggested that epilepsy is a network disease. Graph theory is a mathematical tool that allows for the analysis and quantification of the brain network. We aimed to evaluate the influences of duration of epilepsy on the topological organization of brain network in focal epilepsy patients with normal MRI using the graph theoretical analysis based on diffusion tenor imaging. METHODS: We prospectively enrolled 66 patients with focal epilepsy (18/66 patients were newly diagnosed) and 84 healthy subjects...
January 17, 2018: Acta Neurologica Scandinavica
https://www.readbyqxmd.com/read/29342923/electrical-design-and-evaluation-of-asynchronous-serial-bus-communication-network-of-48-sensor-platform-lsis-with-single-ended-i-o-for-integrated-mems-lsi-sensors
#2
Chenzhong Shao, Shuji Tanaka, Takahiro Nakayama, Yoshiyuki Hata, Masanori Muroyama
For installing many sensors in a limited space with a limited computing resource, the digitization of the sensor output at the site of sensation has advantages such as a small amount of wiring, low signal interference and high scalability. For this purpose, we have developed a dedicated Complementary Metal-Oxide-Semiconductor (CMOS) Large-Scale Integration (LSI) (referred to as "sensor platform LSI") for bus-networked Micro-Electro-Mechanical-Systems (MEMS)-LSI integrated sensors. In this LSI, collision avoidance, adaptation and event-driven functions are simply implemented to relieve data collision and congestion in asynchronous serial bus communication...
January 15, 2018: Sensors
https://www.readbyqxmd.com/read/29340399/landscape-of-gene-networks-for-random-parameter-perturbation
#3
Chunhe Li
Landscape approaches have been exploited to study the stochastic dynamics of gene networks. However, how to calculate the landscape with a wide range of parameter variations and how to investigate the influence of the network topology on the global properties of gene networks remain to be elucidated. Here, I developed an approach for the landscape of random parameter perturbation (LRPP) to address this issue. Based on a self-consistent approximation approach, by making perturbations to parameters in a given range, I obtained the landscape for gene network systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29340074/identification-of-novel-diagnostic-biomarkers-for-thyroid-carcinoma
#4
Xiliang Wang, Qing Zhang, Zhiming Cai, Yifan Dai, Lisha Mou
Thyroid carcinoma (THCA) is the most universal endocrine malignancy worldwide. Unfortunately, a limited number of large-scale analyses have been performed to identify biomarkers for THCA. Here, we conducted a meta-analysis using 505 THCA patients and 59 normal controls from The Cancer Genome Atlas. After identifying differentially expressed long non-coding RNA (lncRNA) and protein coding genes (PCG), we found vast difference in various lncRNA-PCG co-expressed pairs in THCA. A dysregulation network with scale-free topology was constructed...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339311/general-crystallized-and-fluid-intelligence-are-not-associated-with-functional-global-network-efficiency-a-replication-study-with-the-human-connectome-project-1200-data-set
#5
J D Kruschwitz, L Waller, L S Daedelow, H Walter, I M Veer
One hallmark example of a link between global topological network properties of complex functional brain connectivity and cognitive performance is the finding that general intelligence may depend on the efficiency of the brain's intrinsic functional network architecture. However, although this association has been featured prominently over the course of the last decade, the empirical basis for this broad association of general intelligence and global functional network efficiency is quite limited. In the current study, we set out to replicate the previously reported association between general intelligence and global functional network efficiency using the large sample size and high quality data of the Human Connectome Project, and extended the original study by testing for separate association of crystallized and fluid intelligence with global efficiency, characteristic path length, and global clustering coefficient...
January 12, 2018: NeuroImage
https://www.readbyqxmd.com/read/29337088/cross-regulatory-network-in-pseudomonas-aeruginosa-biofilm-genes-and-tio2-anatase-induced-molecular-perturbations-in-key-proteins-unraveled-by-a-systems-biology-approach
#6
Rani Anupama, S Sajitha Lulu, Amitava Mukherjee, Subramanian Babu
A systems biology approach was used to study all the biofilm related genes of P. aeruginosa PAO1, and the interaction of titanium dioxide (TiO2) anatase with biofilm related proteins. Among the 71 genes, the interactions of all the nodal pairs were extracted by STRING 10.5 database. The inter-relationship among these genes was predicted by constructing complete PPI network and visualized in Cytoscape v 3.4.0. Total number of nodes of the network was found to be 335 and edges were 795. The network was further investigated for its clusters and the best cluster was further analyzed for the hub proteins which significantly contribute in cross-regulation of the biofilm related process...
January 11, 2018: Gene
https://www.readbyqxmd.com/read/29335803/contribution-of-transposable-elements-and-distal-enhancers-to-evolution-of-human-specific-features-of-interphase-chromatin-architecture-in-embryonic-stem-cells
#7
Gennadi V Glinsky
Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs...
January 15, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29335680/flows-scaling-and-the-control-of-moment-hierarchies-for-stochastic-chemical-reaction-networks
#8
Eric Smith, Supriya Krishnamurthy
Stochastic chemical reaction networks (CRNs) are complex systems that combine the features of concurrent transformation of multiple variables in each elementary reaction event and nonlinear relations between states and their rates of change. Most general results concerning CRNs are limited to restricted cases where a topological characteristic known as deficiency takes a value 0 or 1, implying uniqueness and positivity of steady states and surprising, low-information forms for their associated probability distributions...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29335434/competitive-influence-maximization-and-enhancement-of-synchronization-in-populations-of-non-identical-kuramoto-oscillators
#9
Markus Brede, Massimo Stella, Alexander C Kalloniatis
Many networked systems have evolved to optimize performance of function. Much literature has considered optimization of networks by central planning, but investigations of network formation amongst agents connecting to achieve non-aligned goals are comparatively rare. Here we consider the dynamics of synchronization in populations of coupled non-identical oscillators and analyze adaptations in which individual nodes attempt to rewire network topology to optimize node-specific aims. We demonstrate that, even though individual nodes' goals differ very widely, rewiring rules in which each node attempts to connect to the rest of the network in such a way as to maximize its influence on the system can enhance synchronization of the collective...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335027/fungi-stabilize-connectivity-in-the-lung-and-skin-microbial-ecosystems
#10
Laura Tipton, Christian L Müller, Zachary D Kurtz, Laurence Huang, Eric Kleerup, Alison Morris, Richard Bonneau, Elodie Ghedin
BACKGROUND: No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes than in cataloging which microbes are present, the variety of microbes in the community should be considered. However, the majority of ecological interaction networks for microbiomes built to date have included only bacteria. Joint association inference across multiple domains of life, e...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29334736/hydration-behavior-along-the-folding-pathways-of-trpzip4-trpzip5-and-trpzip6
#11
Madhulika Gupta, Prabir Khatua, Charusita Chakravarty, Sanjoy Bandyopadhyay
The microscopic properties of water confined within different segments of Trpzip4 (TZ4), Trpzip5 (TZ5) and Trzpip6 (TZ6) have been compared for all the states characterized along their folding pathways. In particular, structural ordering, energetics, and dynamics of water have been examined as the peptide unfolds along the free energy landscape. It is observed that the structuring of tetrahedral network as well as translational and rotational motions of hydration waters confined within the strands and the turn regions are very different, revealing motional heterogeneity in small 16-residue trpzips...
January 15, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29334377/detecting-hierarchical-genome-folding-with-network-modularity
#12
Heidi K Norton, Daniel J Emerson, Harvey Huang, Jesi Kim, Katelyn R Titus, Shi Gu, Danielle S Bassett, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease...
January 15, 2018: Nature Methods
https://www.readbyqxmd.com/read/29333197/solving-moment-hierarchies-for-chemical-reaction-networks
#13
Supriya Krishnamurthy, Eric Smith
The study of chemical reaction networks (CRN's) is a very active field. Earlier well-known results (Feinberg 1987 Chem. Enc. Sci. 42 2229, Anderson et al 2010 Bull. Math. Biol. 72 1947) identify a topological quantity called deficiency, for any CRN, which, when exactly equal to zero, leads to a unique factorized steady-state for these networks. No results exist however for the steady states of non-zero-deficiency networks. In this paper, we show how to write the full moment-hierarchy for any non-zero-deficiency CRN obeying mass-action kinetics, in terms of equations for the factorial moments...
October 20, 2017: Journal of Physics. A, Mathematical and Theoretical
https://www.readbyqxmd.com/read/29331709/what-do-the-genetic-association-data-say-about-the-high-risk-of-suicide-in-people-with-depression-a-novel-network-based-approach-to-find-common-molecular-basis-for-depression-and-suicidal-behavior-and-related-therapeutic-targets
#14
Ali Bozorgmehr, Fatemeh Alizadeh, Sattar Norouzi Ofogh, Mohammad Reza Abdollahzadeh Hamzekalayi, Sara Herati, Atefeh Moradkhani, Ali Shahbazi, Mohammad Ghadirivasfi
BACKGROUND: Available sources indicate that the risk of suicide in people with major depression is higher than other psychiatric disorders. Although it seems that these two conditions may have a shared cause in some cases, no studies have been conducted to identify a common basis for them. METHODS: In this study, following an extensive review of literature, we found almost all the genes that are involved in major depression and suicidal behavior, and we isolated genes shared between the two conditions...
January 8, 2018: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29328377/feature-genes-in-metastatic-breast-cancer-identified-by-metade-and-svm-classifier-methods
#15
Youlin Tuo, Ning An, Ming Zhang
The aim of the present study was to investigate the feature genes in metastatic breast cancer samples. A total of 5 expression profiles of metastatic breast cancer samples were downloaded from the Gene Expression Omnibus database, which were then analyzed using the MetaQC and MetaDE packages in R language. The feature genes between metastasis and non‑metastasis samples were screened under the threshold of P<0.05. Based on the protein‑protein interactions (PPIs) in the Biological General Repository for Interaction Datasets, Human Protein Reference Database and Biomolecular Interaction Network Database, the PPI network of the feature genes was constructed...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29326311/spatial-effects%C3%A2-%C3%A2-site-specific-regulation-of-actin-and-microtubule-organization-by-septin-gtpases
#16
REVIEW
Elias T Spiliotis
The actin and microtubule cytoskeletons comprise a variety of networks with distinct architectures, dynamics and protein composition. A fundamental question in eukaryotic cell biology is how these networks are spatially and temporally controlled, so they are positioned in the right intracellular places at the right time. While significant progress has been made in understanding the self-assembly of actin and microtubule networks, less is known about how they are patterned and regulated in a site-specific manner...
January 11, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29325077/integrating-restriction-site-associated-dna-sequencing-rad-seq-with-morphological-cladistic-analysis-clarifies-evolutionary-relationships-among-major-species-groups-of-bee-orchids
#17
Richard M Bateman, Gábor Sramkó, Ovidiu Paun
Background and Aims: Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus...
January 9, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29322926/construction-and-analysis-of-gene-gene-dynamics-influence-networks-based-on-a-boolean-model
#18
Maulida Mazaya, Hung-Cuong Trinh, Yung-Keun Kwon
BACKGROUND: Identification of novel gene-gene relations is a crucial issue to understand system-level biological phenomena. To this end, many methods based on a correlation analysis of gene expressions or structural analysis of molecular interaction networks have been proposed. They have a limitation in identifying more complicated gene-gene dynamical relations, though. RESULTS: To overcome this limitation, we proposed a measure to quantify a gene-gene dynamical influence (GDI) using a Boolean network model and constructed a GDI network to indicate existence of a dynamical influence for every ordered pair of genes...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322149/exploring-physical-and-chemical-properties-in-new-multifunctional-indium-bismuth-and-zinc-based-1d-and-2d-coordination-polymers
#19
G E Gomez, R F D'vries, D F Lionello, L M Aguirre-Díaz, M Spinosa, C S Costa, M C Fuertes, R A Pizarro, A M Kaczmarek, J Ellena, L Rozes, M Iglesias, R Van Deun, C Sanchez, M A Monge, G J A A Soler-Illia
Main group element coordination polymers (MGE-CPs) are important compounds for the development of multifunctional materials. However, there has been a shortage of studies regarding their structural, optical, catalytic, mechanical, and antibacterial properties. This work presents an exhaustive study of a set of crystalline MGE-CPs obtained from bismuth and indium metals and iminodiacetate, 1,2,4,5-benzenetetracarboxylate, and 2,2'-bipyridine as building blocks. An in-depth topological analysis of the networks was carried out...
January 11, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29318488/disrupted-topological-organization-of-the-frontal-mesolimbic-network-in-obese-patients
#20
Qianqian Meng, Yu Han, Gang Ji, Guanya Li, Yang Hu, Li Liu, Qingchao Jin, Karen M von Deneen, Jizheng Zhao, Guangbin Cui, Huaning Wang, Dardo Tomasi, Nora D Volkow, Jixin Liu, Yongzhan Nie, Yi Zhang, Gene-Jack Wang
Neuroimaging studies have revealed brain functional abnormalities in frontal-mesolimbic regions in obesity. However, the effects of obesity on brain network topology remains largely unknown. In the current study, we employed resting-state functional magnetic resonance imaging and graph theory methods to investigate obesity-related changes in brain network topology in 26 obese patients and 28 normal weight subjects. Results revealed that the whole-brain networks of the two groups exhibited typical features of small-world topology...
January 9, 2018: Brain Imaging and Behavior
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