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https://www.readbyqxmd.com/read/28339276/two-dimensional-platform-for-networks-of-majorana-bound-states
#1
Michael Hell, Martin Leijnse, Karsten Flensberg
We model theoretically a two-dimensional electron gas (2DEG) covered by a superconductor and demonstrate that topological superconducting channels are formed when stripes of the superconducting layer are removed. As a consequence, Majorana bound states (MBSs) are created at the ends of the stripes. We calculate the topological invariant and energy gap of a single stripe, using realistic values for an InAs 2DEG proximitized by an epitaxial Al layer. We show that the topological gap is enhanced when the structure is made asymmetric...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28335718/rnav-2-0-a-visualization-tool-for-bacterial-srna-mediated-regulatory-networks-mining
#2
Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol, Patricia Thébault
BACKGROUND: Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of mRNA targets of bacterial sRNAs is essential to investigate their functional activities. However, this step remains challenging with the lack of knowledge of the topological and biological constraints behind the formation of sRNA-mRNA duplexes. Even with the most sophisticated bioinformatics target prediction tools, the large proportion of false predictions may be prohibitive for further analyses...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#3
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334142/layer-specific-organization-of-local-excitatory-and-inhibitory-synaptic-connectivity-in-the-rat-presubiculum
#4
Yangfan Peng, Federico J Barreda Tomás, Constantin Klisch, Imre Vida, Jörg R P Geiger
The presubiculum is part of the parahippocampal spatial navigation system and contains head direction and grid cells upstream of the medial entorhinal cortex. This position within the parahippocampal cortex renders the presubiculum uniquely suited for analyzing the circuit requirements underlying the emergence of spatially tuned neuronal activity. To identify the local circuit properties, we analyzed the topology of synaptic connections between pyramidal cells and interneurons in all layers of the presubiculum by testing 4250 potential synaptic connections using multiple whole-cell recordings of up to 8 cells simultaneously...
February 25, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28326021/abnormalities-in-structural-covariance-of-cortical-gyrification-in-parkinson-s-disease
#5
Jinping Xu, Jiuquan Zhang, Jinlei Zhang, Yue Wang, Yanling Zhang, Jian Wang, Guanglin Li, Qingmao Hu, Yuanchao Zhang
Although abnormal cortical morphology and connectivity between brain regions (structural covariance) have been reported in Parkinson's disease (PD), the topological organizations of large-scale structural brain networks are still poorly understood. In this study, we investigated large-scale structural brain networks in a sample of 37 PD patients and 34 healthy controls (HC) by assessing the structural covariance of cortical gyrification with local gyrification index (lGI). We demonstrated prominent small-world properties of the structural brain networks for both groups...
2017: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/28326020/pyramidal-neurons-are-not-generalizable-building-blocks-of-cortical-networks
#6
REVIEW
Jennifer I Luebke
A key challenge in cortical neuroscience is to gain a comprehensive understanding of how pyramidal neuron heterogeneity across different areas and species underlies the functional specialization of individual neurons, networks, and areas. Comparative studies have been important in this endeavor, providing data relevant to the question of which of the many inherent properties of individual pyramidal neurons are necessary and sufficient for species-specific network and areal function. In this mini review, the importance of pyramidal neuron structural properties for signaling are outlined, followed by a summary of our recent work comparing the structural features of mouse (C57/BL6 strain) and rhesus monkey layer 3 (L3) pyramidal neurons in primary visual and frontal association cortices and their implications for neuronal and areal function...
2017: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/28323817/hippocampal-and-prefrontal-processing-of-network-topology-to-simulate-the-future
#7
Amir-Homayoun Javadi, Beatrix Emo, Lorelei R Howard, Fiona E Zisch, Yichao Yu, Rebecca Knight, Joao Pinelo Silva, Hugo J Spiers
Topological networks lie at the heart of our cities and social milieu. However, it remains unclear how and when the brain processes topological structures to guide future behaviour during everyday life. Using fMRI in humans and a simulation of London (UK), here we show that, specifically when new streets are entered during navigation of the city, right posterior hippocampal activity indexes the change in the number of local topological connections available for future travel and right anterior hippocampal activity reflects global properties of the street entered...
March 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28323359/atomimetic-mechanical-structures-with-nonlinear-topological-domain-evolution-kinetics
#8
Michael J Frazier, Dennis M Kochmann
A mechanical metamaterial, a simple, periodic mechanical structure, is reported, which reproduces the nonlinear dynamic behavior of materials undergoing phase transitions and domain switching at the structural level. Tunable multistability is exploited to produce switching and transition phenomena whose kinetics are governed by the same Allen-Cahn law commonly used to describe material-level, structural-transition processes. The reported purely elastic mechanical system displays several key features commonly found in atomic- or mesoscale physics of solids...
March 21, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28322823/generating-tissue-topology-through-remodeling-of-cell-cell-adhesions
#9
REVIEW
Katharine Goodwin, Celeste M Nelson
During tissue morphogenesis, cellular rearrangements give rise to a large variety of three-dimensional structures. Final tissue architecture varies greatly across organs, and many develop to include combinations of folds, tubes, and branched networks. To achieve these different tissue geometries, constituent cells must follow different programs that dictate changes in shape and/or migratory behavior. One essential component of these changes is the remodeling of cell-cell adhesions. Invasive migratory behavior and separation between tissues require localized breakdown of cadherin-mediated adhesions...
March 16, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28322230/reconstruction-of-noise-driven-nonlinear-networks-from-node-outputs-by-using-high-order-correlations
#10
Yang Chen, Zhaoyang Zhang, Tianyu Chen, Shihong Wang, Gang Hu
Many practical systems can be described by dynamic networks, for which modern technique can measure their outputs, and accumulate extremely rich data. Nevertheless, the network structures producing these data are often deeply hidden in the data. The problem of inferring network structures by analyzing the available data, turns to be of great significance. On one hand, networks are often driven by various unknown facts, such as noises. On the other hand, network structures of practical systems are commonly nonlinear, and different nonlinearities can provide rich dynamic features and meaningful functions of realistic networks...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28321969/the-pangenome-of-the-genus-clostridium
#11
Zulema Udaondo, Estrella Duque, Juan Luis Ramos
We present the pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species, some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair...
March 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28321948/gene-networks-show-associations-with-seed-region-connectivity
#12
Marie Forest, Yasser Iturria-Medina, Jennifer S Goldman, Claudia L Kleinman, Amanda Lovato, Kathleen Oros Klein, Alan Evans, Antonio Ciampi, Aurélie Labbe, Celia M T Greenwood
Primary patterns in adult brain connectivity are established during development by coordinated networks of transiently expressed genes; however, neural networks remain malleable throughout life. The present study hypothesizes that structural connectivity from key seed regions may induce effects on their connected targets, which are reflected in gene expression at those targeted regions. To test this hypothesis, analyses were performed on data from two brains from the Allen Human Brain Atlas, for which both gene expression and DW-MRI were available...
March 21, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28321444/enantiomeric-two-fold-interpenetrated-3d-zinc-ii-coordination-networks-as-a-catalytic-platform-significant-difference-between-water-within-the-cage-and-trace-water-in-transesterification
#13
Eunkyung Choi, Minjoo Ryu, Haeri Lee, Ok-Sang Jung
Self-assembly of Zn(ClO4)2 with 1,1,2,2-tetramethyl-1,2-di(pyridin-3-yl)disilane (L) as a bidentate N-donor gives rise to 3D coordination networks, [Zn(μ-OH)(L)]3(ClO4)3·5H2O (1·5H2O), of unique, 10(3)-a srs net topology. An important feature is that two enantiomeric 3D frameworks, 4(1)- and 4(3)-[Zn(μ-OH)(L)]3(ClO4)3·5H2O, are interpenetrated to form a racemic two-fold 3D network with cages occupied by two water molecules. Another structural characteristic is a C3-symmetric planar Zn3(μ-OH)3 6-membered ring with tetrahedral Zn(ii) ions...
March 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28320679/synchronization-of-coupled-reaction-diffusion-neural-networks-with-directed-topology-via-an-adaptive-approach
#14
Hao Zhang, Yin Sheng, Zhigang Zeng
This paper investigates the synchronization issue of coupled reaction-diffusion neural networks with directed topology via an adaptive approach. Due to the complexity of the network structure and the presence of space variables, it is difficult to design proper adaptive strategies on coupling weights to accomplish the synchronous goal. Under the assumptions of two kinds of special network structures, that is, directed spanning path and directed spanning tree, some novel edge-based adaptive laws, which utilized the local information of node dynamics fully are designed on the coupling weights for reaching synchronization...
March 15, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28320358/preservation-affinity-in-consensus-modules-among-stages-of-hiv-1-progression
#15
Sk Md Mosaddek Hossain, Sumanta Ray, Anirban Mukhopadhyay
BACKGROUND: Analysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in which a disease progresses. Identifying topological preservation of modular structure also contributes to that understanding. METHODS: HIV-1 disease provides a well-documented progression pattern through three stages of infection: acute, chronic and non-progressor...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28319835/convergent-and-divergent-effects-of-apolipoprotein-e-%C3%AE%C2%B54-and-%C3%AE%C2%B52-alleles-on-amygdala-functional-networks-in-nondemented-older-adults
#16
Liang Gong, Hao Shu, Cancan He, Qing Ye, Feng Bai, Chunming Xie, Zhijun Zhang
Traditionally, in the context of Alzheimer's disease, the apolipoprotein E ε2 (APOEε2) allele is a protective factor and the APOEε4 allele is a destructive factor. However, this inverse relationship has recently been challenged, and the neural mechanisms underlying the effects of APOE genotype on Alzheimer's disease remain unclear. A resting-state functional magnetic resonance imaging study was conducted to investigate the effects of APOE genotype and age on amygdala functional connectivity (AFC) networks in 84 patients with amnestic mild cognitive impairment and 124 cognitively normal order adults...
February 24, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28317991/a-novel-naphthalenediimide-based-lanthanide-organic-framework-with-polyoxometalate-templates-exhibiting-reversible-photochromism
#17
Hai-Long Zhang, Jian-Zhen Liao, Wenbin Yang, Xiao-Yuan Wu, Can-Zhong Lu
The first visible-light-responsive photochromic polyoxometalate-templated lanthanide-organic framework (LOF) has been constructed from a carboxyphenyl-substituted naphthalenediimide (NDI) derivative, which displays an unusual four-fold interpenetration of an srs topological network, featuring a variety of anion-π interactions between polyoxoanions and π-acidic NDI moieties, and undergoes a rapid reversible photochromic transformation upon blue light irradiation.
March 20, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28317894/swim-a-computational-tool-to-unveiling-crucial-nodes-in-complex-biological-networks
#18
Paola Paci, Teresa Colombo, Giulia Fiscon, Aymone Gurtner, Giulio Pavesi, Lorenzo Farina
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317835/reducing-cascading-failure-risk-by-increasing-infrastructure-network-interdependence
#19
Mert Korkali, Jason G Veneman, Brian F Tivnan, James P Bagrow, Paul D H Hines
Increased interconnection between critical infrastructure networks, such as electric power and communications systems, has important implications for infrastructure reliability and security. Others have shown that increased coupling between networks that are vulnerable to internetwork cascading failures can increase vulnerability. However, the mechanisms of cascading in these models differ from those in real systems and such models disregard new functions enabled by coupling, such as intelligent control during a cascade...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28315631/network-analysis-of-urocortins
#20
Shao-Jun Chen
OBJECTIVES: Urocortins (Ucns), members of corticotropin releasing factor family, play critical roles in a number of pathological and physiological conditions. Many proteins have been reported to participate in Ucns signaling pathways, which formed complex interaction networks. METHODS: STITCH ('search tool for interactions of chemicals') is an interaction network database that provides exploration of the known and predicted interactions among large sets of chemicals and proteins...
November 2016: Neuro Endocrinology Letters
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