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https://www.readbyqxmd.com/read/28647368/identification-and-characterization-of-the-leaf-specific-networks-of-inner-and-rosette-leaves-in-brassica-rapa
#1
Man-Sun Kim, Seongmin Hong, Devaraj Sangeeth Prasath, Subin Im, Jeong-Rae Kim, Yong Pyo Lim
Inner and rosette leaves of Chinese cabbage (Brassica rapa) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa. The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone...
June 21, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28645845/the-feature-weighted-receptive-field-an-interpretable-encoding-model-for-complex-feature-spaces
#2
REVIEW
Ghislain St-Yves, Thomas Naselaris
We introduce the feature-weighted receptive field (fwRF), an encoding model designed to balance expressiveness, interpretability and scalability. The fwRFis organized around the notion of a feature map-a transformation of visual stimuli into visual features that preserves the topology of visual space (but not necessarily the native resolution of the stimulus). The key assumption of the fwRFmodel is that activity in each voxel encodes variation in a spatially localized region across multiple feature maps. This region is fixed for all feature maps; however, the contribution of each feature map to voxel activity is weighted...
June 20, 2017: NeuroImage
https://www.readbyqxmd.com/read/28644658/coevolution-of-synchronization-and-cooperation-in-costly-networked-interactions
#3
Alberto Antonioni, Alessio Cardillo
Despite the large number of studies on synchronization, the hypothesis that interactions bear a cost for involved individuals has seldom been considered. The introduction of costly interactions leads, instead, to the formulation of a dichotomous scenario in which an individual may decide to cooperate and pay the cost in order to get synchronized with the rest of the population. Alternatively, the same individual can decide to free ride, without incurring any cost, waiting for others to get synchronized to his or her state...
June 9, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28640829/an-exploration-of-collaborative-scientific-production-at-mit-through-spatial-organization-and-institutional-affiliation
#4
Matthew Claudel, Emanuele Massaro, Paolo Santi, Fiona Murray, Carlo Ratti
Academic research is increasingly cross-disciplinary and collaborative, between and within institutions. In this context, what is the role and relevance of an individual's spatial position on a campus? We examine the collaboration patterns of faculty at the Massachusetts Institute of Technology, through their academic output (papers and patents), and their organizational structures (institutional affiliation and spatial configuration) over a 10-year time span. An initial comparison of output types reveals: 1...
2017: PloS One
https://www.readbyqxmd.com/read/28640816/topographic-independent-component-analysis-reveals-random-scrambling-of-orientation-in-visual-space
#5
Marina Martinez-Garcia, Luis M Martinez, Jesús Malo
Neurons at primary visual cortex (V1) in humans and other species are edge filters organized in orientation maps. In these maps, neurons with similar orientation preference are clustered together in iso-orientation domains. These maps have two fundamental properties: (1) retinotopy, i.e. correspondence between displacements at the image space and displacements at the cortical surface, and (2) a trade-off between good coverage of the visual field with all orientations and continuity of iso-orientation domains in the cortical space...
2017: PloS One
https://www.readbyqxmd.com/read/28640183/bluetooth-low-energy-mesh-networks-a-survey
#6
REVIEW
Seyed Mahdi Darroudi, Carles Gomez
Bluetooth Low Energy (BLE) has gained significant momentum. However, the original design of BLE focused on star topology networking, which limits network coverage range and precludes end-to-end path diversity. In contrast, other competing technologies overcome such constraints by supporting the mesh network topology. For these reasons, academia, industry, and standards development organizations have been designing solutions to enable BLE mesh networks. Nevertheless, the literature lacks a consolidated view on this emerging area...
June 22, 2017: Sensors
https://www.readbyqxmd.com/read/28638123/transient-cell-assembly-networks-encode-stable-spatial-memories
#7
Andrey Babichev, Yuri Dabaghian
One of the mysteries of memory is that it can last despite changes in the underlying synaptic architecture. How can we, for example, maintain an internal spatial map of an environment over months or years when the underlying network is full of transient connections? In the following, we propose a computational model for describing the emergence of the hippocampal cognitive map in a network of transient place cell assemblies and demonstrate, using methods of algebraic topology, how such a network can maintain spatial memory over time...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28638071/emergent-stochastic-oscillations-and-signal-detection-in-tree-networks-of-excitable-elements
#8
Justus Kromer, Ali Khaledi-Nasab, Lutz Schimansky-Geier, Alexander B Neiman
We study the stochastic dynamics of strongly-coupled excitable elements on a tree network. The peripheral nodes receive independent random inputs which may induce large spiking events propagating through the branches of the tree and leading to global coherent oscillations in the network. This scenario may be relevant to action potential generation in certain sensory neurons, which possess myelinated distal dendritic tree-like arbors with excitable nodes of Ranvier at peripheral and branching nodes and exhibit noisy periodic sequences of action potentials...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28636542/niaoduqing-granules-relieve-chronic-kidney-disease-symptoms-by-decreasing-renal-fibrosis-and-anemia
#9
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...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636461/genice-a-novel-framework-for-gene-network-inference-by-clustering-exhaustive-search-and-multivariate-analysis
#10
Ricardo de Souza Jacomini, David Correa Martins-Jr, Felipe Leno da Silva, Anna Helena Reali Costa
Gene network (GN) inference from temporal gene expression data is a crucial and challenging problem in systems biology. Expression data sets usually consist of dozens of temporal samples, while networks consist of thousands of genes, thus rendering many inference methods unfeasible in practice. To improve the scalability of GN inference methods, we propose a novel framework called GeNICE, based on probabilistic GNs; the main novelty is the introduction of a clustering procedure to group genes with related expression profiles and to provide an approximate solution with reduced computational complexity...
June 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28636049/neutral-mixed-metal-coordination-polymers-based-on-a-ditopic-acetylacetonate-mg-ii-and-ag-i-syntheses-characterization-and-solvent-dependent-topologies
#11
Qianqian Guo, Ulli Englert
The complex [Mg(acacCN)2(H2O)2] (acacCN = 3-cyanoacetylacetonate) has been synthesized in good yield and fully characterized. It represents a versatile labile precursor for an anionic tris(ligand) complex which is crosslinked with Ag(i) to five different neutral bimetallic networks; all of them are solvates. Four of these extended structures share the same framework stoichiometry Ag[Mg(acacCN)3] and only differ in their solvent content. The co-crystallized solvent molecules decide the topological outcome of the crosslinking: the four compounds can be classified into two isomorphous 3D networks and two non-isomorphous but related 2D layer structures...
June 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28635674/exploring-wound-healing-genomic-machinery-with-a-network-based-approach
#12
Francesca Vitali, Simone Marini, Martina Balli, Hanne Grosemans, Maurilio Sampaolesi, Yves A Lussier, Maria Gabriella Cusella De Angelis, Riccardo Bellazzi
The molecular mechanisms underlying tissue regeneration and wound healing are still poorly understood despite their importance. In this paper we develop a bioinformatics approach, combining biology and network theory to drive experiments for better understanding the genetic underpinnings of wound healing mechanisms and for selecting potential drug targets. We start by selecting literature-relevant genes in murine wound healing, and inferring from them a Protein-Protein Interaction (PPI) network. Then, we analyze the network to rank wound healing-related genes according to their topological properties...
June 21, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/28635300/pyridine-dinucleotides-from-molecules-to-man
#13
Joshua P Fessel, William M Oldham
SIGNIFICANCE: Pyridine dinucleotides, NAD and NADP, were discovered over 100 years ago as necessary cofactors for fermentation in yeast extracts. Since that time, these molecules have been recognized as fundamental players in a variety of cellular processes, including energy metabolism, redox homeostasis, cellular signaling, and gene transcription, among many others. Given their critical role as mediators of cellular responses to metabolic perturbations, it is unsurprising that dysregulation of NAD and NADP metabolism has been associated with the pathobiology of many chronic human diseases...
June 21, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28633299/structural-covariance-networks-in-children-with-autism-or-adhd
#14
R A I Bethlehem, R Romero-Garcia, E Mak, E T Bullmore, S Baron-Cohen
Background: While autism and attention-deficit/hyperactivity disorder (ADHD) are considered distinct conditions from a diagnostic perspective, clinically they share some phenotypic features and have high comorbidity. Regardless, most studies have focused on only one condition, with considerable heterogeneity in their results. Taking a dual-condition approach might help elucidate shared and distinct neural characteristics. Method: Graph theory was used to analyse topological properties of structural covariance networks across both conditions and relative to a neurotypical (NT; n = 87) group using data from the ABIDE (autism; n = 62) and ADHD-200 datasets (ADHD; n = 69)...
June 13, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28632985/healable-reconfigurable-reprocessable-thermoset-shape-memory-polymer-with-highly-tunable-topological-rearrangement-kinetics
#15
Zizheng Fang, Ning Zheng, Qian Zhao, Tao Xie
The unique capability of topological rearrangement for dynamic covalent polymer networks has enabled various unusual properties (self-healing, solid-state plasticity, and reprocessability) that are not found in conventional thermosets. Achieving these properties in one network in a synergetic fashion can open up new opportunities for shape memory polymer. To accomplish such a goal, the freedom to tune topological rearrangement kinetics is critical. This is, however, challenging to achieve. In this work, two sets of dynamic bonds (urethane and hindered urea) are incorporated into a hybrid network for synthesizing shape memory poly(urea-urethane)...
June 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28631354/cross-population-myelination-covariance-of-human-cerebral-cortex
#16
Zhiwei Ma, Nanyin Zhang
Cross-population covariance of brain morphometric quantities provides a measure of interareal connectivity, as it is believed to be determined by the coordinated neurodevelopment of connected brain regions. Although useful, structural covariance analysis predominantly employed bulky morphological measures with mixed compartments, whereas studies of the structural covariance of any specific subdivisions such as myelin are rare. Characterizing myelination covariance is of interest, as it will reveal connectivity patterns determined by coordinated development of myeloarchitecture between brain regions...
June 20, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28629866/distributed-reconfigurable-control-strategies-for-switching-topology-networked-multi-agent-systems
#17
Z Gallehdari, N Meskin, K Khorasani
In this paper, distributed control reconfiguration strategies for directed switching topology networked multi-agent systems are developed and investigated. The proposed control strategies are invoked when the agents are subject to actuator faults and while the available fault detection and isolation (FDI) modules provide inaccurate and unreliable information on the estimation of faults severities. Our proposed strategies will ensure that the agents reach a consensus while an upper bound on the team performance index is ensured and satisfied...
June 16, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28629533/design-of-new-traditional-chinese-medicine-herbal-formulae-for-treatment-of-type-2-diabetes-mellitus-based-on-network-pharmacology
#18
Rui-Feng Hu, Xiao-Bo Sun
In the present study, 28 Chinese medicinal herbs belonging to traditional Chinese medicine (TCM) for the treatment of type 2 diabetes were selected to explore the application of network pharmacology in developing new Chinese herbal medicine formulae for the treatment of type 2 diabetes mellitus (T2DM). These herbs have the highest appearance rate in the literature, and their compounds are listed. The human protein-protein interaction network and the T2DM disease protein interaction network were constructed...
June 2017: Chinese Journal of Natural Medicines
https://www.readbyqxmd.com/read/28629174/using-coexpression-protein-interaction-network-analysis-to-identify-mechanisms-of-danshensu-affecting-patients-with-coronary-heart-disease
#19
Mengqi Huo, Zhixin Wang, Dongxue Wu, Yanling Zhang, Yanjiang Qiao
Salvia miltiorrhiza, known as Danshen, has attracted worldwide interest for its substantial effects on coronary heart disease (CHD). Danshensu (DSS) is one of the main active ingredients of Danshen on CHD. Although it has been proven to have a good clinical effect on CHD, the action mechanisms remain elusive. In the current study, a coexpression network-based approach was used to illustrate the beneficial properties of DSS in the context of CHD. By integrating the gene expression profile data and protein-protein interactions (PPIs) data, two coexpression protein interaction networks (CePIN) in a CHD state (CHD CePIN) and a non-CHD state (non-CHD CePIN) were generated...
June 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28627424/channeling-in-native-microbial-pathways-implications-and-challenges-for-metabolic-engineering
#20
REVIEW
Mary H Abernathy, Lian He, Yinjie J Tang
Intracellular enzymes can be organized into a variety of assemblies, shuttling intermediates from one active site to the next. Eukaryotic compartmentalization within mitochondrion and peroxisomes and substrate tunneling within multi-enzyme complexes have been well recognized. Intriguingly, the central pathways in prokaryotes may also form extensive channels, including the heavily branched glycolysis pathway. In vivo channeling through cascade enzymes is difficult to directly measure, but can be inferred from in vitro tests, reaction thermodynamics, transport/reaction modeling, analysis of molecular diffusion and protein interactions, or steady state/dynamic isotopic labeling...
June 13, 2017: Biotechnology Advances
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