keyword
MENU ▼
Read by QxMD icon Read
search

network topology

keyword
https://www.readbyqxmd.com/read/28445550/classifying-patents-based-on-their-semantic-content
#1
Antonin Bergeaud, Yoann Potiron, Juste Raimbault
In this paper, we extend some usual techniques of classification resulting from a large-scale data-mining and network approach. This new technology, which in particular is designed to be suitable to big data, is used to construct an open consolidated database from raw data on 4 million patents taken from the US patent office from 1976 onward. To build the pattern network, not only do we look at each patent title, but we also examine their full abstract and extract the relevant keywords accordingly. We refer to this classification as semantic approach in contrast with the more common technological approach which consists in taking the topology when considering US Patent office technological classes...
2017: PloS One
https://www.readbyqxmd.com/read/28443014/the-topographical-mapping-in-drosophila-central-complex-network-and-its-signal-routing
#2
Po-Yen Chang, Ta-Shun Su, Chi-Tin Shih, Chung-Chuan Lo
Neural networks regulate brain functions by routing signals. Therefore, investigating the detailed organization of a neural circuit at the cellular levels is a crucial step toward understanding the neural mechanisms of brain functions. To study how a complicated neural circuit is organized, we analyzed recently published data on the neural circuit of the Drosophila central complex, a brain structure associated with a variety of functions including sensory integration and coordination of locomotion. We discovered that, except for a small number of "atypical" neuron types, the network structure formed by the identified 194 neuron types can be described by only a few simple mathematical rules...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28442534/oncogenic-%C3%AE-catenin-and-pik3ca-instruct-network-states-and-cancer-phenotypes-in-intestinal-organoids
#3
Pamela Riemer, Mattias Rydenfelt, Matthias Marks, Karen van Eunen, Kathrin Thedieck, Bernhard G Herrmann, Nils Blüthgen, Christine Sers, Markus Morkel
Colorectal cancer is driven by cooperating oncogenic mutations. In this study, we use organotypic cultures derived from transgenic mice inducibly expressing oncogenic β-catenin and/or PIK3CA(H1047R) to follow sequential changes in cancer-related signaling networks, intestinal cell metabolism, and physiology in a three-dimensional environment mimicking tissue architecture. Activation of β-catenin alone results in the formation of highly clonogenic cells that are nonmotile and prone to undergo apoptosis. In contrast, coexpression of stabilized β-catenin and PIK3CA(H1047R) gives rise to intestinal cells that are apoptosis-resistant, proliferative, stem cell-like, and motile...
April 25, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28441964/fecal-metagenomic-profiles-in-subgroups-of-patients-with-myalgic-encephalomyelitis-chronic-fatigue-syndrome
#4
Dorottya Nagy-Szakal, Brent L Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G Klimas, Anthony L Komaroff, Susan Levine, Jose G Montoya, Daniel L Peterson, Devi Ramanan, Komal Jain, Meredith L Eddy, Mady Hornig, W Ian Lipkin
BACKGROUND: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained persistent fatigue, commonly accompanied by cognitive dysfunction, sleeping disturbances, orthostatic intolerance, fever, lymphadenopathy, and irritable bowel syndrome (IBS). The extent to which the gastrointestinal microbiome and peripheral inflammation are associated with ME/CFS remains unclear. We pursued rigorous clinical characterization, fecal bacterial metagenomics, and plasma immune molecule analyses in 50 ME/CFS patients and 50 healthy controls frequency-matched for age, sex, race/ethnicity, geographic site, and season of sampling...
April 26, 2017: Microbiome
https://www.readbyqxmd.com/read/28436912/distributed-position-based-consensus-of-second-order-multiagent-systems-with-continuous-intermittent-communication
#5
Qiang Song, Fang Liu, Guanghui Wen, Jinde Cao, Xinsong Yang
This paper considers the position-based consensus in a network of agents with double-integrator dynamics and directed topology. Two types of distributed observer algorithms are proposed to solve the consensus problem by utilizing continuous and intermittent position measurements, respectively, where each observer does not interact with any other observers. For the case of continuous communication between network agents, some convergence conditions are derived for reaching consensus in the network with a single constant delay or multiple time-varying delays on the basis of the eigenvalue analysis and the descriptor method...
April 24, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28436476/multiplex-lexical-networks-reveal-patterns-in-early-word-acquisition-in-children
#6
Massimo Stella, Nicole M Beckage, Markus Brede
Network models of language have provided a way of linking cognitive processes to language structure. However, current approaches focus only on one linguistic relationship at a time, missing the complex multi-relational nature of language. In this work, we overcome this limitation by modelling the mental lexicon of English-speaking toddlers as a multiplex lexical network, i.e. a multi-layered network where N = 529 words/nodes are connected according to four relationship: (i) free association, (ii) feature sharing, (iii) co-occurrence, and (iv) phonological similarity...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432702/tunable-porous-coordination-polymers-for-the-capture-recovery-and-storage-of-inhalation-anesthetics
#7
Brendan Francis Abrahams, David Dharma, Paul Stephen Donnelly, Timothy Adam Hudson, Cameron J Kepert, Richard Robson, Peter D Southon, Keith Forrest White
The uptake of inhalation anesthetics by three topologically identical frameworks is described. The 3D network materials, which possess square channels of different dimensions, are formed from the relatively simple combination of Zn(II) centres and dianionic ligands that contain a phenolate and a carboxylate group at opposite ends. All three framework materials are able to adsorb N2O, Xe and isoflurane. Whilst the framework with the widest channels is able to adsorb large quantities of the various guests from the gas phase, the frameworks with the narrower channels have superior binding enthalpies and exhibit higher levels of retention...
April 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28431175/minepath-org-a-free-interactive-pathway-analysis-web-server
#8
Lefteris Koumakis, Panos Roussos, George Potamias
Minepath (www.minepath.org) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430977/deep-mining-heterogeneous-networks-of-biomedical-linked-data-to-predict-novel-drug-target-associations
#9
Nansu Zong, Hyeoneui Kim, Victoria Ngo, Olivier Harismendy
Motivation: A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. Results: We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430466/evidence-for-anomalous-dynamic-heterogeneities-in-isostatic-supercooled-liquids
#10
M Micoulaut, M Bauchy
Upon cooling, the dynamics of supercooled liquids exhibits a growing transient spatial distribution of relaxation times that is known as dynamic heterogeneities. The relationship between this now well-established crucial feature of the glass transition and some underlying liquid properties remains challenging and elusive in many respects. Here we report on computer simulations of liquids with a changing network structure (densified silicates), and show that there is a deep and important link between the mechanical nature characterized by topological constraints and the spatial extent of such fluctuations...
April 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28426795/properties-of-healthcare-teaming-networks-as-a-function-of-network-construction-algorithms
#11
Martin S Zand, Melissa Trayhan, Samir A Farooq, Christopher Fucile, Gourab Ghoshal, Robert J White, Caroline M Quill, Alexander Rosenberg, Hugo Serrano Barbosa, Kristen Bush, Hassan Chafi, Timothy Boudreau
Network models of healthcare systems can be used to examine how providers collaborate, communicate, refer patients to each other, and to map how patients traverse the network of providers. Most healthcare service network models have been constructed from patient claims data, using billing claims to link a patient with a specific provider in time. The data sets can be quite large (106-108 individual claims per year), making standard methods for network construction computationally challenging and thus requiring the use of alternate construction algorithms...
2017: PloS One
https://www.readbyqxmd.com/read/28425930/the-peculiar-glycolytic-pathway-in-hyperthermophylic-archaea-understanding-its-whims-by-experimentation-in-silico
#12
Yanfei Zhang, Theresa Kouril, Jacky L Snoep, Bettina Siebers, Matteo Barberis, Hans V Westerhoff
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5'-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase...
April 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28424704/draco-stem-an-automatic-tool-to-generate-high-quality-3d-meshes-of-shoot-apical-meristem-tissue-at-cell-resolution
#13
Guillaume Cerutti, Olivier Ali, Christophe Godin
Context: The shoot apical meristem (SAM), origin of all aerial organs of the plant, is a restricted niche of stem cells whose growth is regulated by a complex network of genetic, hormonal and mechanical interactions. Studying the development of this area at cell level using 3D microscopy time-lapse imaging is a newly emerging key to understand the processes controlling plant morphogenesis. Computational models have been proposed to simulate those mechanisms, however their validation on real-life data is an essential step that requires an adequate representation of the growing tissue to be carried out...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424611/modafinil-induced-changes-in-functional-connectivity-in-the-cortex-and-cerebellum-of-healthy-elderly-subjects
#14
Miriam Punzi, Tommaso Gili, Laura Petrosini, Carlo Caltagirone, Gianfranco Spalletta, Stefano L Sensi
In the past few years, cognitive enhancing drugs (CEDs) have gained growing interest and the focus of investigations aimed at exploring their use to potentiate the cognitive performances of healthy individuals. Most of this exploratory CED-related research has been performed on young adults. However, CEDs may also help to maintain optimal brain functioning or compensate for subtle and or subclinical deficits associated with brain aging or early-stage dementia. In this study, we assessed effects on resting state brain activity in a group of healthy elderly subjects undergoing acute administration of modafinil, a wakefulness-promoting agent...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28424527/unified-alignment-of-protein-protein-interaction-networks
#15
Noël Malod-Dognin, Kristina Ban, Nataša Pržulj
Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423909/ripping-rna-by-force-using-gaussian-network-models
#16
Changbong Hyeon, D Thirumalai
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict, studies in the context of proteins have shown that topology is the major determinant of the unfolding landscapes. By building on this finding we study the responses of RNA molecules to force by adapting Gaussian network model (GNM) that represents RNAs using a bead-spring network with isotropic interactions...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28422062/cross-layer-design-for-optimizing-transmission-reliability-energy-efficiency-and-lifetime-in-body-sensor-networks
#17
Xi Chen, Yixuan Xu, Anfeng Liu
High transmission reliability, energy efficiency, and long lifetime are pivotal issues for wireless body area networks (WBANs. However, these performance metrics are not independent of each other, making it hard to obtain overall improvements through optimizing one single aspect. Therefore, a Cross Layer Design Optimal (CLDO) scheme is proposed to simultaneously optimize transmission reliability, energy efficiency, and lifetime of WBANs from several layers. Firstly, due to the fact that the transmission power of nodes directly influences the reliability of links, the optimized transmission power of different nodes is deduced, which is able to maximize energy efficiency in theory under the premise that requirements on delay and jitter are fulfilled...
April 19, 2017: Sensors
https://www.readbyqxmd.com/read/28418442/network-analysis-and-percolation-transition-in-hydrogen-bonded-clusters-nitric-acid-and-water-extracted-by-tributyl-phosphate
#18
Michael J Servis, David T Wu, Jenifer C Braley
Extraction of polar molecules by amphiphilic species results in a complex variety of clusters whose topologies and energetics control phase behavior and efficiency of liquid-liquid separations. A computational approach including quantum mechanical vibrational frequency calculations and molecular dynamics simulation with intermolecular network theory is used to provide a robust assessment of extractant and polar solute association through hydrogen bonding in the tributyl phosphate (TBP)/HNO3/H2O/dodecane system for the first time...
April 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28417576/the-relation-between-chemical-bonding-and-ultrafast-crystal-growth
#19
Tae Hoon Lee, Stephen R Elliott
Glasses are often described as supercooled liquids, whose structures are topologically disordered like a liquid, but nevertheless retain short-range structural order. Structural complexity is often associated with complicated electron-charge distributions in glassy systems, making a detailed investigation challenging even for short-range structural order, let alone their atomic dynamics. This is particularly problematic for lone-pair-rich, semiconducting materials, such as phase-change materials (PCMs). Here, this study shows that analytical methods for studying bonding, based on the electron-charge density, rather than a conventional atomic pair-correlation-function approach, allows an in-depth investigation into the chemical-bonding network, as well as lone pairs, of the prototypical PCM, Ge2 Sb2 Te5 (GST)...
April 18, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28415303/generic-patterns-in-the-evolution-of-urban-water-networks-evidence-from-a-large-asian-city
#20
Elisabeth Krueger, Christopher Klinkhamer, Christian Urich, Xianyuan Zhan, P Suresh C Rao
We examine high-resolution urban infrastructure data using every pipe for the water distribution network (WDN) and sanitary sewer network (SSN) in a large Asian city (≈4 million residents) to explore the structure as well as the spatial and temporal evolution of these infrastructure networks. Network data were spatially disaggregated into multiple subnets to examine intracity topological differences for functional zones of the WDN and SSN, and time-stamped SSN data were examined to understand network evolution over several decades as the city expanded...
March 2017: Physical Review. E
keyword
keyword
74714
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"