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https://www.readbyqxmd.com/read/29150680/potential-landscape-of-high-dimensional-nonlinear-stochastic-dynamics-with-large-noise
#1
Ying Tang, Ruoshi Yuan, Gaowei Wang, Xiaomei Zhu, Ping Ao
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including the cell-fate decision in developmental processes as well as the genesis and progression of cancers. While various attempts have been made to construct potential landscape in high dimensional systems and to estimate transition rates, they are practically limited to the cases where either noise is small or detailed balance condition holds. A general and practical approach to investigate real-world nonequilibrium systems, which are typically high-dimensional and subject to large multiplicative noise and the breakdown of detailed balance, remains elusive...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150626/constructing-genetic-networks-using-biomedical-literature-and-rare-event-classification
#2
Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29149684/combining-benford-s-law-and-machine-learning-to-detect-money-laundering-an-actual-spanish-court-case
#3
Elena Badal-Valero, José A Alvarez-Jareño, Jose M Pavía
OBJECTIVES: This paper is based on the analysis of the database of operations from a macro-case on money laundering orchestrated between a core company and a group of its suppliers, 26 of which had already been identified by the police as fraudulent companies. In the face of a well-founded suspicion that more companies have perpetrated criminal acts and in order to make better use of what are very limited police resources, we aim to construct a tool to detect money laundering criminals...
November 11, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29149350/a-data-fusion-pipeline-for-generating-and-enriching-adverse-outcome-pathway-descriptions
#4
Penny Nymark, Linda Rieswijk, Friederike Ehrhart, Nina Jeliazkova, Georgia Tsiliki, Haralambos Sarimveis, Chris T Evelo, Vesa Hongisto, Pekka Kohonen, Egon Willighagen, Roland C Grafström
Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven and informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development of non-animal based hazard and risk assessment methods. We devised a six-step workflow that integrated diverse types of toxicology data into a novel AOP scheme for pulmonary fibrosis. Mining of literature references and diverse data sources covering previous pathway descriptions and molecular results were coupled in a stepwise manner with informatics tools applications that enabled gene linkage and pathway identification in molecular interaction maps...
November 15, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29148114/on-the-character-and-production-of-active-participation-in-neuro-rehabilitation-an-actor-network-perspective
#5
Simon Horton, Kathryn Mares, Neil Coull, Fiona Poland
The importance of patients' active involvement in neuro-rehabilitation after acquired brain injury has been consistently emphasised in recent years. However, most approaches fail to show how 'active participation' is practically enacted, focusing on individualised explanations of patient choice and behaviours, or notions of inherent patient traits. Using actor-network theory (ANT) as a sensitising concept, we investigated neuro-rehabilitation practices, asking how participation is shaped through biological and socio-material specificities, how rights to knowledge and expertise are constructed, and how a body acclimatises and adjusts within an order of participation and transformation...
November 2017: Sociology of Health & Illness
https://www.readbyqxmd.com/read/29147147/collective-behavior-of-large-scale-neural-networks-with-gpu-acceleration
#6
Jingyi Qu, Rubin Wang
In this paper, the collective behaviors of a small-world neuronal network motivated by the anatomy of a mammalian cortex based on both Izhikevich model and Rulkov model are studied. The Izhikevich model can not only reproduce the rich behaviors of biological neurons but also has only two equations and one nonlinear term. Rulkov model is in the form of difference equations that generate a sequence of membrane potential samples in discrete moments of time to improve computational efficiency. These two models are suitable for the construction of large scale neural networks...
December 2017: Cognitive Neurodynamics
https://www.readbyqxmd.com/read/29146982/photonic-simulation-of-entanglement-growth-and-engineering-after-a-spin-chain-quench
#7
Ioannis Pitsios, Leonardo Banchi, Adil S Rab, Marco Bentivegna, Debora Caprara, Andrea Crespi, Nicolò Spagnolo, Sougato Bose, Paolo Mataloni, Roberto Osellame, Fabio Sciarrino
The time evolution of quantum many-body systems is one of the most important processes for benchmarking quantum simulators. The most curious feature of such dynamics is the growth of quantum entanglement to an amount proportional to the system size (volume law) even when interactions are local. This phenomenon has great ramifications for fundamental aspects, while its optimisation clearly has an impact on technology (e.g., for on-chip quantum networking). Here we use an integrated photonic chip with a circuit-based approach to simulate the dynamics of a spin chain and maximise the entanglement generation...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29145252/identifications-of-potential-therapeutic-targets-and-drugs-in-angiotensin-ii-induced-hypertension
#8
Xiaoli Wu, Ruihua Fan
This study aimed to identify the underlying therapeutic targets of angiotensin II (AngII)-induced hypertension, and screen the related drugs.The gene expression profiles of GSE93579 and GSE75815 were used to identify differentially expressed genes (DEGs) between AngII-induced hypertension and control samples based on meta-analysis. These DEGs were analyzed using Gene-Ontology (GO) function and pathway enrichment methods. Subsequently, the weighed gene coexpression network analysis (WGCNA)-based meta-analysis was applied to determine transcriptional signature with DEGs...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29143332/accurate-prediction-and-elucidation-of-drug-resistance-based-on-the-robust-and-reproducible-chemoresponse-communities
#9
Enyu Dai, Jing Wang, Feng Yang, Xu Zhou, Qian Song, Shuyuan Wang, Xuexin Yu, Dianming Liu, Qian Yang, Hong Dai, Wei Jiang, Hong Ling
Selecting the available treatment for each cancer patient from genomic context is a core goal of precision medicine, but innovative approaches with mechanism interpretation and improved performance are still highly needed. Through utilizing in vitro chemotherapy response data coupled with gene and miRNA expression profiles, we applied a network-based approach that identified markers not as individual molecules but as functional groups extracted from the integrated transcription factor and miRNA regulatory network...
November 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29143250/cliques-and-cavities-in-the-human-connectome
#10
Ann E Sizemore, Chad Giusti, Ari Kahn, Jean M Vettel, Richard F Betzel, Danielle S Bassett
Encoding brain regions and their connections as a network of nodes and edges captures many of the possible paths along which information can be transmitted as humans process and perform complex behaviors. Because cognitive processes involve large, distributed networks of brain areas, principled examinations of multi-node routes within larger connection patterns can offer fundamental insights into the complexities of brain function. Here, we investigate both densely connected groups of nodes that could perform local computations as well as larger patterns of interactions that would allow for parallel processing...
November 16, 2017: Journal of Computational Neuroscience
https://www.readbyqxmd.com/read/29143172/identification-of-key-genes-and-construction-of-microrna-mrna-regulatory-networks-in-bladder-smooth-muscle-cell-response-to-mechanical-stimuli-using-microarray-expression-profiles-and-bioinformatics-analysis
#11
Liao Peng, De-Yi Luo
PURPOSE: To identify keys genes and elucidate miRNA-mRNA regulatory networks in Bladder smooth muscle cell (BSMC) response to mechanical stimuli. METHODS: Human BSMCs, seeded on a silicone membrane, were subjected to mechanical stretch or without stretch. Microarray was used to analyze the differential expression of mRNAs and miRNAs between human BSMCs under mechanical stretch and control static control group. Differentially expressed genes(DEGs) and miRNAs (DEMs) in these two groups were identified...
November 15, 2017: World Journal of Urology
https://www.readbyqxmd.com/read/29142824/system-wide-cofactor-turnovers-can-propagate-metabolic-stability-between-pathways
#12
Y Yang, Y H Guan, J Villadsen
Metabolic homeostasis, or low-level metabolic steady state, has long been taken for granted in metabolic engineering, and research priority has always been given to understand metabolic flux control and regulation of the reaction network. In the past, this has not caused concerns because the metabolic networks studied were invariably associated with living cells. Nowadays, there are needs to reconstruct metabolic networks, and so metabolic homeostasis cannot be taken for granted. For metabolic steady state, enzyme feedback control has been known to explain why metabolites in metabolic pathways can avoid accumulation...
December 2016: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29141044/high-dimensional-linear-state-space-models-for-dynamic-microbial-interaction-networks
#13
Iris Chen, Yogeshwar D Kelkar, Yu Gu, Jie Zhou, Xing Qiu, Hulin Wu
Medical researchers are increasingly interested in knowing how the complex community of micro-organisms living on human body impacts human health. Key to this is to understand how the microbes interact with each other. Time-course studies on human microbiome indicate that the composition of microbiome changes over short time periods, primarily as a consequence of synergistic and antagonistic interactions of the members of the microbiome with each other and with the environment. Knowledge of the abundance of bacteria-which are the predominant members of the human microbiome-in such time-course studies along with appropriate mathematical models will allow us to identify key dynamic interaction networks within the microbiome...
2017: PloS One
https://www.readbyqxmd.com/read/29140525/rsnpbase-3-0-an-updated-database-of-snp-related-regulatory-elements-element-gene-pairs-and-snp-based-gene-regulatory-networks
#14
Liyuan Guo, Jing Wang
Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29140500/the-persuasion-network-is-modulated-by-drug-use-risk-and-predicts-anti-drug-message-effectiveness
#15
Richard Huskey, J Michael Mangus, Benjamin O Turner, René Weber
While a persuasion network has been proposed, little is known about how network connections between brain regions contribute to attitude change. Two possible mechanisms have been advanced. One hypothesis predicts that attitude change results from increased connectivity between structures implicated in affective and executive processing in response to increases in argument strength. A second functional perspective suggests that highly arousing messages reduce connectivity between structures implicated in the encoding of sensory information, which disrupts message processing and thereby inhibits attitude change...
November 11, 2017: Social Cognitive and Affective Neuroscience
https://www.readbyqxmd.com/read/29140278/development-of-gallic-acid-modified-hydrogels-using-interpenetrating-chitosan-network-and-evaluation-of-their-antioxidant-activity
#16
Byungman Kang, Temmy Pegarro Vales, Byoung-Ki Cho, Jong-Ki Kim, Ho-Joong Kim
In this work, antioxidant hydrogels were prepared by the construction of an interpenetrating chitosan network and functionalization with gallic acid. The poly(2-hydroxyethyl methacrylate) p(HEMA)-based hydrogels were first synthesized and subsequently surface-modified with an interpenetrating polymer network (IPN) structure prepared with methacrylamide chitosan via free radical polymerization. The resulting chitosan-IPN hydrogels were surface-functionalized with gallic acid through an amide coupling reaction, which afforded the antioxidant hydrogels...
November 15, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29139200/allosteric-mechanism-of-quinoline-inhibitors-for-hiv-rt-associated-rnase-with-md-simulation-and-dynamics-fluctuation-network
#17
Yi Cai, Hao Liu, Haifeng Chen
The human immunodeficiency virus (HIV) is a retrovirus which infects T lymphocyte of human body and causes Immunodeficiency. Reverse transcriptase inhibitors (RTIs) can inhibit some functions of RT, preventing virus synthesis (double-stranded DNA), so that HIV virus replication can be reduced. Experimental results indicate a series of benzimidazole-based inhibitors which target HIV RT-associate RNase to inhibit the reverse transcription of HIV virus. However, the allosteric mechanism is still unclear. Here, molecular dynamics simulations and dynamics fluctuation network analysis were used to reveal the binding mode between the inhibitors and RT-associate RNase...
November 15, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29139094/investigating-the-therapeutic-potential-and-mechanism-of-curcumin-in-breast-cancer-based-on-rna-sequencing-and-bioinformatics-analysis
#18
Rong Wang, Jinbin Li, Yulan Zhao, Yapeng Li, Ling Yin
BACKGROUND: Breast cancer is a prevalent cancer in female. This study aims to investigate the therapeutic potential and mechanism of curcumin in breast cancer. METHODS: After cultivation, human breast cancer cells (MCF-7 cells) were treated with 0.1% (v/v) 15 µmol/ml curcumin-dimethylsulfoxide solution and 0.1% (v/v) dimethylsulfoxide, respectively, at 37 °C and 5% CO2 for 48 h. Total RNA was extracted, cDNA library was constructed, and cDNAs were amplified and sequenced...
November 14, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/29139049/feedforward-architectures-driven-by-inhibitory-interactions
#19
Yazan N Billeh, Michael T Schaub
Directed information transmission is paramount for many social, physical, and biological systems. For neural systems, scientists have studied this problem under the paradigm of feedforward networks for decades. In most models of feedforward networks, activity is exclusively driven by excitatory neurons and the wiring patterns between them, while inhibitory neurons play only a stabilizing role for the network dynamics. Motivated by recent experimental discoveries of hippocampal circuitry, cortical circuitry, and the diversity of inhibitory neurons throughout the brain, here we illustrate that one can construct such networks even if the connectivity between the excitatory units in the system remains random...
November 14, 2017: Journal of Computational Neuroscience
https://www.readbyqxmd.com/read/29138860/an-rna%C3%A2-sequencing-study-identifies-candidate-genes-for-angiotensin-ii%C3%A2-induced-cardiac-remodeling
#20
Jin Shu, Zhanwen Liu, Li Jin, Haiya Wang
The present study aimed to reveal the underlying mechanism of angiotensin II (AngII)‑induced cardiac remodeling and to identify potential therapeutic targets for prevention. Rat cardiac fibroblasts (CFs) were cultured with 10 nM AngII for 12 h, and CFs without AngII were used as the control. Following RNA isolation from AngII treated and control CFs, RNA‑sequencing was performed to detect gene expression levels. Differentially‑expressed genes (DEGs) were identified using the linear models for microarray analysis package in R software, and their functions and pathways were examined via enrichment analysis...
November 14, 2017: Molecular Medicine Reports
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