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Integrated network

Ravit Malishev, Razan Abbasi, Raz Jelinek, Liraz Chai
Biofilms are aggregates of cells that form surface-associated communities. The cells in a biofilm are interconnected with an extracellular matrix, a network that is made mostly of polysaccharides, proteins and sometimes nucleic acids. Some extracellular matrix proteins form fibers, often termed functional amyloids or amyloid-like fibrils, to differentiate their constructive function from disease-related amyloid fibers. Recent studies of functional amyloid assembly have neglected their interaction with membranes, despite their native assembly in a cellular environment...
March 22, 2018: Biochemistry
Shwu-Feng Tsay, Shih-Chung Chen, Shu-Jen Lu, Li-Ting Liu
Taiwan is projected to become an aged society in 2018. In addition to establishing a comprehensive, long-term care system that is able to deal with the expected impacts of population aging, it is imperative that the government focus on improving the prevention of aging-related conditions. This article introduces the innovative preventive care policy promoted by Taiwan's Ministry of Health and Welfare and its preliminary results. Furthermore, the foundational ideas behind this policy and how it is being executed are explained...
April 2018: Hu Li za Zhi the Journal of Nursing
Suying Bao, Lilong Jia, Xueya Zhou, Zhi-Gang Zhang, Hazel Wai Lan Wu, Zhe Yu, Gordon Ng, Yanhui Fan, Dana S M Wong, Shishu Huang, Kelvin Kai Wang To, Kwok-Yung Yuen, Man Lung Yeung, You-Qiang Song
Host genetic factors play an important role in diverse host outcomes after influenza A (H7N9) infection. Studying differential responses of inbred mouse lines with distinct genetic backgrounds to influenza virus infection could substantially increase our understanding of the contributory roles of host genetic factors to disease severity. Here, we utilized an integrated approach of mRNA-seq and miRNA-seq to investigate the transcriptome expression and regulation of host genes in C57BL/6J and DBA/2J mouse strains during influenza virus infection...
March 21, 2018: Functional & Integrative Genomics
Behdad Parhizi, Mohammad Reza Daliri, Mehdi Behroozi
The present paper concentrates on the impact of visual attention task on structure of the brain functional and effective connectivity networks using coherence and Granger causality methods. Since most studies used correlation method and resting-state functional connectivity, the task-based approach was selected for this experiment to boost our knowledge of spatial and feature-based attention. In the present study, the whole brain was divided into 82 sub-regions based on Brodmann areas. The coherence and Granger causality were applied to construct functional and effective connectivity matrices...
April 2018: Cognitive Neurodynamics
Tatiana V Karpinets, Vancheswaran Gopalakrishnan, Jennifer Wargo, Andrew P Futreal, Christopher W Schadt, Jianhua Zhang
Studies of microbial communities by targeted sequencing of rRNA genes lead to recovering numerous rare low-abundance taxa with unknown biological roles. We propose to study associations of such rare organisms with their environments by a computational framework based on transformation of the data into qualitative variables. Namely, we analyze the sparse table of putative species or OTUs (operational taxonomic units) and samples generated in such studies, also known as an OTU table, by collecting statistics on co-occurrences of the species and on shared species richness across samples...
2018: Frontiers in Microbiology
Johan Tolö, Grit Taschenberger, Kristian Leite, Markus A Stahlberg, Gesche Spehlbrink, Janina Kues, Francesca Munari, Stefano Capaldi, Stefan Becker, Markus Zweckstetter, Camin Dean, Mathias Bähr, Sebastian Kügler
α-Synuclein (α-Syn) is intimately linked to the etiology of Parkinson's Disease, as mutations and even subtle increases in gene dosage result in early onset of the disease. However, how this protein causes neuronal dysfunction and neurodegeneration is incompletely understood. We thus examined a comprehensive range of physiological parameters in cultured rat primary neurons overexpressing α-Syn at levels causing a slowly progressive neurodegeneration. In contradiction to earlier reports from non-neuronal assay systems we demonstrate that α-Syn does not interfere with essential ion handling capacities, mitochondrial capability of ATP production or basic electro-physiological properties like resting membrane potential or the general ability to generate action potentials...
2018: Frontiers in Molecular Neuroscience
Shu-Han You, Szu-Chieh Chen, Chung-Min Liao
Background: It has been found that health-seeking behavior has a certain impact on influenza infection. However, behaviors with/without risk perception on the control of influenza transmission among age groups have not been well quantified. Objectives: The purpose of this study was to assess to what extent, under scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. Materials and methods: A behavior-influenza model was used to estimate the spread rate of age-specific risk perception in response to an influenza outbreak...
2018: Infection and Drug Resistance
Jacob O Brunkard, Tessa M Burch-Smith
Plastids are critical organelles in plant cells that perform diverse functions and are central to many metabolic pathways. Beyond their major roles in primary metabolism, of which their role in photosynthesis is perhaps best known, plastids contribute to the biosynthesis of phytohormones and other secondary metabolites, store critical biomolecules, and sense a range of environmental stresses. Accordingly, plastid-derived signals coordinate a host of physiological and developmental processes, often by emitting signalling molecules that regulate the expression of nuclear genes...
March 21, 2018: Essays in Biochemistry
George C diCenzo, Deelaka Wellappili, G Brian Golding, Turlough M Finan
Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT. The Sinorhizobium meliloti genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid consisting primarily of recently acquired genes. Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic genome reduction produced through the removal of the megaplasmid and/or the chromid...
March 21, 2018: G3: Genes—Genomes—Genetics
Claudia Cava, Gloria Bertoli, Antonio Colaprico, Gianluca Bontempi, Giancarlo Mauri, Isabella Castiglioni
Like other cancer diseases, prostate cancer (PC) is caused by the accumulation of genetic alterations in the cells that drives malignant growth. These alterations are revealed by gene profiling and copy number alteration (CNA) analysis. Moreover, recent evidence suggests that also microRNAs have an important role in PC development. Despite efforts to profile PC, the alterations (gene, CNA, and miRNA) and biological processes that correlate with disease development and progression remain partially elusive. Many gene signatures proposed as diagnostic or prognostic tools in cancer poorly overlap...
March 19, 2018: International Journal of Molecular Sciences
Joanna Alvarado-Uribe, Andrea Gómez-Oliva, Ari Yair Barrera-Animas, Germán Molina, Miguel Gonzalez-Mendoza, María Concepción Parra-Meroño, Antonio J Jara
Nowadays, Physical Web together with the increase in the use of mobile devices, Global Positioning System (GPS), and Social Networking Sites (SNS) have caused users to share enriched information on the Web such as their tourist experiences. Therefore, an area that has been significantly improved by using the contextual information provided by these technologies is tourism. In this way, the main goals of this work are to propose and develop an algorithm focused on the recommendation of Smart Point of Interaction (Smart POI) for a specific user according to his/her preferences and the Smart POIs' context...
March 17, 2018: Sensors
Heitor S P de Souza, Claudio Fiocchi
Despite unquestionable progress in the management of inflammatory bowel disease (IBD) and the much improved clinical results achievable today in Crohn's disease (CD) and ulcerative colitis (UC) patients, the overall therapeutic outcome remains far from optimal. The main reason of this partial success is that all current medications only block individual components of a highly complex disease process that results from the integration of multiple and incompletely identified pathogenic components. Thus, if further progress is to be achieved in IBD therapeutics and we want to move from the current success rate to nearly 100%, bold new ideas must be entertained and new approaches put into practice...
March 19, 2018: Inflammatory Bowel Diseases
Cibele Monteiro Macedo, Paula Orchiucci Miura, Dora Mariela Salcedo Barrientos, Gisele Almeida Lopes, Emiko Yoshikawa Egry
OBJECTIVE: To investigate and analyze in the scientific literature coping strategies for domestic violence against pregnant female adolescents. METHOD: This is an integrative literature review, conducted from July to August 2017 on LILACS, SciELO and PubMed, using the descriptors and the MeSH terms: confrontation, violence, adolescent, pregnant women, prenatal care. RESULT: The sample comprised 9 articles that were organized and characterized according to year, country of study and coping strategy used...
2018: Revista Brasileira de Enfermagem
Yanting Luo, Jianlin He, Xiguang Xu, Ming-An Sun, Xiaowei Wu, Xuemei Lu, Hehuang Xie
Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci and how to interpret the biological meanings of methylation variations remain largely unexplored. To fill in the research gap, we implemented a computational pipeline to analyze single-cell methylome and to perform an integrative analysis with single-cell transcriptome data...
March 2018: PLoS Computational Biology
Claire O'Callaghan, Julie M Hall, Alessandro Tomassini, Alana J Muller, Ishan C Walpola, Ahmed A Moustafa, James M Shine, Simon J G Lewis
BACKGROUND: Models of hallucinations emphasize imbalance between sensory input and top-down influences over perception, as false perceptual inference can arise when top-down predictions are afforded too much precision (certainty) relative to sensory evidence. Visual hallucinations in Parkinson's disease (PD) are associated with lower-level visual and attentional impairments, accompanied by overactivity in higher-order association brain networks. PD therefore provides an attractive framework to explore contributions of bottom-up versus top-down disturbances in hallucinations...
November 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Saori Furuta, Gang Ren, Jian-Hua Mao, Mina J Bissell
How mammalian tissues maintain their architecture and tissue-specificity is poorly understood. Previously, we documented both the indispensable role of the extracellular matrix (ECM) protein, laminin-111 (LN1), in the formation of normal breast acini, and the phenotypic reversion of cancer cells to acini-like structures in 3-dimensional (3D) gels with inhibitors of oncogenic pathways. Here, we asked how laminin (LN) proteins integrate the signaling pathways necessary for morphogenesis. We report a surprising reciprocal circuitry comprising positive players: laminin-5 (LN5), nitric oxide (NO), p53, HOXD10 and three microRNAs (miRNAs) - that are involved in the formation of mammary acini in 3D...
March 21, 2018: ELife
Abha Belorkar, Rajanikanth Vadigepalli, Limsoon Wong
BACKGROUND: Transcriptomic datasets often contain undeclared heterogeneity arising from biological variation such as diversity of disease subtypes, treatment subgroups, time-series gene expression, nested experimental conditions, as well as technical variation due to batch effects, platform differences in integrated meta-analyses, etc. However, current analysis approaches are primarily designed to handle comparisons between experimental conditions represented by homogeneous samples, thus precluding the discovery of underlying subphenotypes...
March 19, 2018: BMC Systems Biology
Sungjoon Park, Jung Min Kim, Wonho Shin, Sung Won Han, Minji Jeon, Hyun Jin Jang, Ik-Soon Jang, Jaewoo Kang
BACKGROUND: Identifying gene regulatory networks is an important task for understanding biological systems. Time-course measurement data became a valuable resource for inferring gene regulatory networks. Various methods have been presented for reconstructing the networks from time-course measurement data. However, existing methods have been validated on only a limited number of benchmark datasets, and rarely verified on real biological systems. RESULTS: We first integrated benchmark time-course gene expression datasets from previous studies and reassessed the baseline methods...
March 19, 2018: BMC Systems Biology
N Jmail, M Zaghdoud, A Hadriche, T Frikha, C Ben Amar, C Bénar
To define the neural networks responsible of an epileptic seizure, it is useful to perform advanced signal processing techniques. In this context, electrophysiological signals present three types of waves: oscillations, spikes, and a mixture of both. Recent studies show that spikes and oscillations should be separated properly in order to define the accurate neural connectivity during the pre-ictal, seizure and inter-ictal states. Retrieving oscillatory activity is a sensitive task due to the frequency overlap between oscillations and transient activities...
February 2018: Heliyon
Eva Skiöldebrand, Anna Thorfve, Ulrika Björklund, Pegah Johansson, Ruth Wickelgren, Anders Lindahl, Elisabeth Hansson
Chondrocytes are effectively involved in the pathophysiological processes of inflammation in joints. They form cellular processes in the superficial layer of the articular cartilage and form gap junction coupled syncytium to facilitate cell-to-cell communication. However, very little is known about their physiological cellular identity and communication. The aim with the present work is to evaluate the physiological behavior after stimulation with the inflammatory inducers interleukin-1β and lipopolysaccharide...
January 2018: Heliyon
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