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network construction

Yimin Wang, Fang Ye, Chanyan Huang, Faling Xue, Yingyuan Li, Shaowei Gao, Zeting Qiu, Si Li, Qinchang Chen, Huaqiang Zhou, Yiyan Song, Wenqi Huang, Wulin Tan, Zhongxing Wang
BACKGROUND: Neuropathic pain is one of the common complications after spinal cord injury (SCI), affecting patients' life quality. The molecular mechanism for neuropathic pain after SCI is still unclear. We aimed to discover potential genes and MicroRNAs(miRNAs) related to neuropathic pain by bioinformatics method. METHODS: Microarray data of GSE69901 were obtained from Gene Expression Omnibus (GEO) database. Peripheral blood samples from patients with or without neuropathic pain after spinal cord injury (SCI) were collected...
March 15, 2018: Clinical Journal of Pain
Ying Hu, Zhonghai Fang, Yichen Yang, Ting Fan, Ju Wang
Nicotine dependence is the primary addictive stage of cigarette smoking. Although a lot of studies have been performed to explore the molecular mechanism underlying nicotine dependence, our understanding on this disorder is still far from complete. Over the past decades, an increasing number of candidate genes involved in nicotine dependence have been identified by different technical approaches, including the genetic association analysis. In this study, we performed a comprehensive collection of candidate genes reported to be genetically associated with nicotine dependence...
March 16, 2018: Journal of Biomolecular Structure & Dynamics
Loïc Peter, Marcel Tella-Amo, Dzhoshkun Ismail Shakir, George Attilakos, Ruwan Wimalasundera, Jan Deprest, Sébastien Ourselin, Tom Vercauteren
PURPOSE: The standard clinical treatment of Twin-to-Twin transfusion syndrome consists in the photo-coagulation of undesired anastomoses located on the placenta which are responsible to a blood transfer between the two twins. While being the standard of care procedure, fetoscopy suffers from a limited field-of-view of the placenta resulting in missed anastomoses. To facilitate the task of the clinician, building a global map of the placenta providing a larger overview of the vascular network is highly desired...
March 15, 2018: International Journal of Computer Assisted Radiology and Surgery
Quan Zhou, Li Hong, Jing Wang
PURPOSE: The aim of this study was to elucidate the molecular mechanisms and to identify the key genes and pathways for pelvic organ prolapse (POP) using bioinformatics analysis. METHODS: The microarray data for GSE53868 included 12 POP and 12 non-POP anterior vaginal wall samples. Differentially expressed genes (DEGs) were identified by GEO2R online tool. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the DAVID database, and a DEG-associated protein-protein interaction (PPI) network was constructed using STRING and visualized in Cytoscape...
March 15, 2018: Archives of Gynecology and Obstetrics
Jianming Luo, Yuetong Li, Jinli Xie, Lijuan Gao, Liu Liu, Shiyi Ou, Long Chen, Xichun Peng
Bacterial interactions in the biological network affect the growth of Bifidobacterium. In the present study, five habitats were constructed by changing animals, their health statuses and their diets. In each of these habitats, different networks of Bifidobacterium were outlined through correlation analysis of the 50 most dominant microbes. Thirty-eight bacterial genera directly correlated with the growth of Bifidobacterium, including 23 genera with a positive correlation and 15 genera with a negative correlation...
March 13, 2018: FEMS Microbiology Letters
Janya McCalman, Roxanne Bainbridge, Catherine Brown, Komla Tsey, Adele Clarke
Introduction: Spreading proven or promising Aboriginal health programs and implementing them in new settings can make cost-effective contributions to a range of Aboriginal Australian development, health and wellbeing, and educational outcomes. Studies have theorized the implementation of Aboriginal health programs but have not focused explicitly on the conditions that influenced their spread. This study examined the broader political, institutional, social and economic conditions that influenced negotiations to transfer, implement, adapt, and sustain one Aboriginal empowerment program-the Family Wellbeing (FWB) program-to at least 60 geographical sites across Australia over 24 years...
2018: Frontiers in Public Health
Zhong Ni, Xiting Wang, Tianchen Zhang, Linlin Li, Jianxue Li
Small cell lung cancer (SCLC) is the subtype of lung cancer with the highest degree of malignancy and the lowest degree of differentiation. The purpose of this study was to investigate the molecular mechanisms of SCLC using bioinformatics analysis, and to provide new ideas for the early diagnosis and targeted therapy of SCLC. Microarray data were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) in SCLC were compared with the normal lung samples and identified. Gene Ontology (GO) function and pathway analysis of DEGs was performed through the DAVID database...
April 2018: Experimental and Therapeutic Medicine
Alfonso Ruiz-Herrera
In this study, I explored the impact of constructing a new dispersal route between two different patches in a metapopulation. My results indicated that its success/failure on the population abundance greatly depends on the patches directly involved and negligibly on the network topology. Specifically, constructing a dispersal route is highly recommended if it connects a source to a source that is close to becoming a sink or a sink that is close to becoming a source. This biological property is the basis for understanding the influence of the network topology on the population abundance...
March 12, 2018: Theoretical Population Biology
Christoph Schran, Felix Uhl, Jörg Behler, Dominik Marx
The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the interactions. We show that this challenge can be met by using a combination of an effective pair potential for the He-He interactions and a flexible high-dimensional neural network potential (NNP) for describing the complex interaction between helium and the solute in a pairwise additive manner...
March 14, 2018: Journal of Chemical Physics
Andrew J Olsen, Priya Katyal, Jennifer S Haghpanah, Matthew B Kubilius, Ruipeng Li, Nicole L Schnabel, Sean C O'Neill, Yao Wang, Min Dai, Navjot Singh, Raymond S Tu, Jin Kim Montclare
Recombinant methods have been used to engineer artificial protein triblock polymers comprised of two different self-assembling domains (SADs) bearing one elastin (E) flanked by two cartilage oligomeric matrix protein coiled-coil (C) domains to generate CEC. To understand how the two C domains improve small molecule recognition and the mechanical integrity of CEC, we have constructed CL44AECL44A, which bears an impaired CL44A domain that is unstructured as a negative control. The CEC triblock polymer demonstrates increased small molecule binding and ideal elastic behavior for hydrogel formation...
March 15, 2018: Biomacromolecules
Akihiro Suzuki, Takashi Morie, Hakaru Tamukoh
This paper proposes a shared synapse architecture for autoencoders (AEs), and implements an AE with the proposed architecture as a digital circuit on a field-programmable gate array (FPGA). In the proposed architecture, the values of the synapse weights are shared between the synapses of an input and a hidden layer, and between the synapses of a hidden and an output layer. This architecture utilizes less of the limited resources of an FPGA than an architecture which does not share the synapse weights, and reduces the amount of synapse modules used by half...
2018: PloS One
Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
Morgan Lawley, Jessica W Wu, Victor M Navas-López, Hien Q Huynh, Matthew W Carroll, Min Chen, Pavel Medvedev, Andrew S Day, Séamus Hussey, Rotem Sigall-Boneh, Arie Levine, Eytan Wine
OBJECTIVES: Exclusive enteral nutrition (EEN) is an effective induction treatment for pediatric Crohn disease. Given the center-based variation in use and diversity in practice we constructed a survey aimed at sharing experience and strategies in administering EEN, stimulating further research, and optimizing therapy. METHODS: This survey was constructed after consultation with experts and designed to address key knowledge gaps. The survey was disseminated through the Paediatric IBD Porto Group of ESPGHAN, Canadian Children IBD Network, selective experts, and was sent twice through the PEDGI-BB...
March 14, 2018: Journal of Pediatric Gastroenterology and Nutrition
Skye N Leedahl, Alicia Sellon, Rosemary K Chapin
A variety of terms and measures have been used in the literature to denote being socially integrated, and many studies of older adults focus on only social networks or social support and often only include those living in the community. The purpose of this study was to assess multiple constructs of social integration (i.e., social networks, social capital, social support, and social engagement) for older adults in nursing homes. Data were collected from 140 older adults at 30 nursing homes in Kansas. We interviewed older adults' in-person using a survey questionnaire, and used multilevel confirmatory factor analysis to analyze the data...
March 15, 2018: Journal of Gerontological Social Work
Hong Xiao, Jian Zhou, Xing Liu
Two new cadmium bromoplumbates [CdPb2 Br2 L2 ]n (1, L = ethylene glycol) and [CdPb6 Br6 L4 ]n (2) have been solvothermally synthesized and structurally characterized. 1 contains 1-D neutral heterometallic chains [CdPb2 Br2 L2 ]n , which are further connected via weak Pb-Br bonds, resulting in a 3-D network structure. The 3-D framework of 2 is constructed by the interconnection of a 2-D neutral layer [CdPb6 Br6 L4 ]n via weak Pb-Br bonds. The [CdPb6 Br6 L4 ]n layer is based on the linkages of dimeric [Pb2 Br4 ] units and heterometallic crown [Cd(Pb4 O4 )Br2 ] clusters containing a rare eight-membered [Pb4 O4 ] ring...
March 15, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Andrew J Lawrence, Daniel J Tozer, Emmanuel A Stamatakis, Hugh S Markus
Objective: MRI measures of network integrity may be useful disease markers in cerebral small vessel disease (SVD). We compared the sensitivity and reproducibility of MRI derived structural and functional network measures in healthy controls and SVD subjects. Methods: Diffusion tractography and resting state fMRI were used to create connectivity matrices from 26 subjects with symptomatic MRI confirmed lacunar stroke and 19 controls. Matrices were constructed at multiple scales based on a multi-resolution cortical atlas and at multiple thresholds for the matrix density...
2018: NeuroImage: Clinical
Leland J Dunwoodie, William L Poehlman, Stephen P Ficklin, Frank Alexander Feltus
Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors...
February 16, 2018: Oncotarget
Yefei Jiang, Shuangge Ma, Ben-Chang Shia, Tian-Shyug Lee
In "classic" biomedical research, diseases have usually been studied individually. The pioneering human disease network (HDN) studies jointly consider a large number of diseases, analyse their interconnections, and provide a more comprehensive description of diseases. However, most of the existing HDN studies are based on molecular information and can only partially describe disease interconnections. Building on the unique Taiwan National Health Insurance Research Database (NHIRD), in this study, we construct the epidemiological HDN (eHDN), where two diseases are concluded as interconnected if their observed probability of co-occurrence deviating that expected under independence...
March 14, 2018: Scientific Reports
François Ancien, Fabrizio Pucci, Maxime Godfroid, Marianne Rooman
The classification of human genetic variants into deleterious and neutral is a challenging issue, whose complexity is rooted in the large variety of biophysical mechanisms that can be responsible for disease conditions. For non-synonymous mutations in structured proteins, one of these is the protein stability change, which can lead to loss of protein structure or function. We developed a stability-driven knowledge-based classifier that uses protein structure, artificial neural networks and solvent accessibility-dependent combinations of statistical potentials to predict whether destabilizing or stabilizing mutations are disease-causing...
March 14, 2018: Scientific Reports
Tiandong Che, Diyan Li, Long Jin, Yuhua Fu, Yingkai Liu, Pengliang Liu, Yixin Wang, Qianzi Tang, Jideng Ma, Xun Wang, Anan Jiang, Xuewei Li, Mingzhou Li
Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar...
2018: PloS One
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