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https://www.readbyqxmd.com/read/28934431/genetic-profiling-and-comorbidities-of-zika-infection
#1
Mohammad Ali Moni, Pietro Lio'
Background: The difficulty in distinguishing infection by Zika virus (ZIKV) from other flaviviruses is a global health concern, particularly given the high risk of neurologic complications (including Guillain-Barré syndrome [GBS]) with ZIKV infection. Methods: We developed quantitative frameworks to compare and explore infectome, diseasome, and comorbidity of ZIKV infections. We analyzed gene expression microarray and RNA-Seq data from ZIKV, West Nile fever (WNF), chikungunya, dengue, yellow fever, Japanese encephalitis virus, GBS, and control datasets...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934196/spatiotemporal-network-coding-of-physiological-mossy-fiber-inputs-by-the-cerebellar-granular-layer
#2
Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas Close, Daqing Guo, Mario Negrello, Erik De Schutter
The granular layer, which mainly consists of granule and Golgi cells, is the first stage of the cerebellar cortex and processes spatiotemporal information transmitted by mossy fiber inputs with a wide variety of firing patterns. To study its dynamics at multiple time scales in response to inputs approximating real spatiotemporal patterns, we constructed a large-scale 3D network model of the granular layer. Patterned mossy fiber activity induces rhythmic Golgi cell activity that is synchronized by shared parallel fiber input and by gap junctions...
September 21, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28934126/a-multi-objective-partition-method-for-marine-sensor-networks-based-on-degree-of-event-correlation
#3
Dongmei Huang, Chenyixuan Xu, Danfeng Zhao, Wei Song, Qi He
Existing marine sensor networks acquire data from sea areas that are geographically divided, and store the data independently in their affiliated sea area data centers. In the case of marine events across multiple sea areas, the current network structure needs to retrieve data from multiple data centers, and thus severely affects real-time decision making. In this study, in order to provide a fast data retrieval service for a marine sensor network, we use all the marine sensors as the vertices, establish the edge based on marine events, and abstract the marine sensor network as a graph...
September 21, 2017: Sensors
https://www.readbyqxmd.com/read/28933120/-explore-anti-atherosclerotic-mechanism-of-component-compatibility-of-danshen-and-shanzha-based-on-network-pharmacology-and-cell-level
#4
Jian-Yong Zhang, Lan Wang, Ri-Xin Liang, Bin Yang
To explore the anti-atherosclerotic mechanism of active component compatibility of Danshen and Shanzha (SC121) based on network pharmacology and in vitro research validation with cell model. On one hand, according to the chemical structures and pharmacological activities of the compounds reported in Danshen and Shanzha, 5 compounds, i.e., salvianolic acid B, tanshinone ⅡA, tanshinol, epicatechin and procyanidin B2 were chosen and used for network pharmacology analysis. Then the TCMSP(http://lsp.nwsuaf.edu...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932904/a-computational-method-using-the-random-walk-with-restart-algorithm-for-identifying-novel-epigenetic-factors
#5
JiaRui Li, Lei Chen, ShaoPeng Wang, YuHang Zhang, XiangYin Kong, Tao Huang, Yu-Dong Cai
Epigenetic regulation has long been recognized as a significant factor in various biological processes, such as development, transcriptional regulation, spermatogenesis, and chromosome stabilization. Epigenetic alterations lead to many human diseases, including cancer, depression, autism, and immune system defects. Although efforts have been made to identify epigenetic regulators, it remains a challenge to systematically uncover all the components of the epigenetic regulation in the genome level using experimental approaches...
September 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28931970/toward-a-versatile-toolbox-for-cucurbit-n-uril-based-supramolecular-hydrogel-networks-through-in-situ-polymerization
#6
Ji Liu, Cindy Soo Yun Tan, Yang Lan, Oren A Scherman
The success of exploiting cucurbit[n]uril (CB[n])-based molecular recognition in self-assembled systems has sparked a tremendous interest in polymer and materials chemistry. In this study, polymerization in the presence of host-guest complexes is applied as a modular synthetic approach toward a diverse set of CB[8]-based supramolecular hydrogels with desirable properties, such as mechanical strength, toughness, energy dissipation, self-healing, and shear-thinning. A range of vinyl monomers, including acrylamide-, acrylate-, and imidazolium-based hydrophilic monomers, could be easily incorporated as the polymer backbones, leading to a library of CB[8] hydrogel networks...
September 15, 2017: Journal of Polymer Science. Part A, Polymer Chemistry
https://www.readbyqxmd.com/read/28931951/screening-of-mirna-profiles-and-construction-of-regulation-networks-in-early-and-late-lactation-of-dairy-goat-mammary-glands
#7
Zhibin Ji, Zhaohua Liu, Tianle Chao, Lei Hou, Rui Fan, Rongyan He, Guizhi Wang, Jianmin Wang
In recent years, studies related to the expression profiles of miRNAs in the dairy goat mammary gland were performed, but regulatory mechanisms in the physiological environment and the dynamic homeostasis of mammary gland development and lactation are not clear. In the present study, sequencing data analysis of early and late lactation uncovered a total of 1,487 unique miRNAs, including 45 novel miRNA candidates and 1,442 known and conserved miRNAs, of which 758 miRNAs were co-expressed and 378 differentially expressed with P < 0...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931825/disrupted-topological-organization-of-structural-brain-networks-in-childhood-absence-epilepsy
#8
Wenchao Qiu, Chuanyong Yu, Yuan Gao, Ailiang Miao, Lu Tang, Shuyang Huang, Wenwen Jiang, Jintao Sun, Jing Xiang, Xiaoshan Wang
Childhood absence epilepsy (CAE) is the most common paediatric epilepsy syndrome and is characterized by frequent and transient impairment of consciousness. In this study, we explored structural brain network alterations in CAE and their association with clinical characteristics. A whole-brain structural network was constructed for each participant based on diffusion-weighted MRI and probabilistic tractography. The topological metrics were then evaluated. For the first time, we uncovered modular topology in CAE patients that was similar to healthy controls...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931644/ufm1-founder-mutation-in-the-roma-population-causes-recessive-variant-of-h-abc
#9
Eline M C Hamilton, Enrico Bertini, Luba Kalaydjieva, Bharti Morar, Dana Dojčáková, Judy Liu, Adeline Vanderver, Julian Curiel, Claudia M Persoon, Daria Diodato, Lorenzo Pinelli, Nathalie L van der Meij, Barbara Plecko, Susan Blaser, Nicole I Wolf, Quinten Waisfisz, Truus E M Abbink, Marjo S van der Knaap
OBJECTIVE: To identify the gene defect in patients with hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC) who are negative for TUBB4A mutations. METHODS: We performed homozygosity mapping and whole exome sequencing (WES) to detect the disease-causing variant. We used a Taqman assay for population screening. We developed a luciferase reporter construct to investigate the effect of the promoter mutation on expression. RESULTS: Sixteen patients from 14 families from different countries fulfilling the MRI criteria for H-ABC exhibited a similar, severe clinical phenotype, including lack of development and a severe epileptic encephalopathy...
September 20, 2017: Neurology
https://www.readbyqxmd.com/read/28931422/pibas-fedsparql-a-web-based-platform-for-integration-and-exploration-of-bioinformatics-datasets
#10
Marija Djokic-Petrovic, Vladimir Cvjetkovic, Jeremy Yang, Marko Zivanovic, David J Wild
BACKGROUND: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources...
September 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28931302/learning-metabolic-brain-networks-in-mci-and-ad-by-robustness-and-leave-one-out-analysis-an-fdg-pet-study
#11
Zhijun Yao, Bin Hu, Xuejiao Chen, Yuanwei Xie, Jürg Gutknecht, Dennis Majoe
This study attempted to better understand the properties associated with the metabolic brain network in mild cognitive impairment (MCI) and Alzheimer's disease (AD). Graph theory was employed to investigate the topological organization of metabolic brain network among 86 patients with MCI, 89 patients with AD, and 97 normal controls (NCs) using 18F fluoro-deoxy-glucose positron emission tomography (FDG-PET) data. The whole brain was divided into 82 areas by Brodmann atlas to construct networks. We found that MCI and AD showed a loss of small-world properties and topological aberrations, and MCI showed an intermediate measurement between NC and AD...
January 1, 2017: American Journal of Alzheimer's Disease and Other Dementias
https://www.readbyqxmd.com/read/28930970/screening-of-critical-genes-and-micrornas-in-blood-samples-of-patients-with-ruptured-intracranial-aneurysms-by-bioinformatic-analysis-of-gene-expression-data
#12
Lijuan Bo, Bo Wei, Zhanfeng Wang, Daliang Kong, Zheng Gao, Zhuang Miao
BACKGROUND This study aimed to identify more potential genes and miRNAs associated with the pathogenesis of intracranial aneurysms (IAs). MATERIAL AND METHODS The dataset of GSE36791 (accession number) was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened for in the blood samples from patients with ruptured IAs and controls, followed by functional and pathway enrichment analyses. In addition, gene co-expression network was constructed and significant modules were extracted from the network by WGCNA R package...
September 20, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28928808/identification-of-novel-methylated-targets-in-colorectal-cancer-by-microarray-analysis-and-construction-of-co-expression-network
#13
Dongsheng Li, Jialin Guo, Song Wang, Liangchen Zhu, Zugang Shen
The present study was conducted to investigate novel methylated targets in colorectal cancer (CRC). The mRNA expression profiles of GSE32323 in 17 cancer and non-cancerous tissues from CRC patients, as well as expression profiles of 5 CRC cell lines prior and subsequent to 5-aza-2'-deoxycytidine (5-aza-dC) treatment, were obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in 5 CRC cell lines prior and subsequent to 5-aza-dC treatment were combined with the CRC-specific gene expression profiling array data...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28928718/analysing-microbial-community-composition-through-amplicon-sequencing-from-sampling-to-hypothesis-testing
#14
REVIEW
Luisa W Hugerth, Anders F Andersson
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28928370/recyclable-polydimethylsiloxane-network-crosslinked-by-dynamic-transesterification-reaction
#15
Huan Zhang, Chao Cai, Wenxing Liu, Dongdong Li, Jiawei Zhang, Ning Zhao, Jian Xu
This article reports preparation of a crosslinked polydimethylsiloxane (PDMS) network via dynamic transesterification reaction between PDMS-diglycidyl ether and pripol 1017 with Zn(OAc)2 as the catalyst. The thermal dynamic nature of the network was investigated by the creep-recovery and stress-relaxation tests. The synthesized PDMS elastomer showed excellent solvent resistance even under high temperature, and could be reprocessed by hot pressing at 180 °C with the mechanical properties maintained after 10 cycles...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928112/influenzanet-citizens-among-10-countries-collaborating-to-monitor-influenza-in-europe
#16
Carl E Koppeschaar, Vittoria Colizza, Caroline Guerrisi, Clément Turbelin, Jim Duggan, W John Edmunds, Charlotte Kjelsø, Ricardo Mexia, Yamir Moreno, Sandro Meloni, Daniela Paolotti, Daniela Perrotta, Edward van Straten, Ana O Franco
BACKGROUND: The wide availability of the Internet and the growth of digital communication technologies have become an important tool for epidemiological studies and health surveillance. Influenzanet is a participatory surveillance system monitoring the incidence of influenza-like illness (ILI) in Europe since 2003. It is based on data provided by volunteers who self-report their symptoms via the Internet throughout the influenza season and currently involves 10 countries. OBJECTIVE: In this paper, we describe the Influenzanet system and provide an overview of results from several analyses that have been performed with the collected data, which include participant representativeness analyses, data validation (comparing ILI incidence rates between Influenzanet and sentinel medical practice networks), identification of ILI risk factors, and influenza vaccine effectiveness (VE) studies previously published...
September 19, 2017: JMIR Public Health and Surveillance
https://www.readbyqxmd.com/read/28927989/identification-of-susceptible-genes-for-complex-chronic-diseases-based-on-disease-risk-functional-snps-and-interaction-networks
#17
Wan Li, Lina Zhu, Hao Huang, Yuehan He, Junjie Lv, Weimin Li, Lina Chen, Weiming He
Complex chronic diseases are caused by the effects of genetic and environmental factors. Single nucleotide polymorphisms (SNPs), one common type of genetic variations, played vital roles in diseases. We hypothesized that disease risk functional SNPs in coding regions and protein interaction network modules were more likely to contribute to the identification of disease susceptible genes for complex chronic diseases. This could help to further reveal the pathogenesis of complex chronic diseases. Disease risk SNPs were first recognized from public SNP data for coronary heart disease (CHD), hypertension (HT) and type 2 diabetes (T2D)...
September 16, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28927418/a-systematic-review-and-integrative-approach-to-decode-the-common-molecular-link-between-levodopa-response-and-parkinson-s-disease
#18
Debleena Guin, Manish Kumar Mishra, Puneet Talwar, Chitra Rawat, Suman S Kushwaha, Shrikant Kukreti, Ritushree Kukreti
BACKGROUND: PD is a progressive neurodegenerative disorder commonly treated by levodopa. The findings from genetic studies on adverse effects (ADRs) and levodopa efficacy are mostly inconclusive. Here, we aim to identify predictive genetic biomarkers for levodopa response (LR) and determine common molecular link with disease susceptibility. A systematic review for LR was conducted for ADR, and drug efficacy, independently. All included articles were assessed for methodological quality on 14 parameters...
September 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28927082/identification-of-target-gene-of-venous-thromboembolism-in-patients-with-lymphoma-via-microarray-analysis
#19
Pengfei Liu, Wenhua Jiang, Huilai Zhang
Patients with lymphoma are at high risk of developing venous thromboembolism (VTE). The purpose of the present study was to identify the target gene associated with VTE for patients with lymphoma. Microarray data was downloaded from the gene expression omnibus database (GSE17078), which comprised the control group, 27 normal blood outgrowth endothelial cell (BOEC) samples, and the case group, 3 BOEC samples of venous thrombosis with protein C deficiency. Differentially expressed genes (DEGs) were identified by the Limma package of R...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28926723/porous-wo3-graphene-polyester-textile-electrode-materials-with-enhanced-electrochemical-performance-for-flexible-solid-state-supercapacitors
#20
Li-Na Jin, Ping Liu, Chun Jin, Jia-Nan Zhang, Shao-Wei Bian
In this work, a flexible and porous WO3/grapheme/polyester (WO3/G/PT) textile electrode was successfully prepared by in situ growing WO3 on the fiber surface inside G/PT composite fabrics. The unique electrode structure facilitates to enhance the energy storage performance because the 3D conductive network constructed by the G/PT increase the electron transportation rate, nanotructured WO3 exposed enhanced electrochemically active surface area and the hierarchically porous structure improved the electrolyte ion diffusion rate...
September 1, 2017: Journal of Colloid and Interface Science
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