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https://www.readbyqxmd.com/read/28100700/pbrowse-a-web-based-platform-for-real-time-collaborative-exploration-of-genomic-data
#1
Peter S Szot, Andrian Yang, Xin Wang, Chirag Parsania, Uwe Röhm, Koon Ho Wong, Joshua W K Ho
Genome browsers are widely used for individually exploring various types of genomic data. A handful of genome browsers offer limited tools for collaboration among multiple users. Here, we describe PBrowse, an integrated real-time collaborative genome browser that enables multiple users to simultaneously view and access genomic data, thereby harnessing the wisdom of the crowd. PBrowse is based on the Dalliance genome browser and has a re-designed user and data management system with novel collaborative functionalities, including real-time collaborative view, track comment and an integrated group chat feature...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28100048/unanticipated-stickiness-of-%C3%AE-pinene
#2
Hilary M Chase, Junming Ho, Mary Alice Upshur, Regan J Thomson, Victor S Batista, Franz M Geiger
Hilary M. Chase1#, Junming Ho2#, Mary Alice Upshur1, Regan J. Thomson1, Victor S. Batista3, Franz M. Geiger1* 1Department of Chemistry, Northwestern University, Evanston, IL. 60208, United States; 2 Agency for Science, Technology and Research, Institute of High Performance Computing, 1 Fusionopolis Way #16-16 Connexis North, Singapore 138632; 3Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT. 06520, United States # These authors contributed equally to this work. *corresponding author: geigerf@chem...
January 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28099803/deep-learning-to-predict-the-formation-of-quinone-species-in-drug-metabolism
#3
Tyler B Hughes, S Joshua Swamidass
Many adverse drug reactions are thought to be caused by electrophilically reactive drug metabolites that conjugate to nucleophilic sites within DNA and proteins, causing cancer or toxic immune responses. Quinone species, including quinone-imines, quinone-methides, and imine-methides, are electrophilic Michael acceptors that are of- ten highly reactive, and comprise over 40% of all known reactive metabolites. Quinone metabolites are created by cytochromes P450 and peroxidases. For example, cy- tochromes P450 oxidize acetaminophen to N-acetyl-p-benzoquinone imine, which is electrophilically reactive and covalently binds to nucleophilic sites within proteins...
January 18, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28098234/maternal-cortisol-stimulates-neurogenesis-and-affects-larval-behaviour-in-zebrafish
#4
Carol Best, Deborah M Kurrasch, Mathilakath M Vijayan
Excess glucocorticoid transferred from stressed mother to the embryo affects developing vertebrate offspring, but the underlying programming events are unclear. In this study, we tested the hypothesis that increased zygotic glucocorticoid deposition, mimicking a maternal stress scenario, modifies early brain development and larval behaviour in zebrafish (Danio rerio). Cortisol was microinjected into the yolk at one cell-stage, to mimic maternal transfer, and the larvae [96 hours post-fertilization (hpf)] displayed increased activity in light and a reduction in thigmotaxis, a behavioural model for anxiety, suggesting an increased propensity for boldness...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096861/5-8s-rrna-sequence-and-secondary-structure-in-parabronema-skrjabini-and-related-habronematidae-species
#5
Seyed Sajjad Hasheminasab
BACKGROUND: Genomic DNA was isolated from Parabronema skrjabini. rRNA region was amplified and sequenced. METHODS: The RNA secondary structure was predicted using mfold software ( http://mfold.rit.albany.edu ). The secondary structure with bulge, hairpins, helices, interior, external and multi loops was predicted for 5.8srDNA of our sequence of P. skrjabini and a sequence of P. skrjabini and two species of Habronema (H. microstoma and H. muscae) in GenBank. RNA motifs were predicted by MEME program version 4...
April 2016: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28096083/lrssl-predict-and-interpret-drug-disease-associations-based-on-data-integration-using-sparse-subspace-learning
#6
Xujun Liang, Pengfei Zhang, Lu Yan, Ying Fu, Fang Peng, Lingzhi Qu, Meiying Shao, Yongheng Chen, Zhuchu Chen
MOTIVATION: Exploring the potential curative effects of drugs is crucial for effective drug development. Previous studies have indicated that integration of multiple types of information could be conducive to discovering novel indications of drugs. However, how to efficiently identify the mechanism behind drug-disease associations while integrating data from different sources remains a challenging problem. RESULTS: In this research, we present a novel method for indication prediction of both new drugs and approved drugs...
January 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28095789/mirna-338-3p-cdk4-signaling-pathway-suppressed-hepatic-stellate-cell-activation-and-proliferation
#7
Bensong Duan, Jiangfeng Hu, Tongyangzi Zhang, Xu Luo, Yi Zhou, Shun Liu, Liang Zhu, Cheng Wu, Wenxiang Liu, Chao Chen, Hengjun Gao
BACKGROUND: Activated hepatic stellate cell (HSC) is the main fibrogenic cell type in the injured liver. miRNA plays an important role in activation and proliferation of HSC. METHODS: Our previous study examined the expression profiles of microRNAs in quiescent and activated HSC. Real-time PCR and western blot were used to detect the expression of Collagen type I (Col 1) and Alpha-Smooth Muscle Actin (α-SMA). CCK-8 and Edu assay was used to measure the proliferation rate of HSC...
January 17, 2017: BMC Gastroenterology
https://www.readbyqxmd.com/read/28093408/vcf-kit-assorted-utilities-for-the-variant-call-format
#8
Daniel E Cook, Erik C Andersen
: The variant call format (VCF) is a popular standard for storing genetic variation data. As a result, a large collection of tools has been developed that perform diverse analyses using VCF files. However, some tasks common to statistical and population geneticists have not been created yet. To streamline these types of analyses, we created novel tools that analyze or annotate VCF files and organized these tools into a command-line based utility named VCF-kit. VCF-kit adds essential utilities to process and analyze VCF files, including primer generation for variant validation, dendrogram production, genotype imputation from sequence data in linkage studies, and additional tools...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28093093/innovations-for-tomorrow-summary-of-the-2016-disaster-health-education-symposium
#9
Kelly Gulley, Kandra Strauss-Riggs, Thomas D Kirsch, Craig Goolsby
In an effort to enhance education, training, and learning in the disaster health community, the National Center for Disaster Medicine and Public Health (NCDMPH) gathered experts from around the nation in Bethesda, Maryland, on September 8, 2016, for the 2016 Disaster Health Education Symposium: Innovations for Tomorrow. This article summarizes key themes presented during the disaster health symposium including innovations in the following areas: training and education that saves lives, practice, teaching, sharing knowledge, and our communities...
January 17, 2017: Disaster Medicine and Public Health Preparedness
https://www.readbyqxmd.com/read/28090732/high-engagement-high-quality-a-guiding-framework-for-developing-empirically-informed-asynchronous-e-learning-programs-for-health-professional-educators
#10
Peter M Sinclair, Tracey Levett-Jones, Amanda Morris, Ben Carter, Paul N Bennett, Ashley Kable
E-learning involves the transfer of skills and knowledge via technology so that learners can access meaningful and authentic educational materials. While learner engagement is important, in the context of healthcare education, pedagogy must not be sacrificed for edu-tainment style instructional design. Consequently, health professional educators need to be competent in the use of current web-based educational technologies so that learners are able to access relevant and engaging e-learning materials without restriction...
January 16, 2017: Nursing & Health Sciences
https://www.readbyqxmd.com/read/28077905/biomedical-scientific-and-professional-social-networks-in-the-service-of-the-development-of-modern-scientific-publishing
#11
Izet Masic, Edin Begic
Information technologies have found their application in virtually every branch of health care. In recent years they have demonstrated their potential in the development of online library, where scientists and researchers can share their latest findings. Academia.edu, ResearchGate, Mendeley, Kudos, with the support of platform GoogleScholar, have indeed increased the visibility of scientific work of one author, and enable a much greater availability of the scientific work to the broader audience. Online libraries have allowed free access to the scientific content to the countries that could not follow the economic costs of getting access to certain scientific bases...
December 2016: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/28077821/ascending-aortic-constriction-promotes-cardiomyocyte-proliferation-in-neonatal-rats
#12
Zhenhua Wang, Sebastian Schmull, Hui Zheng, Jianggui Shan, Rongjiang Zou, Song Xue
Adult heart suffering from increased workload will undergo myocardial hypertrophy, subsequent cardiomyocyte (CM) death, and eventually heart failure. However, the effect of increasing afterload on the neonatal heart remains unknown. We performed ascending aortic constriction (AAC) in neonatal rats 8-12 hours after birth (P0, P indicates postpartum). Seven days after surgery, in vivo heart function was evaluated using cardiac ultrasonography. Haematoxylineosin and Masson staining were used to assess CM diameter and collagen deposition...
January 11, 2017: International Heart Journal
https://www.readbyqxmd.com/read/28077570/ktcnlncdb-a-first-platform-to-investigate-lncrnas-expressed-in-human-keratoconus-and-non-keratoconus-corneas
#13
Michał W Szcześniak, Michal Kabza, Justyna A Karolak, Malgorzata Rydzanicz, Dorota M Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafal Ploski, Jacek P Szaflik, Marzena Gajecka
Keratoconus (KTCN, OMIM 148300) is a degenerative eye disorder characterized by progressive stromal thinning that leads to a conical shape of the cornea, resulting in optical aberrations and even loss of visual function. The biochemical background of the disease is poorly understood, which motivated us to perform RNA-Seq experiment, aimed at better characterizing the KTCN transcriptome and identification of long non-coding RNAs (lncRNAs) that might be involved in KTCN etiology. The in silico functional studies based on predicted lncRNA:RNA base-pairings led us to recognition of a number of lncRNAs possibly regulating genes with known or plausible links to KTCN...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077567/farme-db-a-functional-antibiotic-resistance-element-database
#14
James C Wallace, Jesse A Port, Marissa N Smith, Elaine M Faustman
Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077566/duplicates-redundancies-and-inconsistencies-in-the-primary-nucleotide-databases-a-descriptive-study
#15
Qingyu Chen, Justin Zobel, Karin Verspoor
GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077405/vrprofile-gene-cluster-detection-based-profiling-of-virulence-and-antibiotic-resistance-traits-encoded-within-genome-sequences-of-pathogenic-bacteria
#16
Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28076956/sbolme-a-repository-of-sbol-parts-for-metabolic-engineering
#17
Hiroyuki Kuwahara, Xuefeng Cui, Ramzan Umarov, Raik Gruenberg, Chris J Myers, Xin Gao
The Synthetic Biology Open Language (SBOL) is a community-driven open language to promote standardization in synthetic biology. To support the use of SBOL in metabolic engineering, we developed SBOLme, the first open-access repository of SBOL 2.0-compliant biochemical parts for a wide range of metabolic engineering applications. The URL of our repository is http://www.cbrc.kaust.edu.sa/sbolme.
January 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28076851/pse-analysis-a-python-package-for-dna-rna-and-protein-peptide-sequence-analysis-based-on-pseudo-components-and-kernel-methods
#18
Bin Liu, Hao Wu, Deyuan Zhang, Xiaolong Wang, Kuo-Chen Chou
To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28074633/a-computational-interactome-for-prioritizing-genes-associated-with-complex-agronomic-traits-in-rice
#19
Shiwei Liu, Yihui Liu, Jiawei Zhao, Shitao Cai, Hongmei Qian, Kaijing Zuo, Lingxia Zhao, Lida Zhang
Rice is one of the most important staple foods for more than half of the world's population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet/) using machine-learning with structural relationship and functional information...
January 11, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28074615/a-database-of-optimized-proteomic-quantitative-methods-for-284-human-drug-disposition-related-proteins-for-applications-in-pbpk-modeling
#20
Marc Vrana, Dale Whittington, Vivek Nautiyal, Bhagwat Prasad
The aim of this study was to create an open access repository of validated LC-MS/MS (MRM) methods for quantifying 284 important proteins associated with drug absorption, distribution, metabolism and excretion (ADME). Various in silico and experimental approaches were used to select surrogate peptides and optimize instrument parameters for LC-MS/MS quantification of the selected proteins. The final methods were uploaded to an online public database (ADME QPrOmics(TM); www.qpromics.uw.edu/qpromics/assay/) which provides essential information for facile method development in triple quadrupole MS instruments...
January 11, 2017: CPT: Pharmacometrics & Systems Pharmacology
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