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[PMID]:27770368
[Au] Autor:Ilnytskyy S; Bilichak A
[Ad] Endereço:Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada, T1K 3M4. slava.ilyntskyy@uleth.ca.
[Ti] Título:Bioinformatics Analysis of Small RNA Transcriptomes: The Detailed Workflow.
[So] Source:Methods Mol Biol;1456:197-224, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Next-generation sequencing became a method of choice for the investigation of small RNA transcriptomes in plants and animals. Although a technical side of sequencing itself is becoming routine, and experimental costs are affordable, data analysis still remains a challenge, especially for researchers with limited computational experience. Here, we present a detailed description of a computational workflow designed to take raw sequencing reads as input, to obtain small RNA predictions, and to detect the differentially expressed microRNAs as a result. The exact commands and pieces of code are provided and hopefully can be adapted and used by other researchers to facilitate the study of small RNA regulation.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Perfilação da Expressão Gênica
Pequeno RNA não Traduzido/genética
Transcriptoma
[Mh] Termos MeSH secundário: Brassica/genética
Biblioteca Gênica
Genômica/métodos
MicroRNAs/genética
Controle de Qualidade
RNA Interferente Pequeno/genética
Análise de Sequência de RNA
Software
Navegador
Fluxo de Trabalho
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Small Interfering); 0 (RNA, Small Untranslated)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180112
[Lr] Data última revisão:
180112
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


  2 / 570 MEDLINE  
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[PMID]:27770366
[Au] Autor:Tsuzuki M; Watanabe Y
[Ad] Endereço:Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo, 153-8902, Japan.
[Ti] Título:Profiling New Small RNA Sequences.
[So] Source:Methods Mol Biol;1456:177-188, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Small RNAs are key molecules in RNA silencing pathways that exert the sequence-specific regulation of gene expression and chromatin modifications in many eukaryotes. In plants, endogenous small RNAs, including microRNAs (miRNAs), trans-acting short interfering RNAs (tasiRNAs), and heterochromatic siRNAs (hc-siRNAs), play an important role in switching or orchestrating biological processes during the development and at the onset of stress responses. These endogenous and exogenous small RNAs are mainly 20-24 nucleotides in length. In addition, viral genome-derived siRNAs of similar lengths are produced during viral infection, and they exhibit anti-viral defense activity in RNA silencing pathway.Here, we introduce a method to isolate and characterize small RNA molecules possibly applicable to a wide range of plant resources and tissues. After purification from total RNAs, small RNAs were subjected to Illumina sequencing analysis using compatible reagents kits. Following the sample preparation protocol, small RNAs are ligated first at the 3'- and then at the 5'-end to the respective RNA adapters followed by reverse transcription with a set of primers to produce cDNAs with Index sequences at ends. After PCR amplification, cDNAs are subjected (after gel purification) to RNA-seq analysis. This method could be applied to isolate small RNAs from different sources and characterize small RNA profiles to compare different sets of samples, e.g., wild-type and mutant plants, plants under different stress environments, and virus-infected plants because the starting RNA material is free of contaminated starch or similar material which would block further analysis.
[Mh] Termos MeSH primário: Perfilação da Expressão Gênica
Pequeno RNA não Traduzido/genética
Transcriptoma
[Mh] Termos MeSH secundário: Arabidopsis/genética
Biologia Computacional/métodos
Sequenciamento de Nucleotídeos em Larga Escala
Marchantia/genética
MicroRNAs/genética
RNA de Plantas
RNA Interferente Pequeno/genética
Pequeno RNA não Traduzido/isolamento & purificação
RNA Viral/genética
Reação em Cadeia da Polimerase Via Transcriptase Reversa
Software
Navegador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Plant); 0 (RNA, Small Interfering); 0 (RNA, Small Untranslated); 0 (RNA, Viral)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180112
[Lr] Data última revisão:
180112
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


  3 / 570 MEDLINE  
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[PMID]:27770355
[Au] Autor:Engelhorn J; Turck F
[Ad] Endereço:Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829, Köln, Germany.
[Ti] Título:Meta-analysis of Genome-Wide Chromatin Data.
[So] Source:Methods Mol Biol;1456:33-50, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Genome-wide analyses of chromatin factor-binding sites or histone modification localization generate lists of up to several thousand potential target genes. For many model organisms, large annotation databases are available to help with the characterization and classification of genomic datasets. The term meta-analysis has been coined for this type of multi-database comparison. In this chapter, we describe a workflow to perform a transcriptional and functional analysis of genome-wide target genes. Sources of transcription data and clustering tools to subdivide genes according to their expression pattern are described. For a functional analysis, we focus on the Gene Ontology (GO) vocabulary and methods to uncover over- or underrepresented functions among target genes. Genomic targets of the histone modification H3K27me3 are presented as a case study to demonstrate that meta-analysis can uncover functions that were hidden in genome-wide datasets.
[Mh] Termos MeSH primário: Cromatina/genética
Biologia Computacional/métodos
Estudo de Associação Genômica Ampla/métodos
[Mh] Termos MeSH secundário: Sítios de Ligação
Cromatina/metabolismo
Imunoprecipitação da Cromatina
Análise por Conglomerados
Proteínas de Ligação a DNA/metabolismo
Ontologia Genética
Anotação de Sequência Molecular
Software
Navegador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (DNA-Binding Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180112
[Lr] Data última revisão:
180112
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


  4 / 570 MEDLINE  
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[PMID]:28986425
[Au] Autor:Haussen DC; Doppelheuer S; Schindler K; Grossberg JA; Bouslama M; Schultz M; Perez H; Hall A; Frankel M; Nogueira RG
[Ad] Endereço:From the Grady Memorial Hospital, Emory University, Atlanta, GA.
[Ti] Título:Utilization of a Smartphone Platform for Electronic Informed Consent in Acute Stroke Trials.
[So] Source:Stroke;48(11):3156-3160, 2017 Nov.
[Is] ISSN:1524-4628
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND AND PURPOSE: The informed consent process is a major limitation for enrollment in acute stroke clinical investigations. We aim to describe the novel application of smartphone electronic informed consenting (e-Consent) in trials of cerebral thrombectomy. METHODS: The e-Consent tool consists of a secure/Health Insurance Portability and Accountability Act compliant smartphone platform based on REDCap (Research Electronic Data Capture; Vanderbilt University, TN) that uses a survey project located on a static webpage. A link to the webpage is sent via text message or email to the legally authorized representative. The e-Consent form is filled and a freehand electronic signature added in the smartphone browser; a record ID and an e-Consent Process Attestation form are automatically generated. The e-Consent application was piloted in a randomized trial comparing endovascular versus medical therapy in late presenting patients (DAWN [Clinical Mismatch in the Triage of Wake Up and Late Presenting Strokes Undergoing Neurointervention With Trevo]). Trial enrollment began in January 2015; e-Consent was approved by the local institutional review board in December 2016, and the study was stopped in February 2017. RESULTS: During the trial period, Grady Memorial Hospital performed 273 thrombectomies with 47 patients being consented and 38 patients enrolled in the DAWN trial. Of the randomized patients, 29 (76%) were transferred from outside hospitals. A total of 6 surrogates were e-Consented, with 2 patients being screen failures. Enrolled e-Consented patients (n=4) had similar age (73±14 versus 69±12 years; =0.65) and National Institutes of Health Stroke Scale (16±5 versus 16±5; =0.88) as compared with conventionally consented (n=25). Time from door-to-randomization was decreased with e-Consenting (28±9 versus 57±24 minutes; =0.002). CONCLUSIONS: e-Consenting streamlined the consenting process in a randomized trial of patients with emergent large vessel occlusion strokes.
[Mh] Termos MeSH primário: Termos de Consentimento
Registros Eletrônicos de Saúde
Internet
Smartphone
Acidente Vascular Cerebral/cirurgia
Trombectomia
Navegador
[Mh] Termos MeSH secundário: Doença Aguda
Idoso
Idoso de 80 Anos ou mais
Feminino
Seres Humanos
Masculino
Meia-Idade
[Pt] Tipo de publicação:JOURNAL ARTICLE; RANDOMIZED CONTROLLED TRIAL
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171026
[Lr] Data última revisão:
171026
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171008
[St] Status:MEDLINE
[do] DOI:10.1161/STROKEAHA.117.018380


  5 / 570 MEDLINE  
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[PMID]:28751473
[Au] Autor:Summers KM; Hume DA
[Ad] Endereço:The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom; and.
[Ti] Título:Identification of the macrophage-specific promoter signature in FANTOM5 mouse embryo developmental time course data.
[So] Source:J Leukoc Biol;102(4):1081-1092, 2017 Oct.
[Is] ISSN:1938-3673
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The FANTOM5 consortium used cap analysis of gene expression (CAGE) to analyze the time course of gene expression over development from 11 days postcoitum (dpc) to adult in 16 developing organs and the whole body of the mouse. Every tissue in the body contains a large number of resident macrophages that initially infiltrate the embryo from the yolk sac. These cells contribute to organogenesis, and their functions diversify during development as they acquire tissue-specific adaptations. In each of the FANTOM5 time courses, the expression of known macrophage-specific genes, including CSF1 receptor ( ), epidermal growth factor-like module-containing mucin-like hormone receptor-like 1 ( ), and mer receptor tyrosine kinase ( ), was readily detectable and increased with time. We reasoned that genes expressed by macrophages would be strongly correlated in their expression with these known markers and might vary between tissues. We used the network analysis tool, Miru, to extract the sets of coexpressed genes from the time course and identified a core set of coexpressed genes attributable to embryonic macrophages, including some, such as dehydrogenase/reductase 3 ( ), that may have unique functions in development. The FANTOM5 data also detected the appearance of tissue-specific macrophage-expressed genes, such as T cell Ig and mucin domain-containing 4 ( ) and V-set and Ig domain-containing 4 ( ) in liver and sialic acid-binding Ig-like lectin 5 ( ) in lung, and confirmed that macrophage content increases with time in each organ as the proliferative phases end, and tissue-specific gene-expression increases. The FANTOM5 data are available on a comprehensive browser (http://fantom.gsc.riken.jp/zenbu/), which provides a resource for the study of macrophage transcriptional regulation and roles in mouse development.
[Mh] Termos MeSH primário: Bases de Dados de Ácidos Nucleicos
Embrião de Mamíferos/embriologia
Regulação da Expressão Gênica no Desenvolvimento/fisiologia
Macrófagos/metabolismo
Especificidade de Órgãos
Regiões Promotoras Genéticas
Navegador
[Mh] Termos MeSH secundário: Animais
Camundongos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171009
[Lr] Data última revisão:
171009
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170729
[St] Status:MEDLINE
[do] DOI:10.1189/jlb.1A0417-150RR


  6 / 570 MEDLINE  
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[PMID]:28728979
[Au] Autor:Cheng X; Xiao X; Chou KC
[Ad] Endereço:Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.
[Ti] Título:pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC.
[So] Source:Gene;628:315-321, 2017 Sep 10.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions. This kind of multiplex proteins is particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called "pLoc-mVirus" by extracting the optimal GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mVirus predictor is remarkably superior to iLoc-Virus, the state-of-the-art method in predicting virus protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mVirus/, by which users can easily get their desired results without the need to go through the complicated mathematics involved.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Ontologia Genética
Proteínas Virais/metabolismo
[Mh] Termos MeSH secundário: Algoritmos
Bases de Dados de Proteínas
Espaço Intracelular
Transporte Proteico
Proteínas Virais/genética
Navegador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Viral Proteins)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171009
[Lr] Data última revisão:
171009
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170722
[St] Status:MEDLINE


  7 / 570 MEDLINE  
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[PMID]:28644833
[Au] Autor:Ferdman S; Minkov E; Bekkerman R; Gefen D
[Ad] Endereço:Department of Computer Science, University of Haifa, Haifa, Israel.
[Ti] Título:Quantifying the web browser ecosystem.
[So] Source:PLoS One;12(6):e0179281, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Contrary to the assumption that web browsers are designed to support the user, an examination of a 900,000 distinct PCs shows that web browsers comprise a complex ecosystem with millions of addons collaborating and competing with each other. It is possible for addons to "sneak in" through third party installations or to get "kicked out" by their competitors without user involvement. This study examines that ecosystem quantitatively by constructing a large-scale graph with nodes corresponding to users, addons, and words (terms) that describe addon functionality. Analyzing addon interactions at user level using the Personalized PageRank (PPR) random walk measure shows that the graph demonstrates ecological resilience. Adapting the PPR model to analyzing the browser ecosystem at the level of addon manufacturer, the study shows that some addon companies are in symbiosis and others clash with each other as shown by analyzing the behavior of 18 prominent addon manufacturers. Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market.
[Mh] Termos MeSH primário: Internet
Modelos Teóricos
Navegador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170920
[Lr] Data última revisão:
170920
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170624
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0179281


  8 / 570 MEDLINE  
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[PMID]:28531230
[Au] Autor:Tun STT; Lubell Y; Dondorp AM; Fieldman T; Tun KM; Celhay O; Chan XH; Saralamba S; White LJ
[Ad] Endereço:Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
[Ti] Título:Identifying artemisinin resistance from parasite clearance half-life data with a simple Shiny web application.
[So] Source:PLoS One;12(5):e0177840, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The emergence of artemisinin-resistant Plasmodium falciparum malaria is a major threat to malaria elimination. New tools for supporting the surveillance of artemisinin resistance are critical for current and future malaria control and elimination strategies. We have developed an open-access, user-friendly, web-based tool to analyse parasite clearance half-life data of P. falciparum infected patients after treatment with artemisinin derivatives, so that resistance to artemisinin can be identified. The tool can be accessed at bit.ly/id_artemisinin_resistance.
[Mh] Termos MeSH primário: Antimaláricos/administração & dosagem
Artemisininas/administração & dosagem
Resistência a Medicamentos
Malária Falciparum/tratamento farmacológico
[Mh] Termos MeSH secundário: Animais
Antimaláricos/uso terapêutico
Artemisininas/uso terapêutico
Bases de Dados Factuais
Meia-Vida
Seres Humanos
Publicação de Acesso Aberto
Plasmodium falciparum/efeitos dos fármacos
Navegador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antimalarials); 0 (Artemisinins)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170908
[Lr] Data última revisão:
170908
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170523
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0177840


  9 / 570 MEDLINE  
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[PMID]:28395631
[Au] Autor:Carter B; Bray L
[Ad] Endereço:Faculty of health and social care, Edge Hill University and director of the children's nursing research unit, Alder Hey Children's NHS Foundation Trust.
[Ti] Título:Developing a web-based resource for parents of young children undergoing day surgery.
[So] Source:Nurs Child Young People;29(3):25, 2017 Apr 11.
[Is] ISSN:2046-2344
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Background The shift to day case surgery makes parents more responsible for managing their child's post-operative care after discharge from hospital.
[Mh] Termos MeSH primário: Procedimentos Cirúrgicos Ambulatórios/educação
Pais/educação
Cuidados Pós-Operatórios/educação
Navegador/tendências
[Mh] Termos MeSH secundário: Criança
Pré-Escolar
Seres Humanos
Internet
Manejo da Dor/métodos
Manejo da Dor/psicologia
Pais/psicologia
Inquéritos e Questionários
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170713
[Lr] Data última revisão:
170713
[Sb] Subgrupo de revista:N
[Da] Data de entrada para processamento:170412
[St] Status:MEDLINE
[do] DOI:10.7748/ncyp.29.3.25.s23


  10 / 570 MEDLINE  
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[PMID]:28369462
[Au] Autor:Lin HH; Liao YC
[Ti] Título:drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes.
[So] Source:Gigascience;6(2):1-10, 2017 Feb 01.
[Is] ISSN:2047-217X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment. Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Células Eucarióticas/virologia
Genoma Viral
Metagenoma
Metagenômica/métodos
Software
[Mh] Termos MeSH secundário: Simulação por Computador
Bases de Dados de Ácidos Nucleicos
Conjuntos de Dados como Assunto
Reprodutibilidade dos Testes
Navegador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170629
[Lr] Data última revisão:
170629
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170404
[St] Status:MEDLINE
[do] DOI:10.1093/gigascience/gix003



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