Base de dados : MEDLINE
Pesquisa : L01.313.500.875.500 [Categoria DeCS]
Referências encontradas : 244 [refinar]
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[PMID]:29220439
[Au] Autor:Gutiérrez-Sacristán A; Bravo À; Portero-Tresserra M; Valverde O; Armario A; Blanco-Gandía MC; Farré A; Fernández-Ibarrondo L; Fonseca F; Giraldo J; Leis A; Mané A; Mayer MA; Montagud-Romero S; Nadal R; Ortiz J; Pavon FJ; Perez EJ; Rodríguez-Arias M; Serrano A; Torrens M; Warnault V; Sanz F; Furlong LI
[Ad] Endereço:Research Group on Integrative Biomedical Informatics (GRIB), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), DCEXS, Universitat Pompeu Fabra (UPF), C/Dr. Aiguader 88, Barcelona 08003, Spain.
[Ti] Título:Text mining and expert curation to develop a database on psychiatric diseases and their genes.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL: http://www.psygenet.org. PsyGeNET corpus: http://www.psygenet.org/ds/PsyGeNET/results/psygenetCorpus.tar.
[Mh] Termos MeSH primário: Curadoria de Dados/métodos
Mineração de Dados/métodos
Bases de Dados Genéticas
Transtornos Mentais/genética
Software
[Mh] Termos MeSH secundário: Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1093/database/bax043


  2 / 244 MEDLINE  
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[PMID]:29220432
[Au] Autor:Mottin L; Pasche E; Gobeill J; Rech de Laval V; Gleizes A; Michel PA; Bairoch A; Gaudet P; Ruch P
[Ad] Endereço:Information Science Department, BiTeM Group, HES-SO/HEG Genève, 17 Rue de la Tambourine, Carouge CH-1227, Switzerland.
[Ti] Título:Triage by ranking to support the curation of protein interactions.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL: http://candy.hesge.ch/nextA5.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Curadoria de Dados/métodos
Mineração de Dados/métodos
Bases de Dados de Proteínas
Mapeamento de Interação de Proteínas/métodos
[Mh] Termos MeSH secundário: Interface Usuário-Computador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1093/database/bax040


  3 / 244 MEDLINE  
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[PMID]:29023519
[Au] Autor:Pfaff CT; Eichenberg D; Liebergesell M; König-Ries B; Wirth C
[Ad] Endereço:Department of Special Botany and Functional Biodiversity, University of Leipzig, Germany.
[Ti] Título:Essential Annotation Schema for Ecology (EASE)-A framework supporting the efficient data annotation and faceted navigation in ecology.
[So] Source:PLoS One;12(10):e0186170, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.
[Mh] Termos MeSH primário: Curadoria de Dados/métodos
Ecologia
[Mh] Termos MeSH secundário: Internet
Vocabulário Controlado
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171013
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186170


  4 / 244 MEDLINE  
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[PMID]:28910313
[Au] Autor:Horsch S; Kopczynski D; Kuthe E; Baumbach JI; Rahmann S; Rahnenführer J
[Ad] Endereço:Department of Statistics, TU Dortmund University, Dortmund, Germany.
[Ti] Título:A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations.
[So] Source:PLoS One;12(9):e0184321, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:MOTIVATION: Disease classification from molecular measurements typically requires an analysis pipeline from raw noisy measurements to final classification results. Multi capillary column-ion mobility spectrometry (MCC-IMS) is a promising technology for the detection of volatile organic compounds in the air of exhaled breath. From raw measurements, the peak regions representing the compounds have to be identified, quantified, and clustered across different experiments. Currently, several steps of this analysis process require manual intervention of human experts. Our goal is to identify a fully automatic pipeline that yields competitive disease classification results compared to an established but subjective and tedious semi-manual process. METHOD: We combine a large number of modern methods for peak detection, peak clustering, and multivariate classification into analysis pipelines for raw MCC-IMS data. We evaluate all combinations on three different real datasets in an unbiased cross-validation setting. We determine which specific algorithmic combinations lead to high AUC values in disease classifications across the different medical application scenarios. RESULTS: The best fully automated analysis process achieves even better classification results than the established manual process. The best algorithms for the three analysis steps are (i) SGLTR (Savitzky-Golay Laplace-operator filter thresholding regions) and LM (Local Maxima) for automated peak identification, (ii) EM clustering (Expectation Maximization) and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) for the clustering step and (iii) RF (Random Forest) for multivariate classification. Thus, automated methods can replace the manual steps in the analysis process to enable an unbiased high throughput use of the technology.
[Mh] Termos MeSH primário: Automação Laboratorial/métodos
Curadoria de Dados
Modelos Teóricos
Análise Espectral
[Mh] Termos MeSH secundário: Testes Respiratórios/instrumentação
Testes Respiratórios/métodos
Seres Humanos
Análise Espectral/instrumentação
Análise Espectral/métodos
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171012
[Lr] Data última revisão:
171012
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170915
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0184321


  5 / 244 MEDLINE  
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[PMID]:28710274
[Au] Autor:Broom A; Jacobi Z; Trainor K; Meiering EM
[Ad] Endereço:From the Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
[Ti] Título:Computational tools help improve protein stability but with a solubility tradeoff.
[So] Source:J Biol Chem;292(35):14349-14361, 2017 Sep 01.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Accurately predicting changes in protein stability upon amino acid substitution is a much sought after goal. Destabilizing mutations are often implicated in disease, whereas stabilizing mutations are of great value for industrial and therapeutic biotechnology. Increasing protein stability is an especially challenging task, with random substitution yielding stabilizing mutations in only ∼2% of cases. To overcome this bottleneck, computational tools that aim to predict the effect of mutations have been developed; however, achieving accuracy and consistency remains challenging. Here, we combined 11 freely available tools into a meta-predictor (meieringlab.uwaterloo.ca/stabilitypredict/). Validation against ∼600 experimental mutations indicated that our meta-predictor has improved performance over any of the individual tools. The meta-predictor was then used to recommend 10 mutations in a previously designed protein of moderate thermodynamic stability, ThreeFoil. Experimental characterization showed that four mutations increased protein stability and could be amplified through ThreeFoil's structural symmetry to yield several multiple mutants with >2-kcal/mol stabilization. By avoiding residues within functional ties, we could maintain ThreeFoil's glycan-binding capacity. Despite successfully achieving substantial stabilization, however, almost all mutations decreased protein solubility, the most common cause of protein design failure. Examination of the 600-mutation data set revealed that stabilizing mutations on the protein surface tend to increase hydrophobicity and that the individual tools favor this approach to gain stability. Thus, whereas currently available tools can increase protein stability and combining them into a meta-predictor yields enhanced reliability, improvements to the potentials/force fields underlying these tools are needed to avoid gaining protein stability at the cost of solubility.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Modelos Moleculares
Mutação Puntual
Engenharia de Proteínas
Proteínas Recombinantes/química
[Mh] Termos MeSH secundário: Algoritmos
Substituição de Aminoácidos
Curadoria de Dados
Bases de Dados de Proteínas
Ligações de Hidrogênio
Interações Hidrofóbicas e Hidrofílicas
Internet
Cinética
Aprendizado de Máquina
Conformação Proteica
Dobramento de Proteína
Estabilidade Proteica
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Reprodutibilidade dos Testes
Software
Solubilidade
Propriedades de Superfície
Termodinâmica
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; VALIDATION STUDIES
[Nm] Nome de substância:
0 (Recombinant Proteins)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170716
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M117.784165


  6 / 244 MEDLINE  
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[PMID]:28652195
[Au] Autor:Kotsampasakou E; Montanari F; Ecker GF
[Ad] Endereço:University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria.
[Ti] Título:Predicting drug-induced liver injury: The importance of data curation.
[So] Source:Toxicology;389:139-145, 2017 Aug 15.
[Is] ISSN:1879-3185
[Cp] País de publicação:Ireland
[La] Idioma:eng
[Ab] Resumo:Drug-induced liver injury (DILI) is a major issue for both patients and pharmaceutical industry due to insufficient means of prevention/prediction. In the current work we present a 2-class classification model for DILI, generated with Random Forest and 2D molecular descriptors on a dataset of 966 compounds. In addition, predicted transporter inhibition profiles were also included into the models. The initially compiled dataset of 1773 compounds was reduced via a 2-step approach to 966 compounds, resulting in a significant increase (p-value<0.05) in model performance. The models have been validated via 10-fold cross-validation and against three external test sets of 921, 341 and 96 compounds, respectively. The final model showed an accuracy of 64% (AUC 68%) for 10-fold cross-validation (average of 50 iterations) and comparable values for two test sets (AUC 59%, 71% and 66%, respectively). In the study we also examined whether the predictions of our in-house transporter inhibition models for BSEP, BCRP, P-glycoprotein, and OATP1B1 and 1B3 contributed in improvement of the DILI mode. Finally, the model was implemented with open-source 2D RDKit descriptors in order to be provided to the community as a Python script.
[Mh] Termos MeSH primário: Doença Hepática Induzida por Substâncias e Drogas/etiologia
Simulação por Computador
Curadoria de Dados
Fígado/efeitos dos fármacos
Proteínas de Membrana Transportadoras/efeitos dos fármacos
Modelos Estatísticos
Testes de Toxicidade/métodos
[Mh] Termos MeSH secundário: Algoritmos
Animais
Área Sob a Curva
Doença Hepática Induzida por Substâncias e Drogas/metabolismo
Doença Hepática Induzida por Substâncias e Drogas/patologia
Mineração de Dados
Bases de Dados Factuais
Seres Humanos
Fígado/metabolismo
Fígado/patologia
Proteínas de Membrana Transportadoras/metabolismo
Reprodutibilidade dos Testes
Medição de Risco
[Pt] Tipo de publicação:JOURNAL ARTICLE; VALIDATION STUDIES
[Nm] Nome de substância:
0 (Membrane Transport Proteins)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170911
[Lr] Data última revisão:
170911
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170628
[St] Status:MEDLINE


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[PMID]:28644838
[Au] Autor:Seidlin M; Holzman R; Knight P; Korf B; Rangel Miller V; Viskochil D; Bakker A; Children's Tumor Foundation
[Ad] Endereço:Children's Tumor Foundation, New York, United States of America.
[Ti] Título:Characterization and utilization of an international neurofibromatosis web-based, patient-entered registry: An observational study.
[So] Source:PLoS One;12(6):e0178639, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The neurofibromatoses (neurofibromatosis type 1, neurofibromatosis type 2 and schwannomatosis) are rare disorders having clinical manifestations that vary greatly from patient to patient. The rarity and variability of these disorders has made it challenging for investigators to identify sufficient numbers of patients with particular clinical characteristics or specific germline mutations for participation in interventional studies. Similarly, because the natural history of all types of neurofibromatosis (NF) is variable and unique for each individual, it is difficult to identify meaningful clinical outcome measures for potential therapeutic interventions. In 2012, the Children's Tumor Foundation created a web-based patient-entered database, the NF Registry, to inform patients of research opportunities for which they fit general eligibility criteria and enable patients to contact investigators who are seeking to enroll patients in approved trials. Registrants were recruited through CTF-affiliated NF clinics and conferences, through its website, and by word-of-mouth and social media. Following online consent, demographic information and details regarding manifestations of NF were solicited on the Registry website. Statistical analyses were performed on data from a cohort of 4680 registrants (the number of registrants as of October 9, 2015) who met diagnostic criteria for one of the 3 NF conditions. The analyses support our hypothesis that patient-reported symptom incidences in the NF Registry are congruent with published clinician-sourced data. Between April 26, 2013 and July 8, 2016, the registry has been useful to investigators in recruitment, particularly for observational trials, especially those for development of patient-reported outcomes.
[Mh] Termos MeSH primário: Internet
Neurofibromatoses
Sistema de Registros
[Mh] Termos MeSH secundário: Adolescente
Adulto
Idoso
Idoso de 80 Anos ou mais
Pesquisa Biomédica/métodos
Criança
Pré-Escolar
Ensaios Clínicos como Assunto
Confidencialidade
Curadoria de Dados
Feminino
Seres Humanos
Lactente
Internacionalidade
Masculino
Meia-Idade
Neurofibromatoses/epidemiologia
Participação do Paciente
Controle de Qualidade
Inquéritos e Questionários
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE; OBSERVATIONAL STUDY
[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.0178639


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[PMID]:28542450
[Au] Autor:Perrier L; Blondal E; Ayala AP; Dearborn D; Kenny T; Lightfoot D; Reka R; Thuna M; Trimble L; MacDonald H
[Ad] Endereço:Gerstein Science Information Centre, University of Toronto, Toronto, Ontario, Canada.
[Ti] Título:Research data management in academic institutions: A scoping review.
[So] Source:PLoS One;12(5):e0178261, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:OBJECTIVE: The purpose of this study is to describe the volume, topics, and methodological nature of the existing research literature on research data management in academic institutions. MATERIALS AND METHODS: We conducted a scoping review by searching forty literature databases encompassing a broad range of disciplines from inception to April 2016. We included all study types and data extracted on study design, discipline, data collection tools, and phase of the research data lifecycle. RESULTS: We included 301 articles plus 10 companion reports after screening 13,002 titles and abstracts and 654 full-text articles. Most articles (85%) were published from 2010 onwards and conducted within the sciences (86%). More than three-quarters of the articles (78%) reported methods that included interviews, cross-sectional, or case studies. Most articles (68%) included the Giving Access to Data phase of the UK Data Archive Research Data Lifecycle that examines activities such as sharing data. When studies were grouped into five dominant groupings (Stakeholder, Data, Library, Tool/Device, and Publication), data quality emerged as an integral element. CONCLUSION: Most studies relied on self-reports (interviews, surveys) or accounts from an observer (case studies) and we found few studies that collected empirical evidence on activities amongst data producers, particularly those examining the impact of research data management interventions. As well, fewer studies examined research data management at the early phases of research projects. The quality of all research outputs needs attention, from the application of best practices in research data management studies, to data producers depositing data in repositories for long-term use.
[Mh] Termos MeSH primário: Gestão da Informação
Serviços de Informação
Armazenamento e Recuperação da Informação
Pesquisa
Universidades
[Mh] Termos MeSH secundário: Coleta de Dados
Curadoria de Dados
Disseminação de Informação
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170918
[Lr] Data última revisão:
170918
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170526
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0178261


  9 / 244 MEDLINE  
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[PMID]:28404779
[Au] Autor:Davies TG; Rahman IA; Lautenschlager S; Cunningham JA; Asher RJ; Barrett PM; Bates KT; Bengtson S; Benson RB; Boyer DM; Braga J; Bright JA; Claessens LP; Cox PG; Dong XP; Evans AR; Falkingham PL; Friedman M; Garwood RJ; Goswami A; Hutchinson JR; Jeffery NS; Johanson Z; Lebrun R; Martínez-Pérez C; Marugán-Lobón J; O'Higgins PM; Metscher B; Orliac M; Rowe TB; Rücklin M; Sánchez-Villagra MR; Shubin NH; Smith SY; Starck JM; Stringer C; Summers AP; Sutton MD; Walsh SA; Weisbecker V; Witmer LM; Wroe S; Yin Z; Rayfield EJ; Donoghue PC
[Ad] Endereço:School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
[Ti] Título:Open data and digital morphology.
[So] Source:Proc Biol Sci;284(1852), 2017 Apr 12.
[Is] ISSN:1471-2954
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.
[Mh] Termos MeSH primário: Curadoria de Dados/normas
Conjuntos de Dados como Assunto
[Mh] Termos MeSH secundário: Disciplinas das Ciências Biológicas/estatística & dados numéricos
Reprodutibilidade dos Testes
Pesquisa/normas
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171008
[Lr] Data última revisão:
171008
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170414
[St] Status:MEDLINE


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[PMID]:28301533
[Au] Autor:Lee DJ; Stvilia B
[Ad] Endereço:University Libraries, Texas A&M University, College Station, Texas, United States of America.
[Ti] Título:Practices of research data curation in institutional repositories: A qualitative view from repository staff.
[So] Source:PLoS One;12(3):e0173987, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools.
[Mh] Termos MeSH primário: Academias e Institutos/organização & administração
Curadoria de Dados
Pesquisa
[Mh] Termos MeSH secundário: Estados Unidos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170907
[Lr] Data última revisão:
170907
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170317
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0173987



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