Base de dados : MEDLINE
Pesquisa : L01.224 [Categoria DeCS]
Referências encontradas : 1068 [refinar]
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  1 / 1068 MEDLINE  
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[PMID]:28453669
[Au] Autor:Hanslovsky P; Bogovic JA; Saalfeld S
[Ad] Endereço:HHMI Janelia Research Campus, Ashburn, VA 20147, USA.
[Ti] Título:Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.
[So] Source:Bioinformatics;33(9):1379-1386, 2017 05 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Motivation: Serial section microscopy is an established method for detailed anatomy reconstruction of biological specimen. During the last decade, high resolution electron microscopy (EM) of serial sections has become the de-facto standard for reconstruction of neural connectivity at ever increasing scales (EM connectomics). In serial section microscopy, the axial dimension of the volume is sampled by physically removing thin sections from the embedded specimen and subsequently imaging either the block-face or the section series. This process has limited precision leading to inhomogeneous non-planar sampling of the axial dimension of the volume which, in turn, results in distorted image volumes. This includes that section series may be collected and imaged in unknown order. Results: We developed methods to identify and correct these distortions through image-based signal analysis without any additional physical apparatus or measurements. We demonstrate the efficacy of our methods in proof of principle experiments and application to real world problems. Availability and Implementation: We made our work available as libraries for the ImageJ distribution Fiji and for deployment in a high performance parallel computing environment. Our sources are open and available at http://github.com/saalfeldlab/section-sort, http://github.com/saalfeldlab/z-spacing and http://github.com/saalfeldlab/z-spacing-spark. Contact: saalfelds@janelia.hhmi.org. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Algoritmos
Metodologias Computacionais
Interpretação de Imagem Assistida por Computador/métodos
Microscopia Eletrônica/métodos
[Mh] Termos MeSH secundário: Animais
Sistema Nervoso Central/anatomia & histologia
Drosophila melanogaster/anatomia & histologia
Microtomia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[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:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw794


  2 / 1068 MEDLINE  
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[PMID]:29352322
[Au] Autor:Mohr C; Friedrich A; Wojnar D; Kenar E; Polatkan AC; Codrea MC; Czemmel S; Kohlbacher O; Nahnsen S
[Ad] Endereço:Applied Bioinformatics, Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
[Ti] Título:qPortal: A platform for data-driven biomedical research.
[So] Source:PLoS One;13(1):e0191603, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software's strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on high-performance computing systems via coupling of workflow management systems. Integration of project and data management as well as workflow resources in one place present clear advantages over existing solutions.
[Mh] Termos MeSH primário: Pesquisa Biomédica
Metodologias Computacionais
Software
[Mh] Termos MeSH secundário: Pesquisa Biomédica/estatística & dados numéricos
Biologia Computacional/métodos
Biologia Computacional/estatística & dados numéricos
Sistemas de Gerenciamento de Base de Dados/estatística & dados numéricos
Bases de Dados Factuais/estatística & dados numéricos
Bases de Dados Genéticas/estatística & dados numéricos
Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos
Seres Humanos
Internet
Interface Usuário-Computador
Fluxo de Trabalho
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180121
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191603


  3 / 1068 MEDLINE  
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[PMID]:29293565
[Au] Autor:Schwartz M; Dixon PC
[Ad] Endereço:Digital Human Research Center, Advanced Institutes of Convergence Technology, Seoul National University, Suwon, South Korea.
[Ti] Título:The effect of subject measurement error on joint kinematics in the conventional gait model: Insights from the open-source pyCGM tool using high performance computing methods.
[So] Source:PLoS One;13(1):e0189984, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The conventional gait model (CGM) is a widely used biomechanical model which has been validated over many years. The CGM relies on retro-reflective markers placed along anatomical landmarks, a static calibration pose, and subject measurements as inputs for joint angle calculations. While past literature has shown the possible errors caused by improper marker placement, studies on the effects of inaccurate subject measurements are lacking. Moreover, as many laboratories rely on the commercial version of the CGM, released as the Plug-in Gait (Vicon Motion Systems Ltd, Oxford, UK), integrating improvements into the CGM code is not easily accomplished. This paper introduces a Python implementation for the CGM, referred to as pyCGM, which is an open-source, easily modifiable, cross platform, and high performance computational implementation. The aims of pyCGM are to (1) reproduce joint kinematic outputs from the Vicon CGM and (2) be implemented in a parallel approach to allow integration on a high performance computer. The aims of this paper are to (1) demonstrate that pyCGM can systematically and efficiently examine the effect of subject measurements on joint angles and (2) be updated to include new calculation methods suggested in the literature. The results show that the calculated joint angles from pyCGM agree with Vicon CGM outputs, with a maximum lower body joint angle difference of less than 10-5 degrees. Through the hierarchical system, the ankle joint is the most vulnerable to subject measurement error. Leg length has the greatest effect on all joints as a percentage of measurement error. When compared to the errors previously found through inter-laboratory measurements, the impact of subject measurements is minimal, and researchers should rather focus on marker placement. Finally, we showed that code modifications can be performed to include improved hip, knee, and ankle joint centre estimations suggested in the existing literature. The pyCGM code is provided in open source format and available at https://github.com/cadop/pyCGM.
[Mh] Termos MeSH primário: Metodologias Computacionais
Marcha
Modelos Biológicos
[Mh] Termos MeSH secundário: Articulação do Tornozelo/fisiologia
Fenômenos Biomecânicos
Articulação do Quadril/fisiologia
Seres Humanos
Articulação do Joelho/fisiologia
Amplitude de Movimento Articular
[Pt] Tipo de publicação:JOURNAL ARTICLE; VALIDATION STUDIES
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180129
[Lr] Data última revisão:
180129
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189984


  4 / 1068 MEDLINE  
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[PMID]:28640806
[Au] Autor:Wilson G; Bryan J; Cranston K; Kitzes J; Nederbragt L; Teal TK
[Ad] Endereço:Software Carpentry Foundation, Austin, Texas, United States of America.
[Ti] Título:Good enough practices in scientific computing.
[So] Source:PLoS Comput Biol;13(6):e1005510, 2017 Jun.
[Is] ISSN:1553-7358
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.
[Mh] Termos MeSH primário: Segurança Computacional/normas
Metodologias Computacionais
Acurácia dos Dados
Pesquisa/normas
Ciência/normas
Software/normas
[Mh] Termos MeSH secundário: Documentação/normas
Guias como Assunto
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170818
[Lr] Data última revisão:
170818
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170623
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pcbi.1005510


  5 / 1068 MEDLINE  
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[PMID]:28423800
[Au] Autor:Ramachandran N; Mohamedally D; Taylor P
[Ad] Endereço:University College London Hospital, London.
[Ti] Título:Project PEACH at UCLH: Student Projects in Healthcare Computing.
[So] Source:Stud Health Technol Inform;235:288-292, 2017.
[Is] ISSN:0926-9630
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:A collaboration between clinicians at UCLH and the Dept of Computer Science at UCL is giving students of computer science the opportunity to undertake real healthcare computing projects as part of their education. This is enabling the creation of a significant research computing platform within the Trust, based on open source components and hosted in the cloud, while providing a large group of students with experience of the specific challenges of health IT.
[Mh] Termos MeSH primário: Metodologias Computacionais
Informática Médica/educação
[Mh] Termos MeSH secundário: Computação em Nuvem
Seres Humanos
Londres
Estudantes
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171020
[Lr] Data última revisão:
171020
[Sb] Subgrupo de revista:T
[Da] Data de entrada para processamento:170421
[St] Status:MEDLINE


  6 / 1068 MEDLINE  
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[PMID]:28340552
[Au] Autor:Chhatre VE; Emerson KJ
[Ad] Endereço:Department of Plant Biology, University of Vermont, Burlington, Vermont, USA. vchhatre@uwyo.edu.
[Ti] Título:StrAuto: automation and parallelization of STRUCTURE analysis.
[So] Source:BMC Bioinformatics;18(1):192, 2017 Mar 24.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. RESULTS: We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. CONCLUSION: StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Metodologias Computacionais
[Mh] Termos MeSH secundário: Automação
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170828
[Lr] Data última revisão:
170828
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170326
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1593-0


  7 / 1068 MEDLINE  
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[PMID]:28182275
[Au] Autor:Kusnezov D; Paragas J
[Ad] Endereço:US Department of Energy, Washington, DC, USA.
[Ti] Título:Charting a Course for Precision Oncology.
[So] Source:Clin Pharmacol Ther;101(5):593-594, 2017 May.
[Is] ISSN:1532-6535
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The fields of science have undergone dramatic reorganizations as they have come to terms with the realities of the growing complexities of their problem set, the costs, and the breadth of skills needed to make major progress. A field such as particle physics transformed from principal investigator-driven research supported by an electron synchrotron in the basement of your physics building in the 1950s, to regional centers when costs became prohibitive to refresh technology everywhere, driving larger teams of scientists to cooperate in the 1970s, to international centers where multinational teams work together to achieve progress. The 2013 Nobel Prize winning discovery of the Higgs boson would have been unlikely without such team science. Other fields such as the computational sciences are well on their way through such a transformation. Today, we see precision medicine as a field that will need to come to terms with new organizational principles in order to make major progress, including everyone from individual medical researchers to pharma. Interestingly, the Cancer Moonshot has helped move thinking in that direction for part of the community and now the initiative has been transformed into law.
[Mh] Termos MeSH primário: Oncologia/tendências
Medicina de Precisão/tendências
[Mh] Termos MeSH secundário: Metodologias Computacionais
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1704
[Cu] Atualização por classe:170425
[Lr] Data última revisão:
170425
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:170210
[St] Status:MEDLINE
[do] DOI:10.1002/cpt.654


  8 / 1068 MEDLINE  
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[PMID]:28154362
[Au] Autor:Ito Y; Takimoto H
[Ad] Endereço:Department of Clinical Medicine, Japanese Red Cross Hokkaido College of Nursing.
[Ti] Título:Development of a Digitalized Child's Checkups Information System.
[So] Source:Nihon Eiseigaku Zasshi;72(1):5-9, 2017.
[Is] ISSN:1882-6482
[Cp] País de publicação:Japan
[La] Idioma:jpn
[Ab] Resumo:In Japan, health checkups for children take place from infancy through high school and play an important role in the maintenance and control of childhood/adolescent health. The anthropometric data obtained during these checkups are kept in health centers and schools and are also recorded in a mother's maternal and child health handbook, as well as on school health cards. These data are meaningful if they are utilized well and in an appropriate manner. They are particularly useful for the prevention of obesity-related conditions in adulthood, such as metabolic syndrome and diabetes mellitus. For this purpose, we have tried to establish a scanning system with an optical character recognition (OCR) function, which links data obtained during health checkups in infancy with that obtained in schools. In this system, handwritten characters on the records are scanned and processed using OCR. However, because many of the scanned characters are not read properly, we must wait for the improvement in the performance of the OCR function. In addition, we have developed Microsoft Excel spreadsheets, on which obesity-related indices, such as body mass index and relative body weight, are calculated. These sheets also provide functions that tabulate the frequencies of obesity in specific groups. Actively using these data and digitalized systems will not only contribute towards resolving physical health problems in children, but also decrease the risk of developing lifestyle-related diseases in adulthood.
[Mh] Termos MeSH primário: Metodologias Computacionais
Sistemas de Informação em Saúde
Obesidade/prevenção & controle
Exame Físico
[Mh] Termos MeSH secundário: Adolescente
Antropometria
Índice de Massa Corporal
Peso Corporal
Criança
Pré-Escolar
Diabetes Mellitus/prevenção & controle
Feminino
Seres Humanos
Lactente
Japão
Estilo de Vida
Masculino
Síndrome Metabólica/prevenção & controle
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1703
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170204
[St] Status:MEDLINE
[do] DOI:10.1265/jjh.72.5


  9 / 1068 MEDLINE  
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[PMID]:28034955
[Au] Autor:Plumridge A; Meisburger SP; Pollack L
[Ad] Endereço:School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
[Ti] Título:Visualizing single-stranded nucleic acids in solution.
[So] Source:Nucleic Acids Res;45(9):e66, 2017 May 19.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Single-stranded nucleic acids (ssNAs) are ubiquitous in many key cellular functions. Their flexibility limits both the number of high-resolution structures available, leaving only a small number of protein-ssNA crystal structures, while forcing solution investigations to report ensemble averages. A description of the conformational distributions of ssNAs is essential to more fully characterize biologically relevant interactions. We combine small angle X-ray scattering (SAXS) with ensemble-optimization methods (EOM) to dynamically build and refine sets of ssNA structures. By constructing candidate chains in representative dinucleotide steps and refining the models against SAXS data, a broad array of structures can be obtained to match varying solution conditions and strand sequences. In addition to the distribution of large scale structural parameters, this approach reveals, for the first time, intricate details of the phosphate backbone and underlying strand conformations. Such information on unperturbed strands will critically inform a detailed understanding of an array of problems including protein-ssNA binding, RNA folding and the polymer nature of NAs. In addition, this scheme, which couples EOM selection with an iteratively refining pool to give confidence in the underlying structures, is likely extendable to the study of other flexible systems.
[Mh] Termos MeSH primário: Conformação de Ácido Nucleico
Ácidos Nucleicos/química
[Mh] Termos MeSH secundário: Metodologias Computacionais
DNA de Cadeia Simples/química
Modelos Químicos
Espalhamento a Baixo Ângulo
Soluções/química
Difração de Raios X
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Single-Stranded); 0 (Nucleic Acids); 0 (Solutions)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170829
[Lr] Data última revisão:
170829
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161231
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkw1297


  10 / 1068 MEDLINE  
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[PMID]:27806406
[Au] Autor:de Oliveira GG; Carnevale Neto F; Demarque DP; de Sousa Pereira-Junior JA; Sampaio Peixoto Filho RC; de Melo SJ; da Silva Almeida JRG; Lopes JLC; Lopes NP
[Ad] Endereço:Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
[Ti] Título:Dereplication of Flavonoid Glycoconjugates from Adenocalymma imperatoris-maximilianii by Untargeted Tandem Mass Spectrometry-Based Molecular Networking.
[So] Source:Planta Med;83(7):636-646, 2017 May.
[Is] ISSN:1439-0221
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:The interpretation of large datasets acquired using high performance liquid chromatography coupled with tandem mass spectrometry represents one of the major challenges in natural products research. Here we propose the use of molecular networking to rapid identify the known secondary metabolites from untargeted MS/MS analysis of plant extracts. The leaves, stems and roots of were extracted using different solvents according to Snyder selectivity triangle. The samples were analyzed by HPLC coupled with ion trap mass spectrometer in a collision-induced dissociation MS/MS configuration in both positive and negative electrospray ionization modes. Molecular networking simultaneously organized the spectra by cosine similarity. The chemical identification was performed based on the systematic study of the main fragmentation pathways observed for the resulting network. The untargeted tandem mass spectrometry-based molecular networking allowed for the identification of 63 metabolites, mainly mono-, di- and tri-, - and/or -glycosyl flavones. Molecular networking was capable not only to dereplicate known flavonoids, but also to point out related prenyl derivatives, described for the first time in species. The gas-phase reaction route to form the characteristic [M-H O-(30/60/90)] fragments in -glycosyl flavones was suggested as sequential sugar ring opening followed by retro-aldol elimination involving aldose-ketose isomerization. The use of molecular networking with LC-CID-MS/MS assisted the identification of various isomeric and isobaric flavonoid glycoconjugates by establishing clusters according to the fragmentation similarities. Additionally, the proposed cross-ring sugar cleavages can contribute to the identification of -glycosides by MS/MS analysis.
[Mh] Termos MeSH primário: Bignoniaceae/química
Flavonoides/química
Glicoconjugados/química
Extratos Vegetais/química
[Mh] Termos MeSH secundário: Brasil
Cromatografia Líquida de Alta Pressão
Metodologias Computacionais
Espectrometria de Massas em Tandem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Flavonoids); 0 (Glycoconjugates); 0 (Plant Extracts)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170713
[Lr] Data última revisão:
170713
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161103
[St] Status:MEDLINE
[do] DOI:10.1055/s-0042-118712



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