Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

T-Cell Receptors Binding Orientation over Peptide/MHC Class I Is Driven by Long-Range Interactions.

Crystallographic data about T-Cell Receptor - peptide - major histocompatibility complex class I (TCRpMHC) interaction have revealed extremely diverse TCR binding modes triggering antigen recognition. Understanding the molecular basis that governs TCR orientation over pMHC is still a considerable challenge. We present a simplified rigid approach applied on all non-redundant TCRpMHC crystal structures available. The CHARMM force field in combination with the FACTS implicit solvation model is used to study the role of long-distance interactions between the TCR and pMHC. We demonstrate that the sum of the coulomb interactions and the electrostatic solvation energies is sufficient to identify two orientations corresponding to energetic minima at 0° and 180° from the native orientation. Interestingly, these results are shown to be robust upon small structural variations of the TCR such as changes induced by Molecular Dynamics simulations, suggesting that shape complementarity is not required to obtain a reliable signal. Accurate energy minima are also identified by confronting unbound TCR crystal structures to pMHC. Furthermore, we decompose the electrostatic energy into residue contributions to estimate their role in the overall orientation. Results show that most of the driving force leading to the formation of the complex is defined by CDR1,2/MHC interactions. This long-distance contribution appears to be independent from the binding process itself, since it is reliably identified without considering neither short-range energy terms nor CDR induced fit upon binding. Ultimately, we present an attempt to predict the TCR/pMHC binding mode for a TCR structure obtained by homology modeling. The simplicity of the approach and the absence of any fitted parameters make it also easily applicable to other types of macromolecular protein complexes.

Use of mobile devices to answer online surveys: implications for research.

BACKGROUND: There is a growing use of mobile devices to access the Internet. We examined whether participants who used a mobile device to access a brief online survey were quicker to respond to the survey but also, less likely to complete it than participants using a traditional web browser. FINDINGS: Using data from a recently completed online intervention trial, we found that participants using mobile devices were quicker to access the survey but less likely to complete it compared to participants using a traditional web browser. More concerning, mobile device users were also less likely to respond to a request to complete a six week follow-up survey compared to those using traditional web browsers. CONCLUSIONS: With roughly a third of participants using mobile devices to answer an online survey in this study, the impact of mobile device usage on survey completion rates is a concern. TRIAL REGISTRATION: ClinicalTrials.gov: NCT01521078.

Semantic web adoption: online tools for web evaluation and metadata extraction

This work briefly analyses the difficulties to adopt the Semantic Web, and in particular proposes systems to know the present level of migration to the different technologies that make up the Semantic Web. It focuses on the presentation and description of two tools, DigiDocSpider and DigiDocMetaEdit, designed with the aim of verifYing, evaluating, and promoting its implementation.

Ag Online, January 22, 2002

Monthly newsletter for the College of Agricultural for Iowa State University

Avaliação do curso de gerenciamento online na perspectiva dos egressos

RESUMO Objetivo Avaliar curso online na perspectiva do egresso e verificar a relação entre variáveis. Método Estudo quantitativo, descritivo e exploratório, aplicado aos participantes no final de três versões de um curso de atualização onlinena temática de Gerenciamento em Enfermagem. Resultados Os índices de satisfação nas três categorias elencadas, em três anos, apresentaram resultados acima de 75,0%. Os coeficientes obtidos indicaram alta consistência do questionário. Considerando o índice total, a categoria Desempenho do tutor foi a de índice mais alto. Fortes associações entre Autoavaliação e Desempenho do tutor, Autoavaliação e Programa do curso e Desempenho do tutor e Programa do curso foram identificadas. Não houve associação entre as três categorias referidas com as demais variáveis do estudo. Conclusão Os egressos demonstraram satisfação com o curso, que favoreceu a interação e a promoção do conhecimento coletivo no gerenciamento em enfermagem. Foram reconhecidos, também, aspectos que carecem de melhorias, com destaque à capacitação do tutor para mediar discussões e estimular o envolvimento do estudante ao longo do curso.

Aging and the lateralization of oscillatory activities related to external and internal motor preparation

Selection of action may rely on external guidance or be motivated internally, engaging partially distinct cerebral networks. With age, there is an increased allocation of sensorimotor processing resources, accompanied by a reduced differentiation between the two networks of action selection. The present study examines the age effects on the motor-related oscillatory patterns related to the preparation of externally and internally guided movements. Thirty-two older and 30 younger adults underwent three delayed motor tasks with S1 as preparatory and S2 as imperative cue: Full, laterality instructed by S1 (external guidance); Free, laterality freely selected (internal guidance); None, laterality instructed by S2 (no preparation). Electroencephalogram (EEG) was recorded using 64 surface electrodes. Motor-Related Amplitude Asymmetries (MRAA), indexing the lateralization of oscillatory activities, were analyzed within the S1-S2 interval in the mu (9-12 Hz) and low beta (15-20 Hz) motor-related frequency bands. Reaction times to S2 were slower in older than younger subjects, and slower in the Free than in the Full condition in older subjects only. In the Full condition, there were significant mu MRAA in both age groups, and significant low beta MRAA only in older adults. The Free condition was associated with large mu MRAA in younger adults and limited low beta MRAA in older adults. In younger subjects, the lateralization of mu activity in both Full and Free conditions indicated effective external and internal motor preparation. In older subjects, external motor preparation was associated with lateralization of low beta in addition with mu activity, compatible with an increase of motor-related resources. In contrast, absence of mu and limited low beta lateralization in internal motor preparation was concomitant with reaction time slowing and suggested less efficient cerebral processes subtending free movement selection in older adults, indicating reduced capacity for internally driven action with age.

Comércio Electrónico: Reservas Online da Agência Krioula

O trabalho que ora se apresenta, Comércio Electrónico: Reservas Online da Agência Aliança Krioula”, é um trabalho de final do curso, para obtenção de grau de Licenciatura em Tecnologias de Informação e Comunicação. O objectivo deste trabalho é a elaboração de um site de Comércio Electrónico para a agência de viagem Aliança Krioula, de forma a possibilitar as pessoas efectuarem as suas Reservas Online.Para a elaboração do mesmo, foi utilizado a ferramenta Joomla, visto que é uma ferramenta gratuita e muito poderosa, que serve para conceber sites de forma rápida e eficiente. Também o trabalho tem como principal propósito, conceptualizar alguns termos relacionados com o Comercio Electrónico. O projecto procura mostrar a importância do Comércio Electrónico nas sociedades modernas. A realização deste trabalho possibilitou a chegada de conclusões importantes sobre vários aspectos de Comércio Electrónico e Gestão de Conteúdo, mais concretamente a ferramenta Joomla que serviu de suporte para o Website.

Sistema de Inscrição para Prova de Ingresso Online

Este trabalho visa apresentar o desenvolvimento de um Sistema de Inscrição Para a Prova de Ingresso Online, dando um especial enfoque à inscrição e selecção dos candidatos para a prova de ingresso na Uni-CV. A situação actual da gestão de inscrição para prova de ingresso era efectuada manualmente, sendo que isto causa alguns constrangimentos. Considera-se que deve primar para uma gestão mais eficiente. Neste sentido, define-se como objectivo o desenvolvimento desse Sistema de Inscrição para Prova de Ingresso Online na Uni-CV. Para o efeito, analisa-se neste trabalho o sistema actual numa perspectiva de concepção de uma aplicação que atenda as necessidades específicas e reais desta Instituição. Várias abordagens foram conceptualmente discutidas num referencial teórico para elaboração do sistema, tendo sido privilegiados os conhecimentos apreendidos durante a formação académica designadamente nas disciplinas Técnicas de Programação, Base de Dados, Sistemas de Informação, Desenvolvimento de Projectos Informáticos, Desenvolvimento avançado de aplicações internet, Planeamento e gestão de projectos, Projectos e Metodologias de Desenvolvimento de Sistemas de Informação. A análise do sistema e a geração de documentação da base de dados foram realizadas com os recursos das ferramentas de desenvolvimento. Para o desenvolvimento do sistema foram utilizados as linguagens de programação PHP, HTML, UML. Para a base de dados que elegeu-se o MySQL. Fundamentou-se essa opção, pelo facto de serem tecnologias modernas e que proporcionam ao sistema uma grande fiabilidade e também porque a Instituição utiliza-se as mesmas tecnologias, o que facilita as coisas.