ProbFAST: Probabilistic Functional Analysis System Tool

Background: The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results: We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions: ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Background: High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent powerful techniques that provide global transcription profiles of different cell types through sequencing of short fragments of transcripts, denominated sequence tags. These techniques have improved our understanding about the relationships between these expression profiles and cellular phenotypes. Despite this, more reliable datasets are still necessary. In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability. This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis. Results: This methodology was applied to a public SAGE dataset. In order to compare data before and after filtering, a hierarchical clustering analysis was performed in samples from the same type of tissue, in distinct biological conditions, using these two datasets. Our results provide evidences suggesting that it is possible to find more congruous clusters after using S3T scoring system. Conclusion: These results substantiate the proposed application to generate more reliable data. This is a significant contribution for determination of global gene expression profiles. The library analysis with S3T is freely available at http://gdm.fmrp.usp.br/s3t/.S3T source code and datasets can also be downloaded from the aforementioned website.

CysView: protein classification based on cysteine pairing patterns

CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at http://research.i2r.a-star.edu.sg/CysView/.

Accuracy of store-and-forward diagnosis in leproy

Telemedicine might increase the speed of diagnosis for leprosy and reduce the development of disabilities. We compared the accuracy of diagnosis made by telemedicine with that made by in-person examination. The cases were patients with suspected leprosy at eight public health clinics in outlying areas of the city of Sao Paulo. The case history and clinical examination data, and at least two clinical images for each patient, were stored in a web-based system developed for teledermatology. After the examination in the public clinic, patients then attended a teaching hospital for an in-person examination. The benchmark was the clinical examination of two dermatologists at the university hospital. From August 2005 to April 2006, 142 suspected cases of leprosy were forwarded to the website by the doctors at the clinics. Of these, 36 cases were excluded. There was overall agreement in the diagnosis of leprosy in 74% of the 106 remaining cases. The sensitivity was 78% and the specificity was 31%. Although the specificity was low, the study suggests that telemedicine may be a useful low-cost method for obtaining second opinions in programmes to control leprosy.

Use of the web to provide learning support for a large metabolism and nutrition class

To support student learning in a large Metabolism and Nutrition class, we have introduced a web-based package, using a commercially available program, WebCT. The package was developed at a minimal cost and with limited resources. In addition to downloadable (PDF) versions of lecture Powerpoint presentations, tutorial outlines and a practical class exercise, web-based self-directed learning exercises were included to reinforce and extend lecture material in an active learning environment. The web-site also contained a variety of formative and summative assessment tasks that examined both factual recall and higher order thinking Detailed course information, timetables and a bulletin board were also readily accessible. Student usage of the site was generally high, but varied widely between individual students. Students who achieved a high overall score for the course completed on average three times as many formative assessment items and achieved a higher score for all tests than students who did poorly. Student feedback about the site was very positive with the majority of students reporting that the course material and assessment items that were available were useful to their learning. Administration of the course was also facilitated. (C) 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.

Web 2.0 and its impact on knowledge and business organizations

Today, information overload and the lack of systems that enable locating employees with the right knowledge or skills are common challenges that large organisations face. This makes knowledge workers to re-invent the wheel and have problems to retrieve information from both internal and external resources. In addition, information is dynamically changing and ownership of data is moving from corporations to the individuals. However, there is a set of web based tools that may cause a major progress in the way people collaborate and share their knowledge. This article aims to analyse the impact of ‘Web 2.0’ on organisational knowledge strategies. A comprehensive literature review was done to present the academic background followed by a review of current ‘Web 2.0’ technologies and assessment of their strengths and weaknesses. As the framework of this study is oriented to business applications, the characteristics of the involved segments and tools were reviewed from an organisational point of view. Moreover, the ‘Enterprise 2.0’ paradigm does not only imply tools but also changes the way people collaborate, the way the work is done (processes) and finally impacts on other technologies. Finally, gaps in the literature in this area are outlined.

Analysis of support for modularity in object teams based on design patterns

Dissertação de Mestrado em Engenharia Informática

Web GIS to support irrigation management: a prototype for SAGRA network, Alentejo Portugal

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

A Obra “Faça-você-mesmo” : Estética da Participação nas Artes Digitais

Doutoramento em Ciências da Comunicação - Especialidade de Comunicação e Artes

How can public administration reforms instill (or not) cooperation among the society?

Comunicação apresentada na Conferência Anual do IASIA, em Paris, a 6 de julho de 2015

Design and implementation of 3D buildings integration for a Webgl-Based Virtual Globe: a case study of Valencian Cadastre and Fide Building Mode

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Numerical methods and tangible interfaces for pollutant dispersion simulation

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia do Ambiente, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

A TV do Mundial

No último ano da primeira década do século XXI, quase a entrar na era da televisão digital, importa saber que modelo de TV existe em Portugal. A análise da programação informativa destinada a acompanhar o Campeonato do Mundo de Futebol 2010 ajudará, decerto, a encontrar respostas. Neste artigo, apresentamos um estudo que incidiu em formatos informativos sobre este grande evento mediático, emitidos nos canais generalistas e temáticos entre os dias 11 de Junho e 11 de Julho de 2010 (datas de arranque e fecho do Mundial de Futebol da África do Sul). Essa análise, que incidiu em 604 emissões, procurou conhecer as formas de integração do telespectador nas emissões televisivas e quem foi chamado aos estúdios televisivos para participar nos debates aí promovidos. Os dados apurados demonstram claramente que esta TV do Mundial continua pouco aberta à participação do público e circunscrita a um grupo restrito de convidados, a maior parte dos quais oriundos da classe jornalística. Não é possível falar-se numa terceira fase do audiovisual. A hiper-televisão pode esperar.

A follow-up study on the quality of alcohol dependence-related information on the web.

ABSTRACT: In order to evaluate the one-year evolution of web-based information on alcohol dependence, we re-assessed alcohol-related sites in July 2007 with the same evaluating tool that had been used to assess these sites in June 2006. Websites were assessed with a standardized form designed to rate sites on the basis of accountability, presentation, interactivity, readability, and content quality. The DISCERN scale was also used, which aimed to assist persons without content expertise in assessing the quality of written health publications. Scores were highly stable for all components of the form one year later (r = .77 to .95, p < .01). Analysis of variance for repeated measures showed no time effect, no interaction between time and scale, no interaction between time and group (affiliation categories), and no interaction between time, group, and scale. The study highlights lack of change of alcohol-dependence-related web pages across one year.

General Practitioners' willingness to pay for continuing medical education in a fee-for-service universal coverage health care system

Background: Sponsoring of physicians meetings by life science companies has led to reduced participation fees but might influence physician's prescription practices. A ban on such sponsoring may increase participation fees. We aimed to evaluate factors associated with physicians' willingness to pay for medical meetings, their position on the sponsoring of medical meetings and their opinion on alternative financing options. Methods: An anonymous web-based questionnaire was sent to 447 general practitioners in one state in Switzerland, identified through their affiliation to a medical association. The questionnaire evaluated physicians' willingness to pay for medical meetings, their perception of a bias in prescription practices induced by commercial support, their opinion on the introduction of a binding legislation and alternative financing options, their frequency of exchange with sales representatives and other relevant socioeconomic factors. We built a multivariate predictor logistic regression model to identify determinants of willingness to pay. Results: Of the 115 physicians who responded (response rate 26%), 48% were willing to pay more than what they currently pay for congresses, 79% disagreed that commercial support introduced a bias in their prescription practices and 61% disagreed that it introduced a bias in their colleagues' prescription practices. Based on the multivariate logistic regression, perception of a bias in peers prescription practices (OR=7.47, 95% CI 1.65-38.18) and group practice structure (OR=4.62, 95% CI 1.34-22.29) were significantly associated with an increase in willingness to pay. Two thirds (76%) of physicians did not support the introduction of a binding legislation and 53% were in favour of creating a general fund administered by an independent body. Conclusion: Our results suggest that almost half of physicians surveyed are willing to pay more than what they currently pay for congresses. Predictors of an increase in physicians' willingness to pay were perception of the influence of bias in peers prescription practices and group practice structure. Most responders did not agree that sponsoring introduced prescribing bias nor did they support the 2 introduction of a binding legislation prohibiting sponsoring but a majority did agree to an independent body that would centrally administer a general fund.