GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

Accessibility in Digital Television: Designing Remote Controls

Free to air television is still an important tool to provide information and communication in many countries. Therefore, the universal access to the television system is very important. This paper presents a set of Digital Television accessible remote control devices designed for the Brazilian Digital Television. A research was conducted, interviewing people with disabilities in Brazil. Three remote control models were proposed, consolidating the main identified requirements, being accessible for a diverse group of impairments.

Towards a hybrid approach for adapting web graphical user interfaces to heterogeneous devices using context

Ubiquitous Computing promises seamless access to a wide range of applications and Internet based services from anywhere, at anytime, and using any device. In this scenario, new challenges for the practice of software development arise: Applications and services must keep a coherent behavior, a proper appearance, and must adapt to a plenty of contextual usage requirements and hardware aspects. Especially, due to its interactive nature, the interface content of Web applications must adapt to a large diversity of devices and contexts. In order to overcome such obstacles, this work introduces an innovative methodology for content adaptation of Web 2.0 interfaces. The basis of our work is to combine static adaption - the implementation of static Web interfaces; and dynamic adaptation - the alteration, during execution time, of static interfaces so as for adapting to different contexts of use. In hybrid fashion, our methodology benefits from the advantages of both adaptation strategies - static and dynamic. In this line, we designed and implemented UbiCon, a framework over which we tested our concepts through a case study and through a development experiment. Our results show that the hybrid methodology over UbiCon leads to broader and more accessible interfaces, and to faster and less costly software development. We believe that the UbiCon hybrid methodology can foster more efficient and accurate interface engineering in the industry and in the academy.

Comparison of multiple-input single-output single-user ultra-wideband systems with pre-distortion

This paper presents a performance analysis of a baseband multiple-input single-output ultra-wideband system over scenarios CM1 and CM3 of the IEEE 802.15.3a channel model, incorporating four different schemes of pre-distortion: time reversal, zero-forcing pre-equaliser, constrained least squares pre-equaliser, and minimum mean square error pre-equaliser. For the third case, a simple solution based on the steepest-descent (gradient) algorithm is adopted and compared with theoretical results. The channel estimations at the transmitter are assumed to be truncated and noisy. Results show that the constrained least squares algorithm has a good trade-off between intersymbol interference reduction and signal-to-noise ratio preservation, providing a performance comparable to the minimum mean square error method but with lower computational complexity. Copyright (C) 2011 John Wiley & Sons, Ltd.

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Development of an integrative cessation program for co-smokers of cigarettes and cannabis: demand analysis, program description, and acceptability

Abstract Background Tobacco and cannabis use are strongly interrelated, but current national and international cessation programs typically focus on one substance, and address the other substance either only marginally or not at all. This study aimed to identify the demand for, and describe the development and content of, the first integrative group cessation program for co-smokers of cigarettes and cannabis. Methods First, a preliminary study using expert interviews, user focus groups with (ex-)smokers, and an online survey was conducted to investigate the demand for, and potential content of, an integrative smoking cessation program (ISCP) for tobacco and cannabis co-smokers. This study revealed that both experts and co-smokers considered an ISCP to be useful but expected only modest levels of readiness for participation.Based on the findings of the preliminary study, an interdisciplinary expert team developed a course concept and a recruitment strategy. The developed group cessation program is based on current treatment techniques (such as motivational interviewing, cognitive behavioural therapy, and self-control training) and structured into six course sessions.The program was evaluated regarding its acceptability among participants and course instructors. Results Both the participants and course instructors evaluated the course positively. Participants and instructors especially appreciated the group discussions and the modules that were aimed at developing personal strategies that could be applied during simultaneous cessation of tobacco and cannabis, such as dealing with craving, withdrawal, and high-risk situations. Conclusions There is a clear demand for a double cessation program for co-users of cigarettes and cannabis, and the first group cessation program tailored for these users has been developed and evaluated for acceptability. In the near future, the feasibility of the program will be evaluated. Trial registration Current Controlled Trials ISRCTN15248397

A arquitetura patrimonial através dos jogos digitais

O presente artigo pretende ressaltar o potencial dos jogos digitais como instrumento de assimilação do conhecimento em arquitetura patrimonial, através da pesquisa Patrimônio arquitetônico, design e educação: desenvolvimento de Sistemas Interativos Lúdicos (jogos educativos em meio digital). Nesta pesquisa foram desenvolvidos jogos digitais a partir do levantamento das características arquitetônicas dos edifícios de relevância histórica e cultural da cidade de São Carlos. Através da interação e exploração da interface digital pelo usuário, a apropriação do conhecimento ocorre de uma forma lúdica e criativa. Por meio da manipulação desses jogos, os alunos, cidadãos e visitantes podem aproximar-se da educação patrimonial adquirindo consciência histórica e aprendendo a valorizar as origens da cidade e a arquitetura do município. Ressalta-se a importância das metodologias que permitem viabilizar o desenvolvimento dos jogos eletrônicos (desenho e linguagem de programação) e que se apresentam como importantes ferramentas de representação da arquitetura. Por fim, destaca-se a importância da educação patrimonial para a formação do cidadão e preservação do patrimônio cultural.

Long-term type 1 diabetes impairs decidualization and extracellular matrix remodeling during early embryonic development in mice

Introduction: Endometrial decidualization and associated extracellular matrix (ECM) remodeling are critical events to the establishment of the maternal-fetal interface and successful pregnancy. Here, we investigated the impact of type 1 diabetes on these processes during early embryonic development, in order to contribute to the understanding of the maternal factors associated to diabetic embryopathies. Methods: Alloxan-induced diabetic Swiss female mice were bred after different periods of time to determine the effects of diabetes progression on the development of gestational complications. Furthermore, the analyses focused on decidual development as well as mRNA expression, protein deposition and ultrastructural organization of decidual ECM. Results: Decreased number of implantation sites and decidual dimensions were observed in the group mated 90-110 days after diabetes induction (D), but not in the 50-70D group. Picrosirius staining showed augmentation in the fibrillar collagen network in the 90e110D group and, following immunohistochemical examination, that this was associated with increase in types I and V collagens and decrease in type III collagen and collagen-associated proteoglycans biglycan and lumican. qPCR, however, demonstrated that only type I collagen mRNA levels were increased in the diabetic group. Alterations in the molecular ratio among distinct collagen types and proteoglycans were associated with abnormal collagen fibrillogenesis, analyzed by transmission electron microscopy. Conclusions: Our results support the concept that the development of pregnancy complications is directly related with duration of diabetes (progression of the disease), and that this is a consequence of both systemic factors (i.e. disturbed maternal endocrine-metabolic profile) and uterine factors, including impaired decidualization and ECM remodeling