PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

Estudo das propriedades psicofisiológicas da pintura como actividade criativa remediativa das manifestações de ansiedade

Ao longo das últimas duas décadas, as intervenções de Arte-Terapia baseada nas actividades criativas de Pintura têm sido implementadas em várias instituições e com variados objectivos e fins terapêuticos, diferindo nas suas abordagens (antroposófica, arte-pedagógica e apenas baseada na arte) e nos seus métodos e materiais aplicados. Constatamos que o recurso a actividades criativas, como a Pintura, provocam efeitos positivos nos indivíduos levando-os a resolver problemas e a reduzir ansiedades, melhorando a sua qualidade de vida. Deste modo é objectivo deste estudo pré-experimental efectuar uma análise das propriedades psicofisiológicas da Pintura como actividade criativa remediativa das manifestações de ansiedade em adultos, sem diagnóstico de perturbação ansiosa. De encontro a esse objectivo, perante uma amostra constituída por 7 indivíduos com níveis de ansiedade elevados, desenvolvemos um processo terapêutico, em que foram realizadas dez sessões de pintura, com a periodicidade de duas vezes por semana tendo cada sessão a duração de 45 min. Antes e depois da intervenção pela pintura, foi administrado o inventário para Avaliação do Traço da Ansiedade (STAY-Y), e durante essas sessões foram registadas as manifestações psicofisiológicas da ansiedade, mais especificamente a actividade electrodérmica da pele (EDA) e a frequência cardíaca. (FC), sendo efectuada a sua análise. Na sequência da análise dos dados obtidos nos dois instrumentos aplicados, verificamos que em relação aos marcadores psicofisiológicos EDA e FC não obtivemos diferenças estatísticas significativas para comprovar que de facto existe uma relação entre estes marcadores e a redução da ansiedade. Em relação ao STAY-Y referente à ansiedade traço, aplicado antes e depois das sessões de pintura, verificamos uma diminuição do score, o que evidência a ocorrência de uma diminuição da ansiedade traço nos indivíduos alvo do nosso estudo. Significa isto que apesar de existir uma variância nos resultados obtidos através das duas abordagens, é provavel que a pintura, enquanto actividade terapêutica, reduza o traço de ansiedade em indivíduos normais, com níveis de ansiedade elevados e sem manifestações de ansiedade diagnosticada.

Qualidade de vida relacionada com o exercício em indivíduos com asma: revisão sistemática

Background: A asma condiciona o dia-a-dia do indivíduo asmático do ponto de vista clínico e emocional demonstrando-se muitas vezes como um subtractivo da qualidade de vida (QV). Alguns estudos, com particular incidência nos últimos dez anos, para além de demonstrarem os benefícios da actividade física na componente clínica da doença, têm analisado o seu efeito na QV dos asmáticos. Objectivo: Analisar os efeitos da actividade física na QV de indivíduos com asma tendo por base uma revisão da literatura actual. Métodos: Foi conduzida uma pesquisa dos randomized controlled trials (RCT) compreendidos entre Janeiro de 2000 e Agosto de 2010, bem como as citações e as referências bibliográficas de cada estudo nas principais bases de dados de ciências da saúde (Academic Search Complete, DOAJ, Elsevier – Science Direct, Highwire Press, PubMed, Scielo Global, Scirus, Scopus, SpringerLink, Taylor & Francis e Wiley Interscience) com as palavras-chave: asthma, quality of life, QoL, physical activity, exercise, breathing, training e programme em todas as combinações possíveis. Os estudos foram analisados independentemente por dois revisores quanto aos critérios de inclusão e qualidade dos estudos. Resultados: Dos 1075 estudos identificados apenas onze foram incluídos. Destes, seis apresentaram um score 5/10, três 6/10 e dois 7/10 segundo a escala PEDro. Cinco destes estudos foram realizados em crianças entre os 7 e os 15 anos e os restantes em adultos. Os programas de intervenção dividiram-se em programas de treino aeróbio e programas de exercícios respiratórios. Todos programas de treino aeróbio apresentaram melhorias na QV demonstrando uma influência positiva do treino aeróbio na asma. Principais conclusões: Há uma tendência notória do benefício dos programas de treino aeróbio na QV dos indivíduos asmáticos. Os programas de exercícios respiratórios foram poucos e heterogéneos impossibilitando uma conclusão positiva quanto à sua recomendação para a melhoria da QV nesta patologia. Há uma grande necessidade de mais RCT com rigor metodológico.

O movimento de alcance em indivíduos após AVE. Estratégias compensatórias por parte do tronco

Introdução: O movimento de alcance, fundamental para actividades diárias, encontra-se frequentemente comprometido após AVE, sendo muitas vezes acompanhado por estratégias compensatórias. Objectivo: Avaliar o movimento de alcance em indivíduos após AVE e verificar se utilizam estratégias compensatórias por parte do tronco aquando da sua realização, verificando também se o plano de intervenção a cada caso permitiu reduzir as estratégias compensatórias. Participantes e métodos: Foram seleccionados dois indivíduos por conveniência, após um único evento de AVE, com score de 2 ou mais na escala Chedoke-McMaster Stroke Assessment. Para avaliar o movimento de alcance utilizou-se a escala Reach Performance Scale (RPS) que apresenta duas subcategorias (alvo próximo e distante). A intervenção, baseada no conceito de Bobath, foi dirigida essencialmente para o membro superior. Resultados: Os dois indivíduos utilizaram o movimento do tronco como estratégia compensatória no movimento de alcance principalmente no alvo distante, onde a pontuação foi menor que para o alvo próximo. Nos dois momentos avaliados não foram registadas alterações. Conclusão: Neste estudo verificaram-se estratégias compensatórias do tronco, concluindo-se que quanto maior o comprometimento do membro superior, maior será o movimento do tronco, sendo este mais visível no caso B.

Methods for automatic and assisted image annotation

Personal memories composed of digital pictures are very popular at the moment. To retrieve these media items annotation is required. During the last years, several approaches have been proposed in order to overcome the image annotation problem. This paper presents our proposals to address this problem. Automatic and semi-automatic learning methods for semantic concepts are presented. The automatic method is based on semantic concepts estimated using visual content, context metadata and audio information. The semi-automatic method is based on results provided by a computer game. The paper describes our proposals and presents their evaluations.

Typical load profiles in the smart grid context – a clustering methods comparison

The present research paper presents five different clustering methods to identify typical load profiles of medium voltage (MV) electricity consumers. These methods are intended to be used in a smart grid environment to extract useful knowledge about customer’s behaviour. The obtained knowledge can be used to support a decision tool, not only for utilities but also for consumers. Load profiles can be used by the utilities to identify the aspects that cause system load peaks and enable the development of specific contracts with their customers. The framework presented throughout the paper consists in several steps, namely the pre-processing data phase, clustering algorithms application and the evaluation of the quality of the partition, which is supported by cluster validity indices. The process ends with the analysis of the discovered knowledge. To validate the proposed framework, a case study with a real database of 208 MV consumers is used.

Technical and economic resources management in smart grids using heuristic optimization methods

Intensive use of Distributed Generation (DG) represents a change in the paradigm of power systems operation making small-scale energy generation and storage decision making relevant for the whole system. This paradigm led to the concept of smart grid for which an efficient management, both in technical and economic terms, should be assured. This paper presents a new approach to solve the economic dispatch in smart grids. The proposed methodology for resource management involves two stages. The first one considers fuzzy set theory to define the natural resources range forecast as well as the load forecast. The second stage uses heuristic optimization to determine the economic dispatch considering the generation forecast, storage management and demand response

Electricity markets: transmission prices methods

In the context of electricity markets, transmission pricing is an important tool to achieve an efficient operation of the electricity system. The electricity market is influenced by several factors; however the transmission network management is one of the most important aspects, because the network is a natural monopoly. The transmission tariffs can help to regulate the market, for this reason transmission tariffs must follow strict criteria. This paper presents the following methods to tariff the use of transmission networks by electricity market players: Post-Stamp Method; MW-Mile Method Distribution Factors Methods; Tracing Methodology; Bialek’s Tracing Method and Locational Marginal Price. A nine bus transmission network is used to illustrate the application of the tariff methods.

Comparison between deterministic and meta-heuristic methods applied to ancillary services dispatch

This paper proposes two meta-heuristics (Genetic Algorithm and Evolutionary Particle Swarm Optimization) for solving a 15 bid-based case of Ancillary Services Dispatch in an Electricity Market. A Linear Programming approach is also included for comparison purposes. A test case based on the dispatch of Regulation Down, Regulation Up, Spinning Reserve and Non-Spinning Reserve services is used to demonstrate that the use of meta-heuristics is suitable for solving this kind of optimization problem. Faster execution times and lower computational resources requirements are the most relevant advantages of the used meta-heuristics when compared with the Linear Programming approach.

Ancillary services market clearing simulation: a comparison between deterministic and heuristic methods

Electricity market players operating in a liberalized environment requires access to an adequate decision support tool, allowing them to consider all the business opportunities and take strategic decisions. Ancillary services represent a good negotiation opportunity that must be considered by market players. For this, decision support tool must include ancillary market simulation. This paper proposes two different methods (Linear Programming and Genetic Algorithm approaches) for ancillary services dispatch. The methodologies are implemented in MASCEM, a multi-agent based electricity market simulator. A test case based on California Independent System Operator (CAISO) data concerning the dispatch of Regulation Down, Regulation Up, Spinning Reserve and Non-Spinning Reserve services is included in this paper.

Online versus postal questionnaires: a comparison between two data collection methods

Objectives : The purpose of this article is to find out differences between surveys using paper and online questionnaires. The author has deep knowledge in the case of questions concerning opinions in the development of survey based research, e.g. the limits of postal and online questionnaires. Methods : In the physician studies carried out in 1995 (doctors graduated in 1982-1991), 2000 (doctors graduated in 1982-1996), 2005 (doctors graduated in 1982-2001), 2011 (doctors graduated in 1977-2006) and 457 family doctors in 2000, were used paper and online questionnaires. The response rates were 64%, 68%, 64%, 49% and 73%, respectively. Results : The results of the physician studies showed that there were differences between methods. These differences were connected with using paper-based questionnaire and online questionnaire and response rate. The online-based survey gave a lower response rate than the postal survey. The major advantages of online survey were short response time; very low financial resource needs and data were directly loaded in the data analysis software, thus saved time and resources associated with the data entry process. Conclusions : The current article helps researchers with planning the study design and choosing of the right data collection method.

A comparison of two attenuation correction methods in 111In-Pentetriotide abdominal SPECT

Tomographic image can be degraded, partially by patient based attenuation. The aim of this paper is to quantitatively verify the effects of attenuation correction methods Chang and CT in 111In studies through the analysis of profiles from abdominal SPECT, correspondent to a uniform radionuclide uptake organ, the left kidney.

Neonatal mortality in intensive care units of Central Brazil

OBJECTIVE: To identify potential prognostic factors for neonatal mortality among newborns referred to intensive care units. METHODS: A live-birth cohort study was carried out in Goiânia, Central Brazil, from November 1999 to October 2000. Linked birth and infant death certificates were used to ascertain the cohort of live born infants. An additional active surveillance system of neonatal-based mortality was implemented. Exposure variables were collected from birth and death certificates. The outcome was survivors (n=713) and deaths (n=162) in all intensive care units in the study period. Cox's proportional hazards model was applied and a Receiver Operating Characteristic curve was used to compare the performance of statistically significant variables in the multivariable model. Adjusted mortality rates by birth weight and 5-min Apgar score were calculated for each intensive care unit. RESULTS: Low birth weight and 5-min Apgar score remained independently associated to death. Birth weight equal to 2,500g had 0.71 accuracy (95% CI: 0.65-0.77) for predicting neonatal death (sensitivity =72.2%). A wide variation in the mortality rates was found among intensive care units (9.5-48.1%) and two of them remained with significant high mortality rates even after adjusting for birth weight and 5-min Apgar score. CONCLUSIONS: This study corroborates birth weight as a sensitive screening variable in surveillance programs for neonatal death and also to target intensive care units with high mortality rates for implementing preventive actions and interventions during the delivery period.

Neurokinin-1 receptor, a new modulator of lymphangiogenesis in obese-asthma phenotype

Aims Obesity and asthma are widely prevalent and associated disorders. Recent studies of our group revealed that Substance P (SP) is involved in pathophysiology of obese-asthma phenotype in mice through its selective NK1 receptor (NK1-R). Lymphangiogenesis is impaired in asthma and obesity, and SP activates contractile and inflammatory pathways in lymphatics. Our aim was to study whether NK1-R expression was involved in lymphangiogenesis on visceral (VAT) and subcutaneous (SAT) adipose tissues and in the lungs, in obese-allergen sensitized mice. Main methods Diet-induced obese and ovalbumin (OVA)-sensitized Balb/c mice were treated with a selective NK1-R antagonist (CJ 12,255, Pfizer Inc., USA) or placebo. Lymphatic structures (LYVE-1 +) and NK1-R expression were analyzed by immunohistochemistry. A semi-quantitative score methodology was used for NK1-R expression. Key findings Obesity and allergen-sensitization together increased the number of LYVE-1 + lymphatics in VAT and decreased it in SAT and lungs. NK1-R was mainly expressed on adipocyte membranes of VAT, blood vessel areas of SAT, and in lung epithelium. Obesity and allergen-sensitization combined increased the expression of NK1-R in VAT, SAT and lungs. NK1-R antagonist treatment reversed the effects observed in lymphangiogenesis in those tissues. Significance The obese-asthma phenotype in mice is accompanied by increased expression of NK1-R on adipose tissues and lung epithelium, reflecting that SP released during inflammation may act directly on these tissues. Blocking NK1-R affects lymphangiogenesis, implying a role of SP, with opposite physiological consequences in VAT, and in SAT and lungs. Our results provide a clue for a novel SP role in the obese-asthma phenotype.

Nintendo Wii: uso terapêutico no controlo postural em indivíduos que sofreram um acidente vascular cerebral

Mestrado em Fisioterapia.