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.

Global and local detection of liver steatosis from ultrasound

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. Steatosis is usually a diffuse liver disease, since it is globally affected. However, steatosis can also be focal affecting only some foci difficult to discriminate. In both cases, steatosis is detected by laboratorial analysis and visual inspection of ultrasound images of the hepatic parenchyma. Liver biopsy is the most accurate diagnostic method but its invasive nature suggest the use of other non-invasive methods, while visual inspection of the ultrasound images is subjective and prone to error. In this paper a new Computer Aided Diagnosis (CAD) system for steatosis classification and analysis is presented, where the Bayes Factor, obatined from objective intensity and textural features extracted from US images of the liver, is computed in a local or global basis. The main goal is to provide the physician with an application to make it faster and accurate the diagnosis and quantification of steatosis, namely in a screening approach. The results showed an overall accuracy of 93.54% with a sensibility of 95.83% and 85.71% for normal and steatosis class, respectively. The proposed CAD system seemed suitable as a graphical display for steatosis classification and comparison with some of the most recent works in the literature is also presented.

A influência do local de estimulação ventricular na incidência de taquiarritmias auriculares em doentes com pacemaker permanente

Mestrado em Tecnologia de Diagnóstico e Intervenção Cardiovascular

Global localization with non-quantized local image features

In the field of appearance-based robot localization, the mainstream approach uses a quantized representation of local image features. An alternative strategy is the exploitation of raw feature descriptors, thus avoiding approximations due to quantization. In this work, the quantized and non-quantized representations are compared with respect to their discriminativity, in the context of the robot global localization problem. Having demonstrated the advantages of the non-quantized representation, the paper proposes mechanisms to reduce the computational burden this approach would carry, when applied in its simplest form. This reduction is achieved through a hierarchical strategy which gradually discards candidate locations and by exploring two simplifying assumptions about the training data. The potential of the non-quantized representation is exploited by resorting to the entropy-discriminativity relation. The idea behind this approach is that the non-quantized representation facilitates the assessment of the distinctiveness of features, through the entropy measure. Building on this finding, the robustness of the localization system is enhanced by modulating the importance of features according to the entropy measure. Experimental results support the effectiveness of this approach, as well as the validity of the proposed computation reduction methods.

GLODS: Global and Local Optimization using Direct Search

Locating and identifying points as global minimizers is, in general, a hard and time-consuming task. Difficulties increase in the impossibility of using the derivatives of the functions defining the problem. In this work, we propose a new class of methods suited for global derivative-free constrained optimization. Using direct search of directional type, the algorithm alternates between a search step, where potentially good regions are located, and a poll step where the previously located promising regions are explored. This exploitation is made through the launching of several instances of directional direct searches, one in each of the regions of interest. Differently from a simple multistart strategy, direct searches will merge when sufficiently close. The goal is to end with as many direct searches as the number of local minimizers, which would easily allow locating the global extreme value. We describe the algorithmic structure considered, present the corresponding convergence analysis and report numerical results, showing that the proposed method is competitive with currently commonly used global derivative-free optimization solvers.

Robot visual localization through local feature fusion: an evaluation of multiple classifiers combination approaches

In the last decade, local image features have been widely used in robot visual localization. In order to assess image similarity, a strategy exploiting these features compares raw descriptors extracted from the current image with those in the models of places. This paper addresses the ensuing step in this process, where a combining function must be used to aggregate results and assign each place a score. Casting the problem in the multiple classifier systems framework, in this paper we compare several candidate combiners with respect to their performance in the visual localization task. For this evaluation, we selected the most popular methods in the class of non-trained combiners, namely the sum rule and product rule. A deeper insight into the potential of these combiners is provided through a discriminativity analysis involving the algebraic rules and two extensions of these methods: the threshold, as well as the weighted modifications. In addition, a voting method, previously used in robot visual localization, is assessed. Furthermore, we address the process of constructing a model of the environment by describing how the model granularity impacts upon performance. All combiners are tested on a visual localization task, carried out on a public dataset. It is experimentally demonstrated that the sum rule extensions globally achieve the best performance, confirming the general agreement on the robustness of this rule in other classification problems. The voting method, whilst competitive with the product rule in its standard form, is shown to be outperformed by its modified versions.

As organizações sem fins lucrativos e a estratégia de uma organização patronal sem fins lucrativos na economia local. Um estudo de caso: ACISCP (Associação Comercial, Industrial e de Serviços do Concelho de Peniche)

Mestrado em Contabilidade

A qualidade de vida do indivíduo com perda auditiva segundo o tipo de local de residência

A necessidade de promoção e manutenção da Qualidade de Vida enfatiza a importância de: Programas de Prevenção de Perda Auditiva e de Sensibilização e Manutenção da Saúde Auditiva; Programas de Terapêutica por Adaptação Protética. Objectivos gerais: avaliar o estado de saúde da população com perda auditiva e averiguar as principais repercussões da perda auditiva na Qualidade de Vida. Finalidades do estudo: demonstrar a necessidade e utilidade de programas de sensibilização para a protecção e conservação do sentido auditivo.

Seasonal variation of total particulate matter and children respiratory diseases at Lisbon primary schools using passive methods

In this work, 14 primary schools of Lisbon city, Portugal, followed a questionnaire of the ISAAC - International Study of Asthma and Allergies in Childhood Program, in 2009/2010. The questionnaire contained questions to identify children with respiratory diseases (wheeze, asthma and rhinitis). Total particulate matter (TPM) was passively collected inside two classrooms of each of 14 primary schools. Two types of filter matrices were used to collect TPM: Millipore (IsoporeTM) polycarbonate and quartz. Three campaigns were selected for the measurement of TPM: Spring, Autumn and Winter. The highest difference between the two types of filters is that the mass of collected particles was higher in quartz filters than in polycarbonate filters, even if their correlation is excellent. The highest TPM depositions occurred between October 2009 and March 2010, when related with rhinitis proportion. Rhinitis was found to be related to TPM when the data were grouped seasonally and averaged for all the schools. For the data of 2006/2007, the seasonal variation was found to be related to outdoor particle deposition (below 10 μm).

Análise dos métodos de medição dos parâmetros geométricos de via e correlação entre os dados obtidos

A razão atribuída à escolha do tema do T.F.M. em Caminhos-de-ferro, tem a ver com o facto de ser uma via de comunicação específica. Contrariamente ao que acontece na execução de auto-estradas, no caminho-de-ferro, a gestora da infra-estrutura responsabiliza-se pela execução, exploração (sinalização e controlo de circulação), abastecimento de energia fornecida às vias que dispõem de catenária (tracção eléctrica), manutenção e conservação da via. O processo de análise e inspecção de geometria de via, é usado quando e necessário preservar a infra-estrutura. Este processo iniciou-se nos caminhos-de-ferro portugueses, há muitos anos, depois da inauguração do primeiro troco de linha férrea. A primeira viagem ocorre em Outubro de 1856, sendo o início do processo em 1968, com a dresina “Matisa PV-6”. Em 1991 a C.P. adquiriu outro veículo de inspecção de via, tendo sido escolhido o VIV02 EM 120 da marca Plasser & Theurer, para substituir “Matisa PV-6”. O tema Análise dos Métodos de Medição dos Parâmetros Geométricos de Via e Correlação entre os Dados Obtidos está directamente relacionado com a manutenção e conservação de via. Na Unidade Operacional Sul (hoje ROS – Região Operacional Sul), local onde desenvolvi o T.F.M., não existem obras de construção de caminhos-de-ferro que pudesse acompanhar e constituir tema para o meu trabalho. Na realidade, com a falta de investimento que se perspectiva no futuro próximo, a manutenção da infra-estrutura passa a ser a actividade principal desenvolvida pela REFER, de modo a assegurar a comodidade, segurança e rapidez na deslocação de cargas e pessoas. A Analise Geométrica de Via e actualmente uma das principais actividades no âmbito da manutenção, que é feita por diagnóstico, contrariamente ao que acontecia no passado em que a conservação metódica era realizada num determinado ano num troço seleccionado independentemente da necessidade ou não da mesma. Uma ajuda preciosa, no que se refere à decisão de se realizar um determinado trabalho de conservação, e a do veículo VIV02 EM 120 que faz inspeções ao longo de toda a rede ferroviária e permite recolher dados e classificar através do desvio padrão, troços com extensão de 200 metros, obtendo os dados relevantes sobre a necessidade de intervenção. Para além do referido veículo existem também equipamentos ligeiros de inspecção dos parâmetros geométricos de via. Um desses equipamentos designa-se por Trólei, não sendo motorizado, pois o mesmo é movido manualmente por um operador. Obviamente que este equipamento não faz a inspecção a toda a rede pois a operação de medição é morosa, sendo contudo utilizado para análise de defeitos geométricos em pequenos trocos, tornando-se assim uma mais-valia, evitando o deslocar de um equipamento “pesado” como o VIV 02 EM 120. Para atingir os objectivos deste trabalho realizaram-se testes de medição com ambos (veiculo e equipamento ligeiro), no mesmo espaço temporal e com as mesmas características físicas, como a temperatura, humidade etc. Os resultados, de acordo com os objectivos, são a comparação entre as medições de ambos, com vista a comprovar a sua utilidade e necessidade, de acordo com os vários tipos de superstruturas constituintes da rede ferroviária nacional.

Prevalência de lesões músculo-esqueléticas ligadas ao trabalho (LMELT) em higienistas orais: contributo para a saúde e segurança no local de trabalho

Mestrado em Intervenção Sócio-Organizacional na Saúde - Área de especialização: Qualidade e Tecnologias da Saúde.

Comparação entre coronariografia efectuada via artéria radial e via artéria femoral

Mestrado em Tecnologia de Diagnóstico e Intervenção Cardiovascular. Área de especialização: Intervenção Cardiovascular.

Contributos para uma prospectiva da implementação de um centro de responsabilidade de radiologia numa Unidade Local de Saúde: o caso da Unidade Local de Saúde do Norte Alentejano

Mestrado em Intervenção Sócio-Organizacional na Saúde - Área de especialização: Políticas de Administração e Gestão de Serviços de Saúde.

Structural and Microanalytical Studies of CrO2 Thin Films on c-Sapphire by High Resolution Electron Microscopy Methods

Chromium dioxide (CrO2) has been extensively used in the magnetic recording industry. However, it is its ferromagnetic half-metallic nature that has more recently attracted much attention, primarily for the development of spintronic devices. CrO2 is the only stoichiometric binary oxide theoretically predicted to be fully spin polarized at the Fermi level. It presents a Curie temperature of ∼ 396 K, i.e. well above room temperature, and a magnetic moment of 2 mB per formula unit. However an antiferromagnetic native insulating layer of Cr2O3 is always present on the CrO2 surface which enhances the CrO2 magnetoresistance and might be used as a barrier in magnetic tunnel junctions.