Automatic Small Bowel Tumor Diagnosis by Using Multi-Scale Wavelet-Based Analysis in Wireless Capsule Endoscopy Images

BACKGROUND: Wireless capsule endoscopy has been introduced as an innovative, non-invasive diagnostic technique for evaluation of the gastrointestinal tract, reaching places where conventional endoscopy is unable to. However, the output of this technique is an 8 hours video, whose analysis by the expert physician is very time consuming. Thus, a computer assisted diagnosis tool to help the physicians to evaluate CE exams faster and more accurately is an important technical challenge and an excellent economical opportunity. METHOD: The set of features proposed in this paper to code textural information is based on statistical modeling of second order textural measures extracted from co-occurrence matrices. To cope with both joint and marginal non-Gaussianity of second order textural measures, higher order moments are used. These statistical moments are taken from the two-dimensional color-scale feature space, where two different scales are considered. Second and higher order moments of textural measures are computed from the co-occurrence matrices computed from images synthesized by the inverse wavelet transform of the wavelet transform containing only the selected scales for the three color channels. The dimensionality of the data is reduced by using Principal Component Analysis. RESULTS: The proposed textural features are then used as the input of a classifier based on artificial neural networks. Classification performances of 93.1% specificity and 93.9% sensitivity are achieved on real data. These promising results open the path towards a deeper study regarding the applicability of this algorithm in computer aided diagnosis systems to assist physicians in their clinical practice.

Improving search engines with open Web-based SKOS vocabularies

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Extracting temporal and spatial distributions information about marine mucilage phenomenon based on Modis satellite images; a case study of the Tyrrhenian and the Adriatic Sea, 2010-2012

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

Aconselhamento médico na prevenção da doença e promoção da saúde : análise a propósito do consumo de tabaco

RESUMO - O consumo de tabaco foi responsável por 100 milhões de mortes no século XX. Apesar dos grandes avanços alcançados no controlo deste problema a nível mundial, sob os auspícios da OMS, no contexto da Convenção-Quadro para o Controlo do Tabaco da OMS, se não forem adoptadas medidas consistentes e efectivas de saúde pública, a morbi-mortalidade que lhe está associada continuará a aumentar durante o presente século. A promoção da cessação tabágica constitui a estratégia populacional que permitirá obter ganhos em saúde a mais curto prazo. Embora a larga maioria dos fumadores faça, ao longo da vida, várias tentativas para parar de fumar sem apoio, apenas uma pequena minoria consegue manter-se abstinente a longo prazo. Os médicos de Medicina Geral e Familiar são, de entre todos os profissionais de saúde, os que podem intervir de modo mais consistente e efectivo neste âmbito e que melhores resultados obtêm na cessação tabágica dos pacientes fumadores, dado o vínculo terapêutico e a interacção frequente e continuada que com eles estabelecem ao longo do seu ciclo de vida. O aconselhamento breve, tendo por base a adopção de um estilo de comunicação motivacional centrado no paciente, adaptado aos estádios de mudança comportamental, tem-se revelado efectivo no apoio à mudança de comportamentos relacionados com a saúde e à resolução da ambivalência que caracteriza este processo. A revisão de literatura evidenciou o facto de os médicos nem sempre intervirem nas áreas preventivas e de promoção da saúde, em particular na área da cessação tabágica, com o investimento e a continuidade desejáveis. Por outro lado, muitos pacientes fumadores referem nunca ter sido aconselhados pelo seu médico a deixar de fumar.. Não são conhecidos estudos de âmbito nacional que permitam conhecer esta realidade, bem como os factores associados às melhores práticas de intervenção ou as barreiras sentidas pelos médicos de MGF à actuação nesta área. O presente trabalho teve como objectivos: (i) avaliar a hipótese de que os médicos que disseram adoptar o método clínico centrado no paciente teriam atitudes mais favoráveis relativamente à cessação tabágica e uma maior probabilidade de aconselhar os seus pacientes a parar de fumar; (ii) estudar a relação entre as atitudes, a percepção de auto-eficácia, a expectativa de efectividade e as práticas de aconselhamento sobre cessação tabágica, auto-referidas pelos médicos; (iii) Identificar as variáveis preditivas da adopção de intervenções breves de aconselhamento adaptadas ao estádio de mudança comportamental dos pacientes fumadores; (iv) identificar as barreiras e os incentivos à adopção de boas práticas de aconselhamento nesta área. A população de estudo foi constituída pelo total de médicos de medicina geral e familiar inscritos na Associação Portuguesa de Médicos de Clínica Geral, residentes em Portugal. Para recolha de informação, foi utilizado um questionário de resposta anónima, de autopreenchimento, aplicado por via postal a 2942 médicos, em duas séries de envio. O questionário integrou perguntas fechadas, semifechadas, escalas de tipo Likert e escalas de tipo visual analógico. Para avaliação da adopção do método clínico centrado no paciente, foi usada a Patient Practitioner Orientation Scale (PPOS). O tratamento estatístico dos dados foi efectuado com o Programa PASW Statistics (ex-SPSS), versão 18. Foram utilizados: o índice de α de Cronbach, diversos testes não paramétricos e a análise de regressão logística binária. Foi obtida uma taxa de resposta de 22,4%. Foram analisadas 639 respostas (67,4% de mulheres e 32,6% de homens). Referiram ser fumadores 23% dos homens e 14% das mulheres. Foi identificada uma grande carência formativa em cessação tabágica, tendo apenas 4% dos médicos afirmado não necessitar de formação nesta área. Responderam necessitar de formação em entrevista motivacional 66%, em prevenção da recaída 59%, de treino numa consulta de apoio intensivo 55%, em intervenção breve 54% e em terapêutica farmacológica 55%. Cerca de 92% dos respondentes consideraram que o aconselhamento para a cessação tabágica é uma tarefa que faz parte das suas atribuições, mas apenas 76% concordaram totalmente com a realização de uma abordagem oportunística deste assunto em todos os contactos com os seus pacientes. Como prática mais frequente, perante um paciente em preparação para parar, 85% dos médicos disseram tomar a iniciativa de aconselhar, 79% avaliar a motivação, 67% avaliar o grau de dependência, 60% marcar o “dia D” e 50% propor terapêutica farmacológica. Apenas 21% assumiram realizar com frequência uma intervenção breve com pacientes em preparação (5 Ás); 13% uma intervenção motivacional com pacientes não motivados para mudar (5 Rs) e 20% uma intervenção segundo os princípios da entrevista motivacional, relativamente a pacientes ambivalentes em relação à mudança. A análise multivariada de regressão logística permitiu concluir que as variáveis com maior influência na decisão de aconselhar os pacientes sobre cessação tabágica foram a percepção de auto-eficácia, o nível de atitudes negativas, a adopção habitual do Programa-tipo de cessação tabágica da DGS, a posse de formação específica nesta área e a não identificação de barreiras ao aconselhamento, em particular organizacionais ou ligadas ao processo de comunicação na consulta. Embora se tenha confirmado a existência de associação entre a adopção do método clínico centrado no paciente e as atitudes face à cessação tabágica, não foi possível confirmar plenamente a associação entre a adopção deste método e as práticas autoreferidas de aconselhamento. Os médicos que manifestaram um nível baixo ou moderado de atitudes negativas, uma percepção elevada de auto-eficácia, que nunca fumaram, que referiram adoptar o Programa-tipo de cessação tabágica e que não identificaram barreiras organizacionais apresentaram uma maior probabilidade de realizar uma intervenção breve (“5 Ás”) de aconselhamento de pacientes fumadores em preparação para parar de fumar. Nunca ter fumado apresentou-se associado a uma probabilidade de realizar uma intervenção breve (“5 Ás”) com frequência, superior à verificada entre os médicos que referiram ser fumadores (Odds-ratio ajustado = 2,6; IC a 95%: 1,1; 5,7). Os médicos com o nível de auto-eficácia no aconselhamento mais elevado apresentaram uma probabilidade superior à encontrada entre os médicos com o menor nível de auto-eficácia de realizar com frequência uma intervenção breve de aconselhamento, integrando as cinco vertentes dos “5 Ás” (Odds ratio ajustado = 2,6; IC a 95%: 1,3; 5,3); de realizar uma intervenção motivacional breve com fumadores renitentes a parar de fumar (Odds ratio ajustado = 3,1; IC a 95%: 1,4; 6,5) ou de realizar com frequência uma intervenção motivacional com pacientes em estádio de ambivalência (Odds ratio = 8,8; IC a 95%: 3,8; 19,9). A falta de tempo, a falta de formação específica e a falta de equipa de apoio foram as barreiras ao aconselhamento mais citadas. Como factores facilitadores de um maior investimento nesta área, cerca de 60% dos médicos referiram a realização de um estágio prático de formação; 57% a possibilidade de dispor do apoio de outros profissionais; cerca de metade a melhoria da sua formação teórica. Cerca de 25% dos médicos investiria mais em cessação tabágica se dispusesse de um incentivo financeiro e 20% se os pacientes demonstrassem maior interesse em discutir o assunto ou existisse uma maior valorização desta área por parte dos colegas e dos órgãos de gestão. As limitações de representatividade da amostra, decorrentes da taxa de resposta obtida, impõem reservas à possibilidade de extrapolação destes resultados para a população de estudo, sendo de admitir que os respondentes possam corresponder aos médicos mais interessados por este tema e que optam por não fumar. Outra importante limitação advém do facto de não ter sido estudada a vertente relativa aos pacientes, no que se refere às suas atitudes, percepções e expectativas quanto à actuação do médico neste campo. Pesem embora estas limitações, os resultados obtidos revelaram uma grande perda de oportunidades de prevenção da doença e de promoção da saúde. Parece ter ficado demonstrada a importante influência que as atitudes, em especial as negativas, e as percepções, em particular a percepção de auto-eficácia, podem exercer sobre as práticas de aconselhamento auto-referidas. Todavia, será necessário aprofundar os resultados agora encontrados com estudos de natureza qualitativa, que permitam compreender melhor, por um lado, as percepções, expectativas e necessidades dos pacientes, por outro, as estratégias de comunicação que deverão ser adoptadas pelo médico, atendendo à complexidade do problema e ao tempo disponível na consulta, tendo em vista aumentar a literacia dos pacientes para uma melhor autogestão da sua saúde. Parece ter ficado igualmente patente a grande carência formativa neste domínio. A adopção do modelo biomédico como paradigma da formação médica pré e pós-graduada, proposto, há precisamente cem anos, por Flexner, tem contribuído para a desvalorização das componentes psicoemocionais e sociais dos fenómenos de saúde e de doença, assim como para criar clivagens entre cuidados curativos e preventivos e entre medicina geral e familiar e saúde pública. Porém, o actual padrão de saúde/doença próprio das sociedades desenvolvidas, caracterizado por “pandemias” de doenças crónicas e incapacitantes, determinadas por factores de natureza sociocultural e comportamental, irá obrigar certamente à revisão daquele paradigma e à necessidade de se (re)adoptarem os grandes princípios Hipocráticos de compreensão dos processos de saúde/doença e do papel da medicina.

Development of oxidoreductase based electrochemical biosensors

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Comparative effects of sediments contaminated by carcinogenic and non-carcinogenic PAHs in Dicentrarchus labrax: a semi-quantitative histopathological approach

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente

Human activity data discovery based on accelerometry

Dissertation to Obtain Master Degree in Biomedical Engineering

Bioinspired polyethersulfone-based hollow fiber membranes as the scaffolds in renal assist device for protein-bound toxins removal from blood

Dissertation for obtaining the Master degree in Membrane Engineering

Relating the spatial component and users interests to improve applications based on questions, petitions and participatory processes

Nowadays, participatory processes attending the need for real democracy and transparency in governments and collectives are more needed than ever. Immediate participation through channels like social networks enable people to give their opinion and become pro-active citizens, seeking applications to interact with each other. The application described in this dissertation is a hybrid channel of communication of questions, petitions and participatory processes based on Public Participation Geographic Information System (PPGIS), Participation Geographic Information System (PGIS) and ‘soft’ (subjective data) Geographic Information System (SoftGIS) methodologies. To achieve a new approach to an application, its entire design is focused on the spatial component related with user interests. The spatial component is treated as main feature of the system to develop all others depending on it, enabling new features never seen before in social actions (questions, petitions and participatory processes). Results prove that it is possible to develop a working application mainly using open source software, with the possibility of spatial and subject filtering, visualizing and free download of actions within application. The resulting application empowers society by releasing soft data and defines a new breaking approach, unseen so far.

UAV - based imagery processing using structure from motion and remote sensing technology

With the recent advances in technology and miniaturization of devices such as GPS or IMU, Unmanned Aerial Vehicles became a feasible platform for a Remote Sensing applications. The use of UAVs compared to the conventional aerial platforms provides a set of advantages such as higher spatial resolution of the derived products. UAV - based imagery obtained by a user grade cameras introduces a set of problems which have to be solved, e. g. rotational or angular differences or unknown or insufficiently precise IO and EO camera parameters. In this work, UAV - based imagery of RGB and CIR type was processed using two different workflows based on PhotoScan and VisualSfM software solutions resulting in the DSM and orthophoto products. Feature detection and matching parameters influence on the result quality as well as a processing time was examined and the optimal parameter setup was presented. Products of the both workflows were compared in terms of a quality and a spatial accuracy. Both workflows were compared by presenting the processing times and quality of the results. Finally, the obtained products were used in order to demonstrate vegetation classification. Contribution of the IHS transformations was examined with respect to the classification accuracy.

The brushstroke and materials of Amadeo de Souza-Cardoso combined in an authentication tool

Nowadays, authentication studies for paintings require a multidisciplinary approach, based on the contribution of visual features analysis but also on characterizations of materials and techniques. Moreover, it is important that the assessment of the authorship of a painting is supported by technical studies of a selected number of original artworks that cover the entire career of an artist. This dissertation is concerned about the work of modernist painter Amadeo de Souza-Cardoso. It is divided in three parts. In the first part, we propose a tool based on image processing that combines information obtained by brushstroke and materials analysis. The resulting tool provides qualitative and quantitative evaluation of the authorship of the paintings; the quantitative element is particularly relevant, as it could be crucial in solving authorship controversies, such as judicial disputes. The brushstroke analysis was performed by combining two algorithms for feature detection, namely Gabor filter and Scale Invariant Feature Transform. Thanks to this combination (and to the use of the Bag-of-Features model), the proposed method shows an accuracy higher than 90% in distinguishing between images of Amadeo’s paintings and images of artworks by other contemporary artists. For the molecular analysis, we implemented a semi-automatic system that uses hyperspectral imaging and elemental analysis. The system provides as output an image that depicts the mapping of the pigments present, together with the areas made using materials not coherent with Amadeo’s palette, if any. This visual output is a simple and effective way of assessing the results of the system. The tool proposed based on the combination of brushstroke and molecular information was tested in twelve paintings obtaining promising results. The second part of the thesis presents a systematic study of four selected paintings made by Amadeo in 1917. Although untitled, three of these paintings are commonly known as BRUT, Entrada and Coty; they are considered as his most successful and genuine works. The materials and techniques of these artworks have never been studied before. The paintings were studied with a multi-analytical approach using micro-Energy Dispersive X-ray Fluorescence spectroscopy, micro-Infrared and Raman Spectroscopy, micro-Spectrofluorimetry and Scanning Electron Microscopy. The characterization of Amadeo’s materials and techniques used on his last paintings, as well as the investigation of some of the conservation problems that affect these paintings, is essential to enrich the knowledge on this artist. Moreover, the study of the materials in the four paintings reveals commonalities between the paintings BRUT and Entrada. This observation is supported also by the analysis of the elements present in a photograph of a collage (conserved at the Art Library of the Calouste Gulbenkian Foundation), the only remaining evidence of a supposed maquete of these paintings. The final part of the thesis describes the application of the image processing tools developed in the first part of the thesis on a set of case studies; this experience demonstrates the potential of the tool to support painting analysis and authentication studies. The brushstroke analysis was used as additional analysis on the evaluation process of four paintings attributed to Amadeo, and the system based on hyperspectral analysis was applied on the painting dated 1917. The case studies therefore serve as a bridge between the first two parts of the dissertation.

Modeling and optimization of extracellular polysaccharides production by Enterobacter A47

Polysaccharides are gaining increasing attention as potential environmental friendly and sustainable building blocks in many fields of the (bio)chemical industry. The microbial production of polysaccharides is envisioned as a promising path, since higher biomass growth rates are possible and therefore higher productivities may be achieved compared to vegetable or animal polysaccharides sources. This Ph.D. thesis focuses on the modeling and optimization of a particular microbial polysaccharide, namely the production of extracellular polysaccharides (EPS) by the bacterial strain Enterobacter A47. Enterobacter A47 was found to be a metabolically versatile organism in terms of its adaptability to complex media, notably capable of achieving high growth rates in media containing glycerol byproduct from the biodiesel industry. However, the industrial implementation of this production process is still hampered due to a largely unoptimized process. Kinetic rates from the bioreactor operation are heavily dependent on operational parameters such as temperature, pH, stirring and aeration rate. The increase of culture broth viscosity is a common feature of this culture and has a major impact on the overall performance. This fact complicates the mathematical modeling of the process, limiting the possibility to understand, control and optimize productivity. In order to tackle this difficulty, data-driven mathematical methodologies such as Artificial Neural Networks can be employed to incorporate additional process data to complement the known mathematical description of the fermentation kinetics. In this Ph.D. thesis, we have adopted such an hybrid modeling framework that enabled the incorporation of temperature, pH and viscosity effects on the fermentation kinetics in order to improve the dynamical modeling and optimization of the process. A model-based optimization method was implemented that enabled to design bioreactor optimal control strategies in the sense of EPS productivity maximization. It is also critical to understand EPS synthesis at the level of the bacterial metabolism, since the production of EPS is a tightly regulated process. Methods of pathway analysis provide a means to unravel the fundamental pathways and their controls in bioprocesses. In the present Ph.D. thesis, a novel methodology called Principal Elementary Mode Analysis (PEMA) was developed and implemented that enabled to identify which cellular fluxes are activated under different conditions of temperature and pH. It is shown that differences in these two parameters affect the chemical composition of EPS, hence they are critical for the regulation of the product synthesis. In future studies, the knowledge provided by PEMA could foster the development of metabolically meaningful control strategies that target the EPS sugar content and oder product quality parameters.

Implementation of a probabilistic based framework for safety assessment of existing timber elements

The assessment of existing timber structures is often limited to information obtained from non or semi destructive testing, as mechanical testing is in many cases not possible due to its destructive nature. Therefore, the available data provides only an indirect measurement of the reference mechanical properties of timber elements, often obtained through empirical based correlations. Moreover, the data must result from the combination of different tests, as to provide a reliable source of information for a structural analysis. Even if general guidelines are available for each typology of testing, there is still a need for a global methodology allowing to combine information from different sources and infer upon that information in a decision process. In this scope, the present work presents the implementation of a probabilistic based framework for safety assessment of existing timber elements. This methodology combines information gathered in different scales and follows a probabilistic framework allowing for the structural assessment of existing timber elements with possibility of inference and updating of its mechanical properties, through Bayesian methods. The probabilistic based framework is based in four main steps: (i) scale of information; (ii) measurement data; (iii) probability assignment; and (iv) structural analysis. In this work, the proposed methodology is implemented in a case study. Data was obtained through a multi-scale experimental campaign made to old chestnut timber beams accounting correlations of non and semi-destructive tests with mechanical properties. Finally, different inference scenarios are discussed aiming at the characterization of the safety level of the elements.

Ontology-based representation and generation of workflows for micro-task human-machine computation

Doctoral Program in Computer Science

MOEA/VAN: Multiobjective Evolutionary Algorithm based on Vector Angle Neighborhood

Natural selection favors the survival and reproduction of organisms that are best adapted to their environment. Selection mechanism in evolutionary algorithms mimics this process, aiming to create environmental conditions in which artificial organisms could evolve solving the problem at hand. This paper proposes a new selection scheme for evolutionary multiobjective optimization. The similarity measure that defines the concept of the neighborhood is a key feature of the proposed selection. Contrary to commonly used approaches, usually defined on the basis of distances between either individuals or weight vectors, it is suggested to consider the similarity and neighborhood based on the angle between individuals in the objective space. The smaller the angle, the more similar individuals. This notion is exploited during the mating and environmental selections. The convergence is ensured by minimizing distances from individuals to a reference point, whereas the diversity is preserved by maximizing angles between neighboring individuals. Experimental results reveal a highly competitive performance and useful characteristics of the proposed selection. Its strong diversity preserving ability allows to produce a significantly better performance on some problems when compared with stat-of-the-art algorithms.