DNA nanoprobes for molecular detection

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Biológica – especialidade Engenharia Genética, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Algorithms for time series clustering applied to biomedical signals

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical Engineering

New strategies to detect and understand genotype-by-environment interactions and QTL-by-environment interactions

Dissertação para obtenção do Grau de Doutor em Estatística e Gestão do Risco, especialidade em Estatística

Type-based protocol conformance and aliasing control in concurrent java programs

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

On-line system for faults detection in induction motors based on PCA

Dissertation to obtain the degree of Master in Electrical and Computer Engineering

Atitudes, conhecimentos e práticas dos médicos de família face aos rastreios de autonomia funcional multidimensional em pessoas idosas

RESUMO - O envelhecimento demográfico é uma constatação e ao mesmo tempo uma oportunidade para viver de forma mais saudável e autónoma o mais tempo possível. A principal razão para a admissão de pessoas idosas em instituições e para o uso desproporcionado de serviços de saúde é o declínio funcional que acompanha o envelhecimento. Os Cuidados de Saúde Primários apresentam‐se como contexto ideal para promover cuidados antecipatórios. A avaliação da autonomia funcional multidimensional permite a detecção de perturbações incipientes. Os programas de rastreios facilitam o desencadear de recursos para a detecção precoce e tratamento. Os médicos sentem diversas barreiras na aplicação dos rastreios, como a falta de familiaridade com os testes, bem como a falta de tempo ou recursos. O estudo aqui proposto visa conhecer, a título exploratório, as atitudes dos médicos de família face aos rastreios de autonomia funcional multidimensional em pessoas idosas; avaliar o grau de conhecimento sobre esta abordagem multidimensional, no que diz respeito às áreas e instrumentos a avaliar; caracterizar as práticas na prestação de cuidados preventivos às pessoas idosas e caracterizar as condições genéricas necessárias para a aplicação destes rastreios no contexto dos cuidados de saúde primários. Para tal, irá basear‐se num questionário auto‐administrado aos médicos de família dos 22 Agrupamentos de Centros de Saúde, na Região de Saúde de Lisboa e Vale do Tejo. As suas conclusões poderão contribuir para uma uniformização do conceito de autonomia funcional multidimensional e para a realização de um levantamento de necessidades de formação sobre a abordagem multidimensional e interdisciplinar.

Bullwhip effect, in production control: a comparison between traditional methods and LPS

21th Annual Conference of the International Group for Lean Construction (IGLC 21), July 2013, Fortaleza, Brazil

Development of an equipment to detect and quantify muscular spasticity

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Data fusion with computational intelligence techniques: a case study of fuzzy inference for terrain assessment

Dissertação apresentada para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

A semi-automatic approach to code smells detection

Eradication of code smells is often pointed out as a way to improve readability, extensibility and design in existing software. However, code smell detection remains time consuming and error-prone, partly due to the inherent subjectivity of the detection processes presently available. In view of mitigating the subjectivity problem, this dissertation presents a tool that automates a technique for the detection and assessment of code smells in Java source code, developed as an Eclipse plugin. The technique is based upon a Binary Logistic Regression model that uses complexity metrics as independent variables and is calibrated by expert‟s knowledge. An overview of the technique is provided, the tool is described and validated by an example case study.

Gold nanoparticles for the detection of DNA adducts as biomarkers of exposure to acrylamide

The main objective of this thesis was the development of a gold nanoparticle-based methodology for detection of DNA adducts as biomarkers, to try and overcome existing drawbacks in currently employed techniques. For this objective to be achieved, the experimental work was divided in three components: sample preparation, method of detection and development of a model for exposure to acrylamide. Different techniques were employed and combined for de-complexation and purification of DNA samples (including ultrasonic energy, nuclease digestion and chromatography), resulting in a complete protocol for sample treatment, prior to detection. The detection of alkylated nucleotides using gold nanoparticles was performed by two distinct methodologies: mass spectrometry and colorimetric detection. In mass spectrometry, gold nanoparticles were employed for laser desorption/ionisation instead of the organic matrix. Identification of nucleotides was possible by fingerprint, however no specific mass signals were denoted when using gold nanoparticles to analyse biological samples. An alternate method using the colorimetric properties of gold nanoparticles was employed for detection. This method inspired in the non-cross-linking assay allowed the identification of glycidamide-guanine adducts and DNA adducts generated in vitro. For the development of a model of exposure, two different aquatic organisms were studies: a goldfish and a mussel. Organisms were exposed to waterborne acrylamide, after which mortality was recorded and effect concentrations were estimated. In goldfish, both genotoxicity and metabolic alterations were assessed and revealed dose-effect relationships of acrylamide. Histopathological alterations were verified primarily in pancreatic cells, but also in hepatocytes. Mussels showed higher effect concentrations than goldfish. Biomarkers of oxidative stress, biotransformation and neurotoxicity were analysed after prolonged exposure, showing mild oxidative stress in mussel cells, and induction of enzymes involved in detoxification of oxygen radicals. A qualitative histopathological screening revealed gonadotoxicity in female mussels, which may present some risk to population equilibrium.

Automatic extraction of concepts from texts and applications

The extraction of relevant terms from texts is an extensively researched task in Text- Mining. Relevant terms have been applied in areas such as Information Retrieval or document clustering and classification. However, relevance has a rather fuzzy nature since the classification of some terms as relevant or not relevant is not consensual. For instance, while words such as "president" and "republic" are generally considered relevant by human evaluators, and words like "the" and "or" are not, terms such as "read" and "finish" gather no consensus about their semantic and informativeness. Concepts, on the other hand, have a less fuzzy nature. Therefore, instead of deciding on the relevance of a term during the extraction phase, as most extractors do, I propose to first extract, from texts, what I have called generic concepts (all concepts) and postpone the decision about relevance for downstream applications, accordingly to their needs. For instance, a keyword extractor may assume that the most relevant keywords are the most frequent concepts on the documents. Moreover, most statistical extractors are incapable of extracting single-word and multi-word expressions using the same methodology. These factors led to the development of the ConceptExtractor, a statistical and language-independent methodology which is explained in Part I of this thesis. In Part II, I will show that the automatic extraction of concepts has great applicability. For instance, for the extraction of keywords from documents, using the Tf-Idf metric only on concepts yields better results than using Tf-Idf without concepts, specially for multi-words. In addition, since concepts can be semantically related to other concepts, this allows us to build implicit document descriptors. These applications led to published work. Finally, I will present some work that, although not published yet, is briefly discussed in this document.

Implementation of membrane processes for improvement of the detection of food contaminants

The EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centres and universities (http://www.em3e.eu)