Quality of process modeling using BPMN: a model-driven approach

Dissertação para obtenção do Grau de Doutor em Engenharia Informática

A system’s approach to cache hierarchy-aware decomposition of data-parallel computations

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

A clustering approach for vehicle routing problems with hard time windows

Dissertação para obtenção do Grau de Mestre em Logica Computicional

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.

Studies towards modified chitooligosaccharides: a new approach to NAG-NAM moiety

Dissertação para obtenção do Grau de Mestre em Bioorgânica

Development of an integrative approach for the characterization of ecological risk on marine transition ecosystems: the Sado Estuary as a case study

Estuaries and other transitional waters are complex ecosystems critically important as nursery and shelter areas for organisms. Also, humans depend on estuaries for multiple socio-economical activities such as urbanism, tourism, heavy industry, (taking advantage of shipping), fisheries and aquaculture, the development of which led to strong historical pressures, with emphasis on pollution. The degradation of estuarine environmental quality implies ecologic, economic and social prejudice, hence the importance of evaluating environmental quality through the identification of stressors and impacts. The Sado Estuary (SW Portugal) holds the characteristics of industrialized estuaries, which results in multiple adverse impacts. Still, it has recently been considered moderately contaminated. In fact, many studies were conducted in the past few years, albeit scattered due to the absence of true biomonitoring programmes. As such, there is a need to integrate the information, in order to obtain a holistic perspective of the area able to assist management and decision-making. As such, a geographical information system (GIS) was created based on sediment contamination and biomarker data collected from a decade-long time-series of publications. Four impacted and a reference areas were identified, characterized by distinct sediment contamination patterns related to different hot spots and diffuse sources of toxicants. The potential risk of sediment-bound toxicants was determined by contrasting the levels of pollutants with available sediment quality guidelines, followed by their integration through the Sediment Quality guideline Quotient (SQG-Q). The SQG-Q estimates per toxicant or class was then subjected to georreferencing and statistical analyses between the five distinct areas and seasons. Biomarker responses were integrated through the Biomarkers Consistency Indice and georreferenced as well through GIS. Overall, in spite of the multiple biological traits surveyed, the biomarker data (from several organisms) are accordant with sediment contamination. The most impacted areas were the shipyard area and adjacent industrial belt, followed by urban and agricultural grounds. It is evident that the estuary, although globally moderately impacted, is very heterogeneous and affected by a cocktail of contaminants, especially metals and polycyclic aromatic hydrocarbon. Although elements (like copper, zinc and even arsenic) may originate from the geology of the hydrographic basin of the Sado River, the majority of the remaining contaminants results from human activities. The present work revealed that the estuary should be divided into distinct biogeographic units, in order to implement effective measures to safeguard environmental quality.

Proteomics based approach to understand tissue regeneration

Dissertation presented to obtain the PhD degree in Biochemistry

Wound Healing: a genetic approach in Drosophila

The wound healing response is an essential mechanism to maintain the integrity of epithelia and protect all organisms from the surrounding milieu. In the “purse-string” mechanism of wound closure, an injured epithelial sheet cinches its hole closed via an intercellular contractile actomyosin cable.(...)

Spiteful Strategies. The ontogeny and the practice of spite in human interaction: an experimental game theory approach and empirical applications

As estratégias de malevolência implicam que um indivíduo pague um custo para infligir um custo superior a um oponente. Como um dos comportamentos fundamentais da sociobiologia, a malevolência tem recebido menos atenção que os seus pares o egoísmo e a cooperação. Contudo, foi estabelecido que a malevolência é uma estratégia viável em populações pequenas quando usada contra indivíduos negativamente geneticamente relacionados pois este comportamento pode i) ser eliminado naturalmente, ou ii) manter-se em equilíbrio com estratégias cooperativas devido à disponibilidade da parte de indivíduos malevolentes de pagar um custo para punir. Esta tese propõe compreender se a propensão para a malevolência nos humanos é inerente ou se esta se desenvolve com a idade. Para esse efeito, considerei duas experiências de teoria de jogos em crianças em ambiente escolar com idades entre os 6 e os 22 anos. A primeira, um jogo 2x2 foi testada com duas variantes: 1) um prémio foi atribuído a ambos os jogadores, proporcionalmente aos pontos acumulados; 2), um prémio foi atribuído ao jogador com mais pontos. O jogo foi desenhado com o intuito de causar o seguinte dilema a cada jogador: i) maximizar o seu ganho e arriscar ter menos pontos que o adversário; ou ii) decidir não maximizar o seu ganho, garantindo que este não era inferior ao do seu adversário. A segunda experiência consistia num jogo do ditador com duas opções: uma escolha egoísta/altruísta (A), onde o ditador recebia mais ganho, mas o seu recipiente recebia mais que ele e uma escolha malevolente (B) que oferecia menos ganhos ao ditador que a A mas mais ganhos que o recipiente. O dilema era que se as crianças se comportassem de maneira egoísta, obtinham mais ganho para si, ao mesmo tempo que aumentavam o ganho do seu colega. Se fossem malevolentes, então prefeririam ter mais ganho que o seu colega ao mesmo tempo que tinham menos para eles próprios. As experiências foram efetuadas em escolas de duas áreas distintas de Portugal (continente e Açores) para perceber se as preferências malevolentes aumentavam ou diminuíam com a idade. Os resultados na primeira experiência sugerem que (1) os alunos compreenderam a primeira variante como um jogo de coordenação e comportaram-se como maximizadores, copiando as jogadas anteriores dos seus adversários; (2) que os alunos repetentes se comportaram preferencialmente como malevolentes, mais frequentemente que como maximizadores, com especial ênfase para os alunos de 14 anos; (3) maioria dos alunos comportou-se reciprocamente desde os 12 até aos 16 anos de idade, após os quais começaram a desenvolver uma maior tolerância às escolhas dos seus parceiros. Os resultados da segunda experiência sugerem que (1) as estratégias egoístas eram prevalentes até aos 6 anos de idade, (2) as tendências altruístas emergiram até aos 8 anos de idade e (3) as estratégias de malevolência começaram a emergir a partir dos 8 anos de idade. Estes resultados complementam a literatura relativamente escassa sobre malevolência e sugerem que este comportamento está intimamente ligado a preferências de consideração sobre os outros, o paroquialismo e os estágios de desenvolvimento das crianças.************************************************************Spite is defined as an act that causes loss of payoff to an opponent at a cost to the actor. As one of the four fundamental behaviours in sociobiology, it has received far less attention than its counterparts selfishness and cooperation. It has however been established as a viable strategy in small populations when used against negatively related individuals. Because of this, spite can either i) disappear or ii) remain at equilibrium with cooperative strategies due to the willingness of spiteful individuals to pay a cost in order to punish. This thesis sets out to understand whether propensity for spiteful behaviour is inherent or if it develops with age. For that effect, two game-theoretical experiments were performed with schoolboys and schoolgirls aged 6 to 22. The first, a 2 x 2 game, was tested in two variants: 1) a prize was awarded to both players, proportional to accumulated points; 2), a prize was given to the player with most points. Each player faced the following dilemma: i) to maximise pay-off risking a lower pay-off than the opponent; or ii) not to maximise pay-off in order to cut down the opponent below their own. The second game was a dictator experiment with two choices, (A) a selfish/altruistic choice affording more payoff to the donor than B, but more to the recipient than to the donor, and (B) a spiteful choice that afforded less payoff to the donor than A, but even lower payoff to the recipient. The dilemma here was that if subjects behaved selfishly, they obtained more payoff for themselves, while at the same time increasing their opponent payoff. If they were spiteful, they would rather have more payoff than their colleague, at the cost of less for themselves. Experiments were run in schools in two different areas in Portugal (mainland and Azores) to understand whether spiteful preferences varied with age. Results in the first experiment suggested that (1) students understood the first variant as a coordination game and engaged in maximising behaviour by copying their opponent’s plays; (2) repeating students preferentially engaged in spiteful behaviour more often than maximising behaviour, with special emphasis on 14 year-olds; (3) most students engaged in reciprocal behaviour from ages 12 to 16, as they began developing higher tolerance for their opponent choices. Results for the second experiment suggested that (1) selfish strategies were prevalent until the age of 6, (2) altruistic tendencies emerged since then, and (3) spiteful strategies began being chosen more often by 8 year-olds. These results add to the relatively scarce body of literature on spite and suggest that this type of behaviour is closely tied with other-regarding preferences, parochialism and the children’s stages of development.

State detection in a financial portfolio: a self-organizing maps approach for financial time series

This study analyses financial data using the result characterization of a self-organized neural network model. The goal was prototyping a tool that may help an economist or a market analyst to analyse stock market series. To reach this goal, the tool shows economic dependencies and statistics measures over stock market series. The neural network SOM (self-organizing maps) model was used to ex-tract behavioural patterns of the data analysed. Based on this model, it was de-veloped an application to analyse financial data. This application uses a portfo-lio of correlated markets or inverse-correlated markets as input. After the anal-ysis with SOM, the result is represented by micro clusters that are organized by its behaviour tendency. During the study appeared the need of a better analysis for SOM algo-rithm results. This problem was solved with a cluster solution technique, which groups the micro clusters from SOM U-Matrix analyses. The study showed that the correlation and inverse-correlation markets projects multiple clusters of data. These clusters represent multiple trend states that may be useful for technical professionals.

Efficient paraconsistent reasoning with rules and ontologies for the semantic web

Ontologies formalized by means of Description Logics (DLs) and rules in the form of Logic Programs (LPs) are two prominent formalisms in the field of Knowledge Representation and Reasoning. While DLs adhere to the OpenWorld Assumption and are suited for taxonomic reasoning, LPs implement reasoning under the Closed World Assumption, so that default knowledge can be expressed. However, for many applications it is useful to have a means that allows reasoning over an open domain and expressing rules with exceptions at the same time. Hybrid MKNF knowledge bases make such a means available by formalizing DLs and LPs in a common logic, the Logic of Minimal Knowledge and Negation as Failure (MKNF). Since rules and ontologies are used in open environments such as the Semantic Web, inconsistencies cannot always be avoided. This poses a problem due to the Principle of Explosion, which holds in classical logics. Paraconsistent Logics offer a solution to this issue by assigning meaningful models even to contradictory sets of formulas. Consequently, paraconsistent semantics for DLs and LPs have been investigated intensively. Our goal is to apply the paraconsistent approach to the combination of DLs and LPs in hybrid MKNF knowledge bases. In this thesis, a new six-valued semantics for hybrid MKNF knowledge bases is introduced, extending the three-valued approach by Knorr et al., which is based on the wellfounded semantics for logic programs. Additionally, a procedural way of computing paraconsistent well-founded models for hybrid MKNF knowledge bases by means of an alternating fixpoint construction is presented and it is proven that the algorithm is sound and complete w.r.t. the model-theoretic characterization of the semantics. Moreover, it is shown that the new semantics is faithful w.r.t. well-studied paraconsistent semantics for DLs and LPs, respectively, and maintains the efficiency of the approach it extends.

Enhancement of an implemented rating model and impact on existing risk management processes: A hands-on approach from financial supplier risk management within the automotive industry

The purpose of this paper is to conduct a methodical drawback analysis of a financial supplier risk management approach which is currently implemented in the automotive industry. Based on identified methodical flaws, the risk assessment model is further developed by introducing a malus system which incorporates hidden risks into the model and by revising the derivation of the most central risk measure in the current model. Both methodical changes lead to significant enhancements in terms of risk assessment accuracy, supplier identification and workload efficiency.

Liberdade e tolerância religiosa: "portugueses não católicos" no ultramar do século XIX

The personal legal status of native non catholic people of Portuguese colonial Empire during the nineteenth century, their position in what concerns Portuguese citizenship, is the main subject of this article. While discussing constitutional articles on religion, Portuguese deputies of the nineteenth century were confronted with a set of problems about that status which they find difficult to solve: should non catholic peoples who were born in Portuguese colonial territory be treated as plain Portuguese citizens or where they just “savage people”, “colonial subjects” or, in a more optimistic approach, “civilizing subjects”. The results were not conclusive, giving rise to an “uncertainty principle” which enabled central and local government to decide in an almost casuistic way about native people status and rights.

An integrated approach to Physcomitrella patens transcriptomics reveals importantclues of the evolutionary development of plant organs and sexual reproduction

Land plant evolution required the generation of a new body plan that could resist the harsher and fluctuating environmental conditions found outside of aquatic environments. Unraveling the genetic basis of plant developmental innovations is not only revealing in terms of an evolutionary point of view, but it is also important for understanding the emergence of agronomically important traits. Comparative genetic studies between basal and modern land plants, both at the genome and trancriptome levels, can help in the generation of hypotheses related to the genetic basis of plant evolutionary development.(...)

Fiscal policy under financial stress: A threshold VAR approach

The purpose of the project is to measure the impact of fiscal policy on the Portuguese GDP and how it may vary according to the state of the financial market. A Threshold VAR model is presented in which the two regimes are found using a financial stress index that divides the economy into a situation of financial stress and financial stability.