Simulations of Antigenic Variability in Influenza A

Computational models of the immune system (IS) and pathogenic agents have several applications, such as theory testing and validation, or as a complement to first stages of drug trials. One possible application is the prediction of the lethality of new Influenza A strains, which are constantly created due to antigenic drift and shift. Here, we present several simulations of antigenic variability in Influenza A using an agent-based approach, where low level molecular antigen-antibody interactions are explicitly described. Antigenic drift and shift events are analyzed regarding the virulence of emergent strains against the IS. Results are discussed from a qualitative point of view taking into account recent and generally recognized immunology and influenza literature

A General Framework for Representing, Reasoning and Querying with Annotated Semantic Web Data

We describe a generic framework for representing and reasoning with annotated Semantic Web data, a task becoming more important with the recent increased amount of inconsistent and non-reliable meta-data on the web. We formalise the annotated language, the corresponding deductive system and address the query answering problem. Previous contributions on specific RDF annotation domains are encompassed by our unified reasoning formalism as we show by instantiating it on (i) temporal, (ii) fuzzy, and (iii) provenance annotations. Moreover, we provide a generic method for combining multiple annotation domains allowing to represent, e.g. temporally-annotated fuzzy RDF. Furthermore, we address the development of a query language -- AnQL -- that is inspired by SPARQL, including several features of SPARQL 1.1 (subqueries, aggregates, assignment, solution modifiers) along with the formal definitions of their semantics

Fuzzy logic based approach for object feature tracking

This thesis introduces a novel technique for feature tracking in sequences of greyscale images based on fuzzy logic. A versatile and modular methodology for feature tracking using fuzzy sets and inference engines is presented. Moreover, an extension of this methodology to perform the correct tracking of multiple features is also presented. To perform feature tracking three membership functions are initially defined. A membership function related to the distinctive property of the feature to be tracked. A membership function is related to the fact of considering that the feature has smooth movement between each image sequence and a membership function concerns its expected future location. Applying these functions to the image pixels, the corresponding fuzzy sets are obtained and then mathematically manipulated to serve as input to an inference engine. Situations such as occlusion or detection failure of features are overcome using estimated positions calculated using a motion model and a state vector of the feature. This methodology was previously applied to track a single feature identified by the user. Several performance tests were conducted on sequences of both synthetic and real images. Experimental results are presented, analysed and discussed. Although this methodology could be applied directly to multiple feature tracking, an extension of this methodology has been developed within that purpose. In this new method, the processing sequence of each feature is dynamic and hierarchical. Dynamic because this sequence can change over time and hierarchical because features with higher priority will be processed first. Thus, the process gives preference to features whose location are easier to predict compared with features whose knowledge of their behavior is less predictable. When this priority value becomes too low, the feature will no longer tracked by the algorithm. To access the performance of this new approach, sequences of images where several features specified by the user are to be tracked were used. In the final part of this work, conclusions drawn from this work as well as the definition of some guidelines for future research are presented.Nesta tese é introduzida uma nova técnica de seguimento de pontos característicos de objectos em sequências de imagens em escala de cinzentos baseada em lógica difusa. É apresentada uma metodologia versátil e modular para o seguimento de objectos utilizando conjuntos difusos e motores de inferência. É também apresentada uma extensão desta metodologia para o correcto seguimento de múltiplos pontos característicos. Para se realizar o seguimento são definidas inicialmente três funções de pertença. Uma função de pertença está relacionada com a propriedade distintiva do objecto que desejamos seguir, outra está relacionada com o facto de se considerar que o objecto tem uma movimentação suave entre cada imagem da sequência e outra função de pertença referente à sua previsível localização futura. Aplicando estas funções de pertença aos píxeis da imagem, obtêm-se os correspondentes conjuntos difusos, que serão manipulados matematicamente e servirão como entrada num motor de inferência. Situações como a oclusão ou falha na detecção dos pontos característicos são ultrapassadas utilizando posições estimadas calculadas a partir do modelo de movimento e a um vector de estados do objecto. Esta metodologia foi inicialmente aplicada no seguimento de um objecto assinalado pelo utilizador. Foram realizados vários testes de desempenho em sequências de imagens sintéticas e também reais. Os resultados experimentais obtidos são apresentados, analisados e discutidos. Embora esta metodologia pudesse ser aplicada directamente ao seguimento de múltiplos pontos característicos, foi desenvolvida uma extensão desta metodologia para esse fim. Nesta nova metodologia a sequência de processamento de cada ponto característico é dinâmica e hierárquica. Dinâmica por ser variável ao longo do tempo e hierárquica por existir uma hierarquia de prioridades relativamente aos pontos característicos a serem seguidos e que determina a ordem pela qual esses pontos são processados. Desta forma, o processo dá preferência a pontos característicos cuja localização é mais fácil de prever comparativamente a pontos característicos cujo conhecimento do seu comportamento seja menos previsível. Quando esse valor de prioridade se torna demasiado baixo, esse ponto característico deixa de ser seguido pelo algoritmo. Para se observar o desempenho desta nova abordagem foram utilizadas sequências de imagens onde várias características indicadas pelo utilizador são seguidas. Na parte final deste trabalho são apresentadas as conclusões resultantes a partir do desenvolvimento deste trabalho, bem como a definição de algumas linhas de investigação futura

Business plan: antimalarial solutions

JEL Classification: L65, M13Malaria is an infectious disease that have caused huge losses to the human being, mainly for those who live in malaria endemic regions. In one hand, public entities spend millions in methods to avoid the transmission, in the treatment of infected people or in the eradication of the disease. In the other hand, half of the human population is at risk and there is half million deaths yearly, being considered one of the most dangerous diseases. Additionally to those who live in endemic regions, millions of travellers visit endemic regions yearly, causing an increase of the problem. As follows, the awareness around this infectious disease has been increasing, mainly due to the increase of the tourism around the world. The incorrect use of the existing medicines has induced to increasing the parasite resistance, reducing the efficiency of those medicines. In this way, it is imperative the development and launching of new medicines that could solve this problem. This problem was detected and both pharmaceutical companies and other entities are increasing their efforts in research and development, in order to find new antimalarial medicines that may decrease the malaria burden. However, the investment needed to the development of new medicines is excessively high, which means that not all the companies and entities are capable of performing those activities. Considering what was said above, the main objective of this Business Plan is to analyse the economic and financial viability of the development of a new antimalarial medicine.A malária é uma doença infeciosa que nos últimos anos tem causado enormes prejuízos para o ser humano, principalmente para aqueles que vivem nas regiões endémicas. Por um lado, todos os anos as entidades governamentais gastam milhões de euros em meios para evitar o contágio, no tratamento dos pacientes ou na erradicação da doença. Por outro, esta doença é das mais mortíferas no mundo, estando cerca de metade da população em risco de contágio, havendo centenas de milhar de mortes por ano. Para além das pessoas que vivem diretamente em contacto com a malária, milhões de viajantes visitam aquelas zonas anualmente, aumentando ainda mais o problema. Desta forma, a preocupação em torno desta doença tem vindo a aumentar, um pouco devido ao aumento dos fluxos de turismo mundial. Devido ao uso indevido dos medicamentos existentes, o parasita da malária tem vindo a ganhar resistência aos mesos, sendo estes medicamentos menos eficazes. Desta forma, torna-se urgente o desenvolvimento de novos medicamentos que possam fazer face a este cenário. Ao perceber este problema, tanto empresas farmacêuticas como outras entidades têm vindo a multiplicar esforços para que, através de investigação e desenvolvimento, apareçam novos medicamentos que atenuem as perdas provocadas pela malária. No entanto, o investimento necessário para desenvolver novos medicamentos é demasiado elevado e nem todas as entidades têm a capacidade para o fazer. Posto isto, o principal objetivo deste Plano de Negócios é o estudo da viabilidade económica e financeira do desenvolvimento de um novo medicamento que possa combater a malária

The relative importance of financial and non-financial analysis in project evaluation – evidence from portuguese firms

Project appraisal has traditionally put its emphasis on the financial aspects of projects, mainly the quantitative ones, underestimating other areas of analyses where factors of a qualitative nature, intangible and subjective, may also affect the implementation and value of projects. Non financial evaluation supply information about less tangible factors and is expected to identify competitive advantages and risks that financial techniques cannot capture. In general there are few empirical studies addressing these other aspects. Most surveys are addressed to the financial techniques. We have done a survey, aimed at the non financial aspects of projects, which is the base of two papers. In this first paper, we aimed to identify the importance of non financial aspects at the decision making process and the evaluation of projects, and in particular to investigate the practices of Portuguese companies in this field. The results of our study support the importance of incorporating non financial aspects into the appraisal of projects, and show how some of those aspects have greater relevance than that attributed to the financial elements. The study also points to the strategic and technical aspects of projects as the most relevant non financial factors considered by Portuguese firms. The financial analysis, according to the empirical data collected, comes only in third place of importance, both at the appraisal and at the decision-making stages. Commercial factors, showed similar relevance to the financial ones