Downstream processing development of enveloped viruses for clinical applications: innovative tools for rational process optimization

Dissertation presented to obtain a Ph.D. degree in Engineering and Technology Sciences, Biotechnology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

European institutions at your fingertips: EUROPA gateway tools for dissemination and access to information

This paper intends to present the legal background that support dissemination and access to documents from European institutions, namely the Parliament, the Council and the European Commission. Currently, this legal framework is accomplished with a set of Internet tools that are analyzed regarding official documents types and options searches available. Some statistical data on access to European information published in annual reports from the institutions are also evaluated. The relationship between shadow and light in transparency to access administrative documents and marketing issues of a political communication are underlined. Neo-institutional approach, reputational concept in public organizations and systemic perspective are used as theoretical background.

Adapting Meeting Tools to Agent Decision

Electricity markets are complex environments comprising several negotiation mechanisms. MASCEM (Multi- Agent System for Competitive Electricity Markets) is a simulator developed to allow deep studies of the interactions between the players that take part in the electricity market negotiations. ALBidS (Adaptive Learning Strategic Bidding System) is a multiagent system created to provide decision support to market negotiating players. Fully integrated with MASCEM it considers several different methodologies based on very distinct approaches. The Six Thinking Hats is a powerful technique used to look at decisions from different perspectives. This paper aims to complement ALBidS strategies usage by MASCEM players, providing, through the Six Thinking Hats group decision technique, a means to combine them and take advantages from their different perspectives. The combination of the different proposals resulting from ALBidS’ strategies is performed through the application of a Genetic Algorithm, resulting in an evolutionary learning approach.

Candidin: comparison of two antigens for cutaneous delayed hypersensitivity testing

A candidin, which is a suspension of killed yeast cells, is commonly used for intradermal tests of delayed hypersensitivity, to evaluate the immunological cellular competence of the patient, when the test is applied along with other similar tests. When working with a cellular antigen, the histopathology of positive skin tests reveals a cellular infiltrate which not only presents a characteristic hypersensitivity reaction but also a neutrophilic abscess in the central part. This research presents the results of a comparison between the yeast cell suspension and the polysaccharide antigens, both obtained from the same strains of Candida albicans. The results obtained by skin tests in one hundred individuals were 61.0% with the polysaccharide antigen and 69.0% with the yeast cell suspension antigen. Concordant results concerning the two antigens were observed in 82.0% of the individuals. The discussion section presents an assumption to explain the differences of positivity obtained with the two antigens. We conclude that the polysaccharide antigen can be utilized in the intradermal test of delayed hypersensitivity to Candida albicans.

In vitro susceptibility testing of Fonsecaea pedrosoi to antifungals

Based on the difficulties experienced in the treatment of chromoblastomycosis, 12 primary human isolates of F. pedrosoi, were tested for their in vitro susceptibility to various antimycotics. We adapted the recommendations of the NCCLS for yeasts and followed the indications for mold testing from other authors in order to determine their MIC’s and the MLC’s. It was found that a significant proportion of the isolates were resistant to 3 of the 4 antimycotics tested, as revealed by high MIC values, as follows: 33% were resistant to amphotericin B (AMB), 58.3% to 5 fluocytosine (5 FC) and 66.7% to fluconazole (FLU). Contrarywise, none of the isolates proved resistant to itraconazole (ITZ). Determination of the MLC’s revealed that a larger proportion of the isolates were not killed by AMB, 5 FC (91.7%), FLU (100%) or even, ITZ (41.7%). These data indicate that it would be desirable to determine the susceptibility of F. pedrosoi before initiating therapy, in order to choose the more effective antifungal and avoid clinical failure

Ferramentas para optimização da solução NGIN da PT Inovação

Mestrado em Engenharia Informática

Massive shift in the pneumococcal nasopharyngeal flora after the 7-valent conjugate vaccine: epidemiological studies and testing pathogenic potential in animal models

Dissertation presented to obtain the PhD degree in Biology/Molecular Biology by Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica

Exploring distributed computing tools through data mining tasks

Harnessing idle PCs CPU cycles, storage space and other resources of networked computers to collaborative are mainly fixated on for all major grid computing research projects. Most of the university computers labs are occupied with the high puissant desktop PC nowadays. It is plausible to notice that most of the time machines are lying idle or wasting their computing power without utilizing in felicitous ways. However, for intricate quandaries and for analyzing astronomically immense amounts of data, sizably voluminous computational resources are required. For such quandaries, one may run the analysis algorithms in very puissant and expensive computers, which reduces the number of users that can afford such data analysis tasks. Instead of utilizing single expensive machines, distributed computing systems, offers the possibility of utilizing a set of much less expensive machines to do the same task. BOINC and Condor projects have been prosperously utilized for solving authentic scientific research works around the world at a low cost. In this work the main goal is to explore both distributed computing to implement, Condor and BOINC, and utilize their potency to harness the ideal PCs resources for the academic researchers to utilize in their research work. In this thesis, Data mining tasks have been performed in implementation of several machine learning algorithms on the distributed computing environment.

Models and tools for value systems analysis in collaborative environments

Dissertation to obtain the degree of Doctor in Electrical and Computer Engineering, specialization of Collaborative Networks

The genetic basis of morphological change in convergent evolution of natural populations: identifying candidate genes behind convergent evolution in blind cavefish astyanax mexicanus

Dissertation presented to obtain the Ph.D. degree in Biology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.

Biotyping, serotyping and ribotyping as epidemiological tools in the evaluation of Acinetobacter baumannii dissemination in hospital units, Sorocaba, São Paulo, Brazil

Dissemination of Acinetobacter baumannii strains in different units of a hospital in Sorocaba, São Paulo, Brazil was evaluated over a period of two years. By using biotyping, serotyping and ribotyping, 27 distinct clones were differentiated among 76 strains isolated between 1993-94, from clinical specimens of hospitalized patients. Two clones, 2:O4:A (biotype:serotype:ribotype) and 2:O29:A accounted for the majority of strains widely disseminated in the units during 1993. The introduction in the hospital setting, of a new clone, 6:O13:B, at the end of 1993 and its predominance through 1994 is discussed. Among 15 strains isolated from neonates, 6 (40%) belonged to the same clone, 2:O4:A. Interestingly, this clone was almost all recovered in neonatal intensive care unit, nursery and in pediatric unit. All strains were susceptible to imipenem and polymyxcin B. Multiresistant strains (up to 12 antimicrobial agents) accounted for 66.7% and 84.8% of the strains isolated in 1993 and in 1994, respectively.

Estudo da delaminação em compósitos

As excelentes propriedades mecânicas, associadas ao seu baixo peso, fazem com que os materiais compósitos sejam atualmente dos mais interessantes da nossa sociedade tecnológica. A crescente utilização destes materiais e a excelência dos resultados daí provenientes faz com que estes materiais sejam utilizados em estruturas complexas de responsabilidade, pelo que a sua maquinagem se torna necessária de forma a possibilitar a ligação entre peças. O processo de furação é o mais frequente. O processo de maquinagem de compósitos terá como base os métodos convencionais utilizados nos materiais metálicos. O processo deverá, no entanto, ser convenientemente adaptado, quer a nível de parâmetros, quer a nível de ferramentas a utilizar. As características dos materiais compósitos são bastante particulares pelo que, quando são sujeitos a maquinagem poderão apresentar defeitos tais como delaminação, fissuras intralaminares, arrancamento de fibras ou dano por sobreaquecimento. Para a detecção destes danos, por vezes a inspeção visual não é suficiente, sendo necessário recorrer a processos específicos de análise de danos. Existem já, alguns estudos, cujo âmbito foi a obtenção de furos de qualidade em compósitos, com minimização do dano, não se podendo comparar ainda com a informação existente, no que se refere à maquinagem de materiais metálicos ou ligas metálicas. Desta forma, existe ainda um longo caminho a percorrer, de forma a que o grau de confiança na utilização destes materiais se aproxime aos materiais metálicos. Este trabalho experimental desenvolvido nesta tese assentou essencialmente na furação de placas laminadas e posterior análise dos danos provocados por esta operação. Foi dada especial atenção à medição da delaminação causada pela furação e à resistência mecânica do material após ser maquinado. Os materiais utilizados, para desenvolver este trabalho experimental, foram placas compósitas de carbono/epóxido com duas orientações de fibras diferentes: unidireccionais e em “cross-ply”. Não se conseguiu muita informação, junto do fornecedor, das suas características pelo que se levaram a cabo ensaios que permitiram determinar o seu módulo de elasticidade. Relativamente á sua resistência â tração, como já foi referido, a grande resistência oferecida pelo material, associada às limitações da máquina de ensaios não permitiu chegar a valores conclusivos. Foram usadas três geometrias de ferramenta diferentes: helicoidal, Brad e Step. Os materiais utilizados nas ferramentas, foram o aço rápido (HSS) e o carboneto de tungsténio para as brocas helicoidais de 118º de ângulo de ponta e apenas o carboneto de tungsténio para as brocas Brad e Step. As ferramentas em diamante não foram consideradas neste trabalho, pois, embora sejam reconhecidas as suas boas características para a maquinagem de compósitos, o seu elevado custo não justifica a sua escolha, pelo menos num trabalho académico, como é o caso. As vantagens e desvantagens de cada geometria ou material utilizado foram avaliadas, tanto no que diz respeito à delaminação como á resistência mecânica dos provetes ensaiados. Para a determinação dos valores de delaminação, foi usada a técnica de Raio X. Algum conhecimento já existente relativamente a este processo permitiu definir alguns parâmetros (por exemplo: tempo de exposição das placas ao liquido contrastante), que tornaram acessível o procedimento de obtenção de imagens das placas furadas. Importando estas imagens para um software de desenho (no caso – AutoCad), foi possível medir as áreas delaminadas e chegar a valores para o fator de delaminação de cada furo efetuado. Terminado este processo, todas as placas foram sujeitas a ensaios de esmagamento, de forma a avaliar a forma como os parâmetros de maquinagem afectaram a resistência mecânica do material. De forma resumida, são objetivos deste trabalho: - Caracterizar as condições de corte em materiais compósitos, mais especificamente em fibras de carbono reforçado com matriz epóxida (PRFC); - Caracterização dos danos típicos provocados pela furação destes materiais; - Desenvolvimento de análise não destrutiva (RX) para avaliação dos danos provocados pela furação; - Conhecer modelos existentes com base na mecânica da fratura linear elástica (LEFM); - Definição de conjunto de parâmetros ideais de maquinagem com o fim de minimizar os danos resultantes da mesma, tendo em conta os resultados provenientes dos ensaios de força, da análise não destrutiva e da comparação com modelos de danos existentes e conhecidos.

Evaluation of Etest and macrodilution broth method for antifungal susceptibility testing of Candida sp strains isolated from oral cavities of AIDS patients

A comparison of the Etest and the reference broth macrodilution susceptibility test for fluconazole, ketoconazole, itraconazole and amphotericin B was performed with 59 of Candida species isolated from the oral cavities of AIDS patients. The Etest method was performed according to the manufacturer's instructions, and the reference method was performed according to National Committee for Clinical Laboratory Standards document M27-A guidelines. Our data showed that there was a good correlation between the MICs obtained by the Etest and broth dilution methods. When only the MIC results at ± 2 dilutions for both methods were considered, the agreement rates were 90.4% for itraconazole, ketoconazole and amphotericin B and 84.6% for fluconazole of the C. albicans tested. In contrast, to the reference method, the Etest method classified as susceptible three fluconazole-resistant isolates and one itraconazole-resistant isolate, representing four very major errors. These results indicate that Etest could be considered useful for antifungal sensitivity evaluation of yeasts in clinical laboratories.

Introducing numerical analysis tools in engineering: a Scilab user case in electronics course

Software tools in education became popular since the widespread of personal computers. Engineering courses lead the way in this development and these tools became almost a standard. Engineering graduates are familiar with numerical analysis tools but also with simulators (e.g. electronic circuits), computer assisted design tools and others, depending on the degree. One of the main problems with these tools is when and how to start use them so that they can be beneficial to students and not mere substitutes for potentially difficult calculations or design. In this paper a software tool to be used by first year students in electronics/electricity courses is presented. The growing acknowledgement and acceptance of open source software lead to the choice of an open source software tool – Scilab, which is a numerical analysis tool – to develop a toolbox. The toolbox was developed to be used as standalone or integrated in an e-learning platform. The e-learning platform used was Moodle. The first approach was to assess the mathematical skills necessary to solve all the problems related to electronics and electricity courses. Analysing the existing circuit simulators software tools, it is clear that even though they are very helpful by showing the end result they are not so effective in the process of the students studying and self learning since they show results but not intermediate steps which are crucial in problems that involve derivatives or integrals. Also, they are not very effective in obtaining graphical results that could be used to elaborate reports and for an overall better comprehension of the results. The developed tool was based on the numerical analysis software Scilab and is a toolbox that gives their users the opportunity to obtain the end results of a circuit analysis but also the expressions obtained when derivative and integrals calculations, plot signals, obtain vector diagrams, etc. The toolbox runs entirely in the Moodle web platform and provides the same results as the standalone application. The students can use the toolbox through the web platform (in computers where they don't have installation privileges) or in their personal computers by installing both the Scilab software and the toolbox. This approach was designed for first year students from all engineering degrees that have electronics/electricity courses in their curricula.