Landscape composition and climatic parameters significant in the spread of an invasive species (Pine wood Nematode)

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente

DNA-Protein interaction: a response regulatory protein associated with Mo homeostasis in Desulfovibrio alaskensis G20.

Dissertation for a degree in Doctor in Sustainable Chemistry

Petri net based development of globally-asynchronous locally-synchronous distributed embedded systems

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores

Design of a tool to study the fate of Chlamydia trachomatis infected cells

Chlamydia trachomatis has a unique obligate intracellular developmental cycle that ends by the lysis of the cell and/or the extrusion of the bacteria in order to allow for re-infections. While Chlamydia trachomatis infections are often asymptomatic the diagnosis of Chlamydia trachomatis is usually late, occurring after manifestation of persistency. Investigations on the consequences of long-term infections and the molecular mechanisms behind it will reveal light to what extent bacteria can modulate host cell function and what the ultimate fate of host cells after clearance of an infection is. Such studies on the host cell fate could be greatly facilitated if the infected cells become permanently marked during and after the infection. Therefore, this project intends to develop a new genetic tool that would allow permanently labeling of Chlamydia trachomatis host cells. The plan was to generate a Chlamydia trachomatis strain that encodes a recombinant CRE recombinase, fused to a secretory effector function of the Chlamydia type 3 secretion system (T3SS). Upon translocation into the host cell, this recombinant CRE enzyme could then, owing to its site-specific recombination function, switch a reporter gene contained in the host cell genome. To this end, the reporter line carried a membrane-tagged tdTomato (mT) gene flanked by two LoxP sequences followed by a GFP gene. The translocation of the recombinant CRE recombinase into this cell line was designed to trigger the recombination of the LoxP sites whereby the cells would turn from red fluorescence to green as an irreversible label of the infected cells. Successful execution of this mechanism would allow to draw a direct link between Chlamydia trachomatis infection and the subsequent fate of the infected cell.

Report of a traineeship : audit of antidepressant prescribing in Primary and Mental Care: how to address appropriateness and keep a curb on costs. A tool suitable for all contexts?

RESUMO: Este é o relatório de um estágio realizado na Autoridade de Saúde Local de Bolonha com o objectivo de desenvolver capacidades e competências na área de projectos orientados para a avaliação com base epidemiológica. As prescrições de anti-depressivos aumentaram consideravelmente em todo o mundo durante as últimas décadas. O uso cada vez maior dos agentes mais dispendiosos desempenha um papel na subida do custo dos tratamentos. A Autoridade de Saúde Local de Bolonha implementou um processo de auditoria com o objectivo de melhorar a adequação das prescrições de pacientes externos, centrando-se em dois anti-depressivos de marca ainda protegidos por patente, Escitalopram e Duloxetine. Os Departamentos de Cuidados de Saúde Primários e de Cuidados de Saúde Mental, assim como o Departamento Farmacêutico e a Unidade de Gestão Clínica, estiveram envolvidos na fase de planeamento da auditoria. O grupo da auditoria, maioritariamente composto por médicos de clínica geral e psiquiatras, reuniu e analisou provas da eficácia e segurança dos anti-depressivos. Os dados sobre as prescrições das Unidades de Cuidados de Saúde Primários e dos Centros de Saúde Mental Comunitários da Autoridade de Saúde Local (866.294 habitantes) foram comparados, em particular as taxas de consumo de Escitalopram e Duloxetine. O grupo da auditoria definiu os standards a serem abordados, os indicadores a serem avaliados e as medidas a empreender para atingir os objectivos definidos. As directrizes do NICE sobre a depressão foram escolhidas como referência. O objectivo da auditoria foi definido como evitar o Escitalopram e Duloxetine como medicamentos de primeira escolha num tratamento anti-depressivo. De modo a verificar a eficácia das medidas empreendidas foi seleccionado um indicador, consistindo numa redução de 25% das prescrições de ambos os anti-depressivos na prática clínica de pacientes externos e numa redução de 20% da variabilidade nas Unidades de Cuidados de Saúde Primários. O relatório retrospectivo pré-auditoria (Janeiro a Abril de 2012) revelou que os tratamentos com anti-depressivos para pacientes externos eram prescritos pelos médicos de clínica geral em mais de90% dos casos. As medidas da auditoria foram implementadas entre Novembro de 2012 e Maio de 2013. Algumas medidas relevantes foram integradas com a revisão da auditoria, tais como reuniões educacionais de pequena escala com os médicos de clínica geral e psiquiatras, visitas de apoio do assessor de prescrições da Autoridade de Saúde Local aos médicos de clínica geral e Centros de Saúde Mental Comunitários, panfletos para profissionais com informação retirada das directrizes clínicas do NICE, implementação de um serviço de consulta na Web para médicos de clínica geral sobre provas relativas a anti-depressivos. O relatório de feedback é aguardado em Novembro de 2013 depois de se verificar nos standards atingidos a eficácia das medidas implementadas. Foi realizada uma análise SWOT para comprovar as forças e fraquezas, as oportunidades e ameaças do processo. Como identificação de fraquezas poderá ser útil identificar estratégias relevantes para melhoria interna, para que o conhecimento das ameaças possa amortizar factores que possam ter impactos adversos que fujam ao controlo do Departamento de Saúde Mental. Uma melhor compreensão das forças e das oportunidades facilita a consecução dos objectivos estabelecidos no projecto. O primeiro, mas não o último, resultado deste processo consistiu numa maior integração entre os Cuidados de Saúde Primários e de Saúde Mental, permitindo assim que a Autoridade de Saúde Local coloque as alterações em prática.------------ABSTRACT: This is the report of a traineeship held in the Local Health Authority of Bologna with the aim to develop skills and competencies in the field of epidemiogically based evaluation oriented projects. Antidepressants prescriptions have considerably increased all over the world in the last decades. The increasing use of the most expensive agents plays a part in the rising cost of treatments. The Local Health Authority of Bologna has implemented an audit process aimed at improving the appropriateness of outpatient prescriptions focusing on the two branded antidepressants still protected by patent, Escitalopram and Duloxetine. The Primary Care and the Mental Health Care Departments, as well as the Pharmaceutical Department and the Clinical Governance Unit, were involved in the planning phase of the audit. The audit group, mainly composed of general practitioners and psychiatrists, collected and analyzed scientific evidence on effectiveness and safety of antidepressants. Data on prescriptions of Primary Care Units and Community Mental Health Centers of the Local Health Authority (866.294 inhabitants) were compared, in particular consumption rates of Escitalopram and Duloxetine. The audit group defined the standards to be addressed, the indicators to be evaluated and the actions aimed at reaching the defined goals. NICE guidelines on depression were chosen as reference. The aim of the audit was settled as avoiding Escitalopram and Duloxetine as first choice drugs starting an AD treatment. In order to check the efficacy of the actions undertaken an indicator was selected, consisting in a reduction of 25% of prescriptions of both ADs in outpatient practice and in a 20% reduction of To develop skills and competencies across Primary Care Units. The pre-audit retrospective report (January-April 2012) showed that outpatient antidepressant treatments were prescribed by GPs in over 90% of cases. Audit actions were implemented between November 2012 and May 2013. Some relevant actions have been integrated with the audit review, such as small-scale educational meetings with GPs and psychiatrists, outreach visits of the LHA prescribing adviser to GPs and CMHCs,leaflets for professionals with information extracted from NICE clinical guidelines, implementation of a web consultation service for GPs about evidence on antidepressants. The feedback report is expected in November 2013 after checking through the standards attained the effectiveness of actions implemented. A SWOT Analysis was carried out to evidence the strengths and weaknesses, opportunities and threats of the process. As identification of weaknesses may be useful to identify relevant strategies for internal improvement, so the knowledge of threats can amortize factors that may have adverse impacts beyond the control of the Mental Health Department. Better understanding of the strengths and the opportunities facilitates the achievement of the goals set in the project. The first and not least upshot of this process has consisted in further integration between Primary and Mental Health Care, thus enabling the LHA to put the change into practice.

Doppler ultrasound - a valid and reliable tool to assess spondyloarthritis

Enthesitis is the hallmark of spondyloarthritis and is observed in all subtypes. Namely, a wide information on spondyloarthritis abnormalities, including synovitis, bursitis, tendinitis, enthesitis and cortical bone abnormalities (erosions and enthesophytes), can be efficiently perceived by ultrasound power Doppler. Furthermore, several studies on imaging of enthesis showed that imaging techniques are better than clinical examination to detect pathology at asymptomatic enthesis. Vascularized enthesitis detected by ultrasound power Doppler appears to be a valuable diagnostic tool to confirm spondyloarthritis diagnosis. This article focuses on the validity and reliability of ultrasound enthesitis assessment in the management of spondyloarthritis patients.

Phage display as a tool for development of novel therapeutics for breast cancer

Phage display technology is a powerful platform for the generation of highly specific human monoclonal antibodies (Abs) with potential use in clinical applications. Moreover, this technique has also proven to be a reliable approach in identifying and validating new cancer-related targets. For scientific or medical applications, different types of Ab libraries can be constructed. The use of Fab Immune libraries allows the production of high quality and affinity antigen-specific Abs. In this work, two immune human phage display IgG Fab libraries were generated from the Ab repertoire of 16 breast cancer patients, in order to obtain a tool for the development of new therapeutic Abs for breast cancer, a condition that has great impact worldwide. The generated libraries are estimated to contain more than 108 independent clones and a diversity over 90%. Libraries validation was pursued by selection against BSA, a foreign and highly immunogenic protein, and HER2, a well established cancer target. Preliminary results suggested that phage pools with affinity for these antigens were selected and enriched. Individual clones were isolated, however, it was not possible to obtain enough data to further characterize them. Selection against the DLL1 protein was also performed, once it is a known ligand of the Notch pathway, whose deregulation is associated to breast cancer, making it an interesting target for the generation of function-blocking Abs. Selection resulted in the isolation of a clone with low affinity and Fab expression levels. The validation process was not completed and further effort will have to be put in this task in the future. Although immune libraries concept implies limited applicability, the library reported here has a wide range of use possibilities, since it was not restrained to a single antigen but instead thought to be used against any breast cancer associated target, thus being a valuable tool.

Analysis of the interaction of polycyclic aromatic compounds in a model organism: integration of genotoxic and histopathological effects

Due to their toxicity, especially their carcinogenic potential, polycyclic aromatic hydrocarbons (PAHs) became priority pollutants in biomonitoring programmes and environmental policy, such as the European Water Framework Directive. The model substances tested in this study, namely benzo[b]fluoranthene (B[b]F), considered potentially carcinogenic to humans and an effector carcinogenic PAH to wildlife, and phenanthrene (Phe), deemed a non-carcinogenic PAH, are common PAHs in coastal waters, owning distinct properties reflected in different, albeit overlapping, mechanisms of toxicity. Still, as for similar PAHs, their interaction effects remain largely unknown. In order to study the genotoxic effects of caused by the interaction of carcinogenic and non-carcinogenic PAHs, and their relation to histopathological alterations, juvenile sea basses, Dicentrarchus labrax, a highly ecologically- and economically-relevant marine fish, were injected with different doses (5 and 10 μg.g-1 fish ww) of the two PAHs, isolated or in mixture, and incubated for 48 h. Individuals injected with B[b]F and the PAH mixture exhibited higher clastogenic/aneugenic effects and DNA strand breakage in blood cells, determined through the erythrocytic nuclear abnormalities (ENA) and Comet assays, respectively. Also, hepatic histopathological alterations were found in all animals, especially those injected with B[b]F and the PAH mixture, relating especially to inflammation. Still, Phe also exhibited genotoxic effects in sea bass, especially in higher doses, revealing a very significant acute effect that was accordant with the Microtox test performed undergone in parallel. Overall, sea bass was sensitive to B[b]F (a higher molecular weight PAH), likely due to efficient bioactivation of the pollutant (yielding genotoxic metabolites and reactive oxygen species), when compared to Phe, the latter revealing a more significant acute effect. The results indicate no significant additive effect between the substances, under the current experimental conditions. The present study highlights the importance of understanding PAH interactions in aquatic organisms, since they are usually present in the aquatic environment in complex mixtures.

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Dynamic stiffness of the piled foundation of a onshore wind turbine

One of today's biggest concerns is the increase of energetic needs, especially in the developed countries. Among various clean energies, wind energy is one of the technologies that assume greater importance on the sustainable development of humanity. Despite wind turbines had been developed and studied over the years, there are phenomena that haven't been yet fully understood. This work studies the soil-structure interaction that occurs on a wind turbine's foundation composed by a group of piles that is under dynamic loads caused by wind. This problem assumes special importance when the foundation is implemented on locations where safety criteria are very demanding, like the case of a foundation mounted on a dike. To the phenomenon of interaction between two piles and the soil between them it's given the name of pile-soil-pile interaction. It is known that such behavior is frequency dependent, and therefore, on this work evaluation of relevant frequencies for the intended analysis is held. During the development of this thesis, two methods were selected in order to assess pile-soil-pile interaction, being one of analytical nature and the other of numerical origin. The analytical solution was recently developed and its called Generalized pile-soil-pile theory, while for the numerical method the commercial nite element software PLAXIS 3D was used. A study of applicability of the numerical method is also done comparing the given solution by the nite element methods with a rigorous solution widely accepted by the majority of the authors.

Technology transition towards electric mobility - technology assessment as a tool for policy design

Paper presented at the Colloquium Gerpisa 2013, Paris (http://gerpisa.org/node/2085), Session n°: 19 New kinds of mobility: old and new business models

Tool for discovering sequential patterns in financial markets

The goal of this thesis is the study of a tool that can help analysts in finding sequential patterns. This tool will have a focus on financial markets. A study will be made on how new and relevant knowledge can be mined from real life information, potentially giving investors, market analysts, and economists new basis to make informed decisions. The Ramex Forum algorithm will be used as a basis for the tool, due to its ability to find sequential patterns in financial data. So that it further adapts to the needs of the thesis, a study of relevant improvements to the algorithm will be made. Another important aspect of this algorithm is the way that it displays the patterns found, even with good results it is difficult to find relevant patterns among all the studied samples without a proper result visualization component. As such, different combinations of parameterizations and ways to visualize data will be evaluated and their influence in the analysis of those patterns will be discussed. In order to properly evaluate the utility of this tool, case studies will be performed as a final test. Real information will be used to produce results and those will be evaluated in regards to their accuracy, interest, and relevance.

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.