Long-term behaviour of railway transitions under dynamic loading application to soft soil sites

Dissertação para obtenção do Grau de Doutor em Engenharia Civil

Mining protein structure data

The principal topic of this work is the application of data mining techniques, in particular of machine learning, to the discovery of knowledge in a protein database. In the first chapter a general background is presented. Namely, in section 1.1 we overview the methodology of a Data Mining project and its main algorithms. In section 1.2 an introduction to the proteins and its supporting file formats is outlined. This chapter is concluded with section 1.3 which defines that main problem we pretend to address with this work: determine if an amino acid is exposed or buried in a protein, in a discrete way (i.e.: not continuous), for five exposition levels: 2%, 10%, 20%, 25% and 30%. In the second chapter, following closely the CRISP-DM methodology, whole the process of construction the database that supported this work is presented. Namely, it is described the process of loading data from the Protein Data Bank, DSSP and SCOP. Then an initial data exploration is performed and a simple prediction model (baseline) of the relative solvent accessibility of an amino acid is introduced. It is also introduced the Data Mining Table Creator, a program developed to produce the data mining tables required for this problem. In the third chapter the results obtained are analyzed with statistical significance tests. Initially the several used classifiers (Neural Networks, C5.0, CART and Chaid) are compared and it is concluded that C5.0 is the most suitable for the problem at stake. It is also compared the influence of parameters like the amino acid information level, the amino acid window size and the SCOP class type in the accuracy of the predictive models. The fourth chapter starts with a brief revision of the literature about amino acid relative solvent accessibility. Then, we overview the main results achieved and finally discuss about possible future work. The fifth and last chapter consists of appendices. Appendix A has the schema of the database that supported this thesis. Appendix B has a set of tables with additional information. Appendix C describes the software provided in the DVD accompanying this thesis that allows the reconstruction of the present work.

Vibration control with shape-memory alloys in civil engineering structures

Dissertação apresentada à Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Doutor em Engenharia Civil

Development of molecularly imprinted polymers using supercritical fluid technology

Dissertação para obtenção do Grau de Doutor em Química Sustentável

Effect of sialic acid loss on dendritic cell maturation

Sialic acids are key structural determinants and contribute to the functionality of a number of immune cell receptors. Previously, we demonstrated that differentiation of human dendritic cells (DCs) is accompanied by an increased expression of sialylated cell surface structures, putatively through the activity of the ST3Gal.I and ST6Gal.I sialyltransferases. Furthermore, DC endocytosis was reduced upon removal of the cell surface sialic acid residues by neuraminidase. In the present work, we evaluate the contribution of the sialic acid modifications in DC maturation. We demonstrate that neuraminidase-treated human DCs have increased expression of major histocompatibility complex (MHC) and costimulatory molecules, increased gene expression of specific cytokines and induce a higher proliferative response of T lymphocytes. Together, the data suggest that clearance of cell surface sialic acids contributes to the development of a T helper type 1 proinflammatory response. This postulate is supported by mouse models, where elevated MHC class II and increased maturation of specific DC subsets were observed in DCs harvested from ST3Gal.I(-/-) and ST6Gal.I(-/-) mice. Moreover, important qualitative differences, particularly in the extent of reduced endocytosis and in the peripheral distribution of DC subsets, existed between the ST3Gal.I(-/-) and ST6Gal.I(-/-) strains. Together, the data strongly suggest not only a role of cell surface sialic acid modifications in maturation and functionality of DCs, but also that the sialic acid linkages created by different sialyltransferases are functionally distinct. Consequently, with particular relevance to DC-based therapies, cell surface sialylation, mediated by individual sialyltransferases, can influence the immunogenicity of DCs upon antigen loading.

Cilia motility studies in zebrafish embryos

A thesis submitted in fulfilment of the requirements for the degree of Masters in Molecular Genetics and Biomedicine

Safety function analysis in an industrial production process

Dissertação para obtenção do Grau de Mestre em Engenharia e Gestão Industrial

Characterization of sol-gel matrices with entrapped cutinase

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Using cilia mutants to study left-right asymmetry in zebrafish

A thesis submitted in fulfillment of the requirements for the degree of the Masters in Molecular Genetics and Biomedicine

Precast concrete wall-foundation connection. Development of a seismic dissipative connection

Seismic events are a major factor to consider in structural design of buildings in many countries. With the purpose of saving lives, most of the design codes lead to structural solutions that withstand large seismic actions without collapsing, but without taking into account a possible usage of the structures after the earthquake. As a result, it is necessary to consider the time needed to repair/retrofit the damaged structures (i.e. the downtime) since this period of inactivity may result in huge financial implications for the occupants of the buildings. In order to minimise the damages and simplify repair operations, structural solutions with rocking systems and negligible residual displacements have been developed during the last two decades. Systems with precast concrete rocking walls were studied with the aim of investigat- ing suitable and convenient structural alternatives to minimise the damage in case of an earthquake. Experimental, numerical and analytical analyses on post-tensioned solutions, with and without energy dissipation devices, were carried out in this research. The energy dissipation devices were made from steel angles that were further developed during the research. Different solutions for these devices were experimentally tested under cyclic loading and the results are presented. Numerical and analytical work on steel angles was also carried out. Regarding the concrete rocking wall systems, two concrete rocking wall systems were studied: post-tensioned walls and post-tensioned walls with energy dissipation devices. In the latter, the solution was to fix them externally to the wall, allowing their easy replacement after an earthquake. It is shown that the dissipaters are a viable solution for use in precast concrete rocking wall systems. A building case study is presented. The comparison between a traditional monolithic system and a hybrid solution was carried out, allowing the evaluation of the efficiency of the solution that was developed.

Análise não linear do comportamento dinâmico de passadiços pedonais pré-fabricados

Os terramotos têm sido considerados uma das forças mais destrutivas e violentas da natureza, causando grandes tragédias e perdas económicas significativas. O objetivo principal do presente estudo é avaliar o comportamento global e local de três pontes pedonais, pré-fabricadas, durante a ação sísmica regulamentar. Através destas análises, pretende-se avaliar o risco de colapso das estruturas por “descalçamento” do tabuleiro e, caso necessário, propor soluções para evitar este fenómeno e melhorar o desempenho sísmico dos passadiços. No domínio de pontes, o “descalçamento dos apoios” é um tipo de rotura que pode ocorrer em estruturas com tramos simplesmente apoiados, onde os problemas surgem geralmente na interface de ligação tabuleiro-pilar, podendo conduzir ao derrubamento do primeiro. Este tipo de ligação é geralmente constituído por um conjunto de varões de aço – ferrolhos, chumbados verticalmente ao capitel do pilar e que atravessam placas de neoprene, ficando instalados no negativo das vigas. A selagem dos varões é normalmente realizada com argamassa de alta resistência. Os problemas que surgem neste tipo de ligação estão associados, a maior parte das vezes, à falta de manutenção e ao insuficiente comprimento de entrega do tabuleiro na zona dos aparelhos de apoio. A simulação do comportamento da estrutura durante as várias fases construtivas e aplicação de cargas, até ao colapso total, implica a utilização de uma ferramenta adequada. A modelação numérica foi efetuada com recurso ao programa de cálculo não-linear de estruturas Extreme Loading for Structures, baseado no Método dos Elementos Aplicados. O método considera os efeitos da não-linearidade física e geométrica, permitindo analisar o comportamento das estruturas durante a fase elástica e inelástica, passando pela cedência das armaduras, abertura e propagação de fendas até à separação dos elementos. Com base neste trabalho, foi possível verificar alterações significativas na resposta sísmica da estrutura, nomeadamente devido à eventual degradação dos ferrolhos.

Método dos elementos aplicados na simulação numérica do arrancamento de armaduras

Uma das propriedades do betão armado que foi alvo de maior número de estudos, ao longo dos tempos, é a aderência. Esta é uma das propriedades mais importantes a considerar na construção, pois dela depende o desempenho e estabilidade de uma estrutura. Dada a sua importância, a aderência é a propriedade do betão armado mais estudada ao longo do tempo. A complexidade inerente a esta propriedade torna difícil de compreender e prever o comportamento estrutural. Esta dissertação pretende analisar a capacidade do Método dos Elementos Aplicados em simular o ensaio de arrancamento directo e de reproduzir modos de rotura. Este ensaio, denominado de pull-out test, estuda a aderência entre três materiais: o aço, o betão e o grout. Vários tipos de ligações, com diferentes modos de rotura, são simulados e comparados com um ensaio experimental referido na revisão bibliográfica. Assim, recorrer-se-á ao programa Extreme Loading for Structures, que tem como base o Método dos Elementos Aplicados. Através de uma análise de sensibilidade foi possível calibrar as propriedades dos diferentes elementos e das interfaces entre o betão, aço e grout, de modo a viabilizar o cálculo da força crítica das ligações e reproduzir os modos de rotura observados experimentalmente. Este trabalho pretende dar uma contribuição ao conhecimento no âmbito da simulação numérica, em relação a este tipo de ligações, e ajudar à criação de modelos numéricos fiáveis e eficientes de fácil e rápida execução. Esta dissertação permite concluir que o Método dos Elementos Aplicados, apresenta-se como uma boa solução para o estudo deste tipo de ligações. Os resultados numéricos tiveram uma boa aproximação dos resultados experimentais. Em conformidade com a análise experimental, as ligações com bainha de pré-esforço e comprimento de embebimento a partir de 15 cm são as que melhor desempenho têm ao nível da resistência.

The effect of key process operational conditions on enhanced biological phosphorus removal from wastewater

Enhanced biological phosphorus removal (EBPR) is the most economic and sustainable option used in wastewater treatment plants (WWTPs) for phosphorus removal. In this process it is important to control the competition between polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), since EBPR deterioration or failure can be related with the proliferation of GAOs over PAOs. This thesis is focused on the effect of operational conditions (volatile fatty acid (VFA) composition, dissolved oxygen (DO) concentration and organic carbon loading) on PAO and GAO metabolism. The knowledge about the effect of these operational conditions on EBPR metabolism is very important, since they represent key factors that impact WWTPs performance and sustainability. Substrate competition between the anaerobic uptake of acetate and propionate (the main VFAs present in WWTPs) was shown in this work to be a relevant factor affecting PAO metabolism, and a metabolic model was developed that successfully describes this effect. Interestingly, the aerobic metabolism of PAOs was not affected by different VFA compositions, since the aerobic kinetic parameters for phosphorus uptake, polyhydroxyalkanoates (PHAs) degradation and glycogen production were relatively independent of acetate or propionate concentration. This is very relevant for WWTPs, since it will simplify the calibration procedure for metabolic models, facilitating their use for full-scale systems. The DO concentration and aerobic hydraulic retention time (HRT) affected the PAO-GAO competition, where low DO levels or lower aerobic HRT was more favourable for PAOs than GAOs. Indeed, the oxygen affinity coefficient was significantly higher for GAOs than PAOs, showing that PAOs were far superior at scavenging for the often limited oxygen levels in WWTPs. The operation of WWTPs with low aeration is of high importance for full-scale systems, since it decreases the energetic costs and can potentially improve WWTP sustainability. Extended periods of low organic carbon load, which are the most common conditions that exist in full-scale WWTPs, also had an impact on PAO and GAO activity. GAOs exhibited a substantially higher biomass decay rate as compared to PAOs under these conditions, which revealed a higher survival capacity for PAOs, representing an advantage for PAOs in EBPR processes. This superior survival capacity of PAOs under conditions more closely resembling a full-scale environment was linked with their ability to maintain a residual level of PHA reserves for longer than GAOs, providing them with an effective energy source for aerobic maintenance processes. Overall, this work shows that each of these key operational conditions play an important role in the PAO-GAO competition and should be considered in WWTP models in order to improve EBPR processes.

Novel ready-to-eat mango product using gellan gum as gelling agent: physico-chemical, microbial and sensory characteristics

Este trabalho foi efectuado com o apoio da Universidade de Lisboa, Instituto Superior de Agronomia com o Centro de Engenharia dos Biossistemas (CEER

Fate map of zebrafish left-right organizer

The organizer is a ciliated signalling transient organ, responsible for the patterning of embryo tissues during embryonic development. In higher vertebrates, such as mouse and chick, this organizer (the node and the Hensen’s node, respectively) performs dorsalventral and anteriorposterior axis definition, as well as left-right patterning of the internal organs. In lower vertebrates, such as frog and zebrafish, there is a separate specialized organ for left-right purposes called the Gastrocoel Roof Plate (GRP) and Kupffer’s Vesicle (KV), respectively. It is known that mouse and chick organizer cells give rise to structures like floor plate, notochord, hypochord and somites. Frog GRP originates all these but floor plate. In zebrafish, at 13-14 somite stage (ss) the KV finished its left-right patterning but what happens to this organizer’ cells is still poorly studied. This research attempts to understand the fate and behaviour of the KV cells. We followed the fate of KV cells by live imaging and by tight time-courses with fixed larvae. We assessed in detail their proliferative and death profile, as well as cilia length progression from 9-10 ss until 29-30 ss. We conclude that the KV cells mostly follow the evolutionarily conserved fates described for other organizers. These cells mainly incorporate the notochord and hypochord; few cells incorporate the floor plate and the somites. As a novelty, it is also hypothesized that the hypural cell fate may be among the KV cell fates.