Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Palhetas simples: técnicas de manutenção para aplicação na interpretação e pedagogia do clarinete

Relatório de estágio de mestrado em Ensino da Música

On the Hill estimator: a comparison of methods

Extreme value theory (EVT) deals with the occurrence of extreme phenomena. The tail index is a very important parameter appearing in the estimation of the probability of rare events. Under a semiparametric framework, inference requires the choice of a number k of upper order statistics to be considered. This is the crux of the matter and there is no definite formula to do it, since a small k leads to high variance and large values of k tend to increase the bias. Several methodologies have emerged in literature, specially concerning the most popular Hill estimator (Hill, 1975). In this work we compare through simulation well-known procedures presented in Drees and Kaufmann (1998), Matthys and Beirlant (2000), Beirlant et al. (2002) and de Sousa and Michailidis (2004), with a heuristic scheme considered in Frahm et al. (2005) within the estimation of a different tail measure but with a similar context. We will see that the new method may be an interesting alternative.

Solving large 0–1 multidimensional knapsack problems by a new simplified binary artificial fish swarm algorithm

The artificial fish swarm algorithm has recently been emerged in continuous global optimization. It uses points of a population in space to identify the position of fish in the school. Many real-world optimization problems are described by 0-1 multidimensional knapsack problems that are NP-hard. In the last decades several exact as well as heuristic methods have been proposed for solving these problems. In this paper, a new simpli ed binary version of the artificial fish swarm algorithm is presented, where a point/ fish is represented by a binary string of 0/1 bits. Trial points are created by using crossover and mutation in the different fi sh behavior that are randomly selected by using two user de ned probability values. In order to make the points feasible the presented algorithm uses a random heuristic drop item procedure followed by an add item procedure aiming to increase the profit throughout the adding of more items in the knapsack. A cyclic reinitialization of 50% of the population, and a simple local search that allows the progress of a small percentage of points towards optimality and after that refines the best point in the population greatly improve the quality of the solutions. The presented method is tested on a set of benchmark instances and a comparison with other methods available in literature is shown. The comparison shows that the proposed method can be an alternative method for solving these problems.

Autoimmune diseases and pregnancy: analysis of a series of cases

BACKGROUND: An autoimmune disease is characterized by tissue damage, caused by self-reactivity of different effector mechanisms of the immune system, namely antibodies and T cells. All autoimmune diseases, to some extent, have implications for fertility and obstetrics. Currently, due to available treatments and specialised care for pregnant women with autoimmune disease, the prognosis for both mother and child has improved significantly. However these pregnancies are always high risk. The purpose of this study is to analyse the fertility/pregnancy process of women with systemic and organ-specific autoimmune diseases and assess pathological and treatment implications. METHODS: The authors performed an analysis of the clinical records and relevant obstetric history of five patients representing five distinct autoimmune pathological scenarios, selected from Autoimmune Disease Consultation at the Hospital of Braga, and reviewed the literature. RESULTS: The five clinical cases are the following: Case 1-28 years old with systemic lupus erythematosus, and clinical remission of the disease, under medication with hydroxychloroquine, prednisolone and acetylsalicylic acid, with incomplete miscarriage at 7 weeks of gestation without signs of thrombosis. Case 2-44 years old with history of two late miscarriages, a single preterm delivery (33 weeks) and multiple thrombotic events over the years, was diagnosed with antiphospholipid syndrome after acute myocardial infarction. Case 3-31 years old with polymyositis, treated with azathioprine for 3 years with complete remission of the disease, took the informed decision to get pregnant after medical consultation and full weaning from azathioprine, and gave birth to a healthy term new-born. Case 4-38 years old pregnant woman developed Behcet's syndrome during the final 15 weeks of gestation and with disease exacerbation after delivery. Case 5-36 years old with autoimmune thyroiditis diagnosed during her first pregnancy, with difficult control over the thyroid function over the years and first trimester miscarriage, suffered a second miscarriage despite clinical stability and antibody regression. CONCLUSIONS: As described in literature, the authors found a strong association between autoimmune disease and obstetric complications, especially with systemic lupus erythematosus, antiphospholipid syndrome and autoimmune thyroiditis.

An innovative framework for probabilistic-based structural assessment with an application to existing reinforced concrete structures

A novel framework for probabilistic-based structural assessment of existing structures, which combines model identification and reliability assessment procedures, considering in an objective way different sources of uncertainty, is presented in this paper. A short description of structural assessment applications, provided in literature, is initially given. Then, the developed model identification procedure, supported in a robust optimization algorithm, is presented. Special attention is given to both experimental and numerical errors, to be considered in this algorithm convergence criterion. An updated numerical model is obtained from this process. The reliability assessment procedure, which considers a probabilistic model for the structure in analysis, is then introduced, incorporating the results of the model identification procedure. The developed model is then updated, as new data is acquired, through a Bayesian inference algorithm, explicitly addressing statistical uncertainty. Finally, the developed framework is validated with a set of reinforced concrete beams, which were loaded up to failure in laboratory.

Assistive locomotion strategies for active lower limb devices

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Eletrónica Médica)

Cultural studies as the new humanities

The purpose of this study is to argue that Cultural Studies may be regarded as the new humanities. Cultural Studies focus on ethnic, post-colonial, communication, anthropological, ethnographic and feminist studies, and only ‘very marginally’ have they shown an interest in literature and literary studies (Aguiar & Silva, 2008). But those fields, which ‘Social Science’ rather than the ‘Arts’ have invested in (Ibid., p. 254), are the touchstone of modernity. Today, the concept we have of humankind is, to a large extent, played out in these areas. The questioning of both humankind and modernity has as backdrop the technologically-driven shift of culture from word to image (Martins, 2011 a). My proposal takes into account this debate, while underscoring how Cultural Studies are engaged in what is current and contemporary, which means, in the present and everyday life.

A dimensão interna da responsabilidade social nas organizações: equilíbrio entre o trabalho e a vida familiar

Dissertação de mestrado em Sociologia (área de especialização em Organizações e Trabalho)

Monitorização do risco de dificuldades de aprendizagem específicas na leitura de alunos do 2.º ao 4.ºano no contexto do modelo de resposta à intervenção

Dissertação de mestrado em Educação Especial (área de especialização em Dificuldades de Aprendizagem Específicas)

Ajustamento da criança à separação ou divórcio dos pais

Objetivo: O presente artigo procura relacionar e analisar evidências empíricas e teóricas sobre o impacto e os fatores associados ao impacto da separação ou divórcio dos pais no ajustamento da criança. Método: Realizou-se uma revisão agregativa da literatura, recorrendo às palavras-chave “divorce adjustment”, “child divorce” e “divorce impact”, nas bases de dados JSTOR, PsycInfo, SciELO e Medline e em livros da especialidade. Resultados: Respostas adaptativas e desadaptativas da criança são descritas, assim como potenciais resultados positivos. São principalmente discutidos os fatores mediadores e moderadores frequentemente referenciados na literatura no impacto da separação ou divórcio dos pais no ajustamento da criança. Entre esses estão: características da criança, problemas financeiros, sintomatologia psicopatológica dos pais, qualidade das práticas parentais e conflito interparental. Conclusão: Com base nas evidências empíricas e perspectivando o divórcio como uma transição desenvolvimental, levantamos a hipótese de que os problemas de ajustamento apresentados pelas crianças com pais divorciados possam ser mais bem explicados por outros fatores do que pelo divórcio/separação per se. Finalmente assumimos uma inovação conceptual de que essa transição familiar pode significar uma oportunidade de crescimento e de promoção desenvolvimental.