New strategies to detect and understand genotype-by-environment interactions and QTL-by-environment interactions

Dissertação para obtenção do Grau de Doutor em Estatística e Gestão do Risco, especialidade em Estatística

Full-scale biological phosphorus removal: quantification of storage polymers, microbial performance and metabolic modelling

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

THE INFLUENCE OF HIV-1 SUBTYPES C, CRF31_BC AND B ON DISEASE PROGRESSION AND INITIAL VIROLOGIC RESPONSE TO HAART IN A SOUTHERN BRAZILIAN COHORT

Background: Although most HIV-1 infections in Brazil are due to subtype B, Southern Brazil has a high prevalence of subtype C and recombinant forms, such as CRF31_BC. This study assessed the impact of viral diversity on clinical progression in a cohort of newly diagnosed HIV-positive patients. Methods: From July/2004 to December/2005, 135 HIV-infected patients were recruited. The partial pol region was subtyped by phylogeny. A generalized estimating equation (GEE) model was used to examine the relationship between viral subtype, CD4+ T cell count and viral load levels before antiretroviral therapy. Hazard ratio (Cox regression) was used to evaluate factors associated with viral suppression (viral load < 50 copies/mL at six months). Results: Main HIV-1 subtypes included B (29.4%), C (28.2%), and CRF31_BC (23.5%). Subtypes B and C showed a similar trend in CD4+ T cell decline. Comparison of non-B (C and CRF31_BC) and B subtypes revealed no significant difference in the proportion of patients with viral suppression at six months (week 24). Higher CD4+ T cell count and lower viral load were independently associated with viral suppression. Conclusion: No significant differences were found between subtypes; however, lower viral load and higher CD4+ T cell count before therapy were associated with better response.

The Role of the Humoral Immune Response in the Molecular Evolution of the Envelope C2, V3 and C3 Regions in Chronically HIV-2 Infected Patients

BACKGROUND: This study was designed to investigate, for the first time, the short-term molecular evolution of the HIV-2 C2, V3 and C3 envelope regions and its association with the immune response. Clonal sequences of the env C2V3C3 region were obtained from a cohort of eighteen HIV-2 chronically infected patients followed prospectively during 2-4 years. Genetic diversity, divergence, positive selection and glycosylation in the C2V3C3 region were analysed as a function of the number of CD4+ T cells and the anti-C2V3C3 IgG and IgA antibody reactivity RESULTS: The mean intra-host nucleotide diversity was 2.1% (SD, 1.1%), increasing along the course of infection in most patients. Diversity at the amino acid level was significantly lower for the V3 region and higher for the C2 region. The average divergence rate was 0.014 substitutions/site/year, which is similar to that reported in chronic HIV-1 infection. The number and position of positively selected sites was highly variable, except for codons 267 and 270 in C2 that were under strong and persistent positive selection in most patients. N-glycosylation sites located in C2 and V3 were conserved in all patients along the course of infection. Intra-host variation of C2V3C3-specific IgG response over time was inversely associated with the variation in nucleotide and amino acid diversity of the C2V3C3 region. Variation of the C2V3C3-specific IgA response was inversely associated with variation in the number of N-glycosylation sites. CONCLUSION: The evolutionary dynamics of HIV-2 envelope during chronic aviremic infection is similar to HIV-1 implying that the virus should be actively replicating in cellular compartments. Convergent evolution of N-glycosylation in C2 and V3, and the limited diversification of V3, indicates that there are important functional constraints to the potential diversity of the HIV-2 envelope. C2V3C3-specific IgG antibodies are effective at reducing viral population size limiting the number of virus escape mutants. The C3 region seems to be a target for IgA antibodies and increasing N-linked glycosylation may prevent HIV-2 envelope recognition by these antibodies. Our results provide new insights into the biology of HIV-2 and its relation with the human host and may have important implications for vaccine design.

Caracterização de perfis pultrudidos Híbridos

A pultrusão é uma técnica já sobejamente conhecida de produção de perfis de secção constante, tais como barras, cantoneiras, perfis estruturais ou tubos, em materiais compósitos de matriz polimérica. A necessidade de, em determinadas aplicações, utilizar perfis que proporcionem melhor isolamento térmico, melhor isolamento acústico ou possuam um momento de inércia ligeiramente superior, sem que o peso próprio seja significativamente afectado, levou à produção de perfis pultrudidos híbridos, com núcleos baseados em pré-formas ou na alimentação contínua de resíduos. Realizados os protótipos seguindo as metodologias acima descritas, urge verificar se as propriedades dos perfis híbridos correspondem às expectativas inicialmente neles depositadas, através de testes destrutivos e não-destrutivos. Assim, foram realizados testes à tracção, à compressão e à flexão, no intuito de verificar os ganhos conseguidos e poder analisar o valor-acrescentado trazido por estes novos perfis em termos estruturais. Estes valores, depois de devidamente validados, permitirão a sua inserção em bases de dados agregadas a programas de cálculo estrutural, que efectuam de forma automática o dimensionamento de estruturas baseadas em perfis desta natureza. Complementarmente, foram realizados testes de isolamento térmico e acústico, com vista a quantificar a melhoria conseguida nestas propriedades, extremamente importantes em determinados tipos de aplicações ligadas à construção civil e obras públicas.

Personality, Brain Asymmetry, and Neuroendocrine Reactivity in Two Immune-Mediated Disorders: a Preliminary Report

Development of some immune-mediated disorders may depend on dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis. To explore neuropsychologic mechanisms in relation to the abnormal endocrine reactivity in patients with systemic lupus erythematosus (SLE) and chronic hepatitis C (CHC) we used the corticotropin releasing hormone (CRH) test, the Minnesota Multiphasic Personality Inventory (MMPI), and the Edinburgh Inventory of Manual Preference Inventory (EIMP). Compared to controls, the adrenocorticotrophic hormone (ACTH) response to CRH was reduced in CHC, while SLE presented reduced baseline dehydroepiandrosterone sulfate levels; higher neurotic scores were found in SLE and higher behavior deviant scores in CHC. Peak ACTH levels were a significant factor for the MMPI profile variability, while the manual preference score was a significant factor for the ACTH response. Personality and manual preference contribute to neuroendocrine abnormalities. Different behavioral and neuroimmunoendocrine models emerge for these disorders.

Spatio-temporal analyses of the relationship between armed conflict and climate change in the eastern Africa

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Acute Kidney Injury after Pediatric Cardiac Surgery: Risk Factors and Outcomes. Proposal for a Predictive Model

Objectives: To characterize the epidemiology and risk factors for acute kidney injury (AKI) after pediatric cardiac surgery in our center, to determine its association with poor short-term outcomes, and to develop a logistic regression model that will predict the risk of AKI for the study population. Methods: This single-center, retrospective study included consecutive pediatric patients with congenital heart disease who underwent cardiac surgery between January 2010 and December 2012. Exclusion criteria were a history of renal disease, dialysis or renal transplantation. Results: Of the 325 patients included, median age three years (1 day---18 years), AKI occurred in 40 (12.3%) on the first postoperative day. Overall mortality was 13 (4%), nine of whom were in the AKI group. AKI was significantly associated with length of intensive care unit stay, length of mechanical ventilation and in-hospital death (p<0.01). Patients’ age and postoperative serum creatinine, blood urea nitrogen and lactate levels were included in the logistic regression model as predictor variables. The model accurately predicted AKI in this population, with a maximum combined sensitivity of 82.1% and specificity of 75.4%. Conclusions: AKI is common and is associated with poor short-term outcomes in this setting. Younger age and higher postoperative serum creatinine, blood urea nitrogen and lactate levels were powerful predictors of renal injury in this population. The proposed model could be a useful tool for risk stratification of these patients.

Web-assisted tobacco intervention in Portuguese : intentions to make behavioural changes and behavioural changes

ABSTRACT - The problem of how to support “intentions to make behavioural changes” (IBC) and “behaviour changes” (BC) in smoking cessation when there is a scarcity of resources is a pressing issue in public health terms. The present research focuses on the use of information and communications technologies and their role in smoking cessation. It is developed in Portugal after the ratification of WHO Framework Convention on Tobacco Control (on 8 November 2005). The prevalence of smokers over fifteen years of age within the population stood at 20.9% (30.9% for men and 11.8% for women). While the strategy of helping people to quit smoking has been emphasised at National Health Service (NHS) level, the uptake of cessation assistance has exceeded the capacity of the service. This induced the search of new theoretical and practical venues to offer alternative options to people willing to stop smoking. Among these, the National Health Plan (NHP) of Portugal (2004-2010), identifies the use of information technologies in smoking cessation. eHealth and the importance of health literacy as a means of empowering people to make behavioural changes is recurrently considered an option worth investigating. The overall objective of this research is to understand, in the Portuguese context, the use of the Internet to help people to stop smoking. Research questions consider factors that may contribute to “intentions to make behavioural changes” (IBC) and “behavioural changes” (BC) while using a Web-Assisted Tobacco Intervention Probe (WATIP). Also consideration is given to the trade-off on the use of the Web as a tool for smoking cessation: can it reach a vast number of people for a small cost (efficiency) demonstrating to work in the domain of smoking cessation (efficacy)”? In addition to the introduction, there is a second chapter in which the use of tobacco is discussed as a public health menace. The health gains achieved by stopping smoking and the means of quitting are also examined, as is the use of the Internet in smoking cessation. Then, several research issues are introduced. These include background theory and the theoretical framework for the Sense of Coherence. The research model is also discussed. A presentation of the methods, materials and of the Web-Assisted Tobacco Intervention Probe (WATIP) follows. In chapter four the results of the use of the Web-Assisted Tobacco Intervention Probe (WATIP) are presented. This study is divided into two sections. The first describes results related to quality control in relation to the Web-Assisted Tobacco Intervention Probe (WATIP) and gives an overview of its users. Of these, 3,150 answered initial eligibility questions. In the end, 1,463 met all eligibility requirements, completed intake, decided on a day to quit smoking (Dday) and declared their “intentions to make behavioural changes” (IBC) while a second targeted group of 650 did not decide on a Dday. With two quit attempts made before joining the platform, most of the participants had experienced past failures while wanting to stop. The smoking rate averaged 21 cigarettes per day. With a mean age of 35, of the participants 55% were males. Among several other considerations, gender and the Sense of Coherence (SOC) influenced the success of participants in their IBC and endeavour to set quit dates. The results of comparing males and females showed that, for current smokers, establishing a Dday was related to gender differences, not favouring males (OR=0.76, p<0.005). Belonging to higher Socio-economic strata (SES) was associated with the intention to consider IBC (when compared to lower SES condition) (OR=1.57, p<0.001) and higher number of school years (OR=0.70, p<0.005) favoured the decision to smoking cessation. Those who demonstrated higher confidence in their likelihood of success in stopping in the shortest time had a higher rate of setting a Dday (OR=0.51, p<0.001). There were differences between groups in IBC reflecting the high and low levels of the SOC score (OR=1.43, p=0.006), as those who considered setting a Dday had higher levels of SOC. After adjusting for all variables, stages of readiness to change and SOC were kept in the model. This is the first Arm of this research where the focus is a discussion of the system’s implications for the participants’ “intentions to make behavioural changes” (IBC). Moreover, a second section of this study (second Arm) offers input collected from 77 in-depth interviews with the Web-Assisted Tobacco Intervention Probe (WATIP) users. Here, “Behaviour Change” (BC) and the usability of the platform are explored a year after IBC was declared. A percentage of 32.9% of self-reported, 12-month quitters in continuous abstinence from smoking from Dday to the 12-month follow- up point of the use of the Web-Assisted Tobacco Intervention Probe (WATIP) has been assessed. Comparing the Sense of Coherence (SOC) scores of participants by their respective means, according to the two groups, there was a significant difference in these scores of non smokers (BC) (M=144,66, SD=22,52) and Sense of Coherence (SOC) of smokers (noBC) (M=131,51, SD=21,43) p=0.014. This WATIP strategy and its contents benefit from the strengthening of the smoker’s sense of coherence (SOC), so that the person’s progress towards a life without tobacco may be experienced as comprehensible, manageable and meaningful. In this sample the sense of coherence (SOC) effect is moderate although it is associated with the day to quit smoking (Dday). Some of the limitations of this research have to do with self-selection bias, sample size (power) and self-reporting (no biochemical validation). The enrolment of participants was therefore not representative of the smoking population. It is not possible to verify the Web-Assisted Tobacco Intervention Probe (WATIP) evaluation of external validity; consequently, the results obtained cannot be applied generalized. No participation bias is provided. Another limitation of this study is the associated limitations of interviews. Interviewees’ perception that fabricating answers could benefit them more than telling the simple truth in response to questions is a risk that is not evaluated (with no external validation like measuring participants’ carbon monoxide levels). What emerges in this analysis is the relevance of the process that leads to the establishment of the quit day (Dday) to stop using tobacco. In addition, technological issues, when tailoring is the focus, are key elements for scrutiny. The high number of dropouts of users of the web platform mandates future research that should concentrate on the matters of the user-centred design of portals. The focus on gains in health through patient-centred care needs more research, so that technology usability be considered within the context of best practices in smoking cessation.

Determinants of export diversification and sophistication in sub-saharan Africa

This paper studies the political and economic factors that determine successful export diversification (ED) and export sophistication (ES) strategies in the Sub-Saharan African (SSA) countries and also the way in which successful ED and sophistication strategies contribute to explain the improving in some of the millennium development goals (MDG). We run separate regressions for the determinants of ES and ED, using disaggregated data of the 48 SSA countries, from 1960 to 2005. The results suggest that better governance is an important determinant for the success of diversification and sophistication strategies in SSA. In particular the level of corruption, transparency and accountability are important factors in limiting or promoting the scope of diversification and the level of sophistication of the exports. The results also suggest that increases in human capital in SSA countries promote both ED and ES, showing that the level of education of the workforce is positively related with ES and ED, with higher levels of education (tertiary) playing a more important role in explaining ES, while lower levels of education (primary) being more important as determinants of ED. In the second part we explore the links between ED and ES and growth presenting evidence that ED and ES are linked to growth stability in SSA. This study also suggests that the Sub-Saharan countries that were more successful in achieving ED and ES tend to be more successful in improving the living conditions of their population. Using different variables of Infant Mortality (one of the MDG) and life expectancy as dependent variables, we present evidence that suggests that in SSA higher ED and ES are associated with lower infant mortality and higher life expectancy. We show that this result is robust, presenting positive and significant results even when a large number of different control variables are introduced, or when fixed effects and instrumental variables are considered. The evidence suggests that ED and ES are part of the solution for a successful development of SSA.

Promoting healthy eating standards on children through CSR educational programs: An evaluation of impact on eating preferences, attitude towards the brand and perceived brand reputation

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Macroeconomic impacts of politics and policy: Applications to financial and real markets

A PhD Dissertation, presented as part of the requirements for the Degree of Doctor of Philosophy from the NOVA - School of Business and Economics

De serviteurs de l´Etat à représentants élus. Les parlementaires originaires du secteur public en Europe

This article aims at testing empirically the relevance of the State/civil society dichotomy commonly used by political theorists through the question of the specific weight of MPs having a public sector background in Europe. It uses the DATACUBE data set in order to show that such an opposition is only relative because of the specific weight of the public sector in the parliamentary elite considered in a long-term perspective. The article focuses on the dynamics of this relevance and introduces nuances regarding variations across countries, sub-categories within the public sector and political parties.

Land cover mapping analysis and urban growth modeling using remote sensing techniques

The rapid growth of big cities has been noticed since 1950s when the majority of world population turned to live in urban areas rather than villages, seeking better job opportunities and higher quality of services and lifestyle circumstances. This demographic transition from rural to urban is expected to have a continuous increase. Governments, especially in less developed countries, are going to face more challenges in different sectors, raising the essence of understanding the spatial pattern of the growth for an effective urban planning. The study aimed to detect, analyse and model the urban growth in Greater Cairo Region (GCR) as one of the fast growing mega cities in the world using remote sensing data. Knowing the current and estimated urbanization situation in GCR will help decision makers in Egypt to adjust their plans and develop new ones. These plans should focus on resources reallocation to overcome the problems arising in the future and to achieve a sustainable development of urban areas, especially after the high percentage of illegal settlements which took place in the last decades. The study focused on a period of 30 years; from 1984 to 2014, and the major transitions to urban were modelled to predict the future scenarios in 2025. Three satellite images of different time stamps (1984, 2003 and 2014) were classified using Support Vector Machines (SVM) classifier, then the land cover changes were detected by applying a high level mapping technique. Later the results were analyzed for higher accurate estimations of the urban growth in the future in 2025 using Land Change Modeler (LCM) embedded in IDRISI software. Moreover, the spatial and temporal urban growth patterns were analyzed using statistical metrics developed in FRAGSTATS software. The study resulted in an overall classification accuracy of 96%, 97.3% and 96.3% for 1984, 2003 and 2014’s map, respectively. Between 1984 and 2003, 19 179 hectares of vegetation and 21 417 hectares of desert changed to urban, while from 2003 to 2014, the transitions to urban from both land cover classes were found to be 16 486 and 31 045 hectares, respectively. The model results indicated that 14% of the vegetation and 4% of the desert in 2014 will turn into urban in 2025, representing 16 512 and 24 687 hectares, respectively.

How to optimize Lipton’s business model in order to stimulate tea consumption in Portugal and increase Lipton Leaf tea market share?: The importance of distribution and sales channels management in a B2B2C market

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