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.

Controlo da tuberculose em Portugal : papel e qualidade da detecção de casos

RESUMO - A impressionante evolução da incidência notificada desde 1950 evidencia o quanto o sistema de informação é sensível ao esforço de notificação, reflectindo ainda o impacte das medidas de controlo que foram sendo introduzidas, bem como alguma melhoria nas condições sociais com efeito favorável sobre a doença (Briz, 2005). Sendo a tuberculose uma doença de notificação obrigatória, nos termos da Portaria n.º 766/86, de 26 de Dezembro, os casos deverão ser sempre comunicados à Autoridade de Saúde, em impresso aprovado. O facto de a tuberculose ter um sistema de informação próprio tem permitido um conhecimento relativamente completo da situação epidemiológica. (DGS, 1995) Pretende-se caracterizar o perfil de distribuição da incidência notificada da tuberculose pulmonar, em Portugal Continental, nomeadamente a nível distrital, no período compreendido entre 2000 e 2008, inclusive, partindo-se depois para um estudo mais pormenorizado, relacionado com a sensibilidade do sistema de notificação da tuberculose, no sentido de se quantificarem os problemas de subnotificação. Para validação da notificação, serão utilizados os dados de 2007 e 2008. Procurar-se-á depois obter o perfil da incidência ajustada para a detecção em cada um desses anos, avançando-se de seguida para a identificação e caracterização de parâmetros complementares e de acesso fácil que contribuam para interpretar a distribuição geográfica da incidência notificada, em função da sua provável validade. Perante o eventual confronto com o problema da subnotificação, a identificação das razões da menor adesão à notificação de casos de tuberculose pulmonar apresenta-se quase como inevitável, sendo feita através do recurso a entrevistas a informadores-chave. --------------------------------------ABSTRACT - The impressive development of the incidence reported since 1950 shows how the system is sensitive to the effort of notification, still reflects the impact of control measures have been introduced, and some improvement in social conditions with favorable effect on the disease ( Briz, 2005). As tuberculosis a notifiable disease, according to Ordinance No. 766/86, December 26, cases should be reported to the Health Authority, approved in print. The fact that tuberculosis have an information system itself has allowed a relatively complete knowledge of the epidemiological situation. (DGS, 1995) The aim is to characterize the distribution profile of the reported incidence of pulmonary tuberculosis, in Portugal, particularly at district level in the period between 2000 and 2008, starting from then to a more detailed study, related to the sensitivity of the system notification of tuberculosis, in order to quantify the problems of underreporting. For validation of the notification, we used the data from 2007 and 2008. Search will then obtain the profile of the adjusted incidence for detection in each of those years, advancing is then for the identification and characterization of additional parameters and easy access to contribute to interpret the geographical distribution of reported incidence in according to their likely validity. Given the eventual confrontation with the problem of underreporting, the identification of reasons for the lower adherence to reporting cases of pulmonary tuberculosis has become almost as inevitable, being made through the use of interviews with key informants.

L’instabilité dynamique pendant le Toarcien dans le Moyen Atlas (Maroc): mise en évidence de glissements synsédimentaires dans le synclinal de Bou Angar

During the Toarcian, shelves undergo block-faulting with mechanisms of tilting. It results the break up of the Middle Atlas basin in subsident sectors separated by resistant ridges. This device is highlighted by strong variations of facies, more or less extended lacunar zones, reefs aligned on the ridges and of synsedimentary tectonics structures. Within the framework of mapping survey carried out in the south-west of Middle Atlas, a meticulous prospection of Bou Angar synclinal allowed the description of a new outcrop of Toarcian. This one offers good examples of extensional structures and bio-accumulations. These data, supplemented by other witnesses of the dynamic instability in the rest of the Middle Atlas, permit to propose a paleogeographic map of the Middle Atlas basin during the Toarcian.

Biomarkers in Solea Senegalensis Kaup, 1858 exposed to contaminated estuarine sediments: a multi-level approach

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia for the degree of Doctor of Philosophy in Environmental Sciences

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

Cortisol e testosterona no plasma da grávida e no líquido amniótico: variação com o relaxamento e correlação com o rácio digital 2D:4D no recém-nascido

RESUMO: Conclusão - Este estudo sugere que mulheres grávidas beneficiam da prática rotineira de 30 min de relaxamento perante a eminência de um acontecimento indutor de stress. O benefício será tanto psicológico como fisiológico e será mais marcado de manhã do que de tarde. As mulheres com maior tendência ansiosa, tipicamente as mais jovens e com menos idade gestacional, serão as que mais beneficiam. Entre os tipos de intervenção experimentados, todos eles não dispendiosos, a audição de música foi globalmente o mais eficaz para o propósito pretendido. A variação do cortisol e a variação da testosterona estão altamente correlacionadas, e este efeito poderá ser explorado em futuras intervenções relaxantes. Programas curtos de relaxamento poderão conduzir a benefícios para o bem-estar psicológico e para a saúde da grávida, com benefícios adicionais no desfecho da gravidez. O rácio digital 2D:4D do recém-nascido apresenta características sexualmente dimórficas, sendo mais baixo em rapazes que em raparigas, confirmando a influência dos androgénios pré-natais, mas há grande sobreposição entre os sexos pelo que, isoladamente, não pode ser utilizado como marcador de risco. No entanto, se associado a outros marcadores biológicos, como o peso ao nascer e a circunferência cerebral, entre outros, poderá ser um parâmetro a valorizar desde cedo, possivelmente no acompanhamento pediátrico. Nas raparigas, o RD da mãe e a testosterona no LA explicam uma proporção significativa do seu 2D:4D. Em ambos os sexos, o rácio 2D:4D aumenta após o nascimento e o dimorfismo sexual observado com base em amostras de crianças com mais de dois anos de idade, é afectado pela testosterona pós-natal, especialmente no que se refere à mão direita.----------ABSTRACT: Conclusions - This study suggests that pregnant women would benefit from the routine practice of 30min relaxation when at the imminence of a stressful event. The benefit would be both psychological and physiological and would be more pronounced in the morning than in the afternoon. Women tending to be more anxious, typically younger and at a lower gestational age, are the ones that benefit the most. Among the interventions investigated, all being non-expensive and easy to implement, listening to relaxing music was globally the most efficient for the benefit intended. The variation of cortisol and the variation of testosterone are significantly correlated, an association that might be used in future relaxation interventions. It is feasible to conceive short relaxation programs aimed at benefiting psychological well-being and health in pregnancy, with additional benefits for pregnancy outcome. The digital ratio 2D:4D is sexually dimorphic, being lower in males than in females, confirming the influence of pre-natal androgens. There is however large overlap between sexes, rendering the 2D:4D a risk marker not to be used in isolation but rather in association with other markers, like for instance the weight at birth and the head circumference, wherein it may be a relevant parameter for pediatric follow-up. In newborn females, a significant amount of variability in 2D:4D is accounted for by their mother’s digital ratio and AF testosterone. In both sexes, the 2D:4D ratio increases following birth and sexual dimorphism,as assessed from samples of subjects with more than 2 years of age, is affected by post-natal testosterone, especially in what concerns the right hand.

Taxes and labor supply: Portugal, Europe, and the United States

I relate hours worked with taxes on consumption and labor for Portugal, France, Spain, United Kingdom and United States. From 1986 to 2001, hours per worker in Portugal decreased from 35.1 to 32.6. With the parameters for Portugal, the model predicts hours worked in 2001 with an error of only 12 minutes from the actual hours. Across countries, most predictions differ from the data by one hour or less. The model is not sensible to special assumptions on the parameters. I calculate the long run effects of taxes on consumption, hours, capital and welfare for Portugal. I extend the model to discuss implications for Social Security. I discuss the steady state and the transition from a pay-as-you-go to a fully funded system.