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.

Drawing and use of auxiliary projection nets (the program STEGRAPH)

The development of an algorithm for the construction of auxiliary projection nets (conform, equivalent and orthographic), in the equatorial and polar versions, is presented. The algorithm for the drawing of the "IGAREA 220" counting net (ALYES & MENDES, 1972), is also presented. Those algorithms are the base of STEGRAPH program (vers. 2.0), for MS-DOS computers, which has other applications.

The impact of CdSe/ZnS Quantum Dots in cells of Medicago sativa in suspension culture

Abstract Background: Nanotechnology has the potential to provide agriculture with new tools that may be used in the rapid detection and molecular treatment of diseases and enhancement of plant ability to absorb nutrients, among others. Data on nanoparticle toxicity in plants is largely heterogeneous with a diversity of physicochemical parameters reported, which difficult generalizations. Here a cell biology approach was used to evaluate the impact of Quantum Dots (QDs) nanocrystals on plant cells, including their effect on cell growth, cell viability, oxidative stress and ROS accumulation, besides their cytomobility. Results: A plant cell suspension culture of Medicago sativa was settled for the assessment of the impact of the addition of mercaptopropanoic acid coated CdSe/ZnS QDs. Cell growth was significantly reduced when 100 mM of mercaptopropanoic acid -QDs was added during the exponential growth phase, with less than 50% of the cells viable 72 hours after mercaptopropanoic acid -QDs addition. They were up taken by Medicago sativa cells and accumulated in the cytoplasm and nucleus as revealed by optical thin confocal imaging. As part of the cellular response to internalization, Medicago sativa cells were found to increase the production of Reactive Oxygen Species (ROS) in a dose and time dependent manner. Using the fluorescent dye H2DCFDA it was observable that mercaptopropanoic acid-QDs concentrations between 5-180 nM led to a progressive and linear increase of ROS accumulation. Conclusions: Our results showed that the extent of mercaptopropanoic acid coated CdSe/ZnS QDs cytotoxicity in plant cells is dependent upon a number of factors including QDs properties, dose and the environmental conditions of administration and that, for Medicago sativa cells, a safe range of 1-5 nM should not be exceeded for biological applications.

Iberian peninsula ecosystem carbon fluxes: a model-data integration study

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia do Ambiente pela Universidade Nova de Lisboa,Faculdade de Ciências e Tecnologia

Sigla WEBGIS portal: an open source Web-based GIS application for the portuguese bluetongue Entomologiacal surveillance program.

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Ciência e Sistemas de Informação Geográfica

China's space program : a new tool for PRC "soft power" in international relations?

When China launched an anti-satellite (ASAT) weapon in January 2007 to destroy one of its inactive weather satellites, most reactions from academics and U.S. space experts focused on a potential military “space race” between the United States and China. Overlooked, however, is China’s growing role as global competitor on the non-military side of space. China’s space program goes far beyond military counterspace applications and manifests manned space aspirations, including lunar exploration. Its pursuit of both commercial and scientific international space ventures constitutes a small, yet growing, percentage of the global space launch and related satellite service industry. It also highlights China’s willingness to cooperate with nations far away from Asia for political and strategic purposes. These partnerships may constitute a challenge to the United States and enhance China’s “soft power” among key American allies and even in some regions traditionally dominated by U.S. influence (e.g., Latin America and Africa). Thus, an appropriate U.S. response may not lie in a “hard power” counterspace effort but instead in a revival of U.S. space outreach of the past, as well as implementation of more business-friendly export control policies.

Every normal logic program has a 2-valued semantics: theory, extensions, applications, implementations

Trabalho apresentado no âmbito do Doutoramento em Informática, como requisito parcial para obtenção do grau de Doutor em Informática

Effects of a mental health training program on health care worker's knowledge and attitude and practice in Belize

ABSTRACT This study was conducted to assess mental health knowledge, attitude and practices among health care workers in Belize before and immediately after a competency based training program in mental health. A baseline Knowledge, Attitudes and Practices (KAP) survey was given to health personnel, mainly nurses, working primary and secondary care. The intervention was a 13-week face-to-face training course for health care professionals with the objective of increasing their competency in mental health and reducing stigma. After the training a post intervention KAP survey was conducted among the original respondents. 88 health care workers completed the baseline survey and 61 of those respondents completed the post-intervention questionnaire. The results showed that the level of knowledge of the participants had improved by the training intervention and that in general, the intervention was effective in correcting some misconceptions about mental illness and reducing stigmatizing attitudes among the participants.

Modeling assembly program with constraints. A contribution to WCET problem

Dissertação para obtenção do Grau de Mestre em Lógica Computacional

Electron transfer complex between nitrous oxide reductase and cytochrome c552 from Pseudomonas nautica: kinetic, nuclear magnetic resonance, and docking studies

Biochemistry. 2008 Oct 14;47(41):10852-62. doi: 10.1021/bi801375q

Efectividade de um programa de exercício aquático na osteoartrose do joelho

RESUMO: A osteoartrose do joelho é uma condição clínica cuja prevalência tem aumentado nos últimos anos na população idosa. Trata-se de uma condição que pode ser bastante incapacitante para o idoso, gerando um forte impacto social e económico. O exercício aquático tem sido identificado como um factor de promoção da melhoria do quadro clínico nesta população, mas a sua efectividade não está, ainda, determinada. Objectivo: investigar a efectividade, a curto e médio prazo, de um programa de exercício aquático, realizado em grupo, com a duração de 8 semanas, na amplitude articular, dor e rigidez do joelho, e na função física e qualidade de vida, em idosos com osteoartrose do joelho. Metodologia: Recorreu-se a um estudo quase-experimental, double-blind, controlado, sem aleatorização, cuja amostra, constituída por 43 sujeitos, foi selecionada por conveniência. Os sujeitos do grupo experimental (n=22) foram submetidos ao programa de exercício aquático e os do grupo de controlo (n=21) foram submetidos ao programa de exercício no solo. Ambos os programas foram definidos de acordo com as recomendações internacionais para a prática de exercício físico em idosos com osteoartrose (Arthritis Foundation, 2009a, 2009b). Todo o grupo foi avaliado no início do programa, no final do mesmo (8 semanas) e após 6 semanas de follow-up, nos seguintes indicadores: amplitude articular do joelho (através do goniómetro), dor, rigidez, função e qualidade de vida (através do KOOS). Resultados: A amostra deste estudo foi constituída por sujeitos maioritariamente do género feminino (76,7%), com uma média de 72,7 anos (DP=5,49). O programa de exercício aquático implementado demonstrou um aumento da amplitude articular passiva de flexão (p<0,0001) e extensão (p=0,016) do joelho, uma diminuição da dor e da rigidez articular (p<0,0001), um aumento da função nas AVD’s (p<0,0001) e no desporto/lazer (p=0,031), e ainda, um aumento da qualidade de vida (p<0,0001). Contudo, apenas os níveis de amplitude articular passiva de extensão do joelho (p=0,083) e de função no desporto/lazer (p=0,244) se mantiveram ao longo das seis semanas de follow-up. Conclusões: Apesar de algumas limitações, considera-se que este estudo é de grande importância para a comunidade científica e para os fisioterapeutas preocupados com a crescente prevalência da osteoartrose e dos custos associados. O exercício aquático parece ser uma estratégia importante na melhoria do estado de saúde dos idosos com osteoartrose do joelho.----------------- ABSTRACT: The osteoarthritis of the knee is a clinical condition that has been increasing among the elderly population over the past few years. It’s a condition that can be fairly disabling to the elderly individual, and which generates a strong social and economic impact. Aquatic exercise has been named as a promotional factor in the improvement of the clinical picture in this population, but its effectiveness is yet to be determined. Objective: To investigate the effectiveness, in a short and medium term, of an aquatic exercise program undertaken by a group over eight weeks, in the joint amplitude, pain and stiffness of the knee, and in the physical function and quality of life in elderly people who suffer from knee osteoarthritis. Methodology: was used a double-blind, quasi-experimental study with no randomization and its 43 subjects were selected as a matter of convenience. The subjects of the experimental group (n=22) were subjected to an aquatic exercise program and those of the control group (n=21) were subjected to a land-based exercise program. Both programs have followed international recommendations on the practice of physical exercise in elderly people who suffer from osteoarthritis (Arthritis Foundation, 2009a, 2009b). The entire group was evaluated in the beginning and at the end of the program (8 weeks later), and after a 6 week follow-up, in these parameters: knee range of motion (through a goniometer), pain, stiffness, function and quality of life (through KOOS). Results: This sample was predominantly female (76,7%) with a mean age of 72,7 years (SD=5,49). Aquatic exercise resulted in increase of passive joint flexion (p<0,0001) and knee extension (p=0,016), in the decline of pain and stiffness (p<0,0001), in the increase of function in the ADLs (p<0,0001). However, only the knee extension amplitude (p=0,083) and the function in sports/leisure (p=0,244) were kept through the six-week follow-up. Conclusions: Despite some limitations, this study is of great importance to the community and to the physiotherapists concerned with the growing prevalence of osteoarthritis and the associated costs. Aquatic exercise appears to be an important strategy in the improvement of the health condition of patients who suffer from knee osteoarthritis.

Program Catapultas: Education for development in Bairro Padre Cruz

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

Contract-program evaluation: Impact of the DRG classification system on hospitals' outputs

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

A diabetes: principais parâmetros para o controlo da diabetes

RESUMO: A Diabetes Mellitus é uma doença metabólica crónica, com deficiência a nível do metabolismo dos hidratos de carbono, lípidos e proteínas, resultante de deficiências na secreção ou ação da insulina, ou de ambas, que quando não tratada antecipadamente e de modo conveniente, pode ter consequências muito graves. Dado a incidência a nível mundial da Diabetes Mellitus, torna-se de elevada importância avaliar toda a sua envolvência e estudar bem quais os critérios a ter em consideração. Este trabalho propõe-se estudar para além dos parâmetros bioquímicos relacionados com a doença - Glicose e Hemoglobina Glicada A1c (HbA1c), analisar os resultados dos últimos cinco anos (2008-2012) dos ensaios interlaboratoriais do PNAEQ, do Departamento de Epidemiologia, do Instituto Nacional de Saúde Dr. Ricardo Jorge. Foram também analisadas as metodologias utilizadas e as variações interlaboratoriais, de forma a entender qual ou quais são os parâmetros mais adequados para o seu diagnóstico e controlo. Este estudo utilizou a população de laboratórios portugueses, públicos e privados, de Portugal Continental e Ilhas, um laboratório de Angola e outro de Macau que se inscreveram no PNAEQ nestes cinco anos, sendo a amostra composta pelo n.º de participações. No programa de Química Clinica foram distribuídas 38 amostras e no programa de HbA1c foram distribuídas 22 amostras. Para a glicose, o nível de desempenho nos ensaios é na globalidade das amostras de Excelente, no entanto verifica-se que sempre que a concentração da amostra é de nível patológico, que a maioria dos ensaios o desempenho foi inferior – Bom. O método de eleição e com CV% mais baixos foi o método da hexoquinase. Para a HbA1c, o nível de desempenho nos ensaios é na globalidade das amostras de Excelente. O método de eleição e com CV% mais baixos foi o método de HPLC. O CV% para a glicose ronda desde 2010 a 2012, os 3% e para a HbA1c foi de aproximadamente 4,0% em 2012. A HbA1c tem mostrado ser uma ferramenta muito útil, importante e robusta na monitorização da Diabetes, sendo hoje em dia quase sempre requisitada em análises de rotina a diabéticos de modo a prevenir complicações que possam vir a acorrer. No futuro poderá ser um importante, senão o parâmetro de futuro, para o diagnóstico da Diabetes, no entanto, mesmo já tendo sido muito trabalhada a sua padronização, ainda existem questões por responder como quais são na realidade todos os seus interferentes, qual a verdadeira relação da HbA1c com a glicose média estimada, em todas as populações e com estudos epidemiológicos. Também a própria educação do diabético e clínico deve ser aprimorada, pelo que neste momento as PTGO e os doseamentos de glicose em jejum devem ser utilizados e encontrando-se a Norma da DGS N.º 033/2011 de acordo com as necessidades e com o estado da arte deste parâmetro. A implementação da glicose média estimada será uma mais-valia na monitorização dos diabéticos pelo que deverá ser uma das prioridades a ter em conta no futuro desta padronização, uniformizando a decisão clinica baseada nela e minimizando a dificuldade de interpretação de resultados de laboratório para laboratório. --------------ABSTRACT: Diabetes Mellitus is a chronic metabolic disease, with a deficit in the metabolism of carbohydrates, lipids and proteins, resulting from deficiencies in insulin secretion or action, or both, which if, when not early treated in a proper way, may result in very serious consequences. Given the worldwide incidence of diabetes mellitus, it is highly important to evaluate all its background and study specifically all the criteria to take into consideration. The aim of this thesis is to study and evaluate beyond the biochemical parameters related to the disease - Glucose and Glycated Haemoglobin A1c (HbA1c), analyze the results of the last five years (2008-2012) of the PNAEQ interlaboratorial tests, in the Department of Epidemiology of National Institute of Health Dr. Ricardo Jorge. It is also intended to analyze the methodologies used and the interlaboratorial variations, in order to understand the most suitable parameters for the diagnosis and control. This study was based in a population of Portuguese laboratories, public and private, of Portugal mainland and islands, a laboratory of Angola and other from Macau, who enrolled in PNAEQ in these five years, and the sample was composed by the n. º of holdings. In the Clinical Chemistry Program there were distributed 38 samples and in the program HbA1c were distributed 22 samples. For glucose, the level of performance in the total nº of the samples was Excellent; however, it was found that when the concentration level of the sample was pathological, in most of the tests the performance was Good. The most preferred method with the lowest CV% is the hexokinase method. For the HbA1c, as a whole, the samples’ tests were Excellent, at the level of performance. The method of election with the lower CV% was the HPLC. The CV% for glucose was around 3%, from 2010 to 2012 and the HbA1c was approximately 4.0% in 2012. The HbA1c method has demonstrated to be a very useful tool, important and robust for monitoring diabetes, being nowadays, almost always required in routine analysis to prevent future complications. In the future it may be an important parameter, if not the most important, for the diagnosis of diabetes. However, despite it has already been standardized, there are still some questions that need to be answered, such as, which are in fact all their interferences, which is the true connection of HbA1c, when compared with the estimated average glucose, in all populations and epidemiological studies. Moreover, the education of the patient and the doctor concerning diabetes should be improved. Nowadays, the Oral Glucose Tolerance Test (OGTT) and fasting glucose determinations should be used and, the needs and the state of the art of this parameter, should be in accordance with the Standard DGS N. º 033/2011. The Implementation of the estimated average glucose will be an added value in monitoring diabetics and, therefore, should be a priority to consider in its future standardization and clinical decision based on it, will be uniform and the difficulty of interpreting results from laboratory to laboratory will be minimal.

The effectiveness of a teacher’s training workshop on Media Smart Program

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