Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Human-robot teamwork: a knowledge-based solution

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Playing Newtonian Games with Modellus

This article is a short introduction on how to use Modellus (a computer package that is freely available on the Internet and used in the IOP Advancing Physics course) to build physics games using Newton’s laws, expressed as differential equations. Solving systems of differential equations is beyond most secondary-school or first-year college students. However, with Modellus, the solution is simply the output of the usual physical reasoning: define the force law, compute its magnitude and components, use it to obtain the acceleration components, then the velocity components and, finally, use the velocity components to find the coordinates.

Derivation methods for hybrid knowledge bases with rules and ontologies

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

How human schematization and systematic errors take effect on sketch map formalizations

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

Aplicação do método de aprendizagem baseado na análise de problemas ao ensino da Fisiopatologia

Educação Médica 1991; 2 (2): 29-40

Société rurale, société urbaine: espaces en interaction

La sociologie et les nouveaux défis de la modernisation, Porto, pp. 315-326

Educação alimentar infantil: potencialidades de estudantes de educação de infância

Resumo: Na promoção de comportamentos alimentares saudáveis ao longo da vida. que deve iniciar-se o mais precocemente possível, a educação alimentar é um elemento chave. O jardim-de-infância é um espaço efectivo na implementação de projectos de educação alimentar, onde os educadores de infância são actores imprescindíveis. Este estudo teve como objectivo desenvolver uma metodologia apropriada para identificar as capacidades de estudantes de educação de infância e avaliar as suas aptidões no contexto da educação alimentar infantil. A população alvo do estudo foram estudantes do 4ºano da licenciatura em educação de infância de instituições públicas e privadas da área metropolitana de Lisboa (n=287). Construiu-se um videograma, integrador dos domínios da aprendizagem (cognitivo e afectivo) e dos factores associados aos comportamentos em saúde (predisponentes, capacitadores e de esforço). A construção dos questionários estruturou-se em: conhecimentos-atitudes-comportamentos.Pretendia-se que os estudantes transmitissem a sua opinião, de acordo com os questionários.Os estudantes manifestaram conhecimentos, no âmbito da alimentação infantil e da utilidade e aplicabilidade da educação alimentar.Nenhum estudante apresentou conhecimentos negativos, numa escala de zero a 18 valores, 86,9% obtiveram uma classificação entre 11 e 17 valores e 13,1% a classificação máxima.A atitude dos estudantes revelou-se consensual com o desejável, 98,5% apresentaram atitudes positivas face aos aspectos estruturadores das actividades de educação alimentar.No domínio do "saber fazer" 51,0% dos estudantes demonstraram fragilidades no seu desempenho/comportamento. Em conclusão, a utilização do questionário demonstrou ser apropriado para a medição dos conhecimentos, das atitudes e como forma de os estudantes, após visionarem o videograma, espelharem o seu desempenho/comportamento face à representação do educador de infância. A taxa de resposta nunca foi inferior a 98,9% (n=284). No domínio dos conhecimentos, os estudantes manifestaram concepções positivas no campo da alimentação infantil e da educação alimentar. As atitudes enfatizaram-se no domínio afectivo, nos aspectos relacionais e comunicacionais. No domínio dos comportamentos, 91,8% dos estudantes apresentaram dificuldades na identificação dos aspectos menos correctos do desempenho dos actores do video, o que pode sugerir lacunas no âmbito do "saber fazer". Abstract:Nutrition education is key element to promote lifelong healthy eating behaviours and it must begin since early stages of life. Nursery schools are an effective space in the implementation of nutrition education projects, where the nursery teachers are indispensable actors. The aim of this study was to develop an appropriate methodology to identify nursery education student´s skills and evaluate their attitudes in the childhood nutrition education's context. The study's population were students of the 4th degree in private and public nursery education universities in Lisbon metropolitan area (n=287). A video integrator of learning domains (cognitive and affective) and of factors associated with health behaviours (predisposing, enabling and reinforcing) was developed. Questionnaire´s construction was structured in: knowledge-attitudes-behaviours.According to the questionnaires students were asked to transmit their opinion. Students revealed knowledge, in the scope of the childhood nutrition and in utility and applicability of nutrition education. No students presented negative results in knowledge ina zero - 18 scale; 86,9% students obtained a classification between 11 and 17 and the maximum classification was obtained by 13.1% students. Student's attitude was according to win the desirable, 98,5% student´s revealed positive attitudes in the nutrition education's structure aspects of chilhood activities.In the domain of the "know to do" 51,0% of students showed fragilities in their performance/behaviour. In conclusion, the questionnaire´s utilization confirm to be appropriated in measurement knowledge and attitudes and also, after watching the video, as a way for students reflect their performance/behaviour face to the nursery teacher´s representation. Answer´s rate was never lower than 98.9% (n=284). In the knowledge's domain students demonstrated positive conceptions in the childhood nutrition and nutrition education's fields. Attitudes were emphasized in the effective domain in the communication and relational aspects. In behaviour's domain 91.8% students presented difficulties in identifying the less correct aspects of the video actor's performance what may suggest gaps in the "know to do" scope.

Satisfação profissional e vínculo laboral : prestadores de cuidados directos num hospital distrital

RESUMO - A flexibilidade dos contratos de trabalho é cada vez mais uma realidade. Em 2009, cerca de 18% da população activa em Portugal tinha um vínculo instável. Na instituição onde se realizou o estudo, 38,8% dos profissionais de saúde têm este tipo de vínculo. Este estudo foi realizado num hospital distrital com a participação de 103 prestadores de cuidados directos – assistentes operacionais, enfermeiros, médicos e técnicos de diagnóstico e terapêutica - aos quais foi dado um questionário de auto-resposta. Através deste, fez-se a comparação dos níveis de satisfação dos profissionais com diferentes tipos de vínculo. Concluiu-se que as dimensões mais valorizadas são as relacionais e condições de trabalho e saúde. A dimensão da Segurança no Emprego surge no meio da tabela. Ao contrário do que dizem os estudos, a autonomia e poder foi das menos valorizadas. Os profissionais com vínculo laboral instável dão maior importância à segurança. As dimensões relacionais são as que apresentam maiores níveis de satisfação. As que apresentam menores níveis são a Remuneração, Condições de Trabalho e Saúde e Segurança no Emprego, sendo que nesta ultima se registam diferenças significativas entre profissionais com diferentes tipos de vínculo. Verifica-se com 95% de confiança que existem diferenças significativas na dimensão da Segurança no Emprego, onde os profissionais com vínculo instável apresentam menores níveis de satisfação. Os profissionais com vínculo instável demonstram que este facto lhes trouxe consequências negativas ao nível pessoal e social. Não existe significância na diferença entre os níveis da satisfação dos profissionais de saúde com diferentes vínculos. -----------------------------------ABSTRACT - Employment contract flexibility is becoming a reality with each passing day. In 2009, around 18% of the active population in Portugal had an unstable bond. In the institution where this study was conducted, 38.8% of the health professionals have this kind of arrangement. This study was conducted in a district hospital with the participation of 103 direct care providers - operating assistants, nurses, doctors and technical diagnostic and therapeutic - that were given a self-response questionnaire. Through this questionnaire, the levels of satisfaction of the professionals with different types of employment bond were compared. It was concluded that the most valued dimensions are relational and work and health conditions. Work security appears in the middle of the table. Contrary to what studies say, autonomy and power were less valued. Professionals with an unstable bond give greater importance to safety. The relational dimensions are those with higher levels of satisfaction. Those with lower levels are the wages, working conditions and health and safety in employment, where in health and safety in employment show significant differences between professionals with different types of employment bond. We can verify with a 95% confidence interval that there are significant differences in the work safety dimension, where professionals with unstable employment bonds present lower levels of satisfaction. Professionals with an unstable employment bond show that this fact brought them negative consequences at the personal and social level. There is no significant difference between the levels of satisfaction of health professionals with different types of employment bond.

Automorphisms of partial endomorphism semigroups

Publicationes Mathematicae Debrecen

Intelligent decision support systems for collaboration in industrial plants

Dissertação apresentada para obtenção do Grau de Doutor em Sistemas de Informação Industriais, Engenharia Electrotécnica, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

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

Database repairs with answer set programming

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Aborto recorrente das causas na mulher às consequências para o casal

RESUMO: O aborto recorrente (AR) é um evento extremamente traumático com grande impacto na vida dos casais. Apesar de avanços significativos verificados na investigação médica, cerca de 50% dos casos continua sem uma causa identificada. Alguns aspectos como a caracterização inadequada das doentes e das perdas gestacionais, assim como diferentes metodologias utilizadas no seu estudo, têm influenciado a prevalência de alguns dos factores causais e dificultado a compreensão do AR. Da mesma forma, pouco se sabe sobre as diferenças de género na vivência psicológica do aborto recorrente e das suas eventuais repercussões para o relacionamento do casal, centrando-se os poucos estudos existentes preferencialmente na mulher. Por esta razão, o objectivo desta tese foi a caracterização dos factores médicos associados ao AR e das consequências psicológicas desta entidade, contribuindo para promover estratégias clínicas baseadas na evidência específica. Na primeira parte desta tese (capítulos 1 e 2), após uma breve introdução geral e através de uma revisão da literatura, efectua-se uma reflexão sobre o tema, abordando a epidemiologia do aborto recorrente, os factores médicos e os aspectos psicológicos associados. Nos capítulos 3 e 4 descrevemos três estudos efectuados em mulheres portuguesas com aborto recorrente. O primeiro estudo teve por objectivo caracterizar os factores médicos e determinar o padrão da perda recorrente de gravidez, numa coorte de mulheres submetidas a um protocolo de diagnóstico definido. As participantes foram agrupadas de acordo com a paridade (AR primário ou secundário) e a idade gestacional das perdas (embrionárias ou fetais). As anomalias da cavidade uterina, a SAAF e as translocações equilibradas parentais foram os factores mais prevalentes. 15,6% das participantes eram obesas. Em 55,5% dos casos não foi identificado nenhum factor. A história obstétrica materna influenciou significativamente os resultados encontrados: os factores anatómicos e a SAAF foram mais prevalentes em nulíparas e as perdas inexplicadas foram mais frequentes em mulheres com AR secundário. Assim, os nossos dados reforçam os resultados de pesquisas anteriores sobre a importância da obesidade, da síndrome de anticorpos antifosfolípidos e das anomalias uterinas estruturais como factores associados ao AR e mostram que os a paridade é um moderador da importância desses factores. Capítulo 6 94 A ausência de resultados consensuais na literatura sobre a etiologia do AR condiciona a pesquisa sistemática de alguns factores, envolvendo exames dispendiosos, muitas vezes sem que exista evidência que suporte a sua associação com esta entidade. A trombofilia hereditária é uma das condições frequentemente investigadas nestas doentes. O nosso segundo estudo pretende contribuir para clarificar o papel de duas mutações (factor V Leiden e protrombina G20210A) na perda recorrente de gravidez e esclarecer a necessidade do seu rastreio nestas situações. Foi efectuada a pesquisa destes polimorfismos em 100 mulheres com AR inexplicado e num grupo de controlo de multíparas sem história de perdas de gravidez. Na nossa amostra não se verificou uma associação entre perdas embrionárias recorrentes e estas mutações. Nas mulheres com este tipo de perdas, a prevalência do FLV foi inclusive menor do que a verificada nos controlos. Pelo contrário, nas participantes com perdas fetais a prevalência destes polimorfismos foi muito superior à verificada nos controlos, sugerindo uma possível associação entre estas duas entidades. A pequena dimensão deste último subgrupo de mulheres, não nos permitiu contudo tirar conclusões. Uma investigação prospectiva multicêntrica é necessária antes de recomendar a pesquisa da trombofilia hereditária na investigação do AR. Procurámos incluir também nesta tese uma dimensão psicológica e contribuir assim para o conhecimento dos processos relacionais originados pelo AR. No terceiro estudo foram investigadas as diferenças de género na vivência do AR e o seu impacto no relacionamento e sexualidade do casal. Participaram neste estudo 30 casais sem filhos, com pelo menos 3 abortos espontâneos consecutivos. Cada membro do casal respondeu a um conjunto de questionários (Impact of Events Scale, Perinatal Grief Scale, Partnership Questionnaire e Intimate Relationship Scale). Os resultados mostram que as mulheres sofrem mais intensamente do que os homens com o AR, relacionando-se a intensidade do seu sofrimento com a qualidade do relacionamento conjugal. A sexualidade do casal é também afectada pelo stress e pelo sofrimento associados ao AR. Uma avaliação e acompanhamento deste tipo de problemas são imprescindíveis para ajudar estes casais a manterem a qualidade afectiva e sexual da sua relação. Finalmente, no capítulo 5 sumariámos as conclusões de toda a contribuição pessoal para a investigação sobre os factores associados e repercussões para o casal da perda recorrente de gravidez.-------------------ABSTRACT: Recurrent miscarriage (RM), a rare condition, has been described as a traumatic event for couples. Parental chromosomal anomalies, maternal thrombophilic disorders and structural uterine anomalies have been directly associated with RM. However, despite significant advances in medical research, the vast majority of cases remain unexplained. Aspects as the ethnic diversity of the population with different expression of genes, the inappropriate characterization of patients and of pregnancy losses, as well as different methodologies used in their study, have influenced the prevalence of etiological factors and have hampered the understanding of this problem. Similarly, little is known about gender differences in psychological experience of RM and its implications for the relationship of the couple. The first objective of this thesis is the characterization of the medical factors and of the psychological consequences related with RM, in the Portuguese population, helping to promote specific evidence-based clinical strategies. In the first part of this thesis, and after a brief general introduction (Chapter 1), a critical review of literature on the definition, the epidemiology and the dimensions involved, with a special emphasis on associated medical and psychological aspects of recurrent miscarriage, is presented (Chapter 2). In Chapters 3 and 4 we describe three studies carried out in Portuguese couples with RM. The first study aimed to investigate the etiological factors and the pattern of pregnancy loss in a cohort of women with RM. Subjects were divided in groups according to their parity (primary or secondary RM) and time of pregnancy loss (embryonic or fetal). Parental chromosome anomalies, uterine anomalies and antiphospholipid syndrome were the most prevalent medical factors. 15.6% of the women were obese. In the majority of cases (55.5%) no identifiable cause was detected. Parity influenced significantly our results. There was a higher prevalence of anatomic factors and antiphospholipid syndrome in primary RM. On the other hand, unexplained losses were more frequent in secondary RM. Except for the parental chromosomal abnormalities; the frequency of risk factors was similar among women with fetal or embryonic losses. Our data emphasizes the results of previous research on the importance of obesity, antiphospholipid syndrome and structural uterine abnormalities as known risk factors for RM, and shows that parity is an important moderator of the weight of those risk factors. Our second study aims to clarify the role of two mutations (factor V Leiden and prothrombin G20210A) and elucidate the need for their screening in Portuguese women with RM. FVL and PT G20210A analysis was carried out in 100 women with three or more consecutive miscarriages and a control group of 100 parous controls with no history of pregnancy losses. Secondary analysis was made regarding gestational age at miscarriage (embryonic and fetal loss). Overall the prevalence of FVL and PT G20210A was similar in RM women compared with controls. In the RM embryonic subgroup of women, FVL prevalence was inclusively lower than that of controls. Conversely in women with fetal losses both polymorphisms were much more frequent, although statistical significance was not reached due to the small size of this subgroup of patients. These data indicate that inherited maternal thrombophilia is not associated with RM prior to 10 weeks of gestation. Therefore, its screening is not indicated as an initial approach in Portuguese women with RM and a negative personal history of thromboembolic.96 Our second study aims to clarify the role of two mutations (factor V Leiden and prothrombin G20210A) and elucidate the need for their screening in Portuguese women with RM. FVL and PT G20210A analysis was carried out in 100 women with three or more consecutive miscarriages and a control group of 100 parous controls with no history of pregnancy losses. Secondary analysis was made regarding gestational age at miscarriage (embryonic and fetal loss). Overall the prevalence of FVL and PT G20210A was similar in RM women compared with controls. In the RM embryonic subgroup of women, FVL prevalence was inclusively lower than that of controls. Conversely in women with fetal losses both polymorphisms were much more frequent, although statistical significance was not reached due to the small size of this subgroup of patients. These data indicate that inherited maternal thrombophilia is not associated with RM prior to 10 weeks of gestation. Therefore, its screening is not indicated as an initial approach in Portuguese women with RM and a negative personal history of thromboembolic. In our third study, we investigate gender differences in RM experience and its impact on the couple's relationship and sexuality. Each member of 30 couples with RM answered a set of questionnaires, including the Impact of Events Scale (Horowitz et al., 1979), the Perinatal Grief Scale (Toedter et al., 1988), the Partnership Questionnaire (Hahlweg, 1979) and the Intimate Relationship Scale (Hetherington e Soeken, 1990). Results showed that men do grieve, but less intensely than women. Although the quality of the couple‟s relationship seemed not to be adversely affected by RM, both partners described sexual changes after those events. Grief was related to the quality of communication in the couple for women, and to the quality of sex life for men. An understanding of such issues is critical in helping these couples to maintain sexual and affective quality of their relationship. Finally, in Chapter 5, conclusions and clinical implications of all personal contribution to the investigation on associated factors and relational consequences of recurrent miscarriage are presented.

Building anonymised database samples

Dissertação para obtenção do Grau de Mestre em Engenharia Informática