Copper-containing nitrite reductase from Pseudomonas chlororaphis DSM 50135

Eur. J. Biochem. 271, 2361–2369 (2004)

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.

Extracção de unigramas relevantes

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

Reciclagem de placas de circuitos electrónicos

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

Reciclagem mecânica de placas de circuitos electrónicos

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

Estudo dos principais mecanismos de resistência aos antibióticos β-lactâmicos em bactérias patogénicas de gram negativo

Dissertação apresentada para a obtenção do Grau de Mestre em Genética Molecular e Biomedicina, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Contributo dos músculos respiratórios para a fisiopatologia da hipercápnia na doença pulmonar crónica estabilizada: parte 1 = The role of the respiratory muscles in the pathophisiology of chronic hypercapnia in clinically stable chronic obstructive pulmonary diseases: part 1

Rev Port Pneumol. VII(2): 191-208, 2001

Robustness of corroded reinforced concrete structures. A structural performance approach

Structure and Infrastructure Engineering, 1-17

Caracterização da actividade física nos idosos e a sua relação com a capacidade física, em pessoas com mais de 75 anos

RESUMO: Objectivo: O presente estudo tem como objectivo caracterizar os níveis de actividade física das pessoas com mais de 75 anos e analisar a sua relação com as diferentes componentes da aptidão física. Enquadramento: A actividade física é indispensável para todos mas, os idosos é quem mais beneficia (Fischer, 2005). Actua na prevenção e na reabilitação, fortalecendo a aptidão física, e a autonomia do idoso, permitindo manter, por mais tempo, a capacidade de execução das actividades de vida diárias (Shephard, 2003). A prática de actividade física contribui por exemplo, para a prevenção de quedas, reforçando a aptidão física e o equilíbrio postural. Por outro lado, o baixo nível de aptidão física repercute-se no aumento da actividade sedentária. Os homens têm uma adesão à actividade física de 45% e as mulheres de 28% (Melo et. al., 2007). Métodos: Este é um estudo observacional, correlacional e transversal. Foram avaliados 66 participantes (média de idade de 80,11 ± 3,83 anos), não institucionalizados. O processo de amostragem foi não probabilístico acidental por conveniência. Todos os idosos deram o seu consentimento informado. A actividade física foi avaliada através do questionário do Yale Physical Activity Survey, e foi desenvolvido um diário, para uma semana-tipo, para averiguar os hábitos de actividades diárias, nas últimas quatro semanas. A aptidão física foi avaliada pela bateria de testes de Rikli e Jones (1999),nomeadamente a força, a flexibilidade, a resistência aeróbia e a agilidade e equilíbrio. Os dados foram analisados através da estatística descritiva e para averiguar as possíveis associações entre a actividade física e a aptidão física, recorreu-se á estatística inferencial. Não tendo sido verificada a normalidade da amostra com o teste kolmogorov-smirnov, foram utilizados testes não paramétricos, nomeadamente o teste U Mann – Whitney e o coeficiente de correlação de Spearman (p≤0,05). Resultados: Constatou-se que os idosos em média praticavam 480, 23 minutos por semana de actividade moderada, cerca 11,04% do seu tempo, superior ao recomendado pela literatura (>150 minutos por semana). A actividade física moderada apresentou relações positivas com a aptidão física, na força dos membros inferiores, na resistência aeróbia e na agilidade e equilíbrio. Os homens têm maior agilidade e equilíbrio (p=0,002) e força dos membros inferiores (p=0,025) que as mulheres. Os homens passam mais tempo em actividade moderada do que as mulheres. Ainda superam no gasto energético em cada actividade que praticam durante a semana. As mulheres passam mais tempo em actividade sedentária e actividade ligeira. Conclusão: Quanto mais tempo de prática de actividade física moderada melhor a força dos membros inferiores, a resistência aeróbia, a agilidade e o equilíbrio dinâmico. Recomenda-se uma reflexão sobre a possível intervenção na estruturação das actividades diárias do idoso e uma intervenção mais direccionada às idosas, na força do membro inferior, na agilidade e na resistência aeróbia.----------------------- ABSTRACT:Purpose: The present study aims to characterize the physical activity levels of people over 75 years and analyze their relationship with the different components of physical fitness. Background: Physical activity is essential for all but the elderly who are more benefit (Fischer, 2005). It works on prevention and rehabilitation, strengthening physical fitness,and independence of older people, maintaining, for longer, the ability to implement the activities of daily living (Shephard, 2003). The physical activity contributes for example, for the prevention of falls by strengthening physical fitness and postural balance. Moreover, the low level of physical fitness level is reflected in the increase of sedentary activity. Men have an adherence to physical activity of 45% and women 28% (Melo et. al, 2007) Methods: This was an observational, cross-sectional and correlational. We evaluated 66 participants (mean age 80.11 ± 3.83 years), not institutionalized. The sampling procedure was non accidental probabilistic convenience. All seniors gave their informed consent. Physical activity was assessed by questionnaire at the Yale Physical Activity Survey was developed and a diary-type for a week, to ascertain the habits of daily activities in the last four weeks. Physical fitness was assessed by the battery of tests Rikli and Jones (1999), including strength, flexibility, endurance and agility and balance. Data were analyzed using descriptive statistics and to investigate possible associations between physical activity and physical fitness, we used will inferential statistics. Not having been verified the sample normality with Kolmogorov-Smirnov test, we used non-parametric tests, including the test U Mann - Whitney and Spearman correlation coefficient (p ≤ 0.05). Results: It was found that older people on average practiced 480, 23 minutes per week of moderate activity, about 11,04% of the time, higher than recommended in the literature (> 150 minutes per week). A moderate physical activity had positive correlations with physical fitness, lower limb strength, endurance and aerobic agility and balance. Men have greater agility and balance (p = 0.002) and lower-limb strength (p = 0.025) than women. Men spend more time in moderate activity than women. Still outweigh the energy expenditure for each activity they practice during the week. Women spend more time in sedentary activity and light activity. Conclusion: The more practice time in moderate physical activity best lower-limb strength,aerobic resistance, agility and dynamic balance. It is recommended that a reflection on the possible intervention in structuring the daily activities of the elderly and a more targeted to the woman elderly, especially lower limb strength, agility and endurance.

The international expansion strategy of Striyah in Poland

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

Análise do mercado financeiro baseada em análise técnica com self-organizing maps

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Projeto de web TV no âmbito da assessoria de comunicação da Presidência da República

Trabalho de projeto apresentado para o cumprimento dos requisitos necessários à obtenção do grau de Mestre em em Novos Media e Práticas Web

A cerâmica oriental da carreira da Índia no contexto da carga de uma nau - A presumível Nossa Senhora dos Mártires

Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Arqueologia

The employee policy manual

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

Automatic extraction of concepts from texts and applications

The extraction of relevant terms from texts is an extensively researched task in Text- Mining. Relevant terms have been applied in areas such as Information Retrieval or document clustering and classification. However, relevance has a rather fuzzy nature since the classification of some terms as relevant or not relevant is not consensual. For instance, while words such as "president" and "republic" are generally considered relevant by human evaluators, and words like "the" and "or" are not, terms such as "read" and "finish" gather no consensus about their semantic and informativeness. Concepts, on the other hand, have a less fuzzy nature. Therefore, instead of deciding on the relevance of a term during the extraction phase, as most extractors do, I propose to first extract, from texts, what I have called generic concepts (all concepts) and postpone the decision about relevance for downstream applications, accordingly to their needs. For instance, a keyword extractor may assume that the most relevant keywords are the most frequent concepts on the documents. Moreover, most statistical extractors are incapable of extracting single-word and multi-word expressions using the same methodology. These factors led to the development of the ConceptExtractor, a statistical and language-independent methodology which is explained in Part I of this thesis. In Part II, I will show that the automatic extraction of concepts has great applicability. For instance, for the extraction of keywords from documents, using the Tf-Idf metric only on concepts yields better results than using Tf-Idf without concepts, specially for multi-words. In addition, since concepts can be semantically related to other concepts, this allows us to build implicit document descriptors. These applications led to published work. Finally, I will present some work that, although not published yet, is briefly discussed in this document.