Model morphisms (MoMo) to enable language independent information models and interoperable business networks

MSc. Dissertation presented at Faculdade de Ciências e Tecnologia of Universidade Nova de Lisboa to obtain the Master degree in Electrical and Computer Engineering

Behavioral and synaptic circuit analysis in models of neuropsychiatric disorders: Dissecting the in vivo role of the postsynaptic density proteins nArgBP2 and Shank3 using genetic engineered mice

Dissertation presented to obtain the Ph.D degree in Biology

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.

Risk-based decision support system for life cycle management of industrials plants

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores

The internationalization process of mychild to São Paulo, Brazil

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

Improvement of Lipton’s business model through wholesalers and traditional supermarkets channel

Field Lab in Entrepreneurial Innovative Ventures

Proposta de abordagem para gestão de ocorrências em Serviços de Sangue

RESUMO: A gestão de ocorrências, sendo um requisito, quer legal, ao nível da regulação, quer normativo, tal como surge na ISO 9001, é um componente crítico para garantir a melhoria contínua um Serviço de Sangue, dado ter como objetivo a satisfação contínua dos requisitos dos dadores e recetores. A gestão eficaz, mas com eficiência, depende, também da eficácia da abordagem para gestão de ocorrência, nomeadamente, através da geração de correções, ações corretivas e ações preventiva eficazes. Esta dissertação discute a relevância, propondo um modelo de abordagem de gestão da qualidade conforme com os requisitos da lei fundamental da regulação de Serviços de Sangue, DL 267/2007, e com a norma global para sistemas de gestão da qualidade, ISO 9001. Esta abordagem usada descreve as várias etapas para a gestão eficaz de ocorrências, desde o seu relato, à sua classificação, tratamento com medição e análise risco associado e verificação da eficácia das ações tomadas. A eficácia do modelo teórico proposto foi verificado através da sua passagem para algoritmo informático num software comercial. Foi evidenciado neste software o cumprimento dos requisitos da abordagem teórica, pelo que a aplicação informática está conforme com os requisitos estabelecidos num procedimento documentado. Foi evidenciado, também, a rastreabilidade dos dados ao longo e toda a metodologia. A utilização de uma ferramenta informática também acrescentou valor ao modelo teórico, dado o acesso a toda a informação ser mais célere e de fácil acesso, quando comparado com o uso em suporte de papel.---------ABSTRACT: The issues management is a law requirement intended for regulation of “Blood Banks” and a quality management global requirement from ISO 9001. It is a critical activity, intended to to ensure continuous improvement on “Blood Bank”. Its goal is the continuous satisfaction of blood donors and transfusion recipients. Effective management and efficiency also depend on the effectiveness of the management of occurrence approach, namely in successful corrections, corrective actions and preventive actions. This paper discusses the relevance and it proposes a model approach to quality management according to the requirements of the fundamental law of regulation of “Blood Bank”, DL 267/2007, and according to the global standard for quality management systems, ISO 9001. This approach describes the various steps for effective management of incidents, such as his account, its classification, measurement and treatment using risk analysis and verification of the effectiveness of actions taken. The efficiency of the proposed theoretical model was verified through its transition to a computer algorithm trading software. It was demonstrated in this software that the requirements of the theoretical approach has been fulfilled by the computer application, which complies with the requirements established in a documented procedure. It was also evident that traceability of data across the methodology. The use of a software tool also added value to the theoretical model due to the access to all information to be faster and more easily accessible, when compared to paper.

Strategy definition of a new business opportunity in mobile-casual gaming: Partnership between Nmusic and Rovio Entertainment Ltd.

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

Politicization of non-political events

Spatial analysis and social network analysis typically take into consideration social processes in specific contexts of geographical or network space. The research in political science increasingly strives to model heterogeneity and spatial dependence. To better understand and geographically model the relationship between “non-political” events, streaming data from social networks, and political climate was the primary objective of the current study. Geographic information systems (GIS) are useful tools in the organization and analysis of streaming data from social networks. In this study, geographical and statistical analysis were combined in order to define the temporal and spatial nature of the data eminating from the popular social network Twitter during the 2014 FIFA World Cup. The study spans the entire globe because Twitter’s geotagging function, the fundamental data that makes this study possible, is not limited to a geographic area. By examining the public reactions to an inherenlty non-political event, this study serves to illuminate broader questions about social behavior and spatial dependence. From a practical perspective, the analyses demonstrate how the discussion of political topics fluсtuate according to football matches. Tableau and Rapidminer, in addition to a set basic statistical methods, were applied to find patterns in the social behavior in space and time in different geographic regions. It was found some insight into the relationship between an ostensibly non-political event – the World Cup - and public opinion transmitted by social media. The methodology could serve as a prototype for future studies and guide policy makers in governmental and non-governmental organizations in gauging the public opinion in certain geographic locations.

Efficiency optimization of the transportation supply chain activity: the maritime option for Volkswagen Autoeuropa

Field Lab of Entrepreneurial Innovative Ventures

Análise de risco aplicada à coleção de pintura a óleo da “Casa dos Patudos”

Este trabalho teve como principais objetivos a avaliação de risco para a coleção de pinturas a óleo da “Casa dos Patudos” e a proposta de estratégias para mitigar esses riscos. Escolheu-se o modelo de análise de risco Cultural Property Risk Analysis Model ou Modelo de Análise de Risco para Património Cultural, desenvolvido por Robert Waller (2003), por permitir hierarquizar os riscos a que a coleção está sujeita e por já ter sido aplicado com sucesso noutras coleções. Neste trabalho o modelo CPRAM é aplicado pela primeira vez a uma coleção de pintura a óleo em exibição. A metodologia utilizada passou pela caracterização da coleção, o diagnóstico das obras, inspeções ao edifício, conversas informais com os vários funcionários, colocação de armadilhas e determinação das condições ambientais. Verificou-se que os principais agentes de deterioração a que a coleção está exposta estão relacionados com as elevadas flutuações de humidade relativa, forças físicas, a excessiva exposição à luz e a ocorrência de pragas de insetos xilófagos. Desse modo, algumas das soluções propostas passam pela implementação de uma política de controlo integrado de pragas, colocação de filtros UV nas janelas e claraboias e controlo da humidade relativa e temperatura. As vantagens e desvantagens da aplicação deste modelo a esta coleção são aqui discutidos. Um dos desafios deste estudo passou por encontrar um equilíbrio entre o que são as condições ideais de preservação e o que é possível implementar numa casa histórica, ou seja, um local que não foi originalmente concebido para as funções que desempenha atualmente. Neste caso, a estas restrições, adiciona-se ainda as imposições deixadas em testamento pelo proprietário da casa. Embora o trabalho seja aplicado a uma coleção específica, existem muitas outras instituições, com coleções e situações semelhantes, que certamente partilham do mesmo tipo de problemas. Deste modo, espera-se que este trabalho também contribua para a chamada de atenção e melhoramento dos riscos a que essas coleções se encontram expostas.

Canada, a child's play

Science4you, a Portuguese developer, producer and seller of scientific and educational toys, leveraged the worldwide growth of this category to successfully expand its operations abroad. Following a recent entry into the United States market, the purpose of this report is to help the company define the next step in its international expansion. A customized scoring model, based on a set of relevant macro and micro-criteria was developed for Anglo-Saxon and Asian countries, yielding Canada as the market with the highest potential. The recommended entry mode is direct exporting via an independent distributor, being complemented with a financial and risk analysis.

Models and tools for value systems analysis in collaborative environments

Dissertation to obtain the degree of Doctor in Electrical and Computer Engineering, specialization of Collaborative Networks

MAC regenerative analysis of wireless Ad-Hoc networks

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