Adaption of the Creative Commons approach and the roaming concept to spatial data infrastructures (SDI)

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

The role of objects in creative collaborations

Objects matter when professionals collaborate to create new products. Chapter 1 explains the intention of this work, to apply theories on objects in the empirical context of fashion design. Chapter 2 addresses the question of how creative professionals learn about and use strategy tools to turn their artistic fame into a commercial success. For Chapter 3 I collected ethnographic data on the development of a seasonal collection from the idea to the presentation at Fashion Week. The result is a deep insight into the collaborative processes and material objects used when a stable team of designers works with several outside experts. Chapter 4 applies the knowledge of the role of objects in fashion design gained during the ethnography in the context of online co-creation and crowd sourced fashion items. The synthesis of the empirical studies allows me to present the conceptual leap in Chapter 5. In the theoretical essay I review the findings on the role of objects in collaborations in relation to practice theory, present the new concept of the comprehensive object and conclude by stating the possibilities for future research.

Cognitive models for the concept of angle

Tese de doutoramento em Filosofia

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.

Self-organization and complexity theory to support evolvable production systems

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

Patterns of Associational Life in Western Europe, 1800-2000

Thesis submitted for assessment with a view to obtaining the degree of Doctor of Political and Social Science of the European University Institute

Introduction to fractional linear systems. Part 1 : continuous-time case

IEE Proceedings - Vision, Image, and Signal Processing, Vol. 147, nº 1

Gender and reproductive autonomy : are there second-class citizens in Europe?

EUROPEAN MASTER’S DEGREE IN HUMAN RIGHTS AND DEMOCRATISATION Academic Year 2007/2008

An Ethos Theory of Party Positions on European Integration: Poland and Beyond

Since 1989, five parliamentary elections have been the stage for the foundation and demise of political parties aspiring to govern the new democratic Polish state. The demise of the AWS before the 2001 elections after ten years of attempts to create a centre-right core party resulted in a new splintering of the right-wing, and the centre-right became again devoid of a pivotal formation. While Eurosceptic parties in average gain 8 percent of the vote, in the 2001 Polish parliamentary elections Eurosceptic parties gained around 20 percent of the vote. In Poland right-wing parties show an unusual propensity for Euroscepticism. The persistence and increased importance of nationalism in Poland, which has prevented the development of a strong Christian democratic party, effectively explains the levels of Euroscepticism on the right. After the autumn 2005 parliamentary elections the national conservative party, Law and Justice, formed a governing coalition with the national Catholic League of Polish Families, creating one of the first Eurosceptic governments. Although this work does not intend to provide a theorisation of party systems development, it shows that the context of European integration fostered nationalists’ divisiveness of, and provoked the splitting of the right the unusual propensity of parties for Euroscepticism makes Poland a paradigmatic case of the kind of conflicts over European integration emerging in Central and Eastern European party systems.

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

Health care marketing: the theory of planned behavior applied to patients' choise between private and public providers in the portuguese health care system.

Dissertation submitted in partial fulfillment of the requirements for degree of Master in Statistics and Information Management.

Depositions of rulers in the later middle ages: on the theory of th "useless ruler" and its practical utilization

pp. 157-168

“The past is a foreign country”? Acculturation theory and the anthropology of globalization

Etnográfica, 15 (2): 313-336

New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway

Biochem. J. (2011) 438,485–494 doi:10.1042/BJ20110836

Nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases

J Biol Inorg Chem (2011) 16:443–460 DOI 10.1007/s00775-010-0741-z