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.

Halogen-bonded tris (2,4-Bis(trichloromethyl)-1,3,5,triazapentadienato)-M(III) [M = Mn, Fe, Co] complexes and their catalytic activity in the peroxidative oxidation of 1-phenylethanol to acetophenone

One-pot template condensation of CCl3C=N with ammonia on a metal source [MnCl2 center dot 4H(2)O, FeCl3 center dot 6H(2)O or Co(CH3COO)(2)center dot 4H(2)O] in DMSO led to the formation of tris(2,4-bis(trichloromethyl)-1,3,5-triazapentadienato)-M(III) complexes, [M(NH=C(CCl3)NC(CCl3)=-NH}(3)]center dot n(CH3)(2)SO [M = Mn, n = 1 (1); M = Fe, n = 2 (2); M = Co, n = 2 (3)1, which were characterized using elemental analysis, and IR, ESI-MS and single-crystal X-ray analysis. The role of inter- and intramolecular non-covalent halogen and hydrogen bonds in the synthesis of 1-3 is discussed. It is shown that the crystal ionic radii of the metal ions [68.5 (Co) < 69 (Fe) < 72 (Mn), pm] are related to the corresponding Cl center dot center dot center dot Cl distances [3.178 (3) > 3.155 (2) > 3.133 (1) Al. Compounds 1-3 and the related di(triazapentadienato)-Cu(v) complex [Cu(NH=C(CCl3)NC(CCl3)=NH}2]center dot 2(CH3)(2)SO (4) act as catalyst precursors for the additive-free microwave (MW) assisted homogeneous oxidation of 1-phenylethanol with tert-butylhydroperoxide (TBHP), leading to the formation of acetophenone with yields up to 99% and TONs up to 5.0 x 10(3) after 1 h of low power (10 W) MW irradiation.

Acylated cyanoimido-complexes trans-[Mo(NCN){NCN(O)R}(DPPE)(2)]Cl and their reactons with electrophiles: Chemical, electrochemical and theoretical study

Treatment of a dichloromethane solution of trans-[Mo(NCN){NCNC(O)R}(dppe)(2)]Cl [R = Me (1a), Et (1b)] (dppe = Ph2PCH2CH2PPh2) with HBF4, [Et3O][BF4] or EtC(O)Cl gives trans-[Mo(NCN)Cl-(dppe)(2)]X [X = BF4 (2a) or Cl (2b)] and the corresponding acylcyanamides NCN(R')C(O)Et (R' = H, Et or C(O)Et). X-ray diffraction analysis of 2a (X = BF4) reveals a multiple-bond coordination of the cyanoimide ligand. Compounds 1 convert to the bis(cyanoimide) trans-[Mo(NCN)(2)(dppe)(2)] complex upon reaction with an excess of NaOMe (with formation of the respective ester). In an aprotic medium and at a Pt electrode, compounds 1 (R = Me, Et or Ph) undergo a cathodically induced isomerization. Full quantitative kinetic analysis of the voltammetric behaviour is presented and allows the determination of the first-order rate constants and the equilibrium constant of the trans to cis isomerization reaction. The mechanisms of electrophilic addition (protonation) to complexes 1 and the precursor trans[Mo(NCN)(2)(dppe)(2)], as well as the electronic structures, nature of the coordination bonds and electrochemical behaviour of these species are investigated in detail by theoretical methods which indicate that the most probable sites of the proton attack are the oxygen atom of the acyl group and the terminal nitrogen atom, respectively.

Chimpanzees Share Forbidden Fruit

PLoS ONE - www.plosone.org, V.9, e886

XII Iberian-Italian Congress of Financial and Actuarial Mathematics

"The purpose of the XII Iberian-Italian Congress of Financial and Actuarial Mathematics is to provide a meeting point for researchers in Financial Economics from different countries and research backgrounds in universities, government or financial institutions. In fact, the Congress which is currently taking place in Lisbon has been organized to encourage communication and debate among the participants as well as to reinforce the bonds between us.The current edition of the Congress is characterized by the quality and diversity of the papers that have been submitted with special attention to the International Financial Crisis and measures of risk in different financial markets. However, as the Congress Program indicates, there are also parallel sessions about traditional topics in finance such as asset pricing, insurance, corporate finance, etc.Although this Congress has always been organized alternately between Spain and Italy, this year we have the great pleasure of celebrating it in Portugal which will be included as a permanent partner." [prefácio]

Somewhere near reality: artistic portrayal of violence in post WWII British realistic drama

ABSTRACT - I will explore and present the portrayal of violence in some British plays that were staged between 1951 and 1965, in order to discuss the role, impact and aim of its representation. Thus, I will consider John Whiting’s Saint’s Day (1951), Ann Jelicoe’s The Sport of my Mad Mother (1956), Arnold Wesker (Chicken Soup with Barley (1958), Harold Pinter’s Birthday Party (1958), David Rudkin’s Afore Night Come (1962) and Edward Bond’s Saved (1965). My aim is to discuss the way how theatre in the post WWII changed the traditional ways of representing violence. On one hand, violence and reality became more and more familiar and domestic, permitting a representation of multiple and non-agonic violence; and, on the other hand, the violence that was depicted often changed the way one perceived reality itself, being part of a socially engaged artistic attitude.

An enzymatic route to a benzocarbazole framework using bacterial CotA laccase

The CotA laccase-catalysed oxidation of the meta, para-disubstituted arylamine 2,4-diaminophenyldiamine delivers, under mild reaction conditions, a benzocarbazole derivative (1) (74% yield), a key structural motif of a diverse range of applications. This work extends the scope of aromatic frameworks obtained using these enzymes and represents a new efficient and clean method to construct in one step C-C and C-N bonds.

Generalization of Wertheim's theory for the assembly of various types of rings

We generalize Wertheim's first order perturbation theory to account for the effect in the thermodynamics of the self-assembly of rings characterized by two energy scales. The theory is applied to a lattice model of patchy particles and tested against Monte Carlo simulations on a fcc lattice. These particles have 2 patches of type A and 10 patches of type B, which may form bonds AA or AB that decrease the energy by epsilon(AA) and by epsilon(AB) = r epsilon(AA), respectively. The angle theta between the 2 A-patches on each particle is fixed at 601, 90 degrees or 120 degrees. For values of r below 1/2 and above a threshold r(th)(theta) the models exhibit a phase diagram with two critical points. Both theory and simulation predict that rth increases when theta decreases. We show that the mechanism that prevents phase separation for models with decreasing values of theta is related to the formation of loops containing AB bonds. Moreover, we show that by including the free energy of B-rings ( loops containing one AB bond), the theory describes the trends observed in the simulation results, but that for the lowest values of theta, the theoretical description deteriorates due to the increasing number of loops containing more than one AB bond.

Língua adicional: contextos e continua

O papel de uma língua adicional, seja ela uma língua estrangeira, língua segunda, ou uma variedade não nativa, é fundamental atualmente não só no domínio profissional mas também em termos de investigação científica, mais precisamente sobre o contacto de línguas. Até ao início da segunda metade do século passado, o contacto linguístico que poderá ter estado na origem das línguas crioulas gozou de especial atenção entre os linguistas. Nas últimas décadas a sua atenção virou-se para a língua segunda e as variedades não nativas. Neste artigo, apresentamos,do ponto de vista teórico, os elos de ligação, contextos e continua, entre os quatro conceitos acima referidos, em que o primeiro, língua adicional, é apresentado como hiperónimo dos outros três, língua estrangeira, língua segunda e variedade não nativa.

App mobile “My Corine de Farme”

Trabalho de projeto apresentado à Escola Superior de Comunicação Social como parte dos requisitos para obtenção de grau de mestre em Publicidade e Marketing.

Liquid-vapor interfaces of patchy colloids

We investigate the liquid-vapor interface of a model of patchy colloids. This model consists of hard spheres decorated with short-ranged attractive sites ("patches") of different types on their surfaces. We focus on a one-component fluid with two patches of type A and nine patches of type B (2A9B colloids), which has been found to exhibit reentrant liquid-vapor coexistence curves and very low-density liquid phases. We have used the density-functional theory form of Wertheim's first-order perturbation theory of association, as implemented by Yu and Wu [J. Chem. Phys. 116, 7094 (2002)], to calculate the surface tension, and the density and degree of association profiles, at the liquid-vapor interface of our model. In reentrant systems, where AB bonds dominate, an unusual thickening of the interface is observed at low temperatures. Furthermore, the surface tension versus temperature curve reaches a maximum, in agreement with Bernardino and Telo da Gama's mesoscopic Landau-Safran theory [Phys. Rev. Lett. 109, 116103 (2012)]. If BB attractions are also present, competition between AB and BB bonds gradually restores the monotonic temperature dependence of the surface tension. Lastly, the interface is "hairy," i.e., it contains a region where the average chain length is close to that in the bulk liquid, but where the density is that of the vapor. Sufficiently strong BB attractions remove these features, and the system reverts to the behavior seen in atomic fluids.

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.

Ligação Adesiva de Polímeros Particularmente Difíceis de Colar

As ligações adesivas têm sido cada vez mais utilizadas nos últimos anos em detrimento de outros métodos tais como a soldadura, ligações aparafusadas e ligações rebitadas. Os plásticos de Engenharia têm um papel cada vez mais preponderante na indústria, devido às suas excelentes propriedades. Neste trabalho foram considerados três polímeros diferentes, o Policloreto de Vinilo (PVC) e o Polipropileno (PP) dado o seu baixo custo e peso e a superfície quimicamente inerte e o Politetrafluoretileno (PTFE) devido às suas boas propriedades químicas e excelentes propriedades de deslizamento. No entanto, estes materiais possuem uma baixa energia de superfície e, por isso, são muito difíceis de colar com mais relevância para o PTFE. Assim, após um estudo preliminar foi escolhido, para realizar as colagens necessárias, um adesivo da Tamarron Technology “Tam Tech Adhesive”, próprio para este tipo de substratos difíceis de colar. Posteriormente foi efetuada a sua caraterização através de ensaios de provetes maciços à tração. O principal objetivo deste trabalho foi estudar juntas de sobreposição simples de materiais poliméricos difíceis de colar tais como o PTFE, PP e PVC com recurso a um adesivo que não necessitasse de preparação de superfície. Foram fabricadas juntas de sobreposição simples (JSS) segundo os métodos Lap Shear (LS) e Block Shear (BS) dos três materiais referidos anteriormente e realizados os respetivos ensaios para avaliar o comportamento mecânico das ligações adesivas. Os materiais utilizados como substratos foram também submetidos a ensaios de tração com a finalidade de obter o módulo de elasticidade e as suas propriedades de resistência. Os substratos envolvidos nas juntas adesivas não sofreram qualquer preparação especial das superfícies. Na maioria dos casos consistiu apenas numa limpeza das superfícies com álcool etílico. Contudo, para o PTFE também se experimentou a preparação por abrasão com lixa e por chama. Foi também efetuado um trabalho de simulação numérica por elementos finitos utilizando um modelo de dano coesivo triangular. As resistências ao corte obtidas são superiores em BS comparativamente a LS, exceção feita aos substratos de PTFE aonde os resultados são similares. O tratamento por chama melhorou a resistência mecânica das juntas. Verificou-se também que o modelo numérico simulou adequadamente o comportamento das juntas principalmente das LS.

Estudo de delaminação em compósitos de matriz polimérica

A aplicação do material compósito é neste momento bastante vasta, graças à combinação das suas características específicas, tais como, maior resistência específica e módulos específicos e melhor resistência à fadiga, quando comparados com os metais convencionais. Tais características, quando requeridas, tornam este material ideal para aplicações estruturais. Esta caminhada de sucesso iniciou desde muito cedo, quando o material compósito já era utilizado para fabrico de armas pelos mongóis e na construção civil pelos hebreus e egípcios, contudo, só a partir dos meados do século XX é que despertou interesses para aplicações mais modernas. Atualmente os materiais compósitos são utilizados em equipamentos domésticos, componentes elétricos e eletrónicos, passando por materiais desportivos, pela indústria automóvel e construção civil, até indústrias de grande exigência e visibilidade tecnológica como a aeronáutica, espacial e de defesa. Apesar das boas características apresentadas pelos materiais compósitos, no entanto, estes materiais têm tendência a perderem as suas propriedades quando submetidas a algumas operações de acabamento como a furação. A furação surge da necessidade de ligação de peças de um mesmo mecanismo. Os furos obtidos por este processo devem ser precisos e sem danos para garantir ligações de alta resistência e também precisas. A furação nos materiais compósitos é bastante complexa devido à sua heterogeneidade, anisotropia, sensibilidade ao calor e pelo facto de os reforços serem extremamente abrasivos. A operação de furação pode causar grandes danos na peça, como a delaminação a entrada, defeitos de circularidade do furo, danos de origem térmica e a delaminação à saída que se apresenta como o mais frequente e indesejável. Com base nesses pressupostos é que este trabalho foi desenvolvido de forma a tentar obter processos simples para determinação e previsão de danos em polímeros reforçados com fibras (de carbono neste caso) de forma a precavê-los. De forma a conseguir estes objetivos, foram realizados ensaios de início de delaminação segundo a proposta de Lachaud et al. e ensaios de pin-bearing segundo a proposta de Khashaba et al. Foram também examinadas extensões de danos de acordo com o modelo de Fator de delaminação ajustado apresentado por Davim et al. A partir dos ensaios, de pin-bearing, realizados foram analisadas influências do material e geometria da broca, do avanço utilizado na furação e de diferentes orientações de empilhamentos de placas na delaminação de laminados compósitos e ainda a influências dessas variáveis na força de rutura por pin-bearing. As principais conclusões tiradas daqui são que a delaminação aumenta com o aumento do avanço, o que já era esperado, as brocas em carboneto de tungsténio são as mais recomendas para a furação do material em causa e que a delaminação é superior para a placa cross-ply quando comparada com placas unidirecionais. Para a situação de ensaios de início de delaminação foram analisadas as influências da variação da espessura não cortada por baixo da broca/punção, de diferentes geometrias de brocas, da alteração de velocidade de ensaio e diferentes orientações de empilhamentos de placas na força de início de delaminação. Deste ensaio as principais conclusões são que a força de início de delaminação aumenta com o aumenta da espessura não cortada e a influência da velocidade de ensaio altera com a variação das orientações de empilhamento.

Gold nanoparticle-DNA conjugates for oligonucleotide vectorization towards gene silencing

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina