An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences

Mycologia, Vol. 98, nº6

Glasses' makeup: the simple and the combined effect of color and shape on perceived volume and beverage intake

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

Monotherapy and combined therapy of new potential antitumor compounds: antiproliferative activities and biological targets

Review article Martins, P., Marques, M., Coito, L., Pombeiro, A.J.L., Baptista, P.V., Fernandes, A.R. 2014. Organometallic Compounds in Cancer Therapy: Past Lessons and Future Directions. Anti-cancer Agents in Medicinal Chemistry 14. PMID: 25173559

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.

Adherence to health-related behaviors: effectiveness of implementation intentions and posthypnotic suggestion in college students

Resumo: Com base no conceito de implementação de intenções (Gollwitzer, 1993, 1999) e na teoria do contexto de resposta de Kirsch & Lynn (1997), o presente trabalho testou a eficácia de uma intervenção combinada de implementação de intenções com hipnose e sugestão pós-hipnótica na promoção da adesão a uma tarefa simples (avaliação do humor) e uma tarefa difícil (actividade física). Os participantes são estudantes universitários de uma universidade na Nova Jérsia, (N=124, Estudo 1, EUA) e em Lisboa (N=323, Estudo 2, Portugal). Em ambos os estudos os participantes foram seleccionados a partir de uma amostra mais vasta baseado num escrutínio da sua sugestibilidade hipnótica avaliada por meio da Escala de Grupo de Sugestibilidade Hipnótica de Waterloo-Stanford (WSGC): Forma C. O Estudo 1 usou um desenho factorial do tipo 2x2x3 (tipo de intenção formada x hipnose x nível de sugestionabilidade) e o Estudo 2 usou um desenho factorial do tipo 2 x 2x 2 x 4 (tipo de tarefa x tipo de intenção formada x hipnose x nível de sugestionabilidade). No Estudo 1 foi pedido aos participantes que corressem todos os dias e durante três semanas durante 5 minutos, que medissem a sua pulsação antes e depois da actividade física e que mandassem um e-mail ao experimentador, fornecendo assim uma medida comportamental e uma medida de auto-relato. Aos participantes no grupo de intenções de meta foi apenas pedido que corressem todos os dias. Aos participantes no grupo de implementação de intenções foi pedido que especificasses com exactidão quando e onde iriam correr e enviar o e-mail. Para além disso, cerca de metade dos participantes foram hipnotizados e receberam uma sugestão pós-hipnótica em que lhes foi sugerido que o pensamento de correr todos os dias lhes viria à mente sem esforço no momento apropriado. A outra metade dos participantes não recebeu qualquer sugestão hipnótica. No Estudo 2 foi seguido o mesmo procedimento, mas a cerca de metade dos participantes foi atribuída uma tarefa fácil (enviar um Adherence to health-related behaviors ix SMS com a avaliação diária do seu estado de humor naquele momento) e à outra metade da amostra foi atribuída a tarefa de exercício físico atrás descrita (tarefa difícil). Os resultados do estudo 1 mostraram uma interacção significativa entre o nível de sugestionabilidade dos participantes e a sugestão pós-hipnótica (p<.01) indicando que a administração da sugestão pós-hipnótica aumentou a adesão nos participantes muito sugestionáveis, mas baixou a adesão nos participantes pouco sugestionáveis. Não se encontraram diferenças entre os grupos que formaram intenções de meta e os que formaram implementação de intenções. No Estudo 2 os resultados indicaram que os participantes aderiram significativamente mais à tarefa fácil do que à tarefa difícil (p<.001). Os resultados não revelaram diferenças significativas entre as condições implementações de intenções, hipnose e as duas estratégias combinadas, indicando que a implementação de intenções não foi eficaz no aumento da adesão às duas tarefas propostas e não beneficiou da combinação com as sugestões pós-hipnóticas. A utilização da hipnose com sugestão pós-hipnótica significativamente reduziu a adesão a ambas as tarefas. Dado que não existiam instrumentos em Português destinados a avaliar a sugestionabilidade hipnótica, traduziu-se e adaptou-se para Português Escala de Grupo de sugestibilidade hipnótica de Waterloo-Stanford (WSGC): Forma C. A amostra Portuguesa (N=625) apresentou resultados semelhantes aos encontrados nas amostras de referência em termos do formato da distribuição dos padrões da pontuação e do índice de dificuldade dos itens. Contudo, a proporção de estudantes portugueses encontrada que pontuaram na zona superior de sugestionabilidade foi significativamente inferior à proporção de participantes na mesma zona encontrada nas amostras de referência. No sentido de lançar alguma luz sobre as razões para este resultado, inquiriu-se alguns dos participantes acerca das suas atitudes face à hipnose utilizando uma versão portuguesa da Escala de Valência de Atitudes e Crenças face à Hipnose e comparou-se com a opinião de Adherence to health-related behaviors xAbstract: On the basis of Gollwitzer’s (1993, 1999) implementation intentions’ concept, and Kirsch & Lynn’s (1997) response set theory, this dissertation tested the effectiveness of a combined intervention of implementation intentions with hypnosis with posthypnotic suggestions in enhancing adherence to a simple (mood report) and a difficult (physical activity) health-related task. Participants were enrolled in a university in New Jersey (N=124, Study 1, USA) and in two universities in Lisbon (N=323, Study 2, Portugal). In both studies participants were selected from a broader sample based on their suggestibility scores using the Waterloo-Stanford Group C (WSGC) scale of hypnotic susceptibility and then randomly assigned to the experimental groups. Study 1 used a 2x2x3 factorial design (instruction x hypnosis x level of suggestibility) and Study 2 used a 2 x 2x 2 x 4 factorial design (task x instructions x hypnosis x level of suggestibility). In Study 1 participants were asked to run in place for 5 minutes each day for a three-week period, to take their pulse rate before and after the activity, and to send a daily email report to the experimenter, thus providing both a self-report and a behavioral measure of adherence. Participants in the goal intention condition were simply asked to run in place and send the e-mail once a day. Those in the implementation intention condition were further asked to specify the exact place and time they would perform the physical activity and send the e-mail. In addition, half of the participants were given a post-hypnotic suggestion indicating that the thought of running in place would come to mind without effort at the appropriate moment. The other half did not receive a posthypnotic suggestion. Study 2 followed the same procedure, but additionally half of the participants were instructed to send a mood report by SMS (easy task) and half were assigned to the physical activity task described above (difficult task). Adherence to health-related behaviors vii Study 1 result’s showed a significant interaction between participant’s suggestibility level and posthypnotic suggestion (p<.01) indicating that posthypnotic suggestion enhanced adherence among highly suggestible participants, but lowered it among low suggestible individuals. No differences between the goal intention and the implementation intentions groups were found. In Study 2, participants adhered significantly more (p<.001) to the easy task than to the difficult task. Results did not revealed significant differences between the implementation intentions, hypnosis and the two conditions combined, indicating that implementation intentions was not enhanced by hypnosis with posthypnotic suggestion, neither was effective as single intervention in enhancing adherence to any of the tasks. Hypnosis with posthypnotic suggestion alone significantly reduced adherence to both tasks in comparison with participants that did not receive hypnosis. Since there were no instruments in Portuguese language to asses hypnotic suggestibility, the Waterloo-Stanford Group C (WSGC) scale of hypnotic susceptibility was translated and adapted to Portuguese and was used in the screening of a sample of college students from Lisbon (N=625). Results showed that the Portuguese sample has distribution shapes and difficulty patterns of hypnotic suggestibility scores similar to the reference samples, with the exception of the proportion of Portuguese students scoring in the high range of hypnotic suggestibility, that was found lower than the in reference samples. In order to shed some light on the reasons for this finding participant’s attitudes toward hypnosis were inquired using a Portuguese translation and adaptation of the Escala de Valencia de Actitudes y Creencias Hacia la Hipnosis, Versión Cliente, and compared with participants with no prior hypnosis experience (N=444). Significant differences were found between the two groups with participants without hypnosis experience scoring higher in factors indicating misconceptions and negative attitudes about hypnosis.

Expression of cyclooxygenase enzymes and prostaglandin E2 receptors in inflammatory airway diseases

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

Ankylosing spondylitis: genomic and functional characterization of candidate genes and their repercussion in clinical practice

RESUMO: Introdução: A espondilite anquilosante (EA) é uma doença inflamatória crónica caracterizada pela inflamação das articulações sacroilíacas e da coluna. A anquilose progressiva motiva uma deterioração gradual da função física e da qualidade de vida. O diagnóstico e o tratamento precoces podem contribuir para um melhor prognóstico. Neste contexto, a identificação de biomarcadores, assume-se como sendo muito útil para a prática clínica e representa hoje um grande desafio para a comunidade científica. Objetivos: Este estudo teve como objetivos: 1 - caracterizar a EA em Portugal; 2 - investigar possíveis associações entre genes, MHC e não-MHC, com a suscetibilidade e as características fenotípicas da EA; 3 - identificar genes candidatos associados a EA através da tecnologia de microarray. Material e Métodos: Foram recrutados doentes com EA, de acordo com os critérios modificados de Nova Iorque, nas consultas de Reumatologia dos diferentes hospitais participantes. Colecionaram-se dados demográficos, clínicos e radiológicos e colhidas amostras de sangue periférico. Selecionaram-se de forma aleatória, doentes HLA-B27 positivos, os quais foram tipados em termos de HLA classe I e II por PCR-rSSOP. Os haplótipos HLA estendidos foram estimados pelo algoritmo Expectation Maximization com recurso ao software Arlequin v3.11. As variantes alélicas dos genes IL23R, ERAP1 e ANKH foram estudadas através de ensaios de discriminação alélica TaqMan. A análise de associação foi realizada utilizando testes da Cochrane-Armitage e de regressão linear, tal como implementado pelo PLINK, para variáveis qualitativas e quantitativas, respetivamente. O estudo de expressão génica foi realizado por Illumina HT-12 Whole-Genome Expression BeadChips. Os genes candidatos foram validados usando qPCR-based TaqMan Low Density Arrays (TLDAs). Resultados: Foram incluídos 369 doentes (62,3% do sexo masculino, com idade média de 45,4 ± 13,2 anos, duração média da doença de 11,4 ± 10,5 anos). No momento da avaliação, 49,9% tinham doença axial, 2,4% periférica, 40,9% mista e 7,1% entesopática. A uveíte anterior aguda (33,6%) foi a manifestação extra-articular mais comum. Foram positivos para o HLA-B27, 80,3% dos doentes. Os haplótipo A*02/B*27/Cw*02/DRB1*01/DQB1*05 parece conferir suscetibilidade para a EA, e o A*02/B*27/Cw*01/DRB1*08/DQB1*04 parece conferir proteção em termos de atividade, repercussão funcional e radiológica da doença. Três variantes (2 para IL23R e 1 para ERAP1) mostraram significativa associação com a doença, confirmando a associação destes genes com a EA na população Portuguesa. O mesmo não se verificou com as variantes estudadas do ANKH. Não se verificou associação entre as variantes génicas não-MHC e as manifestações clínicas da EA. Foi identificado um perfil de expressão génica para a EA, tendo sido validados catorze genes - alguns têm um papel bem documentado em termos de inflamação, outros no metabolismo da cartilagem e do osso. Conclusões: Foi estabelecido um perfil demográfico e clínico dos doentes com EA em Portugal. A identificação de variantes génicas e de um perfil de expressão contribuem para uma melhor compreensão da sua fisiopatologia e podem ser úteis para estabelecer modelos com relevância em termos de diagnóstico, prognóstico e orientação terapêutica dos doentes. -----------ABSTRACT: Background: Ankylosing Spondylitis (AS) is a chronic inflammatory disorder characterized by inflammation in the spine and sacroiliac joints leading to progressive joint ankylosis and in progressive deterioration of physical function and quality of life. An early diagnosis and early therapy may contribute to a better prognosis. The identification of biomarkers would be helpful and represents a great challenge for the scientific community. Objectives: The present study had the following aims: 1- to characterize the pattern of AS in Portuguese patients; 2- to investigate MHC and non-MHC gene associations with susceptibility and phenotypic features of AS and; 3- to identify candidate genes associated with AS by means of whole-genome microarray. Material and Methods: AS was defined in accordance to the modified New York criteria and AS cases were recruited from hospital outcares patient clinics. Demographic and clinical data were recorded and blood samples collected. A random group of HLA-B27 positive patients and controls were selected and typed for HLA class I and II by PCR-rSSOP. The extended HLA haplotypes were estimated by Expectation Maximization Algorithm using Arlequin v3.11 software. Genotyping of IL23R, ERAP1 and ANKH allelic variants was carried out with TaqMan allelic discrimination assays. Association analysis was performed using the Cochrane-Armitage and linear regression tests as implemented in PLINK, for dichotomous and quantitative variables, respectively. Gene expression profile was carried out using Illumina HT-12 Whole-Genome Expression BeadChips and candidate genes were validated using qPCR-based TaqMan Low Density Arrays (TLDAs). Results: A total of 369 patients (62.3% male; mean age 45.4±13.2 years; mean disease duration 11.4±10.5 years), were included. Regarding clinical disease pattern, at the time of assessment, 49.9% had axial disease, 2.4% peripheral disease, 40.9% mixed disease and 7.1% isolated enthesopathic disease. Acute anterior uveitis (33.6%) was the most common extra-articular manifestation. 80.3% of AS patients were HLA-B27 positive. The haplotype A*02/B*27/Cw*02/DRB1*01/DQB1*05 seems to confer susceptibility to AS, whereas A*02/B*27/Cw*01/DRB1*08/DQB1*04 seems to provide protection in terms of disease activity, functional and radiological repercussion. Three markers (two for IL23R and one for ERAP1) showed significant single-locus disease associations. Association of these genes with AS in the Portuguese population was confirmed, whereas ANKH markers studied did not show an association with AS. No association was seen between non-MHC genes and clinical manifestations of AS. A gene expression signature for AS was established; among the fourteen validated genes, a number of them have a well-documented inflammatory role or in modulation of cartilage and bone metabolism. Conclusions: A demographic and clinical profile of patients with AS in Portugal was established. Identification of genetic variants of target genes as well as gene expression signatures could provide a better understanding of AS pathophysiology and could be useful to establish models with relevance in terms of susceptibility, prognosis, and potential therapeutic guidance.

Application of ionic liquids and enzymes for the removal of proteinaceous layers from polychrome of works of art and evaluation of the cleaning effectiveness

Dissertação Apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Ciências da Conservação, especialização em Pintura

Nevirapine in an animal model of pre-diabetes: study of drug pharmacokinetic and its effects on fasting glycemia and insulin resistance

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Analysis of chromium behaviour and speciation during the electrodialytic process

The interest in chromium (Cr) arises from the widespread use of this heavy metal in various industrial processes that cause its release as liquid, solid and gaseous waste into the environment. The impact of Cr on the environment and living organisms primarily depends on its chemical form, since Cr(III) is an essential micronutrient for humans, other animals and plants, and Cr(VI) is highly toxic and a known human carcinogen. This study aimed to evaluate if the electrodialytic process (ED) is an appropriate treatment for Cr removal, through a critical overview of Cr speciation, before and after the ED experiments, to assess possible Cr(III)-Cr(VI) interconversions during the treatment. ED was the treatment technique applied to two types of matrices containing Cr: chromate copper arsenate (CCA) contaminated soil and municipal solid waste incineration (MSWI) fly ash. In order to study Cr remediation, three EDR set-ups were used: a new set-up, the combined cell (2/3C or 3/2C), with three compartments, alternating current between two anodes and different initial experimental conditions, one set-up with three compartments (3C cell) and the other set-up with two compartments (2C cell). The Cr removal rates obtained in this study were between 10-36% for the soil, and 1-13% for the fly ash. The highest Cr removal rates were achieved in the 26 days experiments: 36% for the soil, 13% for the fly ash. Regarding the 13 days experiments, the highest Cr removal rates were attained with the 2/3C set-up: 24% for the soil, 5% for the fly ash. The analysis of Cr(VI) was performed before and after ED experiments to evaluate eventual changes in Cr speciation during the treatment. This analysis was conducted by two methods: USEPA Method 3060A, for the extraction of Cr(VI); and Hach Company Method 8023, for the detection of Cr(VI). Despite the differences in Cr total concentration, both matrices presented a similar speciation, with Cr(III) being the main species found and Cr(VI) less than 3% of Cr total, before and after the treatment. For fly ash, Cr(VI) was initially below the detection limit of the method and remained that way after the treatment. For soil, Cr(VI) decreased after the treatment. Oxidation of Cr(III) to Cr(VI) did not occur during the ED process since there was no increase in Cr(VI) in the matrices after the treatment. Hence, the results of this study indicate that ED is an appropriate technique to remediate matrices containing Cr because it contributes to Cr removal, without causing Cr(III)-Cr(VI) interconversions.