G-quadruplex ligands for cancer therapy

DNA may fold into a diversity of structures and topologies such as duplexes and triplexes. Some specific guanine-rich DNA sequences may even fold into a higher order structures denominated guanine G-quadruplexes (G4). These G-quadruplex forming sequences have shown biological interest since were found in telomeres and in promoter region of oncogenes. Thus, these G4 forming sequences have been explored as therapeutic targets for cancer therapy, since G4 formation was demonstrated to inhibit RNA-polymerase and telomerase activity. However, the G4 structures are transient and are only formed under specific conditions. Hence the main objective of this work is to develop new G4-specific ligands which may potentially find applications in the therapeutic area. Several potential G4-binding ligands were synthesized and characterized. The synthesis of these compounds consisted on a procedure based on van Leusen chemistry and a cross-coupling reaction through C-H activation, affording phenanthroline compounds (Phen-1, 50%; Phen-2, 20%), phenyl (Iso-1, 61%; Iso-2, 21%; Ter-1, 85%; Ter-2, 35%), and quinolyl (Quin-1, 85%; Quin-2, 45%) compounds. Screening assays for selecting the potential G4 compounds were performed by FRET-melting, G4-FID, CD-melting and DSF. Qualitative biophysical studies were performed by fluorescence and CD spectroscopy. Two high-specific G-quadruplex ligands, Phen-1 and Phen-2, were found to effectively bind telomeric and c-myc G4 structures. Phen-1 was found to stabilize parallel telomeric 22AG and c-myc sequence by 4.1 and 4.3 ˚C, respectively. Phen-2 also displayed high affinity towards 22AG (

Experimental study of proton induced nuclear reactions in 6,7 Li

This work presents the results of the experimental study of proton induced nuclear reactions in lithium, namely the 7Li(p,α) 4He, 6Li(p,α) 3He and 7Li(p,p)7Li reactions. The amount of 7Li and 6Li identified as primordial and observed in very old stars of the Milky Way galactic halo strongly deviates from the predictions of primordial nucleosynthesis and stellar evolution models which depend, among other factors, on the cross sections of reactions like 7Li(p,α) 4He and 6Li(p,α) 3He. These discrepancies have triggered a large amount of research in the fields of stellar evolution, cosmology, pre-galactic evolution and low energy nuclear reactions. Focusing on nuclear reactions, this work has measured the 7Li(p,α) 4He and 6Li(p,α) 3He reactions cross sections (expressed in terms of the astrophysical S -factor) with higher accuracy, and the electron screening effects in these reactions for different environments (insulators and metallic targets). The 7Li(p,α) 4He angular distributions were also measured. These measurementstook place in two laboratory facilities, in the framework of the LUNA (Laboratory for Undergroud Nuclear Astrophysics) international collaboration, namely the Laboratorio ´ de Feixe de Ioes ˜ in ITN (Instituto Tecnologico ´ e Nuclear) Sacavem, ´ Portugal, and the Dynamitron-TandemLaboratorium in Ruhr-Universitat¨ Bochum, Germany. The ITN target chamber was modified to measure these nuclear reactions, with the design and construction of new components, the addition of one turbomolecular pump and a cold finger. The 7Li(p,α) 4He and 6Li(p,α) 3He reactions were measured concurrently with seven and four targets, respectively. These targets were produced in order to obtain adequate and stable lithium depth profiles. In metallic environments, the measured electron screening potential energies are much higher than the predictions of atomic-physics models. The Debye screening model applied to the metallic conduction electrons is able to explain these high values. It is a simple model, but also very robust. Concerning primordial nucleosynthesis and stellar evolution models, these results are very important as they show that laboratory measurements are well controlled, and the model inputs from these cross sections are therefore correct. In this work the 7Li(p,p)7Li differential cross section was also measured, which is useful to describe the 7Li(p,α) 4He entrance channel.

Study of nuclear reactions relevant for astrophysics by Micro-AMS

Dissertação para obtenção do Grau de Doutor em Física

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.

MBR activated sludge filterability characterization in cross flow filtration

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

Portuguese Red Cross - Conde d´Óbidos Palace National Headquarters

Ano VI; nº 2 - 2008 - p.103-106

Abordagem farmacoepidemiológica da terapêutica no idoso: um ensaio em meio hospitalar

Introdução: O envelhecimento demográfico e o aumento da esperança de vida, criam condições para uma maior incidência de doenças degenerativas. Vários aspectos críticos envolvem a medicação no idoso, tais como: polimedicação frequente, com risco acrescido de ocorrência de reacções adversas, relacionadas com interacções medicamentosas e eventual medicação desaconselhada, em que o risco pode ser superior ao benefício. Estes aspectos são particularmente críticos no idoso hospitalizado. Objectivo: Este estudo teve como objectivo estimar a prevalência da polimedicação em idosos hospitalizados e analisar a medicação considerada inadequada nesta população. Participantes e metodologia: Seguiu-se um modelo retrospectivo descritivo transversal, reportando-se os dados a um período de um ano e meio, incidindo sobre o último internamento. A natureza da medicação, foi analisada de acordo com o Formulário Terapêutico Nacional, Resumo das Caracteristicas do Medicamento e com critérios de Beers-2002.Englobou 100 idosos (>65 anos) utentes do Hospital Cuf Descobertas, em regime de internamento. Os dados pessoais e clínicos e respectivo mapa farmacoterapêutico, foram introduzidos em base de dados construída para este estudo, em Access 2003 SP2. Procedeu-se à analise estatística (SPSS 13,0), descritiva, com cálculo de medidas de tendência central; análise univariada para todas as variáveis relevantes e análise bi-variada para quantificar a prevalência da polimedicação por sexo e grupo etário. Resultados:Dos doentes estudados (65-98 anos), maioritariamente femininos, 7 apresentavam 4 patologias em simultâneo, 13:3 patologias, 27:2 patologias e 30:1 patologia. Em 23 não se verificou qualquer patologia crónica. A hipertensão (n=49:27,5%) e a patologia cardiovascular (n=41:23%) foram as mais frequentemente encontradas na amostra em estudo sendo as de menor frequência a patologia reumática (n=1:0,56%), a osteoporose e os problemas psíquicos (n=2:1,12%. A prevalência de polimedicação foi de 84% e nº de medicamentos prescrito em simultâneo variou entre 2 e 23.Não se observou associação entre a polimedicação, a idade: e o sexo. Em apenas um caso foi identificado um medicamento desaconselhado em função do diagnóstico (metoclopramida:Parkinson), e independentemente do diagnóstico a amiodariona foi o mais frequente (25%), hidroxizina (22%), ticlopidina (2%) e cetorolac (1%). Conclusões: A polimedicação é um fenómeno muito frequente nos idosos hospitalizados; o número de medicamentos envolvidos pode ser elevado e a prevalência de medicamentos que requerem uma ponderação sobre o risco/benefício no idoso, indicia a vantagem da revisão da terapêutica, impondo-se a implementação de estratégias informativas sobre os mesmos. Background: The demographic aging and expansion of life expectancy create conditions for increased occurrence of degenerative illnesses. Several critical aspects involve the medication of the elderly, such as: frequent polipharmacy with increased occurrence of adverse drug reactions, related to medication interactions and inappropriate prescribing, in which the benefits can be inferior to the risks.These aspects are particularly critical in the hospitalized elderly. Aim: This study aimed to estimate the prevalence of polipharmacy in hospitalized elderly and to analyze the medication considered inappropriate in this population. Participants and Methodology: A cross sectional model was followed, in which the data used relate to a period of a year and a half, focussing on the last hospitalization. The nature of the medication was analysed according to National Therapeutic Formulary, Drug Characteristics Summary and according to Beers-2002.It considered 100 elderly (>65 years) hospitalized at Hospital Cuf Descobertas. The personal and clinical data and the corresponding pharmacotherapeutic registration were introduced in a database created for this study in Access 2003 SP2. Descriptive statistics was calculated trough SPSS 13,0,.Exploraty analysis consisted in measures of average and spread for all variable considered relevant and univariate and bivariate analysis to quantify the prevalence of polipharmacy by sex and age and to relate polipharmacy with inappropriate medication. Results: Of the patients studied (65-98 years), the majority were women, 7 presented 4 pathologies, 13:3 pathologies, 27:2 pathologies and 30:1 pathology. In 23 patients there was any chronic pathology. Hypertension (n=49:27,5%) and cardiovascular disease (n=41:23%) were the most frequent disease in our study, and the minimal values were observed in rheumatism (n=1:0,56%), osteoporosis and psychic disorders (n=2:1,12%. The prevalence of polipharmacy was of 84% and the amount of medication simultaneously prescribed varied between 2 and 23.No association was observed between polipharmacy and age or gender. In only one case inappropriate medication was identified concerning diagnosis (metoclopramid: Parkinson), and independent of diagnosis the amiodaron was the most frequent (25%), hydroxyzin (22%), ticlopidin (2%). and ketorolac (1%). Conclusions: Polipharmacy is very prevalent among elderly people admitted to the hospital; the number of inappropriate medication can also be very high and this evidence should be collected in order to accomplish good drug use reviews and informative strategies in the hospital setting.

Electron driven reactions in complexes embedded in superfluid helium droplets

A thesis submitted to the University of Innsbruck for the doctor degree in Natural Sciences, Physics and New University of Lisbon for the doctor degree in Physics, Atomic and Molecular Physics

A study in cross-cultural transmission of natural philosophy: the Kenkon Bensetsu

Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de Doutor em História dos Descobrimentos e da Expansão Portuguesa

In situ measured cross section geometry of old timber structures and its influence on structural safety

Old timber structures may show significant variation in the cross section geometry along the same element, as a result of both construction methods and deterioration. As consequence, the definition of the geometric parameters in situ may be both time consuming and costly. This work presents the results of inspections carried out in different timber structures. Based on the obtained results, different simplified geometric models are proposed in order to efficiently model the geometry variations found. Probabilistic modelling techniques are also used to define safety parameters of existing timber structures, when subjected to dead and live loads, namely self-weight and wind actions. The parameters of the models have been defined as probabilistic variables, and safety of a selected case study was assessed using the Monte Carlo simulation technique. Assuming a target reliability index, a model was defined for both the residual cross section and the time dependent deterioration evolution. As a consequence, it was possible to compute probabilities of failure and reliability indices, as well as, time evolution deterioration curves for this structure. The results obtained provide a proposal for definition of the cross section geometric parameters of existing timber structures with different levels of decay, using a simplified probabilistic geometry model and considering a remaining capacity factor for the decayed areas. This model can be used for assessing the safety of the structure at present and for predicting future performance.

Kinetics studies of the superoxide-mediated electron transfer reactions between rubredoxin-type proteins and superoxide reductases

J Biol Inorg Chem (2006) 11: 433–444 DOI 10.1007/s00775-006-0090-0

Electron impact ionization cross sections and analysis of X-ray spectra

A thesis submitted for the degree of Ph. D. in Physics

Determinants of venture capital and private equity investments in renewable energy: A cross-country study

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Economics from the NOVA – School of Business and Economics

A look into the cross-section of industry stock returns

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics

Children emotional reactions toward advertising and brands: A drawing experiment

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