Quantum dots: synthesis, functionalization and bioconjugation for biological applications

Dissertation presented to obtain the Ph.D degree in Engineering Sciences and Technology

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.

Biotoxicity assays of quantum dots in in vitro cultures of Medicago sativa and Medicago truncatula

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Biotecnologia

The impact of CdSe/ZnS Quantum Dots in cells of Medicago sativa in suspension culture

Abstract Background: Nanotechnology has the potential to provide agriculture with new tools that may be used in the rapid detection and molecular treatment of diseases and enhancement of plant ability to absorb nutrients, among others. Data on nanoparticle toxicity in plants is largely heterogeneous with a diversity of physicochemical parameters reported, which difficult generalizations. Here a cell biology approach was used to evaluate the impact of Quantum Dots (QDs) nanocrystals on plant cells, including their effect on cell growth, cell viability, oxidative stress and ROS accumulation, besides their cytomobility. Results: A plant cell suspension culture of Medicago sativa was settled for the assessment of the impact of the addition of mercaptopropanoic acid coated CdSe/ZnS QDs. Cell growth was significantly reduced when 100 mM of mercaptopropanoic acid -QDs was added during the exponential growth phase, with less than 50% of the cells viable 72 hours after mercaptopropanoic acid -QDs addition. They were up taken by Medicago sativa cells and accumulated in the cytoplasm and nucleus as revealed by optical thin confocal imaging. As part of the cellular response to internalization, Medicago sativa cells were found to increase the production of Reactive Oxygen Species (ROS) in a dose and time dependent manner. Using the fluorescent dye H2DCFDA it was observable that mercaptopropanoic acid-QDs concentrations between 5-180 nM led to a progressive and linear increase of ROS accumulation. Conclusions: Our results showed that the extent of mercaptopropanoic acid coated CdSe/ZnS QDs cytotoxicity in plant cells is dependent upon a number of factors including QDs properties, dose and the environmental conditions of administration and that, for Medicago sativa cells, a safe range of 1-5 nM should not be exceeded for biological applications.

Epidemiological studies of Streptococcus pneumoniae carriage in the post-vaccination era among two risk groups: children and the elderly

Dissertation presented to obtain the Ph.D. degree in Biology/ Molecular Biology

Portuguese business groups at the beginning of the 21st century: Trends, characteristics and configurations

This study considers the literature on the persistence of business groups in developed economies and analyzes the Portuguese case. The reconstruction of the largest business groups assembles information relevant to define characteristics that enable them to thrive. Increasing internationalization, more specialization in core activities and family control define these types of big businesses. New sectors also emerge as a characteristic of these business groups when compared to the ones existing 40 years ago.

Empirical evidence on the difference between the effective and the statutory tax rates for listed groups in Germany

The difference between the statutory and effective tax rate for listed groups is a complex variable influenced by a variety of factors. This paper aims to analyze whether this difference exists for listed groups in the German market and tests which factors have an impact on it. Thus the sample consists of 130 corporations listed in the three major German stock indices. The findings suggest that the companies that pay less than the statutory rate clearly outweigh the ones that pay more, and that the income earned from associated companies has a significant impact on this difference.

Solution processed quantum dot photodetectors

To find sustainable solutions for the production of energy, it is necessary to create photovoltaic technologies that make every photon count. To pursue this necessity, in the present work photodetectors of zinc oxide embedded with nano-structured materials, that significantly raise the conversion of solar energy to electric energy, were developed. The novelty of this work is on the development of processing methodologies in which all steps are in solution: quantum dots synthesis, passivation of their surface and sol-gel deposition. The quantum dot solutions with different capping agents were characterized by UVvisible absorption spectroscopy, spectrofluorimetry, dynamic light scattering and transmission electron microscopy. The obtained quantum dots have dimensions between 2 and 3nm. These particles were suspended in zinc acetate solutions and used to produce doped zinc oxide films with embedded quantum dots, whose electric response was tested. The produced nano-structured zinc oxide materials have a superior performance than the bulk, in terms of the produced photo-current. This indicates that an intermediate band material should have been produced that acts as a photovoltaic medium for solar cells. The results are currently being compiled in a scientific article, that is being prepared for possible submission to Energy and Environmental Science or Nanoscale journals.

Rating corporate groups a modelling experience

This paper aims to provide a model that allows BPI to measure the credit risk, through its rating scale, of the subsidiaries included in the corporate groups who are their clients. This model should be simple enough to be applied in practice, accurate, and must give consistent results in comparison to what have been the ratings given by the bank. The model proposed includes operational, strategic, and financial factors and ends up giving one of three results: no support, partial support, or full support from the holding to the subsidiary, and each of them translates in adjustments in each subsidiary’s credit rating. As it would be expectable, most of the subsidiaries should have the same credit rating of its parent company.

Contribution of Mental Health Service User Groups to Mental Health Services and Policy in Ghana : The Case of Mental Health Society of Ghana

RESUMO: Este estudo procurou documentar a perspectiva (s) dos utentes de saúde mental e das associações de prestadores de cuidados sobre a prestação, o papel e a contribuição de serviços de saúde mental da comunidade tal como foram percebidos por um número de informadores-chave, incluindo os utentes do serviço mentais e os próprios prestadores de cuidados. O caso específico da Sociedade Saúde Mental do Gana (MEHSOG) foi o foco deste estudo. O modelo foi o de um estudo de caso, utilizando discussões de grupo e entrevistas com informadores-chave como instrumentos de recolha de dados. Estas ferramentas de colheita de dados foram complementadas por observações dos participantes e pela revisão de documentos da MEHSOG e dos vários grupos de apoio da comunidade de auto-ajuda que compõem a associação nacional. O estudo revelou que os utentes dos serviços de saúde mental e seus prestadores de cuidados constituem um importante grupo de partes interessadas na prestação de serviços de saúde mental da comunidade e no desenvolvimento de políticas que tenham em conta as necessidades e os direitos das pessoas com doença mental ou epilepsia. O envolvimento da MEHSOG promove a mobilização de membros e famílias relacionadas com a doença mental de beneficiar de serviços de tratamento bem organizados com um impacto significativo na melhoria da saúde e da participação dos utentes dos serviços e seus prestadores de cuidados primários em processos de tomada de decisão da família e na comunidade processos de desenvolvimento. Os utentes dos serviços por beneficiarem de tratamento, e os prestadores de cuidados primários, por se tornarem mais livres e menos sobrecarregados com a responsabilidade de cuidar, podem passar a envolver-se mais em atividades que melhoramo seu estado, o de suas famílias e das comunidades. A advocacia dos membros da MEHSOG para conseguir que a “Mental Health Bill” se transforme numa Lei foi também um desenvolvimento significativo resultante da participação ativa dos utentes do serviço em chamar a atenção para uma nova e inclusiva legislação de saúde mental para o Gana. Entre os fatores e oportunidades que permitiram aos utentes dos serviços de saúde mental e aos prestadores de cuidados primários de pessoas com doença mental apoiar activamente a prestação de serviços de saúde mental comunitária e o desenvolvimento de políticas conta-se a contribuição da sociedade civil do Gana, particularmente o movimento da deficiência, e os esforços anteriores de ONGs em saúde mental e dos profissionais de saúde mental para ter uma nova lei em saúde mental. Observámos um certo número de desafios e barreiras que actuam de forma a limitar a influência dos utentes dos serviços de saúde mental na provisão da saúde mental comunitária e no desenvolvimento de políticas. Entre elas o estigma social contra a doença mental e pessoas com doença mental ou epilepsia e seus cuidadores primaries é um factor chave. O estigma tem alterado a percepção e as análises do público em geral, especialmente dos profissionais de saúde e das autoridades políticas afetando a priorização dos problemas de saúde mental nas políticas e programas. Outro desafio foi a deficiente infra-estrutura disponível para apoiar serviços de saúde mentais que assegurem aos utentes permanecerem em bom estado de saúde e bem-estar para serem advogados de si próprios. A recomendação do presente estudo é que os movimentos de utentes dos serviços de saúde mental são importantes e que eles precisam de ser apoiados e encorajados a desempenhar o seu papel como pessoas com experiência vivida para contribuir para a organização e prestação de serviços de saúde mental, bem como para a implementação, monitorização e avaliação de políticas e programas. ------------------------------------ ABSTRACT: This study sought to document the perspective(s) of mental health users and care-givers associations in community mental health service provision and their role and contribution as it was perceived by a number of key informants including the mental service users and care-givers themselves. The specific case of the Mental Health Society of Ghana (MEHSOG) was the focus of this study. A case study approach was used to with Focus Group Discussions and Key Informants Interviews being the data collection tools that were used. These data collection tools were complemented by participant observations and review of documents of the MEHSOG and the various community self-help peer support groups that make up the national association. The study revealed that mental health service users and their care-givers constitute an important stakeholder group in community mental health service provision and development of policies that factor in the needs and rights of persons with mental illness or epilepsy. MEHSOG’s involvement in mobilising members and education families to come forward with the relations with mental illness to benefit from treatment services were well made a significant impact in improving the health and participation of service users and their primary carers in family decision-making processes and in community development processes. Service users, on benefiting from treatment, and primary care-givers, on becoming freer and less burdened with the responsibility of care, move on to engage in secure livelihoods activities, which enhanced their status in their families and communities. The advocacy MEHSOG members undertook in getting the mental health Bill become Law was also noted as significant development that was realised as a result of active involvement of service users in calling for a new and inclusive mental health legislation for Ghana. Enabling factors and opportunities that enabled mental health service users and primary care-givers of people with mental illness to actively support community mental health service provision and policy development is with the vibrant civil society presence in Ghana, particularly the disability movement, and earlier efforts by NGOs in mental health in Ghana long-side mental health professionals to have a new law in mental health. A number of challenges were also noted which were found to limit the extent to which mental health service users can be influential in community mental health service provision and policy development. Key among them was the social stigma against mental illness and people with mental illness or epilepsy and their primary carers. Stigma has affected perceptions, analyses of the general public, especially health practitioners and policy authorities that it has affected their prioritisation of mental health issues in policies and programmes. Another challenge was the poor infrastructure available to support enhanced mental health care services that ensure mental health service users remain in a good state of health and wellbeing to advocate for themselves. The recommendation from the study is that mental health service user movements are important and need to be supported and encouraged to play their role as persons with lived experience to inform organisation and provision of mental health services as well as design and implementation, monitoring and evaluation of policies and programes.