Artificial Intelligence in geospatial analysis: applications of self-organizing maps in the context of geographic information science.

A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Information Systems.

UMA ABORDAGEM YEAST TWO-HYBRID PARA O ESTUDO DA REPLICAÇÃO E PATOGÉNESE DO VÍRUS DA HEPATITE DELTA

O vírus da hepatite delta (HDV) é o agente etiológico de uma das formas mais graves de hepatite viral e é ainda endémico em diversas regiões do globo, nomeadamente em África, na Amazónia e no Extremo Oriente. O HDV co-infecta ou super-infecta hepatócitos infectados com o vírus da hepatite B (HBV) aumentando em cerca de 10 vezes o risco de cirrose e hepatite fulminante. A associação clínica entre os dois vírus deve-se ao facto do invólucro do HDV ser constituído pelos antigénios de superfície do HBV (HBsAgs) que são necessários para a propagação da infecção. O genoma do HDV é constituído por uma molécula de RNA de cadeia simples, circular, com cerca de 1.7 Kb, que possui cerca de 70% de emparelhamento interno. Foi identificada uma única grelha de leitura aberta (ORF) no RNA viral que codifica para o antigénio delta (HDAg). A ocorrência de um mecanismo de editing do RNA, resulta na expressão de duas formas do HDAg, a pequena (S-HDAg) e a grande (L-HDAg). Várias funções essenciais para a replicação do HDV têm sido atribuídas a ambas as formas do HDAg, sendo a S-HDAg essencial para a acumulação de RNA viral e a L-HDAg responsável pela interacção com os HBsAgs para formar partículas virais. No entanto, dada a simplicidade dos seus componentes, admite-se que a replicação viral depende das interacções estabelecidas entre os HDAgs e factores celulares do hospedeiro. Apesar do número considerável de factores celulares descritos como interactores dos HDAgs ou RNA virais, a importância de muitas destas interacções não foi elucidada e muitas etapas do ciclo de replicação do HDV permanecem pouco claras. Para além disso, dado o número limitado de factores do hospedeiro que estão envolvidos na sua replicação, é muito provável que um número elevado de interactores do HDV permaneça por identificar. Este trabalho teve como objectivo a identificação de proteínas de fígado humano capazes de interagir com os HDAgs, utilizando o sistema yeast Two-Hybrid (YTH). Identificaram-se trinta proteínas com capacidade de interagir com a S-HDAg no sistema YTH, sendo que estas proteínas se encontram envolvidas em diferentes processos celulares. Com base nas características funcionais, foram seleccionadas três destas proteínas e as suas interacções com a S-HDAg foram investigadas com maior detalhe. As três proteínas seleccionadas foram a ribonucleoproteína nuclear heterogénea C (hnRNPC), a embryonic lethal abnormal vision like1 (ELAVL1/HuR) e a proteína 2 de ligação a EBNA1 (EBP2). As duas primeiras são proteínas de ligação a RNA, previamente descritas como envolvidas em processos de replicações de outros vírus com genoma RNA, enquanto a EBP2, é uma proteína de localização preferencialmente nucleolar, tal como por vezes acontece com os HDAgs. As interacções foram analisadas recorrendo a vários ensaios bioquímicos. No caso da hnRNPC e da HuR, após validação no sistema YTH, a capacidade de interacção com a S-HDAg foi confirmada quer in vitro por blot overlay quer in vivo por co-imunoprecipitação em células de hepatoma humano. Nas mesmas células, observou-se uma co-localização considerável entre os HDAgs e os RNAs virais. Finalmente, de modo a investigar a contribuição das proteínas hnRNPC e HuR na replicação do HDV, procedeu-se ao silenciamento destas proteínas pela utilização de short hairpin RNAs (shRNAs) específicos para os mRNAs correspondentes Observou-se que o silenciamento de ambas as proteínas hnRNPC e HuR endógenas, individualmente resultou numa diminuição acentuada nos níveis de expressão dos HDAgs. No que respeita à EBP2, a interacção com a S-HDAg foi confirmada em condições in vitro com recurso a ensaios de blot overlay e de cromatografia de afinidade. A análise por imunofluorescência indirecta e microscopia confocal revelou co-localização elevada entre os HDAgs e a EBP2, principalmente nos nucléolos de células de hepatoma humano. Finalmente, foi ainda utilizado o sistema YTH para estudar os mecanismos de importação dos HDAgs. Assim, este sistema foi utilizado com o propósito de identificar proteínas celulares capazes de interagir com um domínio específico dos HDAgs, o sinal de localização nuclear (NLS). Na pesquisa YTH realizada obtiveram-se 161 clones positivos, sendo que um deles mostrou codificar para a carioferina α4 (KPNA4). A interacção da KPNA4 com a S-HDAg foi reproduzida em condições in vitro através de um ensaio de cromatografia de afinidade tendo sido utilizadas formas recombinantes das duas proteínas. Este trabalho permitiu identificar várias proteínas celulares que interagem com a S-HDAg. Obtiveram-se evidências sugestivas de que algumas das proteínas identificadas podem desempenhar funções importantes no ciclo de replicação do HDV e que abrem novas perspectivas para o estudo do ciclo de replicação do vírus.

Models and tools for value systems analysis in collaborative environments

Dissertation to obtain the degree of Doctor in Electrical and Computer Engineering, specialization of Collaborative Networks

Hybrid systems biology: application to Escherichia coli

Dissertation presented to obtain a Master degree in Biotechnology

Hybrid Maneuver for Gradient Search with Multiple Coordinated AUVs

This work presents a hybrid maneuver for gradient search with multiple AUV's. The mission consists in following a gradient field in order to locate the source of a hydrothermal vent or underwater freshwater source. The formation gradient search exploits the environment structuring by the phenomena to be studied. The ingredients for coordination are the payload data collected by each vehicle and their knowledge of the behaviour of other vehicles and detected formation distortions.

Comparative analysis of two-dimensional electrophoresis maps (2-DE) of Helicobacter pylori from Brazilian patients with chronic gastritis and duodenal ulcer: a preliminary report

Helicobacter pylori is a bacterium recognized as the major cause of peptic ulcer and chronic gastritis. Recently, a proteome-based approach was developed to investigate pathogenic factors related to H. pylori. In this preliminary study, H. pylori strains were isolated from gastric biopsies of patients with chronic gastritis and duodenal ulcers. A partial proteomic analysis of H. pylori strains was performed by bacterial lyses and proteins were separated by two-dimensional gel electrophoresis (2-DE). A comparative analysis was performed to verify a differential protein expression between these two 2-DE maps. These data should be useful to clarify the role of different proteins related to bacterial pathogenesis. This study will be completed using a larger number of samples and protein identification of H. pylori by MALDI-TOF mass spectrometry.

Life Cycle Assessment of the Hybrid Vehicle – Toyota Prius

Die Luftverschmutzung, die globale Erwärmung sowie die Verknappung der endlichen Ressourcen sind die größten Bedenken der vergangenen Jahrzehnte. Die Nachfrage nach jeglicher Mobilität steigt rapide. Dementsprechend bemüht ist die Automobilindustrie Lösungen für Mobilität unter dem Aspekt der Nachhaltigkeit und dem Umweltschutz anzubieten. Die Elektrifizierung hat sich hierbei als der beste Weg herausgestellt, um die Umweltprobleme sowie die Abhängigkeit von fossilen Brennstoffen zu lösen. Diese Arbeit soll einen Einblick über die Umweltauswirkungen des Hybridfahrzeuges Toyota Prius geben. Hierbei findet eine Gliederung in vier verschiedene Lebensphasen statt. Im Anschluss bietet die Sachbilanz die Möglichkeit die Umweltauswirkungen mit verschiedenen Antriebsmöglichkeiten und Brennstoffen zu vergleichen. Das Modell hat gezeigt, dass der Toyota Prius während der Nutzung einen hohen Einfluss auf das Treibhauspotenzial aufweist. Durch die Nutzung anderer Brennstoffe, wie beispielsweise Ethanol oder Methanol lassen sich die Auswirkungen am Treibhauspotenzial sowie der Verbrauch an abiotischen Ressourcen reduzieren. Vergleicht man die Elektromobilität mit der konventionellen, so ist festzustellen, dass diese Art der Mobilität die derzeit beste Möglichkeit zur Reduzierung der Umweltbelastungen bietet. Die Auswirkungen der Elektromobilität sind im hohen Maße abhängig von der Art des verwendeten Strommixes.

Hybrid link-state path-vector protocol ++

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores Mestrado Integrado em Engenharia Electrotécnica e de Computadores

Post-MAPS: An interactive acquisition platform for gastroenterology

Post-MAPS is a web platform that collects gastroenterological exam data from several european hospital centers, to be used in future clinical studies and was developed in partnership with experts from the gastroenterological area and information technology (IT) technicians. However, although functional, this platform has some issues that are crucial for its functioning, and can render user interaction unpleasant and exhaustive. Accordingly, we proposed the development of a new web platform, in which we aimed for an improvement in terms of usability, data uni cation and interoperability. Therefore, it was necessary to identify and study different ways of acquiring clinical data and review some of the existing clinical databases in order to understand how they work and what type of data they store, as well as their impact and contribution to clinical knowledge. Closely linked to the data model is the ability to share data with other systems, so, we also studied the concept of interoperability and analyzed some of the most widely used international standards, such as DICOM, HL7 and openEHR. As one of the primary objectives of this project was to achieve a better level of usability, practices related to Human Computer-Interaction, such as requirement analysis, creation of conceptual models, prototyping, and evaluation were also studied. Before we began the development, we conducted an analysis of the previous platform, from a functional point of view, which allowed us to gather not only a list of architectural and interface issues, but also a list of improvement opportunities. It was also performed a small preliminary study in order to evaluate the platform's usability, where we were able to realize that perceived usability is different between users, and that, in some aspects, varies according to their location, age and years of experience. Based on the information gathered during the platform's analysis and in the conclusions of the preliminary study, a new platform was developed, prepared for all potential users, from the inexperienced to the most comfortable with technology. It presents major improvements in terms of usability, also providing several new features that simplify the users' work, improving their interaction with the system, making their experience more enjoyable.

Comparison of Methods and Co-Registration Maps of EEG and fMRI in Occipital Lobe Epilepsy

Clinically childhood occipital lobe epilepsy (OLE) manifests itself with distinct syndromes. The traditional EEG recordings have not been able to overcome the difficulty in correlating the ictal clinical symptoms to the onset in particular areas of the occipital lobes. To understand these syndromes it is important to map with more precision the epileptogenic cortical regions in OLE. Experimentally, we studied three idiopathic childhood OLE patients with EEG source analysis and with the simultaneous acquisition of EEG and fMRI, to map the BOLD effect associated with EEG spikes. The spatial overlap between the EEG and BOLD results was not very good, but the fMRI suggested localizations more consistent with the ictal clinical manifestations of each type of epileptic syndrome. Since our first results show that by associating the BOLD effect with interictal spikes the epileptogenic areas are mapped to localizations different from those calculated from EEG sources and that by using different EEG/fMRI processing methods our results differ to some extent, it is very important to compare the different methods of processing the localization of activation and develop a good methodology for obtaining co-registration maps of high resolution EEG with BOLD localizations.

Unsupervised classification of remote sensing images combining Self Organizing Maps and segmentation techniques

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

The Hybrid Approach for Palliation of Hypoplastic Left Heart Syndrome: Intermediate Results of a Single-Center Experience

INTRODUCTION: Hypoplastic left heart syndrome (HLHS) is a major cause of cardiac death during the first week of life. The hybrid approach is a reliable, reproducible treatment option for patients with HLHS. Herein we report our results using this approach, focusing on its efficacy, safety and late outcome. METHODS: We reviewed prospectively collected data on patients treated for HLHS using a hybrid approach between July 2007 and September 2014. RESULTS: Nine patients had a stage 1 hybrid procedure, with seven undergoing a comprehensive stage 2 procedure. One patient completed the Fontan procedure. Five patients underwent balloon atrial septostomy after the hybrid procedure; in three patients, a stent was placed across the atrial septum. There were three deaths: two early after the hybrid procedure and one early after stage two palliation. Overall survival was 66%. CONCLUSIONS: In our single-center series, the hybrid approach for HLHS yields intermediate results comparable to those of the Norwood strategy. The existence of dedicated teams for the diagnosis and management of these patients, preferably in high-volume centers, is of major importance in this condition.

A systems biology framework for pathway level culture media engineering: pplication to Pichia pastoris cultures

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Criação de clusters de clientes de um banco através do self-organizing maps hierárquico: comparação entre HSOM e SOM

Trabalho de Projeto apresentado como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Análise do mercado financeiro baseada em análise técnica com self-organizing maps

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação