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.

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.

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.

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

Construção e caracterização de um transformador de 562,5 VA com núcleo de ferro amorfo

Nos sistemas de geração, transmissão e distribuição de energia, os transformadores de potência são um dos componentes mais comuns e importantes. Deste modo, o desempenho dos transformadores é fundamental para a eficiência global dos sistemas. Para optimizar a eficiência dos transformadores, a escolha do material ferromagnético a usar para a construção do núcleo, é um factor muito importante. Por exemplo, o uso de um material ferromagnético amorfo no núcleo de um transformador, em vez de aço silício, reduz as perdas magnéticas totais do dispositivo. Outra possível solução para aumentar a eficiência dos sistemas de distribuição de energia, é a instalação de transformadores supercondutores de alta temperatura (SAT), normalmente arrefecidos em azoto líquido a 77 K. Deste modo, um transformador de 562,5 VA com núcleo de ferro amorfo foi projectado e construído e as suas propriedades magnéticas mais importantes foram medidas à temperatura ambiente, e à temperatura criogénica para deste modo contribuir para uma melhoria da eficiência dos transformadores supercondutores. De seguida, foram comparadas com as propriedades magnéticas de um transformador com núcleo de aço silício de grão orientado. As perdas magnéticas totais do material amorfo à temperatura ambiente e criogénica, os parâmetros do esquema equivalente de Steinmetz e a impedância de curto-circuito são apresentadas e discutidas. Foi também caracterizado o comportamento do transformador em carga determinando, por exemplo, o rendimento e a regulação da tensão em função da carga do transformador. Aspectos de construção do transformador são também abordados.

State detection in a financial portfolio: a self-organizing maps approach for financial time series

This study analyses financial data using the result characterization of a self-organized neural network model. The goal was prototyping a tool that may help an economist or a market analyst to analyse stock market series. To reach this goal, the tool shows economic dependencies and statistics measures over stock market series. The neural network SOM (self-organizing maps) model was used to ex-tract behavioural patterns of the data analysed. Based on this model, it was de-veloped an application to analyse financial data. This application uses a portfo-lio of correlated markets or inverse-correlated markets as input. After the anal-ysis with SOM, the result is represented by micro clusters that are organized by its behaviour tendency. During the study appeared the need of a better analysis for SOM algo-rithm results. This problem was solved with a cluster solution technique, which groups the micro clusters from SOM U-Matrix analyses. The study showed that the correlation and inverse-correlation markets projects multiple clusters of data. These clusters represent multiple trend states that may be useful for technical professionals.

Variação espaço-temporal na atividade forrageira da Saúva (Atta laevigata)

Na Amazônia, a regeneração natural da floresta em pastos e cultivos abandonados pode ser afetada pelas saúvas, pois estas são importantes predadoras das plântulas e das sementes das espécies arbóreas que eventualmente ali se estabelecem. Entretanto, pouco se sabe sobre como as chances de uma dada planta ser atacada ou de uma semente ser removida pelas saúvas varia no tempo e no espaço. Com este intuito, estabeleci uma parcela de 80 χ 120 m, subdividida em quadrantes de 10 χ 10m, em um campo abandonado próximo a Manaus. Na periferia desta parcela haviam 3 ninhos da saúva Atta laevigata. Ao longo de 1 ano, determinei quais plantas (das espécies arbóreas somente) foram atacadas pelas formigas. Determinei também como variou a atividade de coleta de sementes por A. laevigata. Para isto utilizei grãos de feijão (Phaseolus vulgaris). Iscas, com cerca de 20 feijões cada, foram distribuídas pela parcela ao longo do ano. Finalmente, determinei se plantas (mudas de Bellucia imperialis) estabelecidas em solo desnudo tinham uma maior chance de serem atacadas do que aquelas estabelecidas em solo com cobertura de gramíneas. Os resultados mostram que a atividade de coleta de sementes foi espacialmente agregada. A maior atividade foi observada nas regiões sudeste e noroeste da parcela, em geral, próximo aos ninhos. Forte variação temporal na coleta de sementes também foi observada. O pico máximo de atividade ocorreu em meados de julho e o de menor atividade em meados de janeiro. A atividade de corte seguiu um padrão similar. Houve uma clara diminuição no número de plantas atacadas entre novembro e janeiro. A proporção de plantas atacadas por parcela variou entre 6 e 89%. A incidência de ataques por saúvas sobre mudas de B. imperialis não variou em função da cobertura vegetal (com ou sem gramíneas). Isto possivelmente em função da forte heterogeneidade espacial na atividade de A. laevigata, que encobriu qualquer efeito devido a cobertura vegetal.

Where@UM - Dependable organic radio maps

In the past decade, the research community has been dedicating considerable effort into indoor positioning systems based on Wi-Fi fingerprinting techniques, mainly due to their capability to exploit existing infrastructures. Crowdsourcing approaches, also known as organic, have been proposed recently to address the problem of creating and maintaining the corresponding radio maps. In these organic systems, the users of the system build the radio map themselves while using it to estimate their own position/location. However, most of these collaborative methods, proposed by several authors, assume that all the users are honest and committed to contribute to a good quality radio map. In this paper we assess the quality of a radio map built collaboratively and propose a method to classify the credibility of individual contributions and the reputation of individual users. Experimental results are presented for an organic indoor location system that has been used by more than one hundred users over a period of around 12 months.

An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds

For a given self-map f of M, a closed smooth connected and simply-connected manifold of dimension m ≥ 4, we provide an algorithm for estimating the values of the topological invariant Dm r [f], which equals the minimal number of r-periodic points in the smooth homotopy class of f. Our results are based on the combinatorial scheme for computing Dm r [f] introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63–84]. An open-source implementation of the algorithm programmed in C++ is publicly available at http://www.pawelpilarczyk.com/combtop/.

Estudio de la vía intraperitoneal y sus células presentadoras de antígenos en la inducción de tolerancia a EAE

La Esclerosis Múltiple es una de las enfermedades autoinmunes del Sistema Nervioso Central más frecuentes en adultos jóvenes. Un modelo experimental de la misma es la Encefalomielitis Autoinmune Experimental (EAE). Numerosos trabajos demuestran que en EAE, los clones patogénicos capaces de transferir la enfermedad son células T cooperadoras tipo 1 (Th1), mientras que las células T cooperadoras tipo 2 (Th2) actuarían como clones protectivos. Debido a las funciones opuestas de estas dos poblaciones existe la posibilidad de que la desregulación inmune asociada a Esclerosis Múltiple y su modelo experimental EAE se relacione a un desbalance Th1-Th2. La célula presentadora de antígeno (CPA), la dosis de antígeno, su ruta de entrada, el tipo de interleuquina presente en el medio, las moléculas co-estimulatorias de la CPA, etc., son fundamentales para la inducción de poblaciones Th1 ó Th2. Las estrategias terapéuticas actuales intentan suprimir la enfermedad administrando el autoantígeno por distintas vías, como por ejemplo la vía oral, intragástrica, endovenosa, etc. La inducción de tolerancia utilizando la vía intraperitoneal (ip) no ha sido muy explorada. Recientemente hemos iniciado una nueva línea de trabajo en la cual se suprimió la EAE inyectando i.p. antígenos de mielina en días previos a la inmunización. El objetivo de este proyecto será estudiar la vía i.p. y las CPA peritoneales en la inducción de supresión de la EAE. Se analizará: 1) El mecanismo inmunológico por el cual se induce supresión al inyectar antígenos de mielina por la vía i.p., estudiando si en los animales suprimidos se genera un estado de anergia al autoantígeno y/o células capaces de regular negativamente la respuesta autoinmune. 2) Si las CPA peritoneales pulsadas in vivo con antígenos de mielina al ser transferidas a animales receptores singénicos en días previos a la inmunización con mielina bovina son capaces de inducir supresión de la respuesta autoinmune en los animales receptores. 3) El fenotipo de las CPA peritoneales ya que se sabe que CPA que expresen determinadas moléculas de superficie tales como antígenos del Complejo Mayor de Histocompatibilidad, moléculas de adhesión, moléculas coestimulatorias, etc., participan activamente en el destino final de la respuesta inducida.

Estudio de los mecanismos moleculares involucrados en la inmunosupresión observada durante la infección con Trypanosoma cruzi: Rol de la vía PD-1/PD1-L y E3 ubiquitina ligasas. Molecular mechanismns involved in the immunosupression during Tryapanosoma cruzi infection. Role of PD1-PD1-L pathway and E3 ubiquitin ligases.

Trypanosoma cruzi es el agente causal de la enfermedad de Chagas, un problema de salud importante en América Latina, así como también en América Central, ya que causa infección crónica afectando a millones de personas [1]. Durante esta enfermedad se han descripto varias alteraciones de la respuesta inmune, entre ellas una severa inmunosupresión durante la etapa aguda de la infección, tanto en humanos como en ratones. Células T provenientes de ratones infectados activadas in vitro, muestran reducción en la respuesta proliferativa a mitógenos, característica de un estado de inmunosupresión [2-4]. La falla del sistema inmune durante estadios tempranos de la infección probablemente colabore con la diseminación y el establecimiento del parásito. Un gran número de estudios se han focalizado en la identificación de mecanismos moleculares responsables del fenómeno de inmunosupresión, entre los mecanismos citados se ha demostrado presencia de células supresoras [5-9], factores inmunosupresores presentes en el parásito [2, 3, 10-13], producción excesiva de óxido nítrico [14], disminuida producción de IL-2 y reducida expresión del receptor de IL2 en células de bazo de animales infectados [9, 15-17]. Muchos de estos mecanismos han sido exhaustivamente investigados, sin embargo no está del todo claro si existen mecanismos adicionales involucrados en la inmunosupresión de la célula T. Adicionalmente, en los últimos años nuevas moléculas que median la regulación negativa de la célula T, entre las cuales están PD-1/PD1-L [18], arginasa [19] y E3 ubiquitina ligasas [20-22], han sido reportadas durante inmunosupresión en diversas infecciones. Trypanosoma cruzi, the etiological agent of Chagas’ disease, is parasite causing chronic infections in human and other mammalian species. There is an important immunosupresion during the acute phase of the infection that contribute to the dissemination and installation of the parasite. Several studies have been focused on identifying the mechanisms involved in the immunosupresion; however it is not clear if there are additional mechanisms implicated. In addition, during the last years new molecules involved in the negative T cell regulation such as PD-1/PD1-L pathway and E3 ubiquitin ligases (E3-Ub-Lig) have been reported. It has been demonstrated, that E3-Ub-Lig control the amount and localization of intracellular signal mediators, limiting T cell activation. Moreover, these mechanisms mediate the immunosupresion observed during several infections leading to the persistence of the pathogen in the host. In this project the role of E3-Ub-Lig on the T cell immunosupresion and hipo-response mechanisms observed during T. cruzi infection will be studied. On the other hand, it has been reported that some pathogens release proteins with E3-Ub-Lig activity modifying the ubiquitination process to promote their survival and replication in the host. Recently, a protein with E3-Ub-Lig activity was identified in T. cruzi, however its target molecule has not been discovered yet. Therefore, one of the aims of this project consists on studying different potential target molecules for this novel E3-Ub-Lig. In addition, during the last years, important progress has been done about the biological rol of PD-1/PD1-L pathway on the regulation of the immune response in several infections. However, it is not well known how PD-1/PD1-L pathway transduces signals at intracelular level to block T cell response. Because of this, it is interesting to study if there is any relation between the PD-1/PD1-L pathway and E3-Ub-Lig on the mechanism of T cell immunosupression during T. cruzi infection.

Evaluación de la enfermedad alérgica respiratoria: el concepto de unidad de la vía aérea.

Introducción: Existen evidencias epidemiológicas, funcionales y patológicas que vinculan las vías aéreas superior e inferior, reconocidas clínicamente como una vía aérea única. Objetivos: 1.Estudiar la enfermedad alérgica en la vía aérea. 2. Investigar el impacto pulmonar de la enfermedad de la vía aérea superior. 3. Comparar el efecto bronquial de la enfermedad de la vía aérea superior de etiología alérgica y no alérgica. Población y métodos: Estudio prospectivo, observacional, descriptivo y analítico. Se incluirán niños y adolescentes entre 6 y 18 años con síntomas de rinitis alérgica y no alérgica de diferentes grados de gravedad clínica, sin asma. Se establecerá por historia clínica, edad, sexo, índice de masa corporal y duración de la rinitis. Se realizarán pruebas cutáneas con aeroalergenos, espirometría por curva flujo-volumen y estudio de citología nasal, dosaje de inmunoglobulinas. Se calculará un tamaño muestral mínimo con un poder de 80%, una confianza de 95% y una precisión de 10%, para una prevalencia estimada de rinitis pura de 30% en 150 sujetos, aplicando la fórmula n=Zα2 p(1-p)/i2. Se realizará un muestreo no aleatorio sucesivo. Resultados esperados: La rinitis produciría alteraciones subclínicas en los parámetros de funcionalidad pulmonar. Dicho impacto podría variar de acuerdo al grado clínico de rinitis y su etiología. Utilidad potencial de los resultados: Profundizar el conocimiento de la fisiología de la vía aérea como una unidad y detectar el posible impacto funcional de la rinitis sobre la vía aérea inferior y sus potenciales implicancias terapéuticas.