Medical information extraction in European Portuguese

The electronic storage of medical patient data is becoming a daily experience in most of the practices and hospitals worldwide. However, much of the data available is in free-form text, a convenient way of expressing concepts and events, but especially challenging if one wants to perform automatic searches, summarization or statistical analysis. Information Extraction can relieve some of these problems by offering a semantically informed interpretation and abstraction of the texts. MedInX, the Medical Information eXtraction system presented in this document, is the first information extraction system developed to process textual clinical discharge records written in Portuguese. The main goal of the system is to improve access to the information locked up in unstructured text, and, consequently, the efficiency of the health care process, by allowing faster and reliable access to quality information on health, for both patient and health professionals. MedInX components are based on Natural Language Processing principles, and provide several mechanisms to read, process and utilize external resources, such as terminologies and ontologies, in the process of automatic mapping of free text reports onto a structured representation. However, the flexible and scalable architecture of the system, also allowed its application to the task of Named Entity Recognition on a shared evaluation contest focused on Portuguese general domain free-form texts. The evaluation of the system on a set of authentic hospital discharge letters indicates that the system performs with 95% F-measure, on the task of entity recognition, and 95% precision on the task of relation extraction. Example applications, demonstrating the use of MedInX capabilities in real applications in the hospital setting, are also presented in this document. These applications were designed to answer common clinical problems related with the automatic coding of diagnoses and other health-related conditions described in the documents, according to the international classification systems ICD-9-CM and ICF. The automatic review of the content and completeness of the documents is an example of another developed application, denominated MedInX Clinical Audit system.

Portuguese georesources suitability for medical hydrology applications

In Portugal, there is an old tradition in using clayey materials for therapeutic purposes. They are applied in pelotherapy, at several beaches of the Atlantic coast in the form of clay-sea water mixtures (peloids) to treat skin and rheumatic diseases. During many generations, peloids have been applied without scienti c studies that prove their therapeutic validity. In the last decade, the Portuguese scienti c community has become increasingly more interested in assessing the properties that make clayey materials suitable for therapeutic purposes. The abundance of clayey formations and the established practices of medical hydrology in our country turned this interest into a new perspective of application. The studied materials include di erent clays (in age and origin) mainly collected from well-known Mesozoic-Cenozoic formations, in some cases outcropping at beaches where empirical applications occur. This thesis focus in the study of silt-clay fraction (< 63 m).To determine their suitability for therapy, compositional, physicochemical, technological, thermal and rheological properties were assessed. Conventional techniques (XRD, XRF and Sedigraph) were used to assess compositional features of silt-clay fraction. Electron microscopy (SEM, VPSEM, HREM) was used to study the micromorphology and composition of clay fraction (< 2 m). Physicochemical properties (cation exchange and speci c surface) were assessed using the Ammonium Acetate and BET methods. Technological properties (plasticity and abrasivity indices) were assessed using the Atterberg limits and Einlehner abrasion tests. Thermal properties (speci c heat and cooling kinetics) were estimated by DSC analysis and cooling tests. Pharmacotechnical tests (compressibility index, sediment volume and Brook eld viscosity) were used to assess the powder owability as well as the physical stability and viscosity of clay-water dispersions. We selected as suitable Portuguese clays for health applications the samples A-Pe, A-Be2, A-Sd, J-Fr , M-To, C-Lu1, C-Lu2, Pl-Ba, M-Ga and J-Ab because they represent safe materials, with an adequate composition, good technological, physicochemical and thermal properties for application, also presenting an adequate rheology when dispersed in water. Their most relevant characteristics are the high clay minerals content, abundant smectite, illite and kaolinite, and safe hazardous concentrations. They also showed moderate capacity to exchange Ca 2+, high plasticity, low abrasivity, high speci c heat and slow cooling kinetics. They evidenced fair powder owability and good potential to formulate viscous dispersions when stabilized. Because the majority of the assessed characteristics are in accordance with those presented by clays applied in European spas for pelotherapy, we considered this group of clays also suitable for medical hydrology treatments in Portuguese spas.

Hole-type gaseous detectors for medical imaging and HEP experiments

This work presents the results on the development of a high pressure Xe gaseous detector envisaging medical imaging. The detector uses two VUV photosensors operating face-to-face, based on the CsI-MHSP with position discrimination capability. The known effect of the charge gain decrease with the gas pressure is compensated with a light gain using the electroluminescence process. Studies of signal amplitude, energy and position resolution are presented. On the second part, gaseous detectors based on THGEM where studied in order to fulfill the requirements of present and future high energy physics experiments. The work is focused on the application of THGEM in RICH detectors elements: a triple THGEM detector using CsI photocathodes in Ne mixtures was suggested. The ion backflow to the photocathode remains a concern and a limitation; to minimize it, the application of a new hole-structure, THCOBRA, was suggested. Preliminary results foresee good perspectives for the successful application of THCOBRA in ion back-flow suppression. This work contains several methods and measurements of the CsI photocathodes behaviour in radiation gaseous detectors. A long discussion on its issues and possible solutions are presented.

Micropropagation in elite corck oak trees: a tool for suber production improvement?

Dada a extrema importância económica e ambiental que o montado de sobro tem em Portugal, e dado o declínio deste devido a várias razões (e.g. doença, idade das plantas) é premente desenvolver estratégias de preservação de sobreiros elite e optimizar técnicas para a propagação destes genótipos. No primeiro Capítulo expõe-se uma breve introdução sobre o montado actual e as técnicas actuais de regeneração/propagação do sobreiro. Descreve-se ainda as principais técnicas de preservação e avaliação de estabilidade genética referidas na literatura para sobreiro e outras lenhosas. No Capítulo II é apresentado um estudo de melhoramento das condições actuais de maturação de embriões somáticos de sobreiro com vista a aperfeiçoar o processo de conversão em plantas. Neste capítulo é apresentado um protocolo melhorado em relação ao actual que permite um desenvolvimento dos embriões somáticos dum modo semelhante aos embriões zigóticos em termos de substâncias de reserva. O Capítulo III mostra um estudo efectuado com o objectivo principal de avaliar estabilidade genética durante todo o processo de embriogénese somática. Neste capítulo são apresentados resultados duma análise feita por RAPD em fases distintas da embriogénese somática de sobreiro. Neste estudo mostra-se que não existem diferenças significativas entre plantas de campo, embriões somáticos e plantas regeneradas. No Capítulo VI, pretende-se complementar o estudo anterior. Neste Capítulo descreve-se a dinâmica do ciclo celular durante as primeiras fases de embriogénese somática na presença de reguladores de crescimento. Este trabalho permitiu concluir a importância dos reguladores de crescimento na indução e perceber o peso do factor genótipo durante o processo. Considerando os resultados anteriores, a necessidade de um processo eficiente de preservação de genótipos elite torna-se fundamental. No Capítulo V descreve-se um protocolo de criopreservação eficiente sem recursos a substâncias tóxicas. Nesta secção é ainda feita uma análise de variabilidade genética após criopreservação através de FCM, AFLP e SSR. Todos os resultados obtidos anteriormente são postos a prova no Capítulo VI onde se faz uma monitorização extensiva de 10 genótipos elite, tendo em conta a sua capacidade de produção de cortiça, através do processo de embriogénese somática. Durante esta secção são utilizados os protocolos desenvolvidos anteriormente e avaliados na sua eficiência. Neste capítulo é descrita a integração de vários segmentos deste estudo num só protocolo eficiente de regeneração e preservação de sobreiros através de embriogénese somática. Finalmente, no Capítulo VI são apresentadas as conclusões da presente Tese de Doutoramento, com especial incidência para linhas de investigação futuras a serem tomadas. Discute-se a importância deste novo protocolo na optimização da produção da cortiça e traçam-se possíveis aplicações alternativas.