Thesis (M.S. in Electrical Engineering)--Vanderbilt University, Aug. 2001. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--Washington State University, August 2007. / Includes bibliographical references (p. 168-179).

Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2007. / Includes bibliographical references (leaves 188-198). Also available in electronic version.

Telemedicine systems represent significant achievements in the provision of clinical medicine and health care service using telecommunication and information technologies for the purpose of remote monitoring. Almost all telemedicine systems require a network-enabled device, ranging from server machine to smart phone, which delivers the data as a transmission gateway. The research in this thesis introduces the hardware and software design of a novel Internet-based real time DSP system in the application of telemedicine. Before this work, it was not previously achievable or economically feasible to develop a telemedicine system with a truly embedded measurement platform for real-time monitoring of clinical information on a global scale. The novelty of this design consists in embedding the Internet-based monitoring into the real-time signal processing system, as well as incorporating the merits of wireless communication and global distributed measurement. To demonstrate this concept, a prototype of a truly embedded device incorporating either a browser-based application or a LabVIEW software application has been designed and developed, which is able to provide real-time biomedical signal acquisition, processing, wired/wireless transmission, visualisation, storage and retrieval via the Internet. The concept-to-prototype manipulates multiple biomedical signals from multi-sensors during studies and distributes them to the Internet. The prototype was evaluated on volunteers in vivo under ethical approval. The designed system was also tested under various physiological conditions and different Internet speeds. It manifests desirable performance regarding multi-functionality, ubiquitous accessibility, robustness, and adaptability. The full functionality of this innovative system successfully enables clinicians to remotely monitor a patient's physical condition in real-time globally. The experimental results obtained from the host are in close agreement with the expected performance of the designed system, which proffers evidence that this system represents a true innovation in the realm of telemedicine.

L'objectif de notre thèse est d'appliquer la génomique en temps réel pour déchiffrer les caractéristiques génomiques bactériennes et les événements de recombinaison du génome des bactéries atypiques ainsi que leur impact sur les maladies infectieuses. Au cours de ma thèse, nous avons effectué une revue sur les outils bioinformatiques les plus courants utilisés en microbiologie clinique et mis en évidence l’impact de la recombinaison sur le comportement des bacteries. Le deuxième projet de notre thèse est de déchiffrer une epidémis de Staphylococcus saprophyticus causant des infections urinaires en utilisant la technologie MALDI-TOF MS et une analyse comparative du génome de S. saprophyticus pour comprendre leur évolution génomique. Nous avons démontré qu'il existe un groupe de S. saprophyticus géographiquement restreint à Marseille comparé au souches de Nice. De plus, nous avons montré que S. saprophyticus qui était initialement considéré comme une bactérie saprophyte a evolué pour devenir une bactérie pathogène à travers des recombinaisons massives et des « single nucleotide polymorphism », résultant d'une perte significative de gènes. Le troisième projet de notre thèse est une analyse comparative des génomes d'Enterococcus faecalis et d'E.faecium isolé chez l'homme, les animaux et l'environnement pour déchiffrer la différence de propagation et l'acquisition de déterminants antimicrobiens. Nous avons démontré qu'il existe une association directe entre l'absence de système CRISPR, la présence du gène ardA et l'acquisition de gènes de résistance à la vancomycine, qui différencient E. faecalis de E. faecium. Enfin nous avons decrit un nouveau genre bacterien Nissabacter. / The objective of our thesis is to applied the Real-time genomic approaches to decipher bacterial genomic features and genome recombination events of atypical bacteria and their impact on infectious diseases. During my thesis, we have reviewed the most common bioinformatics tools applicable in clinical microbiology and highlight how bacterial genome recombination have impacted their behaviour. The second project of our PhD is to decipher a community outbreak of Staphylococcus saprophyticus involved in (UTI) using MALDI-TOF MS technology and a comparative genome analysis of clinical and non-clinical S. saprophyticus to understand their genomic evolution. We demonstrated that there is a geographically restricted cluster of S. saprophyticus circulating in Marseille community as compared to Nice. Moreover, we showed that S. saprophyticus which was initially considered as a saprophytic bacterium has drifted to becoming a pathogenic bacterium through massive genome recombination and single nucleotide polymorphism events, resulting from a significant loss of genes. The third project of our work is a comparative genome evolutionary analysis of Enterococcus faecalis and Enterococcus faecium isolated from human, animals, and environment to decipher the difference in spread and the acquisition of antimicrobial determinants. We demonstrated that there is a direct association between the absence of CRISPR system, the presence of gene ardA and the acquisition of vancomycin resistance genes, which differentiate E. faecalis from E. faecium. Our final project was focused on the discovering of a new genus Nissabacter and its description.

In this diploma thesis we investigate how wine characteristics is influenced by the apiculate wine yeast Metschnikowia pulcherrima. For this purpose, two wines of a grape variety Welschriesling were manufactured using an identical technological approach with the only distinction: two separated musts were supplied with broth containing different yeasts. The literary part of the thesis discusses yeasts used in winery in general. We describe both apiculate yeasts and Saccharomyces. In this part, we also further discuss the polymer chain reaction and similar methods. The experimental part deals with possibilities of Metschnikowia pulcherrima DNA isolation from fermenting must and the subsequent quantification of yeasts with help of the real-time PCR method. After evaluation and comparison of the wines, where both general and expert public participated, it was concluded that the yeasts substantially influence the wine cha-racteristics.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2012-06-25T21:03:51Z No. of bitstreams: 1 Cristiane Santos Nascimento Uso de método de biologia molecular....pdf: 1323686 bytes, checksum: caf3acf13d85858d02cc05e45a821e9c (MD5) / Made available in DSpace on 2012-06-25T21:03:51Z (GMT). No. of bitstreams: 1 Cristiane Santos Nascimento Uso de método de biologia molecular....pdf: 1323686 bytes, checksum: caf3acf13d85858d02cc05e45a821e9c (MD5) Previous issue date: 2011 / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, Bahia, Brasil / INTRODUÇÃO: A leishmaniose visceral humana (LVH) é uma importante causa de morbidade e mortalidade no Brasil. Apesar dos avanços no conhecimento da epidemiologia da LVH, ainda existem lacunas importantes nas informações sobre os principais reservatórios desta zoonose. A técnica validada para avaliação da infectividade de reservatórios, xenodiagnóstico, é um método laborioso, demorado e difícil de executar, portanto, inapropriado para a triagem de grande número de animais. A padronização de método capaz de quantificar a carga parasitária presente em diferentes tecidos pode oferecer respostas importantes sobre a epidemiologia e a prevenção da LVH. OBJETIVO: Avaliar a carga parasitária em diferentes amostras biológicas de cães naturalmente infectados por Leishmania chagasi, utilizando método de biologia molecular quantitativo, PCR real-time (qPCR). MÉTODOS:Entre nov/2004 e abr/2007, foram realizados seis inquéritos soro-epidemiológicos em duas áreas endêmicas para LVH. Os cães soropositivos foram eutanasiados e submetidos a: exame de cultura, parasitológico direto e exame histológico para confirmação da infecção. Amostras de sangue periférico e fragmento de pele foram coletadas em todos os animais para determinação da carga parasitária. Adicionalmente, coletou-se também swab da conjuntiva, aspirado de medula óssea e linfonodo para realização do teste de qPCR nos cães incluídos no último inquérito (abr/2007). A técnica de qPCR foi padronizada utilizando um par de primers LEIF e LEIR e sonda LEIP selecionados no gene SSu rRNA. A seleção dos primers e sonda foi realizada utilizando o programa Primer Express (Perkin-Elmer-Applied Biosystems). A sonda fluorogênica foi sintetizada utilizando uma molécula FAM ligada na extremidade 5‟ e TAMRA ligada à extremidade 3‟(Perkin-Elmer -Applied Biosystems). Para determinar a carga parasitária foi realizada curva padrão com o DNA obtido da cultura de L. chagasi em concentrações variando de 101 a 107 parasitas/ml. Cada ponto da curva foi testado em triplicata. RESULTADOS: Dos 98 cães soropositivos identificados, foi detectado DNA de Leishmania em 57% das amostras de sangue total, em 56% das amostras de pele e em 100% das amostras de medula óssea, linfonodos e swab da conjuntiva. A carga parasitária em sangue periférico e swab da conjuntiva não ultrapassou 103 parasitas/ml sendo mais comumente detectado 1 a 10 parasitas/ml. Por outro lado, em pele, medula óssea e linfonodos a carga parasitária passou de 104 parasitas/ml, além disso, as quantidades de DNA detectadas se distribuíram com maior freqüência na categoria acima de 104 parasitas/ml, notadamente em amostras de linfonodos. CONCLUSÕES: O qPCR apresentou alta sensibilidade nas amostras biológicas estudadas, particularmente em linfonodos , medula óssea e pele. Nossos resultados indicam que o qPCR pode ser utilizado numa variedade de amostras biológicas para a quantificação da carga parasitária de cães naturalmente infectados por Leishmania sp. Estudos de validação do qPCR para avaliar a capacidade de reservatórios da LV, em lugar do xenodiagnóstico, e para investigar o papel do qPCR na triagem de cães em programas de controle/prevenção da LV devem ser conduzidos. / INTRODUCTION: Human visceral leishmaniasis (LVH) is an important cause of morbidity and mortality in Brazil. Despite advances in knowledge of the epidemiology of LVH, there are still important gaps in information on the main reservoirs of this zoonotic disease. The validated technique for assessing the infectivity of reservoirs, xenodiagnosis, is laborious, time consuming and difficult to implement, therefore, inappropriate for screening large numbers of animals. A standardized method to quantify the parasite load present in different tissues may provide important answers on the epidemiology and prevention of LVH. OBJECTIVE: To assess the parasite load in different biological samples from dogs naturally infected by Leishmania chagasi using a molecular biology quantitative method, real-time PCR (qPCR). METHODS: From nov/2004 to apr/2007, six seroepidemiological surveys were conducted in two endemic areas for LVH. The seropositive dogs were euthanized and submitted to: culture, direct parasitological and histological examination to confirm infection. Blood samples and skin fragments were collected in all animals to determine the parasite load. Additionally, conjuntival swabs, bone marrow and lymph node aspirates were also collected to do qPCR in dogs included in the last survey (apr/2007). The qPCR technique was standardized using a pair of primers and probe and LEIF /LEIR and LEIP selected in the SSU rRNA gene. The selection of primers and probe was performed using the program Primer Express (Perkin-Elmer-Applied Biosystems). The fluorogenic probe was synthesized using a FAM molecule attached at the 5 'end and TAMRA linked to the 3' end (Perkin-Elmer-Applied Biosystems). In order to determine the parasite load a DNA standard curve was plotted with DNA obtained from L. chagasi culture in concentrations ranging from 101 to 107 parasites/ ml. Each point on the curve was tested in triplicate. RESULTS: Of the 98 seropositive dogs identified Leishmania DNA was detected in 57% of the whole blood samples, 56% of the skin samples and 100% of bone marrow, lymph nodes and conjuntival swabs samples. The parasite load in peripheral blood and conjuntival swab did not exceed 103 parasites/ml, and was more commonly in the range of 1-10 parasites /ml. On the other hand, skin, bone marrow and lymphnode parasite burden exceeded 104 parasites / ml, in addition, the quantities of DNA detected were distributed more frequently in the category above 104 parasites/ml, especially in lymphnodes samples. CONCLUSIONS: qPCR showed high sensitivity in biological samples studied, particularly in lymphnodes, bone marrow and skin. Our results indicate that qPCR could be used in a variety of biological samples to quantify the parasite load in dogs naturally infected by Leishmania sp. qPCR validation studies to assess potential reservoirs for VL (replacing xenodiagnosis), and to investigate the role of qPCR in dog screening programs for the control/prevention of LV should be conducted.

In this study a 3D-application was developed to use for visualizing a website and its visitors in real time. The 3D application was developed to be used in websites developed in the CMS Episerver. This study has investigated the benefits of being able to see how website visitors navigate between webpages in real time, how scalable the implemented 3D application is, if its possible to develop a 3D application that can be implemented in Episerver websites and what the benefits of using 3D compared to 2D or text logs for the end user are. The 3D visualisation was built using the JavaScript library Babylon.js and works by modifying the Episerver Controller class to store relevant visitor data each time a visitor makes a HTTP request to the webserver. The data is then used with Babylon to render animations and visitor representations in the 3D application. Results show that a real time view of a website can be beneficial to be able to see load distribution, where visitors are positioned before restarting the server, to be used in user tests and in customer service cases and that the majority of questioned webadministrators thinks that it would be beneficial to be able to see their visitors in real time. Results also show that the application is not very scalable and that the use of 3D may not be beneficial for the end user. Finally recommendations for future development is presented and discussed. / I detta projekt utvecklades en 3D-visualisering av en webbplats vars syfte var att synliggöra besökares rörelser på webbplatsen i realtid. Visualiseringen skulle utvecklas på ett vis som gav enkel implementation på webbplatser byggda i Episerver. Studien undersöker huruvida det är möjligt att utveckla en 3D- visualisering för Episerver, eventuella fördelar med att se besökare i realtid, hur skalbar applikationen är samt vilka fördelar 3D har för slutanvändaren. 3D- visualiseringen byggdes i JavaScript-biblioteket Babylon.js och fungerar genom att modifiera Episervers controller-klass till att spara nödvändig information från besökaren vid varje förfrågan till servern. Datan används till att rita ut och animera besökares positioner på den 3D-renderade webbplatsen. Resultaten visar att det kan vara användbart att se besökare i realtid för att se lastdistribution på webbplatsen, för att undvika att besökare är i kritiska lägen vid omstart av servern, för att handleda besökare i kundserviceärenden eller för att samla information vid användartest. Vidare visar resultaten att applikationen inte är särskilt skalbar och att 3D inte är ger mervärde för slutanvändaren annat än för imponatoreffekt.

Fast, automated segmentation of the thalamic nuclei in the brain has long been desired as it provides for direct visualization of the target for certain procedures like Deep Brain Stimulation (DBS) that target a specific nucleus. It is also beneficial in the study of other pathologies that pertain to different nuclei. In this thesis, a novel approach to fast automated segmentation of thalamic nuclei called Shortened Template and THalamus for Optimal Multi Atlas Segmentation (ST THOMAS) was developed using the multi-atlas segmentation approach. It was designed with a focus on robustness and speed by making use of an averaged template for registration and cropping the inputs and the template. The performance of ST THOMAS was first evaluated on 7T MRI data by comparing with manual delineation (ground truth) by an expert neuroradiologist. Dice coefficients and Volumetric Similarity Indices were used as metrics. To extend the applicability of this method, 3T MRI data were also evaluated. Finally, applications to real time ventralintermideiate (VIM) nucleus targeting for DBS and study of the effects of alcoholism are demonstrated.

ABB SA Products designs and manufactures complex real-time systems. The real-time properties of the system are hard to measure and test especially in the long run, e.g.  monitoring a system for months out in the real environment. ABB have started developing their own tool called JobMon for monitoring timing requirements, but they needed to measure more properties than time and in a more dynamic way than JobMon is constructed today. The tool must be able to measure different kind of data and be able to be monitor as long as the system itself. This thesis first does a survey and evaluation on existing commercial tools and if there exists a tool that can be integrated to the system and fulfill all demands. Different trace recorders and system monitoring tools are presented with its properties and functions. The conclusion is that there is no such tool and the best solution is to design and develop a new tool. The result is SysMon, a dynamic generic framework for measuring any type of data within a real-time system. The main focus for measuring during this thesis is time measurements, but no limits or assumptions of data types are made, and during late steps of the development new types of measurements are integrated. SysMon can also handle limits for measurements and, if required, take pre-defined actions e.g. triggering a logging function and saving all information about the measurement that passed the limit. The new tool is integrated to the system and evaluated thoroughly. It is an important factor to not steal too much resource from the system itself, and therefore a measurement of the tool’s intrusiveness is evaluated. / ABB SA Products designar och konstruerar komplexa realtidssystem. Realtidsegenskaperna för systemen är svåra att mäta och testa, speciellt under långa tidsperioder, t.ex. under drift i dess riktiga miljö under månader av online tid. ABB SA Products har börjat utvecklat ett eget verktyg, JobMon, för att kunna övervaka och mäta egenskaper i form av tid. Men behovet är större än att endast mäta tid och alla möjliga slags data behöver övervakas och utvärderas. Det här examensarbetet gör först en undersökning och utvärdering av existerande kommersiella verktyg och om det redan finns ett verktyg som uppfyller alla krav. Olika tracerecorders och systemövervakningsverktyg är presenterade med dess egenskaper och funktioner. Slutsatsen är till sist att det inte finns något existerande verktyg och att den bästa lösningen är att utveckla ett nytt verktyg. Resultatet är SysMon, ett dynamisk generisk ramverk för att mäta vilken form av data som helst. Huvudfokus under examensarbetet är tidsmätningar, men inga antaganden om vilka datatyper som kan användas görs. Under den senare delen av examensarbetet implementeras också en ny typ av mätning i system ticks. SysMon kan också hantera gränser för mätningar och, om nödvändigt, exekvera fördefinierade funktioner, t.ex. trigga en loggning och spara nödvändig information om mätningen som överskred gränsen. Det nya verktyget blir integrerat i systemet och testat noggrant. Det är viktigt att verktyget inte tar för mycket resurser från det normala systemet och därför utförs även en utvärdering av hur resurskrävande verktyget är.