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

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.

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.

The present thesis is concerned with the problem of robust pose estimation for planar targets in the context of real-time mobile vision. As a consequence of this research, individual developments made in isolation by earlier researchers are here considered together. Several adaptations to the existing algorithms are undertaken yielding a unified framework for robust pose estimation. This framework is specifically designed to meet the growing demand for fast and robust estimation on power-constrained platforms. For robust recognition of targets at very low computational costs, we employ feature based methods which are based on local binary descriptors allowing fast feature matching at run-time. The matching set is then fed to a robust parameter estimation algorithm in order to obtain a reliable homography. On the basis of our experimental results, it can be concluded that reliable homography estimates can be obtained using a device-friendly implementation of the Gaussian Elimination algorithm. We also show in this thesis that our simplified approach can significantly improve the homography estimation step in a hypothesize-and-verify scheme. The author's attention is focused not only on developing fast algorithms for the recognition framework but also on the optimized implementation of such algorithms. Any other recognition framework would similarly benefit from our optimized implementation.

This work deals with the problem of accurately rendering mirror reflections on curved surfaces in real-time. While planar mirrors do not pose a problem in this area, non-planar surfaces are nowadays rendered mostly using environment mapping, which is a method of approximating the reflections well enough for the human eye. However, this approach may not be suitable for applications such as CAD systems. Accurate mirror reflections can be rendered with ray tracing methods, but not in real-time and therefore without offering interactivity. This work examines existing approaches to the problem and proposes a new algorithm for computing accurate mirror reflections in real-time using accelerated searching for intersections with depth profile stored in cubemap textures. This algorithm has been implemented using OpenGL and tested on different platforms.

Diplomová práce se zabývá návrhem a realizací vestavěného řídicího systému určeného pro autonomní mobilní robot Advee. Řídicí systém tvoří vrstvu abstrakce mezi hardwarovými prostředky robotu a vyššími vrstvami řízení, které provádějí lokalizaci robotu a plánování pohybu. V rámci návrhu byla vyvinuta modulární struktura systému a zvoleny prostředky mezimodulové komunikace. Navržený systém byl pak implementován včetně podpory komunikačních standardů EIA-485 a CAN bus. Zvolená architektura systému se v praxi osvědčila --- prototyp robotu Advee řízený popsaným systémem má za sebou více než 500 hodin komerčního provozu s minimem poruch.

Jedes Jahr werden am Universitätsklinikum Würzburg etwa 100 PatientInnen allogen stammzelltransplantiert. Für den Erfolg einer allogenen Stammzelltransplantation ist neben einer passenden Spenderauswahl und einer optimalen Vorbereitung auch die regelmäßige Nachkontrolle wichtig. Im Rahmen dieser Nachkontrollen werden unter anderem Chimärismusuntersuchungen durchgeführt. Als Chimäre wird in der Wissenschaft ein Lebewesen bezeichnet, das Zellen in sich trägt, die aus zwei oder mehr Zygoten entstanden ist. Der Begriff kommt aus der griechischen Mythologie, in der die Chimäre als Mischwesen aus Löwe, Ziege und Schlange (oder manchmal Drache) beschrieben wurde. Lange Zeit galt die STR/VNTR Methode als Goldstandard für die Nachkontrolle der Chimärismusuntersuchung. Durch Alizadeh et al. wurde bereits im Jahr 2002 eine neuartige Methode beschrieben, die mittels RT-PCR den genauen Chimärismusgrad messen kann. Diese Arbeit beschäftigte sich mit der Etablierung und Evaluierung dieser Methode der Chimärismusuntersuchung am Universitätsklinikum Würzburg. Es konnte gezeigt werden, dass sie für den klinischen Alltag geeignet ist und wurde auch im Hinblick auf äußere Störfaktoren untersucht. Darüber hinaus wurde eine Methode zur Bestimmung des CD3+ Chimärismus etabliert. Diese Untersuchung ist wichtig für die Abschätzung eines möglichen Abstoßungs- und GvHD Risikos. Seit 2013 finden auf Basis dieser Arbeit regelmäßige Chimärismusuntersuchungen am Universitätsklinikum Würzburg statt. / Every year, hematopoietic stem cell transplantations are being performed on approximately 100 patients at the university hospital Würzburg. Apart from finding a fitting stem cell donor and a perfect preparation of the recipient, follow-up examinations are essential for the long-term success of this procedure. Monitoring the chimerism after allogeneic stem cell transplantation is an essentialpart of those follow-up examinations. In science, a chimera is defined as a living organism, that contains cells deriving from different zygotes. In greek mythology, the „Chimera“ was described as a creature with the head of a lion, the body of a goat and the tail of a snake. For many years, the STR/VNTR method was the standard for post-transplant chimerism testing. In 2002, Alizadeh et al. developed a new method using RT-PCR to monitor chimerism. This dissertation evaluated and established this new method for engraftment analysis of transplanted patients at the university hospital Würzburg. It could be shown that the method was suitable for routine use in clinical practice. In addition, a method to measure CD3 + chimerism was established to evaluate the risks of GvHD or graft failure. Since 2013, chimerism is being tested at the university hospital Würzburg based on the results of this graduate thesis.

This research focuses on the development of a novel adaptive dynamical system approach to vector quantization or clustering based on only ordinary differential equations (ODEs) with potential for a real-time implementation. The ODE-based approach has an advantage in making it possible real-time implementation of the system with either electronic or photonic analog devices. This dynamical system consists of a set of energy functions which create valleys for representing clusters. Each valley represents a cluster of similar input patterns. The proposed system includes a dynamic parameter, called vigilance parameter. This parameter approximately reflects the radius of the generated valleys. Through several examples of different pattern clusters, it is shown that the model can successfully quantize/cluster these types of input patterns. Also, a hardware implementation by photonic and/or electronic analog devices is given In addition, we analyze and study stability of our dynamical system. By discovering the equilibrium points for certain input patterns and analyzing their stability, we have shown the quantizing behavior of the system with respect to its parameters. We also extend our model to include competition mechanism and vigilance dynamics. The competition mechanism causes only one label to be assigned to a group of patterns. The vigilance dynamics adjust vigilance parameter so that the cluster size or the quantizing resolution can be adaptive to the density and distribution of the input patterns. This reduces the burden of re-tuning the vigilance parameter for a given input pattern set and also better represents the input pattern space. The vigilance parameter approximately reflects the radius of the generated valley for each cluster. Making this parameter dynamic allows the bigger cluster to have a bigger radius and as a result a better cluster. Furthermore, an alternative dynamical system to our proposed system is also introduced. This system utilizes sigmoid and competitive functions. Although the results of this system are encouraging, the use of sigmoid function makes analyze and study stability of the system extremely difficult.