Ability to diagnose cancer before it progresses into advanced stages is highly desirable for the best treatment outcome. A sensitive test to analyze complex samples for specific cancer biomarkers would provide with important prognostic information and help to select the best treatment regimen. A highly robust, ultra sensitive and cost-effective electronic chip platform was used to detect nucleic acid biomarkers in heterogeneous biological samples without any amplification or purification. Chronic myelogenous leukemia (CML) was chosen as a model disease due to its hallmark genetic abnormality. This disease state therefore has an ideal market to test the detection of the fusion transcripts in complex samples, such as blood. It was shown that the CML-related fusion can be detected from unpurified cell lysates and as low as 10 cells were needed for detection. Finally, patient samples were analyzed using the assay and the fusion transcripts were accurately identified in all of them.

This doctoral thesis describes the investigation carried out by the author in pursuit of a better understanding of the mechanism of cavitation. To create cavitation bubbles under laboratory conditions, an intense Q-switched Nd:YAG laser was used and the event was captured using a high-speed photography system. Three different aspects concerning the cavitation phenomenon were studied and they were the propagation of acoustic waves in a liquid, the resultant stress waves in a nearby solid medium and the interactions between a bubble and the nearby boundary. Optical measurement techniques, based on Mach-Zehnder interferometry, shadowgraphy, Schlieren photography and photoelasticity, were employed to assist the observation and analysis of a cavitation event.

Les particules de suie émises lors de la combustion d’hydrocarbures ont un impact important sur le réchauffement climatique et sur la santé. La compréhension des mécanismes de formation des particules de suie dans les flammes présente donc un fort intérêt environnemental. Cependant, le mécanisme de formation de ces particules pose toujours de nombreuses questions. En particulier la phase de nucléation, qui conduit à la formation des particules primaires de suie (nuclei) à partir de molécules HAPs (Hydrocarbures Aromatiques Polycycliques) en phase gazeuse, reste incomprise. Au cours de ce travail de thèse, nous avons mis en œuvre deux méthodes expérimentales de diagnostic laser, la Fluorescence Induite par Laser en Jet Froid (JCLIF) et l’Incandescence Induite par Laser (LII), respectivement pour la mesure de HAPs (naphtalène, pyrène et fluoranthène) et des particules de suies formées dans des flammes de CH4/O2/N2 stabilisées à basse-pression et de C2H4/air stabilisées à pression atmosphérique. Les résultats obtenus offrent une base de données expérimentale tout à fait originale pour l’amélioration de la compréhension des voies réactionnelles prépondérantes menant à la formation des particules de suie. Par ailleurs, nous avons également mis en évidence l’existence de flammes de nucléation, i.e des flammes dans lesquelles les particules de suie sont essentiellement formées par nucléation, sans subir de croissance de surface. Dans ce travail de thèse, nous montrons que ces flammes pourraient ainsi constituer un cas test unique et très pertinent pour la compréhension du processus de nucléation. / Soot particles emitted during fuel combustion have an important impact on global warming and health. Therefore, the improvement of the knowledge on soot particle formation mechanisms in flames shows an important environmental interest. However, this mechanism is not fully understood. Indeed, the nucleation step, forming primary particles (nuclei) from gaseous PAHs (Polycyclic Aromatic Hydrocarbons), is still speculative and needs accurate experimental data to be fully understood. In this work, two experimental techniques based on laser diagnostics have been implemented, the Jet-Cooled Laser Induced Fluorescence (JCLIF) and the Laser Induced Incandescence (LII), respectively for the measurement of PAHs (naphthalene, pyrene and fluoranthene) and soot particles formed in low-pressure CH4/O2/N2 flames and atmospheric pressure C2H4/air flames. These results offer an original experimental database for the improvement of the understanding of the main chemical pathways leading to soot particle formation. Besides, we also highlight the possibility of generating nucleation flames, i.e flames in which soot particles are essentially formed by nucleation, without growth by soot surface processes. In this thesis, we show that these specific flame conditions could be a unique test case, very well suited for the understanding of the soot nucleation process.

A Z-pinch plasma, suitable for the study of C0₂ laser-plasma interaction mechanisims, is thoroughly diagnosed using a number of non-perturbing, optical probe techniques. Simple streak and shadow methods give an important preliminary view of the spatial distribution and radial dynamics of plasma during the high compression phase. The electron density and temperature are determined as a function of time by spectrally resolving the ion feature of Thomson scattered ruby laser light. Peak electron densities well in excess of 1 x 10¹⁹ cm⁻³ and temperatures near 50 eV are observed. Complementing the scattering results, holographic interferometry is performed to examine both the temporal and spatial variation of electron density. The diagnostics used are well suited to the examination of moderately dense, hot plasma and have been developed specifically for application in our laser-plasma interaction studies. / Science, Faculty of / Physics and Astronomy, Department of / Graduate

The etiological agent of rabies, rabies virus, is a member of the fatal Lyssavirus genus that accounts for the death of more than 55 000 humans per annum, with the number of infected animals far exceeding that number. The process of post-mortem diagnosis of rabies plays a crucial role in general disease surveillance as well as in the implementing and monitoring of disease control programs in animal populations. Although post mortem diagnostic techniques play a crucial role in impeding disease spread, the routine diagnosis of rabies in resource-limited developing countries remains limited due to a lack of stable infrastructures, power supplies, technical expertise and general resources required to perform the routine gold standard fluorescent antibody test (FAT) diagnosis. Based on the aforementioned facts, the development of diagnostic assays that are suitable for application in the resource-limited developing countries has recently gained a lot of consideration, with numerous novel assays being developed and applied in small-scale investigations. Of all the novel diagnostic assays, the direct rapid immunohistochemical test (dRIT) has, to date, shown the most promise in terms of applicability because of its diagnostic sensitivity and specificity, which has been shown to be equal to that of the FAT in five pilot studies. The main drawback with the current application of the dRIT diagnostic assay is that the Centres for Disease Control and Prevention (CDC) are the only supplier of the required cocktail of two-biotinylated monoclonal antibodies. The singular source of biotinylated antibody thus limits the widespread application of the dRIT diagnostic assay because of the limited availability of the cocktail of biotinylated antibodies. This study endeavoured to ascertain whether an alternative antibody preparation could be biotinylated and applied to the dRIT diagnostic assay in order to act as a routine replacement for the cocktail of biotinylated monoclonal antibodies supplied by the CDC. In order to gain comparative data pertaining to the diagnostic efficacy and versatility of the dRIT diagnostic test relying on the locally produced biotinylated polyclonal antibody, the research involved a multi-faceted investigation. The investigated facets included the comparison of the dRIT test relying on the locally produced biotinylated polyclonal antibody to the FAT test. Apart from the comparison to the gold standard FAT, the three versions of the dRIT test, each relying on one of three-biotinylated antibodies used in the study was performed. The antibodies involved in the comparison included the locally produced biotinylated polyclonal antibody preparation as well as the two-biotinylated monoclonal antibodies (monoclonal antibody 1 and monoclonal antibody 2) that make up the antibody cocktail supplied by the CDC. Apart from the said investigation into the diagnostic efficacy of the dRIT diagnostic assay, the versatility of the given assay was also investigated by adapting the standard operating procedure to accommodate an acetone fixation step. The sample set used for the study included a significant number of central nervous system (CNS) tissues samples (n=250) derived from five of the major mammalian reservoir species in southern Africa as well as a subset of CNS tissue samples derived from mice inoculated with seven representative African rabies-related lyssavirus isolates. The results indicated that the dRIT diagnostic assay, relying on the biotinylated polyclonal antibody preparation, had a diagnostic sensitivity (100%) and specificity (100%) that was marginally higher than that of the widely recognised gold standard FAT diagnostic test that had produced a single false negative result (diagnostic sensitivity of 99,5%) once applied to the known true positive and negative samples included in the study. The dRIT diagnostic test, relying on either of the two-biotinylated monoclonal antibodies, had reduced levels of diagnostic efficacy compared to the FAT assay in terms of the sensitivity of the given assays (monoclonal antibody 1: 83,08% and monoclonal antibody 2: 90,55%) once applied to the known true positive and negative samples included in the study. Monoclonal antibody 2, once applied to the dRIT assay in this study, was the only antibody to produce a single false positive result (diagnostic specificity of 97,96%). The adaptation of the dRIT protocol to include the acetone fixation step had no influence on the diagnostic efficacy of the dRIT test, while the results of the study were indicative of the fact that the dRIT diagnostic assay could be used to detect the viral antigen of all the representative rabies-related viruses, irrespective of the biotinylated antibody used. While the data obtained from the study was used to interpret the diagnostic efficacy of the various biotinylated antibodies applied to the dRIT diagnostic assay, a simulation framework was also developed to analyse the costs involved in performing routine rabies diagnosis with either the FAT or dRIT diagnostic tests in order to broaden the scope of the research. The only cost in the simulation framework that resulted in a significant difference between the two assays was the capital expenditure required to set up a new diagnostic facility, with the costs indicating that five dRIT diagnostic facilities could be established for the price of one FAT diagnostic facility. In summary, the work presented in this study has shown that not only is it indeed possible to apply alternative biotinylated antibody preparations to the dRIT diagnostic assay, but that it is also necessary to optimize the concentration of the biotinylated antibody preparation of the dRIT diagnostic assay before routine application can occur. In the case of this specific study, the dRIT diagnostic assay relying on the biotinylated polyclonal antibody preparation was shown to be an ideal complimentary diagnostic assay to the FAT due to its high diagnostic efficacy, adaptability and calculated costs. / Dissertation (MSc)--University of Pretoria, 2013. / Microbiology and Plant Pathology / MSc / Unrestricted

また、この研究は、特定の動作条件で生成されたシートプラズマで、プラズマやシートプラズマの寸法を決定する動作パラメータなどのプラズマ条件を理解し、最適化パラメータと将来の産業用アプリケーションの条件を導き出すことも目的としています。 そのため、この研究は、表面技術アプリケーション用のシートプラズマデバイスの開発と理解に貢献することを試みています。 / Sheet plasmas have the advantage of producing thin films and functional surfaces by generating localized high-density and temperature gradient regions suitable for specific reactions. A stream of high energy electrons from a plasma cathode efficiently excites and/or ionizes atomic and molecular species which are confined in a linear magnetic field. An electron cyclotron resonance (ECR) sheet plasma device employing a 2.45 GHz microwave source and combination of permanent magnets and field coils was designed and operated. The combined field realized a linear magnetic field that sustained a rectilinear confinement of the plasma. / 博士(工学) / Doctor of Philosophy in Engineering / 同志社大学 / Doshisha University

No description available.

La validité analytique et clinique des analyses de diagnostic moléculaire est régulièrement remise en doute. Parmi les modalités d’analyse d’acides nucléiques les plus répandues en laboratoire clinique, le génotypage par PCR allèle-spécifique et le séquençage massivement parallèle pour la détection prénatale non-invasive d’aneuploïdies (DPNI) représentent deux des applications les plus importantes en termes de volume. La perte allélique (« allele drop-out »), d’une part, ainsi que l’identification des variables déterminant la performance diagnostique, la disponibilité de matériel de référence et l’estimation de la fraction d’ADN fœtal, d’autre part, sont autant d’enjeux de validité analytique et clinique dont l’impact et la prise en compte dans la translation clinique demeurent à évaluer pour chacune de ces applications respectivement. Des cas représentatifs de ces deux applications furent donc sélectionnés afin d’étudier certains aspects pertinents à chacun de ces enjeux. En accord avec les doutes soulevés par plusieurs auteurs, des lacunes de validité analytique et clinique furent notées pour tous les aspects examinés. En particulier, la plupart des erreurs diagnostiques causées par les événements de perte allélique étaient dues à des phénomènes stochastiques ne pouvant être prévenus par un design d’amorces méticuleux, et les niveaux de précision de la PCR limitent la validité analytique et clinique de la DPNI par séquençage, bien que ce paramètre ne soit pas toujours quantifié et rapporté de façon rigoureuse dans la littérature. Malgré des impacts cliniques potentiels relativement faibles lorsqu’évalués au niveau populationnel, des impacts significatifs peuvent néanmoins affecter les patients au niveau individuel. Des solutions sont disponibles afin de corriger certaines des lacunes identifiées, alors que d’autres posent des défis plus importants. Les causes possibles de ces lacunes de validité affectant le domaine du diagnostic moléculaire sont en partie communes aux causes impliquées dans le problème de reproductibilité des résultats scientifiques en général et en partie le résultat de la complexité technique, relative nouveauté et de la nature historiquement qualitative des méthodes de génétique moléculaire. Une intégration des standards cliniques en amont du processus de découverte pourrait contribuer à améliorer la validité analytique et clinique des tests de diagnostic moléculaire et iii possiblement augmenter le rendement translationnel de la recherche vers la clinique. / The analytical and clinical validity of molecular diagnostic assays are regularly questioned. Among the most commonly used nuclei acid analysis modalities in clinical laboratories, genotyping by allele-specific PCR and non-invasive prenatal aneuploidy testing (NIPT) by massively parallel sequencing, represent two of the most important applications in terms of volume. Allele drop-out on the one hand, as well as identification of variables determining diagnostic performances, reference material availability and fetal fraction estimation on the other, are all examples of analytical and clinical validity issues for which both the impact, and how well they are taken into account, remain to be evaluated for each of these applications respectively. Representative cases of both applications were therefore selected in order to study certain aspects relevant to each of these issues. In accordance with the doubts raised by several authors, lack of analytical and clinical validity was noted for all aspects examined. In particular, most diagnostic errors caused by allele dropout events were due to stochastic phenomena that cannot be prevented by careful primer design, and PCR precision levels were a limiting factor for analytical and clinical validity of NIPT assays, even though this parameter is seldomly adequately quantified and reported in the literature. Although potential clinical impacts were likely modest at the population level, at the individual level, some of the impacts may nevertheless be significant. Solutions to correct some of these problems are available, while others raise more difficult challenges. The possible causes of this lack of validity affecting molecular diagnostics are partly shared with the general problem of lack of repeatability of scientific results and are partly the result of the technical complexity, relative novelty, and the historically qualitative nature of molecular genetic methods. Integrating clinical standards upstream of the discovery process could contribute to improve analytical and clinical validity of molecular diagnostic tests and possibly to increase “bench-to-bedside” translational yield.

The jet mixing of water in crude oil pipelines by single nozzle and multi-nozzle mixers was studied by dividing the mixing domain into to three regions. the penetration. near field and farfield regions. At the penetration region the quantitative experimental data were aided by a flow visualisation study in an attempt to to form fundamental semi-empirical correlations to estimate the entrainment rate of stratified water from the bottom and the Sauter mean diameter of the entrained water droplets for a single nozzle jet mixer. The flow field diagnostics into the near field region. defined as the region where high level of swirl and mixing is occuring. were conducted theoretically using computational fluid dynamic code "Phoenics" and experimentally through LOA measurements and flow visualisation. The entrainment rate found in penetration region was treated as a source term for theoretical analysis. Experimental analysis of this region was conducted in single phase flow for two mixer nozzles i) Single nozzle mixer and ii). Existing multi-nozzle mixer. Experimental results have revealed that the swirl velocities decay faster for higher velocity ratios and their dependence on Reynolds number (in the range 27600 to 48400) is weak. Higher velocity ratios would generate and dissipate higher levels of energy, therefore break up water droplets to smaller sizes and increase the eddy viscosity. The dispersion strength due to swirl decays faster and the gravity settling begins earlier. As the flow reaches downstream. approximately four diameters. the distribution of velocities (mean and RMS) flattens out and their magnitude begins to close up for the two mixers. when their momentum ratios are equal. It was also shown that the swirl velocities (at axis) die away. approximately at the same axial point for both of the nozzles. The multi-nozzle mixer is shown to be better in two characteristics; i). The mixing is faster and ii) The jet energy is more evenly distributed in the vicinity of the injection cross section. hence improving the quality of the droplet size distribution. Besides providing information to aid understanding of the complex flow in the mixer zone. the experimental data is believed to be of sufficient quality and quantity to improve the present simple modelling procedures as well as to be used as test cases for assessment of the predictive accuracy of more elaborate computational models. Comparision with computational results (of low velocity ratios) shows the agreement with swirl velocities is reasonable. but not always acceptable for mean axial velocities. However. the computational model predicts the near field jet trajectory reasonably well. The flow visualisation of dispersion of passive contaminant agrees qualitatively with the contours of the passive contaminant. In the far field region. where the swirl has decayed. the flow behaves two dimensionally. Therefore. an exact solution was obtained for two dimensional water conservation equation. The boundary conditions were specified by using sticking probability constants. A relationship was obtained to specify eddy viscosity through turbulent kinetic energy. The turbulent kinetic energy and swirl decay were estimated from LDA experimental data. This solution can be used to study the developing characteristics of water concentration profiles along the far field region of the pipeline.

No description available.