Thesis (MScMedSc (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: South Africa is currently facing a major multidrug-resistant tuberculosis (MDR-TB) epidemic and has one of the highest incidences in the world. Aminoglycoside antibiotics are commonly used in this country as a treatment against MDR-TB. A well known side-effect of aminoglycosides is permanent hearing loss and this is thought to have a significant genetic component. To date, at least six mutations in the mitochondrial genome are known to confer susceptibility to aminoglycosideinduced hearing loss. It is imperative that we investigate the frequency of these mutations in our populations and determine whether certain sub-groups are at increased risk. The aim of the present study was therefore to investigate the genetic aetiology of aminoglycoside-induced hearing loss in the South African population. A multiplex method using the ABI Prism® SNaPshotTM Multiplex system was optimised to screen for six mutations in the MT-RNR1: A1555G, C1494T, T1095C, 961delT+C(n), A827G and T1291C. A total of 115 MDR-TB patients from the Brooklyn Chest Hospital in Cape Town who were receiving high doses of either streptomycin, kanamycin or capreomycin were recruited for this study. Furthermore, 439 control samples, comprising of 93 Afrikaner, 104 Caucasian, 112 Black and 130 Mixed Ancestry individuals were recruited and screened for the presence of the six mutations. Identification of novel variants in the MT-RNR1 and the entire mitochondrial genome was performed using High Resolution Melt analysis (HRM) and whole mitochondrial DNA sequencing, respectively. A total of 97 family members from a South African family known to harbour the A1555G mutation were recruited and genotyped using SNaPshot analysis. In addition, mitochondrial functioning in the presence of different streptomycin drug concentrations, in transformed lymphoblasts of an individual harbouring the A1555G, was assessed by means of the MTT colorimetric assay. Detection of heteroplasmic mutations was performed using PCRRestriction Fragment Length Polymorphism (RFLP) analysis and UN-SCAN-IT software. We successfully developed a robust and cost-effective method that detects the presence of all six mutations simultaneously. The method worked equally well on both blood (from adults) and buccal swabs (from children). The C1494T, T1095C and T1291C mutations were not detected in any of the MDR-TB or control groups. Alarmingly, the A1555G mutation was detected in 0.9% of the Black control samples and in 1.1% of the Afrikaner controls (in one sample in the heteroplasmic state 25%). The A827G mutation was present at a frequency of 0.9% in the MDR-TB patients and in 1.1% of the Afrikaner controls. The 961delT + insC(n) mutation was found in relatively high frequencies in both the MDR-TB patients (3.5%) and control groups (1.1% of the Afrikaner, 1.5% of the Mixed Ancestry and 7.1% of the Black samples). Similarly, the T961G mutation was III detected at high frequencies in the Caucasian (2.9%) and Afrikaner (3.2%) controls. Screening for novel variants in MT-RNR1 in MDR-TB patients experiencing ototoxicity revealed two novel variants (G719A and T1040C). However, G719A and T1040C are not likely to be pathogenic since they were detected in ethnic-matched controls: Mixed Ancestry (20.7%) and Black (1.8%) controls. Furthermore, a total of 50 novel variants were identified within the mitochondrial genome of eight MDR-TB patients with ototoxicity. Only five of the 50 variants (one in the MT-TH, ND3, COX3 and two in the CYTB gene) were shown to reside at positions that are evolutionarily conserved across five species from human to frog, and the four variants in the protein coding genes resulted in missense changes. A total of 76 of the 97 family members recruited were found to be A1555Gpositive (on mitochondrial haplogroup L0d) and are therefore at risk of developing irreversible hearing loss. Genes and variants known to act as genetic modifiers: tRNASer(UCN), homozygous A10S in TRMU and 35delG in GJB2 were not present in this family. For the MTT assay, decreased mitochondrial functioning of cells harbouring the A1555G mutation in the presence of streptomycin were (compared to wild type) observed but this was not statistically significant (p-value: 0.615- 0.999). The high frequency of the A1555G mutation (0.9%) in the Black population in South Africa is of concern given the high incidence of MDR-TB in this particular ethnic group. However, future studies with larger numbers of samples are warranted to determine the true frequencies of the aminoglycoside deafness mutations in the general South African population. Our data suggests that the 961delT + insC(n) and T961G variants are common non-pathogenic polymorphisms due to the high frequencies observed in controls (>1%). The identification of the first novel variants within protein coding genes that could possibly be associated with aminoglycoside-induced hearing loss holds great possibilities with regards to the identification of a second gene involved in drug induced hearing loss. Future studies where the possible effect of these variants on the normal functioning of these genes could be assessed would contribute greatly to this field of research. All 76 A1555Gpositive members of the family were given genetic reports and counseled about their risk and that of their children for developing hearing loss due to aminoglycoside use. The development of a rapid and cost-effective genetic method facilitates the identification of individuals at high risk of developing hearing loss prior to the start of aminoglycoside therapy. This is of critical important in a low-resource country like South Africa where, despite their adverse sideeffects, aminoglycosides will be continue to be used routinely and are accompanied with very limited or no audiological monitoring. Future studies and greater public awareness is therefore needed to address this serious problem. / AFRIKAANSE OPSOMMING: Suid Afrika beleef tans „n grootskaalse tuberculose epidemie (veral weerstandige vorme van tuberculose) (MDR-TB), met een van die hoogste voorkomssyfers in die wêreld. Aminoglikosied antibiotikums word baie algemeen gebruik in Suid Afrika vir die behandeling van MDR-TB. ‟n Bekende newe effek van die middels is permanente gehoor verlies en dit is van mening dat dit gekoppel is aan „n genetiese component. Daar is tans ses mutasies in die mitochondriale genoom wat vatbaarheid tot aminoglikosied-geinduseerde gehoor verlies veroorsaak. Daarom is dit van uiterse belang dat die frekwensie van die mutasies in ons populasies bepaal word sodat daar vasgestel kan word watter groepe „n hoë risiko het om gehoor verlies te kan ontwikkel. Die ABI Prism® SNaPshotTM Multipleks sisteem is gebruik en geoptimiseer om te toets vir die ses mutasies in die MT-RNR1: C1494T, T1095C, 961delT+C(n), A827G and T1291C. „n Totaal van 115 MDR-TB pasiente van die Brooklyn Chest Hospital in Kaap Stad is gewerf vir die studie. Hierdie pasiente ontvang daaglikse hoë dosese van een van die volgende aminoglikosiede: streptomycin, kanamycin of capreomycin. Verder is „n totaal van 439 kontrole DNA monsters gewerf vanuit die volgende etniese groepe: 93 Afrikaner, 104 Blank, 112 Swart and 130 Kleurling. Hierdie monsters is ook getoets vir die ses mutatsies. Hoë Resolusie Smelt analise (HRS) is gebruik om nuwe DNS volgorde veranderinge in die MT-RNR geen te identifiseer. Die hele mitochondriale genoom is blootgestel aan DNA volgorde bepaling in „n poging om nuwe DNS volgorde verandering in die genoom te identifiseer wat moontlik betrokke kan wees by aminoglikosied-geinduseerde gehoor verlies. „n Total van 97 lede van „n Suid Afrikaanse familie waar die A1555G mutasie teenwoordig is, is deur middle van die SNaPshot metode gegenotipeer. Verder is die normale funcitoneering van die mitochondrion in getransformeerde witbloed selle, getoets in die teenwoordigheid van verskillende konsentrasies streptomycin met behulp van die MTT kleurmetrie toets. Deteksie van heteroplasmiese mutasies is gedoen deur middle van die PCR-RFLP tegniek en alle analises is gedoen op die UN-SCAN-IT program. Ons was suksesvol in die ontwikkeling van „n vinnige, koste effektiewe en kragtige tegniek wat al ses die mutasies in MT-RNR1 in een reaksie kan optel. Hierdie tegniek het goed gewerk met DNA monsters van bloed en van selle verkry vanuit die wangholte (geneem van kinders jonger as 12 jaar). Die C1494T, T1095C en T1291C mutasies is glad nie waargeneem in enige van ons MDR-TB patiente of kontroles nie. Skrikwekkend is die hoë frekwensie (0.9%) waarby die A1555G mutasie in die Swart kontrole groep waargeneem is. Hierdie mutasie is ook in 1.1% van die Afrikaner kontrole groep opgemerk in heteroplasmie van 25%. Die A827G mutasie was teenwoordig in 0.9% en 1.1% van die MDR-TB patiente en Afrikaner kontrole monsters, onerskeidelik. Die 961delT + insC(n) mutasie is opgemerk in baie hoë frekwensies in beide die MDR-TB (3.5%) en kontrole groepe (1.1% van die Afrikaner, 1.5% van die Kleurling en 7.1% van die Swart monsters). Die T961G mutasie is ook in hoë frekwensies in slegs die Blanke (2.9%) en die Afrikaner (3.2%) kontrole groepe waargeneem. Nuwe DNS volgorde veranderinge in MT-RNR1 is gesoek in „n groep MDR-TB patiente wat gehoor verlies ondervind. Slegs twee nuwe verandering is ontdek (G719A en T1040C). Dit is onwaarskynlik dat hierdie veranderinge patogenies is siende dat hulle teen frekwensies van 20.7% en 1.8% waargeneem is in die Kleurling en Swart kontrole groepe onderskeidelik. Tydens die soeke na nuwe DNS volgorde veranderinge wat moontlik geassosieer is met aminoglikosied-geinduseerde gehoor verlies in die mitochondriale genoom is 50 onbekende veranderinge ontdek (een in die MT-TH, ND3, COX3 en twee in die CYTB gene). Die veranderinge is verder ondersoek vir evolusionêre konservasie op beide die nukliotied en amino suur vlak van mens to padda. Dit is bevind dat 76 uit die 97 familie lede positief is vir die A1555G mutasie en het dus „n hoë risiko om aminoglikosied-geinduseerde gehoor verlies te ontwikkel as hul bloot gestel word aan hierdie antibiotikums. Verder is gevind dat hierdie familie op die L0d mitochondriale haplogroep lê. Geen van die sogenaamde genetiese modifiseerde gene of DNS volgorde veranderinge in hierdie gene (tRNASer(UCN), A10S in TRMU in homosigotiese vorm en die 35delG in GJB2) is gevind in die familie nie. Die MTT toets het „n afname in die mitochondriale funksioneering van selle waar die A1555G mutasie teenwoordig was getoon, alhoewel die verskil tussen selle wat nie die A1555G mutasie het nie, nie statisties betekenisvol was nie (p-waarde: 0.615-0.999). Die hoë frekwensie van die A1555G mutasie (0.9%) in die Swart populasie van Suid Afrika is skrikwekkend siende dat die voorkomssyfer van MDR-TB in hierdie groep baie hoog is. Toekomstige studies met grooter getalle is nodig om die ware frekwensie van die mutasies geassosieer met aminoglikosied-geinduseerde gehoor verlies in die algemende Suid Afrikaanse populasie te bepaal. Ons data dui aan dat die 961delT + insC(n) en die T961G mutasies slegs algemene nie-patogeniese polimorphismis is siende dat dit in sulke hoë frekwensies (>1%) in kontroles opgemerk is. Die identifiseering van die eerste DNS volgorde veranderinge in proteïen kodeerende gene wat moontlik geassosieer is met aminoglikosied-geinduseerde gehoor verlies hou groot en belowende moontlikehede in, interme van die identifiseering van „n tweede geen. Toekomstige studies waarin die effek van hierdie veranderinge op die normale funktioneering van hierdie gene ondersoek word sal „n besondere groot bydrae lewer tot hierdie veld van navorsing. Al 76 van die A1555G positiewe familie lede is voorsien van genetiese verslae en het berading ontvang in verband met hul risiko en die risiko van hul kinders om aminoglikosied-geinduseerde gehoor verlies te ontwikkel. Die ontwikkeling van „n kragtige, vinnige en koste-effektiewe genetiese metode vergemaklik die vinnige identifiseering van hoë risiko individue vir die ontwikkeling van gehoor verlies voordat hulle met hul aminoglikosiede behandeling begin. Dit is veral noodsaaklik in „n derde wêreld land soos Suid Afrika waar, ten spyte van hul gevaarlike newe effekte, aminoglikosied antibiotikums steeds gebruik sal word. Daarom is grooter publieke bewusmaking nodig om hierdie problem te probeer oplos en te verhoed.

Cette thèse apporte des solutions théoriques et pratiques à deux problèmes soulevés par la photographie numérique en présence de mouvement, et par la photographie infrarouge. La photographie d'objets en mouvement semblait ne pouvoir se faire qu'avec des temps d'exposition très courts, jusqu'à ce que deux travaux révolutionnaires proposent deux nouveaux types de caméra permettant un temps d'exposition arbitraire. Le flutter shutter de Agrawal et al. crée en effet un flou inversible, grâce à un obturateur aux séquences d'ouverture-fermeture bie{\it n choisies. Le motion invariant photography de Levin et al. obtient ce même effet avec une accélération constante de la caméra. Les deux méthodes suivent ainsi un nouveau paradigme, la computational photography, selon lequel les caméras sont repensées, car elles incluent un traitement numérique sophistiqué. Cette thèse propose une méthode pour évaluer la qualité image des nouvelles caméras. Le fil conducteur de l'analyse est donc l'évaluation du SNR (signal to noise ratio) de l'image obtenue après déconvolution. La théorie fournit des formules explicites pour le SNR, soulève deux paradoxes de ces caméras, et les résout. Elle permet d'obtenir le modèle de mouvement sous-jacent à chaque flutter shutter, notamment tous ceux qui sont brevetés. Une seconde partie plus brève aborde le problème de qualité principal en imagerie vidéo infrarouge, la non-uniformité. Il s'agit d'un bruit évolutif et structuré en colonnes causé par le capteur. La conclusion des travaux est qu'il est non seulement possible mais également efficace et robuste d'effectuer la correction sur une seule image. Cela permet de contourner le problème récurrent des "ghost artifacts"résultant d'une incohérence du traitement par rapport au modèle d'acquisition. / This thesis provides theoretical and practical solutions to two problems raised by digital photography of moving scenes, and infrared photography. Until recently photographing moving objects could only be done using short exposure times. Yet, two recent groundbreaking works have proposed two new designs of camera allowing arbitrary exposure times. The flutter shutter of Agrawal et al. creates an invertible motion blur by using a clever shutter technique to interrupt the photon flux during the exposure time according to a well chosen binary sequence. The motion-invariant photography of Levin et al. gets the same result by accelerating the camera at a constant rate. Both methods follow computational photography as a new paradigm. The conception of cameras is rethought to include sophisticated digital processing. This thesis proposes a method for evaluating the image quality of these new cameras. The leitmotiv of the analysis is the SNR (signal to noise ratio) of the image after deconvolution. It gives the efficiency of these new camera design in terms of image quality. The theory provides explicit formulas for the SNR. It raises two paradoxes of these cameras, and resolves them. It provides the underlying motion model of each flutter shutter, including patented ones. A shorter second part addresses the the main quality problem in infrared video imaging, the non-uniformity. This perturbation is a time-dependent noise caused by the infrared sensor, structured in columns. The conclusion of this work is that it is not only possible but also efficient and robust to perform the correction on a single image. This permits to ensure the absence of ``ghost artifacts'', a classic of the literature on the subject, coming from inadequate processing relative to the acquisition model.

Obwohl das dokumentarische Bild als beglaubigte Aufzeichnung einer außermedialen Realität als Diskursgegenstand bereits seit Längerem dekonstruiert ist, scheint die Faszination am Dokumentarischen nahezu ungebrochen. Die stete Bezugnahme auf das Dokumentarische in unterschiedlichen Diskursen der Fotografie zeugt davon. Auch zahlreiche künstlerische Auseinandersetzungen rekurrieren seit den 80er-Jahren verstärkt auf dokumentarische Konzepte und Formate. Ausgehend von diesem Paradoxon, der Dekonstruktion des Dokumentarischen in Theoriekontexten und dem Wiedererstarken dokumentarischer Formate in der Fotografie und Kunst, sucht die vorliegende Arbeit nach den Ursachen einer offenkundig anhaltenden Faszination am Dokumentarischen. Dabei richtet sie den Blick speziell auf künstlerische Fotografien, die Gebrauchsweisen der Fotografie aufgreifen, welche per se mit dem Dokumentarischen affiziert werden, wie die Pressefotografie, die kriminalistische Fotografie und die Amateurfotografie. Sie zeigt, über welche Strategien das Dokumentarische dort produktiv umgesetzt wird. Lässt sich jeder Dokumentarismus erst einmal als Versuch lesen, in der Repräsentation das Reale zu verbildlichen, beziehen sich die vorgestellten künstlerischen Arbeiten von Jeff Wall, Thomas Demand, Sophie Calle und Richard Billingham zwar auf ein Begehren nach dem Realen, machen aber gleichzeitig den Verlust des Realen in ihren Erzählungen von der Wirklichkeit erfahrbar. In ihrer Ambivalenz vermitteln die künstlerischen Arbeiten ein Konzept des Dokumentarischen als mobiles System, das dieses nicht als Kategorie, Genre oder Stil festschreibt, sondern als Handlung begreift, die das permanente Ineinandergreifen von Konstruktion und Dekonstruktion des Dokumentarischen nachvollzieht. Insofern erweisen sich die Kunst und das Dokumentarische als nicht polar, denn über ihre Beziehung zum Realen kristallisiert sich dieses als das gemeinsame Dritte der beiden heraus. / Although the documentary image as authenticated record of a reality beyond the media has, as the object of discourse, long been deconstructed, the fascination with the documentary would appear to be ongoing. The constant references to the documentary in a variety of photography discourses bears witness to this. In addition, countless artistic treatments since the Eighties have referred back to documentary concepts and formats. In the light of this paradox as well as the deconstruction of the documentary in theoretical contexts and the renewed gaining of strength of documentary formats in photography and art, this study investigates the reasons for the evident persistent fascination with the documentary. In the process, artistic photographs in particular are examined which reference conventions in photography that are associated per se with the documentary, such as for example press photography, criminalistic photography, and amateur photography. The strategies by which the documentary is productively implemented are demonstrated here. If every form of documentarism can be read first of all as an attempt to express the real visually in the representation, then the artistic works by Jeff Wall, Thomas Demand, Sophie Calle and Richard Billingham that are presented here may indeed reference a desire for the real, but at the same time they make it possible in their telling of reality to experience the loss of the real. It is through their ambivalence that the artistic works convey a concept of the documentary as a mobile system that does not codify it as a category, genre or style, but rather perceives it as an act that comprehends the documentary''s constant intertwining of construction and deconstruction. As such, it is shown that art and the documentary are not polar, because through their relationship to reality this relationship is shown to crystalize out as the common third party for both.

Fast detection and identification of unknown substances is an area of interest for many parties. Raman spectroscopy is a laser-based method allowing for long range no contact investigation of substances. A Coded Aperture Snapshot Spectral Imaging (CASSI) system allows for fast and efficient measurements of hyperspectral images of a scene, containing a mixture of the spatial and spectral data. To analyze the scene and the unknown substances within it, it is required that the spectra in each spatial position are known. Utilizing the theory of compressed sensing allows for reconstruction of hyperspectral images of a scene given their CASSI measurements by assuming a sparsity prior. These reconstructions can then be utilized by a human operator to deduce and classify the unknown substances and their spatial locations in the scene. Such classifications are then applicable as decision support in various areas, for example in the judicial system. Reconstruction of hyperspectral images given CASSI-measurements is an ill-posed inverse problem typically solved by utilizing regularization techniques such as total variation (TV). These TV-based reconstruction methods are time consuming relative to the time needed to acquire the CASSI measurements, which is in the order of seconds. This leads to a reduced number of areas where the technology is applicable. In this thesis, a Generative Adversarial Network (GAN) based reconstruction method is proposed. A GAN is trained using simulated training data consisting of hyperspectral images and their respective CASSI measurements. The GAN provides a learned prior, and is used in an iterative optimization algorithm seeking to find an optimal set of latent variables such that the reconstruction error is minimized. The results of the developed GAN based reconstruction method are compared with a traditional TV method and a different machine learning based reconstruction method.  The results show that the reconstruction method developed in this thesis performs better than the compared methods in terms of reconstruction quality in short time spans.

In manufacturing, metrological inspection is a time-consuming process. The higher the required precision in inspection, the longer the inspection time. This is due to both slow devices that collect measurement data and slow computational methods that process the data. The goal of this work is to propose methods to speed up some of these processes. Conventional measurement devices like Coordinate Measuring Machines (CMMs) have high precision but low measurement speed while new digitizer technologies have high speed but low precision. Using these devices in synergy gives a significant improvement in the measurement speed without loss of precision. The method of synergistic integration of an advanced digitizer with a CMM is discussed. Computational aspects of the inspection process are addressed next. Once a part is measured, measurement data is compared against its model to check for tolerances. This comparison is a time-consuming process on conventional CPUs. We developed and benchmarked some GPU accelerations. Finally, naive data fitting methods can produce misleading results in cases with non-uniform data. Weighted total least-squares methods can compensate for non-uniformity. We show how they can be accelerated with GPUs, using plane fitting as an example. / Thesis / Doctor of Philosophy (PhD)

This master's thesis describes possibilities of Oracle Database 10g and 11g monitoring. It let the reader know about practical tools for monitoring and describes the database's internal catalogs preserving statistics and the information about running database instances within history. Next, it describes design of an Oracle database monitoring tool, describtion of its implementation and at the end its evaluation and comparison with other similar applications.

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