The purpose of this work is split into two categories, the first was to analyse the application of real-time Physics Engine software libraries for use in calculating a geological numerical model. Second was the analysis of the applicability of glyph and implicit surface based visualization techniques to explore fault systems produced by the model. The current state of the art in Physics Engines was explored by redeveloping a Discrete Element Model to be calculated using NVIDIA's PhysX engine. Analyses regarding the suitability of the engine in terms of numerical accuracy and developmental capabilities is given, as well as the definition of a specialised and bespoke parallelisation technique. The use of various glyph based visualizations is explored to define a new standardised taxonomy for geological data and the MetaBall visualization technique was applied to reveal three dimensional fault structures as an implicit surface. Qualitative analysis was undertaken in the form of a user study, comprising of interviews with expert geologists. The processing pipeline used by many Physics Engines was found to be comparable to the design of Discrete Element Model software, however, aspects of their design, such as integration accuracy, limitation to single precision floating point and imposed limits on the scale of n-body problem means their suitability is restricted to specific modelling cases. Glyph and implicit surface based visualization have been shown to be an effective way to present a geological Discrete Element Model, with the majority of experts interviewed able to perceive the fault structures that it contained. Development of a new engine, or modification of one that exists in accordance with the findings of this thesis would result in a library extremely well suited to the problem of rigid-body simulation for the sciences.

Lumpy skin disease (LSD) and Rift Valley fever (RVF) are transboundary viral diseases occurring in Africa and the Middle East (e.g. Israel, Saudi Arabia and Yemen) with increasing potential for global spread. Although the role of wildlife in the epidemiology of these diseases is still not clearly understood, the African buffalo (Syncerus caffer) is thought to play a role in the epidemiology of these diseases. This study sought to expand our understanding of the role of buffalo in the maintenance of RVF and LSD by determining seroprevalence to these viral diseases in buffalo during the inter-epidemic period. Lumpy skin disease is endemic in Africa, and has spread to the Middle East (e.g. Israel); consequently there is a high risk of lumpy skin disease virus (LSDV) expanding its geographical distribution to other areas and due to its economic importance it is included in the list of Notifiable Diseases of the World Organization of Animal Health (OIE). The African buffalo is also suspected to play a role in the epidemiology of RVF. Like LSD, RVF was, until recently, only endemic in Africa. However, it spread to the Arabian Peninsula (Saudi Arabia and Yemen) in 2000 exacerbating concerns that it will extend to other regions of the world. Studies have already established that competent mosquito vectors for RVFV exist in North America and other parts of the world. A total of 248 buffalo sera was tested for antibodies to capripoxviruses and neutralising antibodies against LSDV and RVFV using an indirect enzyme-linked immunosorbent assay (I-ELISA) as well as the serum neutralisation test (SNT). The samples were obtained from the Kruger National Park (KNP) and Hluhluwe-iMfolozi Park (HiP) in South Africa. The prevalence of antibodies to LSDV and RVFV in the sera tested was 70/248 (28.2%) and 15/248 (6.1%), respectively using an I-ELISA. The LSDV I-ELISA, using a sheeppox virus as antigen, has not been validated for use in African buffalo. The high percentage of LSDV positive antibody results obtained in this study is however a concern. Results obtained is in contrast with other published results as well as results obtained with the SNT for antibodies against LSDV. The SNT is currently the gold standard for LSDV antibody testing. Using this test for LSDV in this study, 5/66 (7.6 %) samples tested positive. The results of the RVF I-ELISA, which had previously been validated for use in the African buffalo, correlated with the SNT results. From 12 SNT RVFV-positive sera, 3 (25%) had very high SNT titres of 1:640. Neutralising antibody titres of more than 1:80 were found in 80% of the positive sera tested. Eleven buffaloes (4.4% of the total samples) also showed evidence of antibodies to both LSDV and RVFV. The results obtained in this study complement other reports indicating the role of African buffalo in the epidemiology of these diseases during inter-epidemic periods. / Dissertation (MSc)--University of Pretoria, 2012. / Veterinary Tropical Diseases / unrestricted

Deforestation and land use change are widespread in western Uganda. However, the spatial patterns and time-series of change and the reasons why it is occurring remain to be fully investigated. In this work a combination of satellite imagery and social surveys is used to quantify forest gains and loss over the last three decades in the region close to Lake Albert, whilst also providing an account of possible drivers of change. This area proves to be interesting as it covers regions with both formally protected areas (gazetted regions) and un-protected forest, the latter being largely under private ownership. Remote sensing data from the Landsat satellites were gathered for forest change detection, and were processed using standard remote sensing techniques, then quantified using GIS and regression methods. Fieldwork allowed these data to be ground truthed while gathering (quantitative) household surveys and (qualitative) key informant interviews. Quantitative surveys were analysed using Principal Components Analysis (PCA) and cluster analysis, and were compared qualitatively with the satellite analysis and stakeholder interviews. The results show that forest cover declined significantly outside gazetted areas at the expense of varying local?scale processes, although the protection of the gazetted forests was remarkably successful. In forest corridors outside gazetted regions, losses exceeded 90% (p<0.05). Survey data suggest that rural poor households were more likely to be situated in forested regions, and were more dependent on forest resources for their livelihoods. However, the drivers of change were spatially variable, with expansion of sugarcane farming being a likely driver in the northern areas, but small?scale agricultural expansion a significant factor in the more southern parts of the study region. While there is wide agreement within the data that the patterns of forest cover and land use changes are anthropogenically driven, more specific drivers are swamped by intricacies of the bio-physical and socio-economic preconditions that are inseparable in both space and time, although agricultural expansion and population growth were evident and pervasive. The analyses provide insights into complex anthropogenic processes at various spatial scales, and policy recommendations provided are widely applicable for developing countries struggling to conserve nature whilst boosting economic growth.

The Ottawa Embayment is a intracratonic rift basin that preserves a unique and eventful history through deep time. Its evolution records opening of the Iapetus Ocean with the break-up of Rodinia, followed by the formation of a continental passive margin, trapping siliciclastic sediments eroded from the adjacent Grenville Province. Samples were collected from a transect across the crystalline rift flank and through the embayment. We investigate the influence of crystallinitiy and non-ideal crystal chapes on He diffusion and resulting zircon (U-Th)/He age with the use of zircon (U-Th)/He thermochronometry, raman spectroscopy and x-ray micro-computed tomography. We then integrate our thermochronology data with regional geology to utilize multi-sample numerical modelling to improve our understanding of the thermal history of the Ottawa Embayment and the evolution of intracratonic rift basins. The works collected within define a comprehensive temperature-time history for the basin and rift flank from the Late-Mesoproterozoic to present day.

Impulsive differential equations are useful for modelling certain biological events. We present three biological applications showing the use of impulsive differential equations in real-world problems. We also look at the effects of stability on a reduced two-dimensional impulsive HIV system. The first application is a system describing HIV induction-maintenance therapy, which shows how the solution to an impulsive system is used in order to find biological results (adherence, etc). A second application is an HIV system describing the interaction between T-cells, virus and drugs. Stability of the system is determined for a fixed drug level in three specific regions: low, intermediate and high drug levels. Numerical simulations show the effects of varying drug levels on the stability of a system by including an impulse. We reduce these two models to a two-dimensional impulsive model. We show analytically the existence and uniqueness of T-periodic solutions, and show how stability changes when varying the immune response rate, the impulses and a certain nonlinear infection term. The third application shows how seasonal changes can be incorporated into an impulsive differential system of Rift Valley Fever, and looks at how stability may differ when impulses are included. The analysis of impulsive differential systems is crucial in developing more realistic mathematical models for infectious diseases.

>Magister Scientiae - MSc / The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomics studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites. The actinobacterial OTUs detected belonged to both the Rubrobacterales and Actinomycetales orders with members of the genus Arthrobacter being found in all three lakes. Geochemical properties were significantly different between the lakes, although more than one property attributed to the variance between community compositions. The diversity detected in the culture-based study differed significantly and all isolates belonged to the genus Streptomyces. Two novel strains were characterized by means of phylogenetic (16S rRNA gene sequence), physiological, morphological and biochemical analyses. Both novel isolates were capable of growing under "extreme" conditions- pH 12, 10% NaCl and 45°C. Partial enzyme characterization revealed that both strains produced xylanase enzymes that were active at pH 6.5 and 8.5 with an increase in activity up to 45°C. The results obtained revealed a previously undetected diversity of actinobacteria in the Ethiopian Rift Valley with a potentially novel subpopulation adapted to haloalkaline conditions. The low 16S rRNA sequence similarity of a substantial proportion of the libraries suggests that culture-based isolation may play a vital role in deciphering the community fingerprint. / The National Research Foundation and the Norwegian Research Council

The lower Mount Rogers Formation (LMRF) is described by Rankin (1993) as a sequence of intercalated metabasalts and volcanogenic sediments with minor metarhyolite. We have chosen to examine the sequence of the LMRF units exposed along Elk Garden Ridge, a high shoulder between the summits of Whitetop Mountain and Mount Rogers in the Mount Rogers National Recreation Area in SW Virginia. This sequence represents an uplifted block of LMRF units enclosed by exposures of Whitetop and Wilburn metarhyolites. In the field, progressive lithologic changes can be observed walking up-section along Elk Garden ridge that are indicative of changes in lava compositions and eruptive environments. From the bottom of the section, massive basalts with distinctive 1-2 cm long swallowtail plagioclase phenocrysts grade into vesicular basalts, then into sheet flow basalts, followed by a thick sequence of aphyric and amygdaloidal pillow basalts. Further up section, eruptive products transition into rhyolitic ignimbrites and ash and lapilli tuffs. Boulders of cobble conglomerates near the middle of the sequence and sedimentary layers in between individual sheet flows suggest short periods of relative eruptive quiescence. The only unit broken out in the LMRF by Rankin (1993), Fees Rhyolite, is not observed in the field area, suggesting local differences in topography, eruptive products and eruptive styles across the outcrop area during the deposition of these eruptive products. Petrographically, the rocks reflect the regional greenschist facies metamorphic conditions with chlorite and epidote as primary metamorphic minerals, and unakite-like zones of mineralization. Relict plagioclase and pyroxene phenocrysts persist, as do primary igneous textures and structures. Compositionally, all of the rocks in the Elk Garden Ridge sequence are strongly enriched in alkali metals, with elevated Na2O and K2O contents, and high TiO2 in the basalts. Major and trace element systematics suggest that the chemical signatures of the metabasalts are primary controlled by shallow-level crystallization processes. The LMRF metabasalts share many compositional affinities with later (~570 Ma) rift-related basalts preserved in the Appalachians, suggesting that all of these lavas were formed by melting of a compositionally uniform mantle source, followed by shallow crystallization, despite being separated from one another by large stretches of time and space.

During March 2008 a suspected outbreak of Rift Valley fever was reported on a farm in the Bela-Bela area, Limpopo Province of South Africa. The affected dairy farm, where no vaccination programme against RVF were practiced, applies an intensive farming system with 300 Holstein Friesland cattle (calves included) as well as 200 Pedi sheep on the farm. Seven calves died on this farm but no apparent clinical disease was reported in cattle as well as in sheep. During the outbreak blood samples from cattle and sheep were taken and the animals were re-sampled 8 weeks later. A set of sera was also collected from cattle on a neighbouring farm. The aim of the study was to determine the extent of the outbreak by evaluating if the virus had also infected other animals on the affected farm as well as on a neighbouring farm. During the first blood collection 233 samples were taken from cattle and 73 from sheep on the affected farm; 55 blood samples were taken from cattle on a neighbouring farm. A second blood collection was only done on the affected farm and 234 cattle and 85 sheep were bled. All the sera collected were tested by an IgM-capture ELISA and by an indirect IgG ELISA. Selected IgM positive (n=14), IgG positive (n=23) and samples negative for both IgM and IgG (n=19) were then tested by the serum neutralization test (SNT). Sera from IgM positive (14) and negative (20) animals were also tested by a TaqMan PCR. Results from the affected farm showed that 7% (16/233) of cattle samples were IgMpositive and 13.7% (32/233) IgG positive at the first collection of samples, and 2% were IgM-positive at the second sample collection. The number of cattle positive for RVF virus-specific IgG antibodies increased by 20.3% when compared to the first bled. Only 1.4% of sheep were both positive for anti-RVF virus IgM and IgG antibodies at the first collection; IgM-positive cases decreased to 1.2%, while IgG-positive cases increased to 2.4% at the second bled. Although no IgM-positive cattle could be found on the neighbouring farm, 5.5% of cattle were IgG-positive. The SNT confirmed most of the ELISA results. Three samples that tested positive for anti-RVF virus IgM and one anti-RVF virus IgG positive sample using ELISA tested negative using the SNT. Two samples that tested negative for both IgM and IgG antibodies using ELISA, tested low positive (1:10 and 1:20) using the SNT. All samples tested using a TaqMan PCR were negative. On the affected farm, apart from the seven calves that died, cattle were also infected. There was evidence of virus circulation on the neighbouring farm but the negative PCR results indicate that at the time the animals were sampled they were not viraemic. How the virus was introduced onto the farm is not clear. The possibility of low level virus circulation in animals and the reactivation of virus from endemic foci by the breeding of vector competent mosquitoes on the low-lying area on the farm in Bela-Bela may have led to ideal circumstances for an outbreak to occur. The fact that mostly cattle seroconverted suggests a higher host preference of the local population of mosquitoes for cattle rather than sheep. Copyright / Dissertation (MSc)--University of Pretoria, 2011. / Veterinary Tropical Diseases / unrestricted

No description available.

No description available.