Theses and Dissertations (University of Pretoria)

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Consequence management for minimising financial mismanagement in the City of Johannesburg Metropolitan Municipality
Shokane, Thabane (University of Pretoria, 2024-07)
The study aimed to assess whether consequence management concerning municipal financial management in the local sphere of government is adhered to. There are regulatory bodies, such as the Office of the Auditor-General, Financial DC Boards, Internal Audit, Audit Committees and Oversight Council Committees, which mandated both constitutionally as well as legislatively to ensure that public financial reports, which include recommendations are provided on the municipal performance. Despite the annual recommendations, most South African municipalities still fail to manage public monies properly, which result in a worrying increase in irregular, unauthorised, fruitless, and wasteful (IUFW) expenditure.The CJMM was used as a focus case study to observe the extent to which municipalities comply with consequence management. In doing so, the study utilised a qualitative research approach, that is, secondary data was gathered from, inter alia, municipal audit reports, financial statements, consolidated general reports and accredited journal articles. The adopted research methodology was utilised to analyse audit reports from 2018 - 2022 to provide a descriptive analysis of how the CJMM utilised its finances. The findings revealed an increase in financial mismanagement because of by non-compliance with legislation, lack of performance management, and poor governance and leadership. The Auditor-General of South Africa (AGSA) often highlights these factors as a problem for municipalities. The study also provides recommendations to retain these components to both control financial mismanagement and adhere to the principles of consequence management.
Genomic study of Bacillus anthracis and Bacillus species isolated from anthrax outbreaks in South Africa
Lekota, Kgaugelo Edward (University of Pretoria, 2019)
Anthrax is a zoonotic disease that naturally occurs in wild and domestic animals. The causative agent of anthrax is Bacillus anthracis that consist of a single chromosome and the two virulence plasmids (pXO1 and pXO2) with the capsule and toxin gene regions that makes up a total genome size of 5.5 Mb. Bacillus anthracis and B. endophyticus isolated from anthrax outbreaks (mainly 2008/9 outbreaks in the northen Cape Province, NCP) in South Africa had similar microbiological and genetic features. Whole genome sequencing (WGS) was used to characterize and differentiate B. anthracis from the closely related B. endophyticus as well as other Bacillus species. The identification of morphological and homologous capsule (polyglutamate) genes present in both B. anthracis and B. endophyticus species resolved the non-conformance of the diagnosis of anthrax. Bacillus anthracis is considered to be monomorphic and single nucleotide polymorphisms (SNPs) are the ideal signatures for subtyping monomorphic species. Globally, most B. anthracis strains cluster into the major A-clade into different sub-clades using phylogenetic analysis. In South Africa, anthrax outbreaks in animals have been reported in the Kruger National Park (KNP) and NCP regions with most B. anthracis strains clustering in the A-clade. The rare Kruger B-clade reported to be restricted to the endemic Pafuri (northern) region in KNP was also investigated. In order to subtype and understand these outbreaks, the study generated a B. anthracis genetic database based on WGS to identify SNPs across sequenced genomes. The sequenced genomes were further compared with other available genomes. In conclusion, this study discovered novel SNPs and defined the phylogenetic structure of B. anthracis in South Africa. WGS-SNP analysis could trace some of the anthrax case outbreaks using similar SNP profiles of B. anthracis strains from different case outbreaks. WGS-SNPs specific to NCP were identified and developed into high-resolution melting SNP (melt-MAMA assays) discriminative assays for the purpose of molecular epidemiology. The sequenced KNP B-clade consisted of heterogeneous B. anthracis genomes that were distinctive from the previously sequenced genomes in KNP. South Africa has diverse SNP sub-clades and branches in the A-clade that are not commonly found world-wide.
Discrimination of Hypotrigona species (Apidae : Meliponinae) in Kenya using nest architecture, cephalic secretions and molecular tools
Ndungu, Nelly (University of Pretoria, 2019-01)
Stingless bees are important pollinators contributing significantly to biodiversity and food security. Stingless bees produce honey that has high medicinal value that fetches higher prices compared to the honey produced by honey bees (Apis mellifera). However, identification and classification of Afrotropical stingless bees, which is key and important for their domestication, still remains ambiguous and solely reliant on the use of morphological features. In this study, an integrative taxonomy approach was applied to identify and differentiate three Hypotrigona species: Hypotrigona gribodoi, H. ruspolii and H. araujoi that are found in Kenya. Nesting sites, nest architecture, morphometrics, DNA barcoding and chemotaxonomy using whole head extracts were employed as complementary tools to identify and differentiate the Hypotrigona species. Colonies of the three Hypotrigona species from Kakamega forest and Mwingi, Kenya were nested at meliponary on the campus of icipe in Nairobi, Kenya. Nest sites, nest entrance (colour and sizes) and nest architecture (brood cells arrangement and sizes, honey and pollen pots sizes, presence or absence of involucrum and colour of propolis) were recorded. It was found that nest sites are specific with Hypotrigona gribodoi nesting mostly in crevices of mud walls in homesteads, while H. ruspolii and H. araujoi nest in specific indigenous tree species found in Kakamega forest. The colour of external nest entrances varies between species. Those in H. araujoi were yellowish-brown; white or cream in H. gribodoi while H. ruspolii’s were dark brown. There is an internal nest entrance in H. gribodoi, which is absent in the other species. Brood cells are clustered in H. gribodoi’s and H. ruspolii’s nests, whereas H. araujoi’s form vertical semicomb-like layers. The surface area of the apical opening of the entrance tube and volumes of brood cells, honey and pollen pots differ significantly between the three Hypotrigona species. Using veins on the right forewing and hind leg for morphometrics analysis, H. gribodoi and H. ruspolii were separated from H. araujoi. However, there is an overlap between H. gribodoi and H. ruspolii. On the other hand, using mitochondrial DNA, COI gene, the three Hypotrigona species were clearly separated. A lower genetic distance exists between H. araujoi and H. gribodoi from Kakamega (1.4%) than between H. gribodoi collected from Kakamega and H. gribodoi from Mwingi (4.3%). Using gas chromatography and mass spectrometry, analysis of extracts from the head of workers, 50 components belonging to six chemical classes; hydrocarbons, aldehydes, alcohols, terpenoids, steroids and fatty acids were identified. Twenty-nine compounds were found in the cephalic extracts of H. araujoi, 26 in H. gribodoi and 33 in H. ruspolii. Workers were successfully grouped into their respective species and colonies using sixteen components among which: heptacosene, heptacosanol and octadecanol contributed most to the separation into species. In conclusion, nest entrance and nest architecture show variation between the three Hypotrigona species. Use of morphometrics and molecular taxonomic approaches (DNA barcoding) provides a convenient, robust and reliable way to identify Hypotrigona species. The large genetic distance between H. gribodoi collected from Kakamega and Mwingi suggests that H. gribodoi ex-Mwingi may be a new undescribed putative species. Gas chromatographic and mass spectrometric analysis of head extract reveals differences in secretions among the Hypotrigona species. Thus, integrative taxonomy tools applied in this study provides a valuable alternative to identify Hypotrigona species. In addition, this study indicates the need for a thorough revision of Hypotrigona species.
An evaluation of stripe pattern and niche variation in Cape mountain zebra (Equus zebra zebra)
Prinsloo, Nicolas D. (University of Pretoria, 2018-12)
Phenotypic variation represents an interface between the environment and animal inhabitants to conserve, monitor and study for evolutionary understanding. Confidence in the extent and development of methods to quantify such variation requires an ideal model. The vulnerable Cape mountain zebras (CMZ; Equus zebra zebra) have clearly contrasting stripes, interesting niche dynamics and a historic genetic bottleneck. Morphology was quantified using automated 3D photogrammetry and a novel geometric morphometric approach for stripe patterns. The isotopic niche was defined using isotopic chronologies from tail hair and evaluated at various levels. I observed differences within respective individual replicates for morphology and along isotopic chronologies, individual variation within groups and the population, and between groups in morphological, behavioural and physiological culminations of phenotypic variation. I derived CMZ pattern uniqueness and baseline morphological variation with which to compare over time or with other populations. Individual similarity was maintained, despite allometric distortion of the coat pattern (F1,51 = 7.8; R2 = 0.13; p = 0.001). Branching of the first four torso stripes varied geometrically, accounting for 19.3% of total shape variation, of which 41.82% can only be feasibly measured with geometric morphometrics. Internal neural and gut morphologies, associated with behaviour and physiology, and thus dietary niche, may be similarly affected. Cape MZ are obligate grazers that rarely deviate (4.46% of subsamples), but the timing of mixed feeding contrasts expectations, occurring more in summer and narrowing to obligate grazing in winter. These trends in niche (delimited by δ13C and δ15N) differed between groups (p < 0.001) and demographics (p = 0.002). By increasing the hierarchical resolution to include group dynamics in a gregarious species, I improved the informativeness of niche variation and specialization: group- (0.55 ± 0.04) and individual-level specialisation (0.53 ± 0.02) were similar. Resouce use fills in some behavioural and physiological aspects of phenotype.The methods proposed herein quantify CMZ phenotypic variation. Understanding its hierarchical nature locates it within a broader context for comparison with similarly placed tiers, i.e. species, populations, groups, etc. to understand constraints and the level where action is required. Combined geometric morphometrics with current identification may improve efficiency and informativeness for individual identification and proxy morphological variation at the group and population-levels. Varied group behaviour, and juvenile inexperience are important to consider when moving individuals to suboptimal habitat with limited graze. Each ecological tier has a different association with intrinsic and extrinsic factors that informs management action.In achieving my objectives, I have opened avenues for further study. Modified geometric approaches could quantify shape indices of condition with surface sliding landmarks or study skin cell expansion and migration. Where morphological variation helps us understand the organism and its development, niche may help us understand its interaction with the environment and inform conservation management. Overall, future studies need to consider informative measures of phenotypic variation including easily measurable morphological indices and isotopic niche variation for comparison within a broader context.
Diversity and relationships of South Africa's fig-associated nematodes
Kruger , Meike S (University of Pretoria, 2019-01)
Parasitic nematodes of the fig microcosm have received limited attention in South Africa. I have assessed the molecular diversity of nematodes present in the native South African species and discovered 24 undescribed species. Two were previously described but the descriptions need reviewing. I have revised one of these descriptions in Chapter 3 and Chapter 4 is a description of a new species with unique features that may well be a new genus of nematode. How these nematodes interact with their hosts, fig and/or wasp, has not yet been fully established and I did a co-phylogenetic study to determine how these three organisms interact on an evolutionary scale. The plant parasitic nematodes Schistonchus and Ficophagus showed no coevolutionary patterns with the hosts. Parasitodiplogaster is necrophagous and relies on the wasp for its food sources but showed coevolutionary patterns with both fig and wasp. The latter pattern could be because the fig syconia can influence the nematode survival. To determine if presence of nematodes in a wasp influences the fitness of the wasp I did a biogeography study of the wasps and nematodes associated with Ficus burkei. The dataset obtained was not optimal, but I could generate haplotype networks for Parasitodiplogaster sycophilon, the pollinator wasp Elisabethiella stuckenbergi and the parasitic wasp Seres barbarus. The parasitic wasp showed the highest dispersal, which was expected, because nematodes do not generally pick these wasps as rides to the next generation of figs. The pollinator wasps were not observed in areas where F. burkei has only recently been cultivated and no specific patterns of dispersal were observed. As expected, the nematodes were only associated with figs that contained the pollinator wasp but did show some geographical isolation of haplotypes.
Development of new recombinant vaccines for rabies and dog population management
Wright, Nicolette (University of Pretoria, 2019-02)
Development of new recombinant vaccines for rabies and dog population management Domestic dogs are responsible for the majority of human rabies cases. To eliminate rabies from a given population, two components are crucial, namely mass vaccination of dogs and provision of PEP to bite victims. Achieving the recommended 70% vaccination coverage can be difficult in developing countries. This study aimed to develop recombinant vaccines that could address two factors that hinder the success of vaccination campaigns: 1) vaccinating unreachable dogs and 2) preventing high population turnover. In considering the first aim, oral vaccination of dogs in developing countries can be a useful adjunct in remote areas or communities with large numbers of free-roaming dogs. Given its host specificity (canines), transmission mechanism (oral) and safety, a recombinant canine adenovirus type 2 expressing the rabies glycoprotein gene (CAV2- RG) could be an ideal candidate oral vaccine. To assess the potential use of this vaccine in dog populations, we investigated the prevalence of antibodies against canine adenovirus type 2 (CAV2) in South African dogs. Blood was collected from 241 dogs from 2 provinces in South Africa. Sampled dogs had not previously been vaccinated against canine adenovirus (CAV1 or CAV2). The high seropositivity observed (45% and 62%) in animals from both provinces suggests that CAV2 circulates extensively among domestic dogs in South Africa. Given this finding, we evaluated the effect of pre-existing CAVspecific antibodies on the efficacy of the CAV2-RG vaccine in dogs. Purpose-bred Beagle dogs, which received prior vaccination against CAV, were immunized by oral administration of CAV2-RG. After rabies lyssavirus (RABV) infection, all animals, except one vaccinated dog, developed rabies. This study demonstrated that pre-existing antibodies against CAV, such as naturally occurs in South African dogs, inhibits the development of neutralizing antibodies against RABV when immunized with a CAV-based rabies recombinant vaccine. Considering the second aim of this study, high population turnover in free-roaming dogs is a major factor that influences the efficiency and cost of vaccination programmes. As a population management intervention, surgical sterilization is cost-prohibitive in developing countries while chemical sterilization presents many difficulties associated with safety and acceptance of such practices. Immunocontraceptives may offer an ideal, non-permanent mechanism to interrupt breeding cycles and contribute to population management. We have therefore developed 6 candidate immunocontraceptive vaccines expressing gonadotropin-releasing hormone (GnRH). Two human adenovirus type 5 (HAd5) vaccines and four DNA-based vaccines were constructed. Expression of the GnRH-gene from all inserts was confirmed in cell culture and vaccines were evaluated for immunogenicity in a murine model. No animals developed anti-GnRH antibody responses after 2 intramuscular doses of the DNA vaccines. In a heterologous primeboost strategy all animals that received DNA vaccines also received a booster dose of one HAd5 vaccine but failed to develop any anti-GnRH antibodies. After 2 intramuscular vaccinations with the respective HAd5 constructs, mice from both groups developed GnRH-specific antibody responses. This study demonstrated the potential of recombinant viral vectored vaccines to induce an antibody response against GnRH. These findings may represent an important step in the development of an effective immunocontraceptive vaccine for use in domestic dogs
Occurrence of non-tuberculous mycobacteria in a chloraminated drinking water distribution system
Mlambo, Tlangelani (University of Pretoria, 2018-12)
Nontuberculous mycobacteria are environmental mycobacteria commonly found in natural environments as well as human-engineered environments. The diversity of non-tuberculous mycobacteria (NTM) within drinking water distribution systems (DWDS) has not been fully explored, especially in South Africa. Furthermore, several species of NTM are known to be important opportunistic human pathogens causing nosocomial infection and occupational illness in immunocompromised patients. The objective of this study was to detect and identify nontuberculous mycobacteria in drinking water distribution system using culture-dependent and culture-independent approaches. Mycobacteria were previously identified by phenotypic traits such as colony morphology, growth rates, pigment production and biochemical profile but these methods have proved to be laborious and results are sometimes unreliable as different species may have indistinguishable morphological and biochemical profiles. With the development of molecular approaches for identification it has become easier to determine the specific identity and prevalence on mycobacterial isolates. In this study, NTM were initially detected and identified from different points within a large drinking water distribution system by culture-dependent techniques which included PCR, sequencing of specific gene regions and phylogenetic analyses. However, cultures can take a week to several months to grow since mycobacteria are slow growing bacteria and isolation can also be hindered by overgrowth of other bacteria as currently used media are not selective and decontamination techniques could eliminate some of the mycobacteria. In addition to the first culture-based approach, NTM were also detected using a culture-independent approach consisting of direct extraction of DNA from the water samples, followed by PCR. Mycobacteria were isolated from 125 samples. The most frequently isolated species based on phylogenetic analysis of the sequence data were Mycobacterium mucogenicum (46%) and M. fluoranthenivorans (2%). A total of 33/59 (56%) samples were positive for Mycobacterium using PCR. Although the results could not be further verified, it is clear from the percentage of positive samples that they are present and prevalent within DWDS. Furthermore, these results indicate a need for development and/or improvement of extraction methods which will yield higher DNA levels with good amplifiable quality to be used for culture-independent techniques.
A critical analysis of wrongful life claims in South Africa
Cooper, Ronley C. (University of Pretoria, 2019-02)
With the Constitution as the supreme law of South Africa and the first ever Bill of Rights in the Republic, South African law is in the process of being developed to be in accordance with the spirit, purport and objects of the Bill of Rights. This begs the question whether the wrongful life claim can be recognised within the new democratic dispensation of South Africa. Previously, South African courts have failed to recognise the child-plaintiff’s claim as it is contra bonos mores1 and does not provide a cause of action. However, this research aims to prove that the South African legal framework is capable of recognising the wrongful life claim. In order to do so it is important to consider the common law, more specifically the law of delict, and whether it can be developed to recognise the child’s claim. Most importantly, the element of wrongfulness must be examined and whether the boni mores2 have developed to recognise the child’s claim. Post-Constitutional legislation supports the notion that the boni mores have developed as the Children’s Act3 recognises the rights of children and that their interests are of paramount importance. Also, the Choice on Termination of Pregnancy Act4 provides women with a choice when it comes to reproduction and whether to terminate the pregnancy. This provides a basis for the wrongful life claim and illustrates the change in the community’s legal convictions. Furthermore, in a new Constitutional dispensation, international law plays a role in the recognition of children’s rights within a jurisdiction and imposes obligations on State Parties. These conventions have been examined and it has been determined that they correlate with the child’s claim and support its recognition
Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa
Maswanganye, K.A (University of Pretoria, 2018)
Understanding the processes and patterns of gene flow and diversity within species requires detailedknowledge of how different life history traits enable organisms to adapt to their environments. Another valuable insight stems from the inference of past population distributions as reflected by contemporary phylogeographic patterns. The present study uses a multilocus approach to elucidate the evolutionary mechanisms underlying species distributions and diversity of three small mammals from southern Africa. The study explores the evolutionary history within two species of Hyracoidea, namely the rock hyrax (Procavia capensis) and the yellow-spotted hyrax (Heterohyrax brucei) and the diversification of the Grassland-Savanna clade of a murine rodent, the Namaqua rock mouse (Micaelamys namaquensis). All three species are rock-dwelling and distributed throughout southern Africa. Procavia capensis has a wide distribution spanning most of the African continent, whilst H. brucei is intermittently distributed from the northern parts of South Africa extending into the centre of east and central Africa. Micaelamys namaquensis is a widely distributed species able to adapt to different habitats, although rocky areas are preferred. Individuals of P. capensis, H. brucei and M. namaquesnsis were analysed using mitochondrial DNA (cytochrome b) and nuclear (introns & microsatellites) regions. The cyt b gene was used to study the matrilineal relationships, with a subset of individuals used to amplify the nuclear introns (AP5 and / or PRKC1) in each species. The intron and microsatellite data were used to identify patterns of genetic diversity and gene flow exhibited. Analyses of cyt b in P. capensis revealed two distinct groupings, the southern and northern lineages, with more than 30 unique haplotypes found within each group. In Heterohyrax two deeply divergent lineages were revealed; their taxonomic and conservation status should be evaluated. Although constrained by small sample size, unique haplotypes were discovered, with potential restrictions on gene flow between disjunct locations. The cyt b data of the Namaqua rock mouse displayed high levels of genetic diversity, with 52 maternal haplotypes. This revealed that the grasslands of southern Africa are complex, with signals of admixture between haplogroups. Grasslands are also characterised by a high species turnover and are extremely variable, with increased expansions and declines in response to changing environment. The microsatellite data were used to elucidate the extent of gene flow found between the different areas and to further investigate if this process is sex-biased. For the hyrax species I found minimal unidirectional gene flow between lineages, whilst the Namaqua rock mouse exhibited bi-directional gene flow. I identified areas within hyrax that could have served as refugia during unfavourable times, in turn acting as sources for reestablishment of contact when climate conditions improved. Hyrax distribution seems to be driven by food availability. By contrast the Namaqua rock mouse seems to be able to subsist and recover quickly from bottlenecks. With the dwindling habitat due to several anthropogenic factors (e.g. habitat fragmentation, climate change), improved management of biological diversity, especially in threatened environments, together with knowledge of drivers of species distributions and population dynamics within different landscapes are crucial.
Evaluation of the ability of health care providers and patients to distinguish different colour shades and accuracy of visual glucose estimation when using colorimetric glucose measurement strips
Mhishi, Simbarashe B. (University of Pretoria, 2018-11)
INTRODUCTION: The prevalence and incidence of diabetes has been on the rise globally and in South Africa is now considered an epidemic. Blood glucose monitoring has become crucial in managing diabetic patients. The accuracy of glucose measures in self-blood glucose monitoring are paramount in making treatment discisions by diabetic patients. METHODS: Diabetes patients attending the diabetic clinic at Kalafong Hospital in Pretoria, South Africa as well as staff attending to patients in the clinics were enrolled to participate in this study. A cross-sectional study was conducted in two phases, Phase 1 enrolled 53 individuals, phase 2 enrolled 150 patients and 10 healthcare professionals. Phase 1 assessed ability of patients and healthcare professionals to visually estimate glucose concentration of solutions over a defined range, and phase 2 assessed visual estimation of blood glucose on whole blood. In both phases Accu-chek active glucose strips were used. RESULTS: In Phase 1, the 95% CI of mean visually acquired estimates by patients did not intersect with the true readings despite showing proportional change as glucose values increased. Bland-Altman plots for phase 1 showed a bias of 5.65 mmol/L (95% CI 4.85 – 6.44 mmol/L). The agreement between classifications based on the two methods (visual estimates vs glucometer readings) gave a weighted Kappa statistic of 0.18. In phase 2 Bland-Altman plots showed a bias of -0.372 mmol/L (95% CI -1.2 to 0.531) for visual estimates by patents, healthcare professionals had a bias of -0.801 mmol/L (95% CI -1.30 to -0.309 mmol/L). Weighted kappa statistic for classifications of estimates by healthcare professionals was 0.428 and of patients <0.001. CONCLUSION: Colorimetric matching to estimate blood glucose is inexact, and generally results in over or under-estimating glucose levels
Composition, functional and nutritional quality of marama (Tylosema esculentum) storage root tuber (or tubers) and starch
Adeboye, Adedola S. (University of Pretoria, 2018)
Composition, functional and nutritional quality of marama (Tylosema esculentum) storage root tuber (or tubers) and starch
An ultrastructural, biochemical and viscoelastic investigation into the hypercoagulable state of breast cancer patients and the implications for the disease
Nunes Gonçalves, Julien (University of Pretoria, 2018-11)
Breast cancer patients are at an increased risk for thrombotic events such as deepvein thrombosis (DVT) and venous thromboembolism (VTE), drastically affecting their chance of survival and quality of life post-treatment. It has been proposed that this increased risk is caused by cancer associated inflammation-induced hypercoagulation, a key factor involved in thrombus formation. This study utilized microscopy and rheological techniques to examine coagulation components during clot formation, in order to obtain a better understanding of how changes to these components may increase thrombus formation and thus the risk of thrombotic events. Whole blood from treatment-naïve breast cancer patients were compared to whole blood from healthy controls. Routine clinical tests were used to obtain an overall clinical picture of each participant, and these showed no useful trend which could identify patients at an increased thrombotic risk. Scanning electron microscopy (SEM), revealed that red blood cells (RBCs) from patients showed more irregular surface membranes, increased agglutination and eryptosis when compared to healthy controls. Platelets also appeared to be further activated and fibrin fiber formation was increased. Thromboelastography (TEG®) was used to study the changes in clot dynamics during coagulation. Results showed that clots form faster in breast cancer patients, with increased strength and rigidity, thus revealing the hypercoagulable nature of whole blood in this patient group. The results in this study have revealed the marked differences in coagulation and associated blood components between healthy controls and treatment-naïve breast cancer patients. They provide a greater understanding of clot formation dynamics and has shown that even in a small sample size, breast cancer patients are at an increased risk of thrombotic events, traceable through rheological techniques. This justifies further investigation into the utilization of these techniques in a clinical, point-of-care setting, in order to increase the chance of survival and quality of life of these patients post-treatment
Temporal and spatial patterns of anthrax outbreaks in Lesotho (2005-2016)
Lepheana, Relebohile J. (University of Pretoria, 2018-09)
Background: Despite anthrax being endemic in Lesotho, limited information is available on the epidemiology of the disease. Therefore, this study investigated the temporal and spatial patterns of anthrax outbreaks and cases in the ten districts of Lesotho. Methods: The present study used secondary data of anthrax outbreaks and cases reported to the Department of Livestock Services (DLS) from 2005 and 2016. Outbreaks and cases were geocoded at the village level and aggregated at the district level. Proportions of anthrax outbreaks and cases and their corresponding 95% confidence interval were calculated using SAS 9.4 (SAS Institute Inc., Cary, NC) and compared across the year, season, month and region using the Chi-square test. However, when more than 20% of the cells had expected frequencies of < 5, Fisher’s exact test was used. Autoregression model was used to evaluate annual trends of anthrax outbreaks and cases. Global Moran’s I was used to assess the spatial autocorrelation of anthrax outbreaks and cases. Cartographic maps were used to display the distribution of anthrax outbreaks and cases at village and district level in ArcGIS 10.5 (Esri 2016, United States). Results: While no outbreaks were reported in the Highlands, a total of 38 outbreaks correlating to 526 cases were reported in the Lowlands districts of Lesotho. Maseru district had the highest proportions of outbreaks (52.6%) and cases (70.2%) Significantly (p=0.0004) higher proportions of anthrax outbreaks (78.9%) and cases (95.1%) were reported in the rainy-hot season compared to the dry-cold season. There was a significant association (p<0.0001) between cases and species affected, with the majority of cases (70.3%) reported in cattle. Out of 38 outbreaks that were reported, at village level, 18% (n=7) of outbreaks were in Maseru Urban followed by Ratau (16%, n=6), and Mofoka (13%, n=5). The highest proportion of cases over the population at risk were reported in Leribe district (14.3%) with the least proportion of cases (0.2%) reported in Mohale’s Hoek district (Table 4.2 and Figure 4.5). Among the villages, Mahobong had the highest proportion of cases 20.0%, followed by Pitseng 12.5%, and Kolo 10.5% (Table 4.2 and Figure 4.6). The result of the Moran’s I indicated no spatial autocorrelation at the village level in the Lowlands districts (I=- 0.199518; p-value=0.3684). Conclusion: The burden of anthrax in Lesotho was significantly higher in cattle compared to other species. Outbreaks were restricted to the Lowlands districts and occurred mainly in the hot-rainy season. The prevalence of anthrax outbreaks was higher in certain villages of Leribe, Mafeteng and Maseru. Therefore, anthrax control programs in Lesotho should focus on the high-risk areas and population to curb future outbreaks
Two-level multilevel models focusing on inference and diagnostics
Magagula, Zwelakhe L. (University of Pretoria, 2018)
This mini-dissertation is aimed at introducing multilevel analysis and how it can be applied to data with a hierarchical structure. Chapter 1 gives an introduction and background of multilevel modeling. In Chapter 2 we start with the theory of linear mixed models (LMMs), which includes the examples and structures of data sets for multilevel models, the general speci cation of LMMs, the di erent types of LMMs, and the multilevel linear model (MLM) speci cation of an LMM. In Chapter 3 we give the theory of estimation of parameters. Three estimation methods are given, namely the maximum likelihood estimation, the restricted maximum likelihood estimation and the iterative generalized least squares method of estimation. We proceed to illustrate the estimation of parameters in Chapter 4. In this chapter data is simulated from a multilevel model having covariates on both level-1 and level-2 of the MLM. We then explore the e ect that tting di erent models to the simulated data have on the within and between covariance parameter estimates. In Chapter 5 we discuss hypothesis testing and model selection. Data is simulated from a speci c MLM. We assume that the model is unknown and proceed to explain how a model is selected through various hypotheses tests. These tests include likelihood ratio test, the t-test, F-test and z-test. Di erent model t statistics are also introduced in this chapter. In Chapter 6 some of the diagnostic tools for multilevel linear models are discussed. The focus is on residual and in uence diagnostics. These tools are again illustrated on simulated data. Chapter 7 illustrates the analysis of multilevel models by making use of a practical example. In the analysis attention is given to centering of explanatory variables to obtain more interpretable coe cients and also the analysis of certain diagnostics to detect in uential observations in the data.
Respectful Treatment of Women in Midwife Obstetric Units: An Interventional Study to Improve Clinical Care in Tshwane District, South Africa
Oosthuizen, Susara J. (University of Pretoria, 2018-11)
South Africa did not meet its Millennium Development Goals 4 and 5. In 2014/2015 the country had a maternal mortality of ratio of 132.5 per 100 000 live births, a national stillbirth rate of 21.5 per 1000 total births and a child mortality rate of 39 per 1000 live births. A large proportion of child deaths occur in the perinatal and early neonatal period. Furthermore, many birthing women in South Africa, and worldwide, do not receive intrapartum care with empathy and endure disrespectful and abusive care, seldom voicing their complaints after these events. The consequence of not addressing mistreatment during labour could possibly contribute to the high maternal and perinatal mortality and morbidity in labour wards in South Africa. The aim of this study was to identify, implement and evaluate interventions to reduce mistreatment and to promote respectful, high-quality maternity care in five midwife obstetric units (MOUs) in Tshwane District, South Africa. A mixed-methods study was conducted in three phases in 10 MOUs. A purposive sample of five units was selected for the intervention. The study took place in three phases: (1) baseline measurements in all 10 units (health-systems building blocks, perinatal outcomes and women’s perceptions and experiences of care received during delivery); (2) the development of an intervention package – called CLEVER’ – based on the results of the first phase and implementation in the five intervention units; and (3) an end-line review of health-systems improvements and a repeat assessment of perinatal outcomes and respectful care in all 10 MOUs. The intervention had three pillars: (1) feedback of the results of the baseline measurements to the intervention units to raise awareness and solicit participation; (2) health-systems strengthening; and (3) an intensive weekly engagement with each intervention unit for three months, with monthly support for a further six months afterwards. Perinatal outcome indicators were compared over a period of three years: one year before the intervention (2015); the year of the intervention (2016); and the year after the intervention (2017). In the intervention units, significant reductions were observed between the baseline and end-line assessment for in-facility fresh stillbirths (from 8.50 to 1.30 per 1000 births), meconium aspiration (from 12.18 to 4.55 per 1000 live births) and birth asphyxia (from 15.56 to 8.12 per 1000 live births). For all three indicators the slope of change was much faster in the intervention MOUs than in the control units. Some improvements in the control units could possibly be ascribed to the supportive supervision programme of the district clinical specialist team. Women’s perceptions and experiences of the care received during childbirth were measured at baseline and end-line for all 10 MOUs with an anonymous, self-administered questionnaire completed by 653 women at baseline and 679 women at end-line. Six key items were used as proxies for clinical and respectful care. The end-line measurement recorded a significant improvement of 11 to 20% in women’s perceptions and experiences in the intervention MOUs with regard to consented care before pelvic examinations, positive communication behaviour, respectful treatment and overall satisfaction with birthing care. Working ‘CLEVER’, a clinically-focused intervention package, has the potential to reduce key perinatal mortality rates in midwife obstetric units and improve survival and health for newborns delivered at district health care level. Respectful care embedded in the package has the potential to improve communication and empathetic care to birthing women.
A spin on compressive sensing imaging : reticle-based single-pixel imaging system
Van der Merwe, Marco Marselle (University of Pretoria, 2024-09)
Various aspects of a single-pixel imaging (SPI) system are analyzed using a spinning reticle often referred to as a spinning coded aperture. The cost of imaging outside of the visual spectrum using FPA detectors becomes very expensive and an affordable alternative can have major implications in the commercial and military markets leading to more affordable imaging systems. The first documented use of a spinning disk imaging system came from the development of infrared (IR) missile seeker heads during the Second World War. These systems modulated the incoming light in amplitude of frequency to track a target. The use of spinning frequency modulation (FM) reticles as imaging devices was analyzed to determine the capability of such a system in general imaging scenarios. It was found that the frequency versus angle and radius reticle, termed FM-AR reticle, could only image simple scenes consisting of only a few targets. Using the simpler frequency versus radius reticle and modulating only a single column of pixels for each reticle rotation proved to be a viable option for imaging a wider range of scenes. However, the major drawback was that the imaging time to produce a single image was a factor of the number of columns in the image and the use of compressive sensing techniques was investigated as imaging of the entire scene in one reticle rotation was desired. compressive sensing (CS) is a signal acquisition technique to recover a sparse vector from only a few linear measurements. CS assumes a sparse vector being sampled and the use of sparsifying dictionaries is required for sampling non-sparse vectors such as images. Optimizing the sensing matrix to improve the recovery quality of the sparse vector uses coherence or cumulative coherence to determine a theoretical bound on the signal sparsity to guarantee successful recovery. SPI imaging systems employing CS techniques typically use a digital-micromirror-device (DMD) to modulate the incoming light and random binary patterns are often used. Using a reticle instead of a DMD has the potential to reduce the cost of such SPI systems as DMDs operating outside of the visual spectrum are also very expensive. The two types of reticle patterns considered related to where the patterns are constructed on the reticle. The edge-coded reticle has the reticle pattern constructed radially onto the surface and shifted towards the edge of the disk. The full-coded reticle used the entire surface for the reticle pattern. The edge-coded reticle was found to be a better alternative to the full-coded reticle as the edge-coded reticle allows controlling the CS compression ratio independently of the image dimension. Furthermore, the edge-coded reticle produces an image with a more consistent resolution compared to the full-coded reticle which consists of very small inner pixel dimensions and larger outer pixel dimensions. The genetic algorithm (GA) algorithm is a population-based metaheuristic method based on the Darwinian theory of survival of the fittest. The GA also allows the optimization of binary patterns that correspond to the opaque and transparent pixels on the reticle. Recovering sparse vectors with sensing matrices optimized by the GA for coherence and cumulative coherence generally showed improved reconstruction quality using sparse recovery algorithms. Op- timized sensing matrices consisting of floating point values showed improved recovery quality using OMP but the binary sensing matrices showed higher recovery quality using basis pursuit recovery algorithms. It was observed that the restrictions posed on the binary sensing matrix using an edge-coded reticle did not limit the resulting sensing matrix recovery ability and even improved the capability compared to the non-restricted binary sensing matrices. Training a sensing matrix on a separate image set, referred to as GA-TRAIN, using a sparse recovery algorithm to determine an average fitness score for each candidate in the GA’s population proved to be the better sensing matrix optimization technique. Using GA-TRAIN, improvements of up to 53.1% were observed compared to the GA optimizing coherence or cumulative coherence. Recovering real images using an edge-coded reticle only showed improvements comparing the first to final sensing matrix using the GA with the dB1 Daubechies wavelet dictionary in its second decomposition level (2dB1). This was only observed on the ImageNet dataset for optimizing coherence and cumulative coherence. The other dictionaries considered in this work, namely 1dB4, 5dB1 wavelet dictionary and the discrete cosine transform (DCT) dictionary, showed no noteworthy improvements in reconstruction quality when optimizing coherence and cumulative coherence on the MNIST and ImageNet datasets. The GA-TRAIN method was again used to train sensing matrices on real images and improved recovery quality was observed for all dictionaries and recovery algorithms except for the 2dB1 dictionary using GA-TRAIN. The coherence and cumulative coherence optimization showed slightly improved recovery quality on the ImageNet dataset compared to GA-TRAIN optimization method for the 2dB1 dictionary. It was generally noted that wavelet dictionaries with decomposition levels of one and two proved superior in sparse recovery compared to higher-level decomposition wavelets and the DCT in certain scenarios. The weight of a binary sensing matrix directly influences the signal-to-noise ratio (SNR) of the sampled vector and introducing noise into the sampling vector saw the coherence and cumulative coherence optimized sensing matrices struggle more than the GA-TRAIN optimized sensing matrix to accurately reconstruct the signals.
Black women navigating leadership advancement in the South African financial services sector
Freddy, Mandisa (University of Pretoria, 2025)
Black women remain critically underrepresented in South African financial services leadership despite three decades of democracy and comprehensive equality legislation. This study investigates how Black women navigate advancement into senior and executive leadership positions, examining the adaptive strategies they employ, the organisational systems that enable or constrain these strategies, and the persistent barriers that remain. Using an intersectional framework, the research explores how race and gender interact to create unique barriers that cannot be understood by examining either dimension in isolation. Through qualitative, phenomenological methodology, the study conducted in-depth semi-structured interviews with 13 Black women executives and senior leadership, and 5 organisational enablers in South Africa’s financial services sector. Thematic analysis revealed that whilst Black women employ sophisticated adaptive strategies. Their advancement depends critically on organisational transformation beyond individual adaptation. Findings demonstrate significant gaps between organisational diversity policies and actual structural and cultural levels, despite both individual and organisational efforts. The study contributes to intersectionality theory by measuring strategy effectiveness rather than merely documenting barriers, providing evidence-based guidance for Black women, organisations, and policymakers.
Pastoral perspectives on lived pain in maternal bereavement
Tsautse, Thato Abegail (University of Pretoria, 2026-06)
This study explored the lived experiences of maternal bereavement within the Anglican Church of Southern Africa, focusing on the Dioceses of Pretoria, Natal, and Eswatini. Using a hermeneutic phenomenological methodology, the research sought to uncover how bereaved mothers interpreted and lived through their grief, and how their experiences resonated with theological traditions and cultural frameworks. Data were gathered through in-depth interviews and written narratives and were analysed manually through iterative cycles of coding, use of the hermeneutic circle, and thematic reflection. Rigour was ensured through member-checking, reflexive journaling, and triangulation across diverse data sources. The findings revealed five central themes: the silence of the Church and pastoral neglect; the inadequacy of existing liturgical and ritual responses to maternal bereavement; the embodied and existential dimensions of grief, aligning with Heideggerian concepts of uncanniness, a disassembled world, and being-with; theological tensions involving faith, doubt, and divine providence; and the mediating role of cultural practices and community solidarity. Across the three dioceses, similarities emerged in mothers’ accounts of isolation and unmet pastoral needs, while contextual differences, such as geography, leadership styles, and local cultural practices which shaped bereavement experiences and coping strategies. Pastoral theological reflection highlighted the urgent need for the Church to re-imagine maternal bereavement care by extending support beyond the funeral, fostering communal and embodied practices of remembrance, and integrating Christological compassion with liturgical reform. The study concluded that maternal bereavement was both deeply disruptive and potentially transformative: a space where memory, lament, and resilience converged. A holistic pastoral response must therefore draw on interdisciplinary insights to accompany bereaved mothers with sensitivity, authenticity, and sustained care.
Bearing Witness: histories of black clergy wives in South African churches from 1948 to the present
Masango, Tshepo Morongwa (University of Pretoria, 2026-06)
Across the mid to late twentieth century, more than 85 percent of Black clergy within South Africa’s mainline Protestant churches entered ministry as married men. For many, marriage functioned as a central source of stability and support in their professional lives. Clergy who began their service unmarried often married shortly after ordination in response to expectations expressed by their congregations. The numbers matter because they reveal that marriage among clergymen was not an incidental occurrence. Marriage was an expectation, almost a prerequisite for ministry. The expectation was not simply wrapped up in the politics of respectability but in the understanding that clergy wives served a particular and important purpose in the Black church, even if the church did not openly acknowledge it. Even without degrees, titles, or formal training, clergy wives served alongside their husbands: preaching, teaching, praying, and organizing the mainline protestant churches, especially at the start of the twentieth century forward. Thus, clergy wives have long been an integral part of the Black church experience in southern African congregations. This pattern of joint ministerial service had regional echoes across Southern Africa, specifically in Zimbabwe, Zambia, and Malawi, where clergy wives were even more of a fixture n these more socially conservative contexts. These echoes throughout the region are quite telling, with South Africa often being the denominational hub for these countries. These findings remind us that missionaries made marriage a model for church leadership. This arrangement came to bear as European missionaries aimed to convert Africans beyond the missionary station, which was often established within or adjacent to the colonial city created by Europeans representing the governance of the metropole. When Europeans set their sights on implementing the mandate Jesus Christ had given his followers as stated in Matthew 28:18-20, "Make disciples of all nations, baptizing them in the name of the Father and of the Son and of the Holy Spirit, teaching them to observe all that I have commanded you," they worked together with their African colleagues to achieve it. European missionaries often relied on their African colleagues to carry out the Great Commission and lead conversion work in the interior of the nations, where they had less presence, despite the Africans’ subordinated position as evangelists. Many accounts of their work recognize that African evangelists worked in tandem with their spouses to spread the Christian gospel among their people. African church leaders, often coupled, worked beyond the initial framework that missionaries envisioned, cultivating a unique church culture. Long after the structure of the mission station gave way to colonial order, African clergy and their spouses remained an organizing force. To think of a congregation was to think of a minister; to think of a minister was to imagine his wife at his side. Clergy wives did not function merely as extensions of their husbands or of their husbands’ ministerial roles. They worked alongside them; more precisely, they were expected to do so. That expectation was cultural; it was spiritual; it was communal. Ministry was not conceived as solitary. It was firstly a covenant with God through ordination and then, secondly, in this context, a covenant with their wives. Ministry was interlocking and coterminous. This shared vocation did not stop at the church; the ministerial home was also an important site of ministry. It is important to note that for African clergy and their wives, the ministry extended far beyond physical walls, as it does with most church leaders. Within the physical church itself, ministers’ wives preached, led prayers, and organized associations. Beyond the church walls, they visited the sick, mentored young women, and often represented districts in denominational structures. Together, clergy and their wives engaged in important work even without the full authority vested in their vocational status. Only a small number of ministers’ wives pursued formal theological training or enrolled in seminaries during the mid to late twentieth century. Instead, training came through immersion; through mentorship; through song and prayer; through constitutions read aloud at kitchen tables; through the prayer meetings established and maintained, and through constant improvisation. The wives were revered, yes, but also burdened by the assumption that they could simply be a clergy wife from the beginning of their marriage. Their leadership was complementary, but not in the conservative sense articulated by the complementarian doctrine of U.S. evangelicals (Council on Biblical Manhood and Womanhood, 1988). Ministers’ wives defined their dominions and brought other women within their fold. The notion of a minister’s wife being complementary has never been steeped in the ideology of gendered deficient difference but instead was birthed out of a clear understanding of gendered spiritual need articulated by African women for African women. Among U.S. evangelicals, complementarianism is the sharp demarcation of women’s roles often defined by men (Aune, 2008; Gallagher, 2004; Ruether, 1985). It is a patriarchal exercise, emanating from the church. In contrast, African clergy wives’ complementarity has meant occupying distinct registers of ministry, never mere exclusion. Clergy wives have held an important vector of power in the church, all of it emerging from an expectation that came with marrying a religious cleric.
An autoethnographical witness on the long-term effects of child sexual abuse: a pastoral approach
Matseke, Sarah (University of Pretoria, 2026-05)
Child sexual abuse is not a new phenomenon, yet its occurrence remains hidden, with long-lasting effects that can impair many aspects of a victim’s life. Despite awareness of this human crisis, how victims carry permanent psychological, physical, psychosomatic, and spiritual scars is a subject rarely explored. This study aimed to examine child sexual abuse, its definitions and variations, as well as the long-term effects. Using an autoethnographic approach, the incidents of child sexual abuse, its long-term effects, and the environmental factors contributing to its incidence were investigated through the writer's personal story of CSA and validated against existing literature. By utilising Osmer's framework, this autoethnographic study goes beyond the personal narration of the story of child sexual abuse. The study serves as both an analytical and action-focused exploration of events that link individual experiences to broader systemic issues and possible solutions. This is conducted by examining the nature of the occurrences - what is happening, the underlying reasons - why it is happening, the standard approaches to the issues - what ought to be happening and providing practical solutions and actionable strategies - how might we respond.

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