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Analysis of The Demographics, Pathways to Diagnosis, Burden of Disease and Long-term Outcomes of Patients with Spinal Muscular Atrophy Managed at Red Cross War Memorial Children's Hospital
Full text linkSpinal muscular atrophy (SMA) is an autosomal recessive disorder of anterior horn cell degeneration which results in symmetrical muscle weakness that affects multiple systems. This study was conducted to determine the burden of disease of SMA on children under the neuromuscular service at Red Cross War Memorial Children's Hospital. A quantitative retrospective audit identified 86 DNA confirmed patients with SMA who attended the service from 2000 to August 2023. Thirty-six medical folders were accessible, 6 were excluded and 50 had been destroyed. An in-depth analysis of 30 folders showed a median age of diagnosis of 3.5 months for SMA1 (4 patients), 19 months for SMA2 (17 patients) and 34 months for SMA3 (9 patients). Five patients had demised and 4 were transferred to adult services. Over the study period, 172 chest infections were reported among the 30 children with SMA. Forty-three percent required home ventilation, 70% had scoliosis, 70% had contractures, 33% received feeding support via a percutaneous endoscopic gastrostomy tube and 44% of SMA3 patients had lost ambulation. Our SMA numbers are less than expected and delays in diagnosis were common. Strategies to improve diagnosis and minimize delays are needed and retaining medical records will provide more comprehensive insights on the long-term outcomes
The Panopticon, the State and Non-Profit Organisations in South Africa: A Systematic Review of Literature
No full textThe role of civil society, including non-profit organisations (NPOs), in promoting and protecting democratic processes is one of the key global debates about democracy. One indicator of the development of an enabling democratic environment is the nature of the relations between NPOs – especially advocacy NPOs - and the state. Advocacy NPOs tend to play a “watchdog” role in society and are often critical of the state, which can lead to an antagonistic relationship and repression of state critics. Monitoring relations between advocacy NPOs and the state is critically important as a barometer of the health of any democracy. With the ushering in of democracy in 1994, the adoption the new constitution (based on the principles of liberal democracy), and constructive working relations between many NPOs and the state during the Mandela administration, there was a general perception that a healthy democracy was evolving. However, relations between advocacy NPOs and the ruling party in South Africa soon became strained and at times adversarial. Over the past 25 years various scholars have contributed to a growing body of literature (e.g. Swilling & Russell, 2002; Habib, 2005; De Wet, 2010 & 2012; Leonard, 2014: Duncan, 2016; Volmink & Van de Elst, 2017; Maboya & McKay, 2019) which has analysed the nature of relations between NPOs and state in post-apartheid South Africa. While these authors sometimes reference each other, no single literature review has emerged. For this reason, I have undertaken a systematic literature review of a substantial portion of the relevant literature published in the past 25 years. I focus on relations between the South African state and NPOs in the context of a bigger debate about how the nature of this relationship is a proxy for the health of democracy in the country. The analytical lens used in my literature review is informed by Foucault's panopticon metaphor. In this regard, I was interested in understanding how the state has used its power and surveillance apparatus to control NPOs - especially advocacy NPOs that play a pro-democracy social watchdog role and where necessary challenge the behaviour of organs of the state. Methodologically and procedurally, I employed the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) protocol for this literature review. While there are some common patterns which emerge in the literature across the 25 years under review and covering the Mbeki, Zuma and Ramaphosa administrations, relations between NPOs (especially advocacy NPOs) and the state in post-apartheid South Africa have also changed somewhat over time and under different presidents. At times advocacy NPOs have experienced more state repression and at other times less. My findings show that across all three presidencies there are some overarching patterns that can be explained by Foucault's theory. These patterns reveal that the South African democratic state has adopted a disciplinary approach in its relations with NPOs. This disciplinary approach starts with the naming of some NPOs by Mbeki as “enemies of the party”, implying that others are “friends of the party” and by extension a third category, namely “frenemies”, has emerged. The introduction of such classificatory language during the Mbeki administration contributed to all NPOs experiencing varying kinds of control from incentives (e.g. state grants) to repression (e.g. surveillance and intimidation) depending where along the spectrum they fell. While during the Mbeki era, the state tended to rely more on incentivised cooperation with NPOs, the Zuma era was more crude in generously rewarding NPOs which cooperated with the state and severely punishing watchdog organisations critical of the state. However, more recently under the Ramaphosa's administration, the crude intimidatory and often illegal tactics used by the Zuma government to control NPOs are being replaced by more sophisticated systems of control. In particular, the General Intelligence Laws Amendment Bill has been recently introduced into the South African law making process in an attempt to legally institutionalise mass surveillance of civil society and the regulation of NPOs by state security agencies through a sophisticated legal apparatus which mainstreams and normalises the panoptic state. If this sophisticated legal approach by the state to control civil society becomes law then the South Africa state will take on more features of the panopticon with the infringement of the rights of citizens and NPOs, curtailment of their freedom to organise and their ability to criticise the state's abuses of power and ultimately undermine the country's constitutional democracy
Exploring topological data analysis in gene expression data topology-driven biomarker discovery and clinical outcome prediction in oncology
No full textThis thesis is grounded in the fundamental observation that biological data has shape and this shape matters. Beneath the high-dimensional, often noisy landscape of gene expression profiles lie hidden topological structures (connected components, loops and voids) that capture the complex relationships driving cancer development and progression. By embracing this perspective, we position Topological Data Analysis (TDA) and persistent homology at the core of a novel analytical framework designed to tackle two key challenges in cancer research: clinical outcome prediction and biomarker discovery. In this study, we employ Weighted Gene Topological Data Analysis (WGTDA) to extract topological features from gene expression data, which serve as prognostic biomarkers for cancer classification, staging, and treatment response. Moreover, by integrating these topological features with machine learning models we aim to enhance the predictive accuracy for clinical outcomes. For clinical outcome prediction, we transformed gene expression profiles into topological fingerprints using multiple co-expression measures—namely, Pearson Correlation, Distance Correlation, and Weighted Topological Overlap (wTO) computed with both Pearson and Distance-based adjacencies. These topological features were analyzed using Random Forests. In parallel, we compared the predictive performance of traditional machine learning models (SVM, Gradient Boosting Decision Trees, Random Forest, and Neural Networks) trained on raw gene expression data against models incorporating the topological fingerprints. This comparative analysis was conducted across three classification tasks: cancer type (using TCGA-SARC, TCGA-PCPG, and TCGA-ESCA datasets), cancer staging (using TCGA-HNSC for stages I–IV), and treatment response (responders vs. non-responders). For biomarker identification, the same three tasks were applied using the best performing co-expression measure to generate a global topological representation of the patient population. This provided a disease-level view, highlighting shared homological patterns to facilitate biomarker discovery. Additionally, a dedicated visualization tool has been developed to aid in interpreting these topological signatures and identifying critical biomarkers. The tool is available at https://nnyase.github.io/MSc-Thesis/ WGTDA significantly enhanced phenotype prediction tasks by overcoming common pitfalls of traditional ML models in RNA-Seq data, such as overfitting and poor handling of class imbalance. TDA-derived features improved generalizability of ML models in tasks such as cancer staging and treatment response prediction. Our findings strongly support the integration of TDA into clinical outcome prediction, demonstrating its value in capturing nuanced patterns that allow ML methods to learn more effectively. Moreover, WGTDA remarkably identified key gene signatures for cancer type, staging, and treatment response without relying on pre-existing biological assumptions, yielding biomarkers that are strongly supported by the existing literature. These results underscore the method's reliability and potential clinical utility in precision oncology
Should Kenya repeal its domestic limitation of benefits rule in favour of the simplified limitation of benefits rule in the MLI?
No full textThe Limitation of Benefits (LoB) rule is a recommended measure to fight treaty abuse by the Organization for Economic Cooperation and Development (OECD). It works by preventing residents of third-party states from accessing treaty benefits between states where they do not have sufficient connection in the contracting state based on set criteria. The rule originates from US tax treaty practices and has since been embraced in domestic and treaty practice by other countries worldwide. Kenya is one of the countries that have a domestic LoB rule, which was enacted in 2014. In addition to the domestic LoB rule, Kenya has also elected to include in its treaty practice a version of the rule known as the simplified LoB (SLoB). This has been done under the auspices of the OECD's multilateral tax treaty (MLI). While the two rules operate in different legal realms, there are similarities and differences in their construction and application. Similary, there are different challenges and opportunities in applying each rule in its own legal realm. By analyzing the current law in Kenya, the study highlights the history of the rule and examines its utility for anti-abuse purposes in Kenya today. The SLoB, which is poised to be applied at the treaty level once Kenya ratifies the MLI, is also discussed in detail in contrast to the domestic law provision. The study finds that while the two rules can co-exist, there is a convincing case for why the domestic LOB rule should be repealed. This is because of the main challenge it poses in jurisdictions where it is use which is allowing domestic law to override treaty law. Its repeal will also be a step towards bringing the practice in this area on par with best practices, as reflected in the drafting and content of the treaty version of the rule espoused by the SLoB. The study concludes that for Kenya and other developing countries that have the rule in their domestic law, the MLI presents an opportunity to align with international best practices
Fostering entrepreneurial mindsets in underserved communities - a multiple case study of Cape Flats in Western Cape, South Africa
Full text linkEntrepreneurship is increasingly viewed as a solution for employment creation and poverty alleviation in developing countries, specifically underserved communities. In developed countries, individuals usually possess both entrepreneurial intentions and competencies and have access to various resources and opportunities to start and scale their businesses. However, those in developing countries do not have access to this. Those who engage in entrepreneurial activities do so for survival and are identified as being part of the informal economy. This study aimed to evaluate a strategy that encourages entrepreneurial mindsets among individuals living in underserved communities on the Cape Flats in the Western Cape by examining three groups and their sustainability methods. To understand the different mindsets regarding entrepreneurship among people living in underserved communities, multiple case studies were conducted with three groups and analysed using thematic analysis. Group 1 was constantly seeking relief from daily life challenges, Group 2 were survivalist entrepreneurs, and Group 3 were opportunity-based or growth-oriented entrepreneurs. The goal was to develop a strategy informed by the experiences, attitudes, practices, and perspectives of individuals in Groups 2 and 3. By understanding their mindsets, we aimed to assist those in Group 1 by providing similar strategies to help them move forward. The research revealed that participants in Group 1 wanted to change their environmental circumstances; however, owing to a lack of entrepreneurial training and resources, they felt trapped and helpless. Some managed to face challenges by starting small businesses, either self-taught or inheriting skills, which mainly consist of artisanal skills. The study suggests that an increase in informal learning in these communities could be a strategy to help lift people out of difficult situations. This approach was explored further by incorporating skill development and entrepreneurial training as constructive interventions facilitated by individuals or groups. These initiatives can help reduce unemployment and address various social issues
Does one size fit all? exploring the effect of hearing aid impulse noise reduction on isiXhosa click sounds: a pilot study
Full text linkGender diversity remains a significant challenge in the Information Technology (IT) industry, particularly in South Africa, where the workforce composition does not reflect the nation's demographic diversity. This disparity results in the underrepresentation of women despite policies aimed at fostering inclusion. Existing research highlights a decline in women's participation in the IT sector but often overlooks the perceptions and treatment of women within IT workplaces. This study investigates women's experiences working in Agile project environments in South African IT companies. Agile is a popular software development methodology emphasizing collaboration, communication, and collective decision-making. Using intersectionality theory, this cross-sectional study examines how gender and background factors affect women's work performance. Data were collected through semi-structured interviews with twenty-five women IT professionals recruited via snowball sampling. Key findings indicate that gender discrimination persists in Agile environments. The study revealed that South African women in Agile project environments exist within a male- dominated, Gendered Organisational Culture, which privileges behaviours and actions that benefit men. Women in these environments often experience feelings of inadequacy due to their minority status in predominantly male teams. Other specific persistent issues emerged such as gendered recognition bias, gender pay gap, job insecurity, lack of support for motherhood, work-life balance, and scarcity of women mentors. The study further reveals that the high attrition rate of women in IT is not due to the technical demands of the roles but rather the negative impact of organisational culture and gender bias on their professional development. The study's limitations include its reliance on a small, non-random sample, which may not fully represent the broader population. Additionally, the focus on Agile environments may limit the generalizability of the findings to other IT settings. Future research should explore the intersection of gender with other factors, such as socioeconomic status and motherhood, providing a more comprehensive understanding of the barriers women face in IT. It should also investigate strategies to create more inclusive and supportive workplace cultures
Navigating extreme weather events: An anthropological investigation
Full text linkThe aim of this study was to investigate how do people respond to extreme weather events (EWEs), paying special attention to heavy rainfall. The data and literature gathered unearths strategies and tactics embedded in the social structure of the area of Crawford. These strategies and tactics are either manipulated or reconfigured in patterns of individuality, to gauge what necessary actions are required to mitigate the impacts of heavy rainfall. These approaches were used to answer the foundational question of this study, what roles do existing social relationships play in people's perceptions and responses to extreme weather events? By utilising qualitative research techniques, this study argues that residents of a middle-income neighbourhoods like Crawford respond, adapt and prepare for extreme rainfall in individualised manners. Contrary to areas of less socioeconomic standing who utilise communal strategies such as conviviality to address the challenges heavy rainfall brings
Quantification of fatigue damage in AISI 316L stainless steel using X-Ray powder diffraction (XRD)
Full text linkIn an electricity generation utility, there exists an enduring insistence on improving the efficiency, performance, and reliability of mechanical components with respect to economic challenges. Thus, the comprehension of materials and their behaviour in a typical operating environment is key to enabling and aiding capabilities in component life assessments. Fatigue damage is among the major issues in engineering, because it increases with the number of applied loading cycles in a cumulative manner and can lead to fracture and failure of the considered part. This study systematically investigates the microstructural changes in a material due to cyclic stressing using a non-destructive examination Power X-ray diffraction (PXRD). In industry, the evaluation of material deformation post cycling loading is often performed using microscopic techniques such as transmission electron microscopy (TEM) and electron backscattered diffraction (EBSD). However, each of these techniques have their own limitations. The PXRD technique is advantageous when applied to crystalline materials, as it is sensitive to changes in the crystalline structure of the metal, thus providing a foundation for the development of a capability to enable the early detection of fatigue damage with the aim of improving asset management. The microstructural baseline undertaken in the study involves the calculation of dislocation density in the material. The evolution of dislocation density in steels is an important aspect of the mechanical response. It could potentially be used as a fingerprint to relate the material state to the life-consumption fraction in materials subject to fatigue conditions. To mimic the fatigue damage mechanism, cyclic loading of material specimen is performed in a laboratory. In view of the exploratory nature of the present study, a stable single-phase austenitic microstructure, namely AISI316L stainless steel, was selected for the relative ease of characterizing dislocation development and comparison with PXRD analysis. The initial step included plotting an S-N curve for the AISI316L material in the material annealed state following fatigue testing in the INSTRON machine. A specific stress level was selected to ensure sufficient data retrieval prior to point of failure for the material specimen. Thereafter candidate specimen for fatigue including as received and annealed specimens formed part of the material states used in the study for microstructure analysis using three evaluation techniques. The EBSD results mostly show good qualitative agreement with the PXRD analysis. TEM analysis was used to qualitatively visualise the individual dislocations but is very time-consuming to perform quantitatively and the results are subject to large scatter. Validation of the PXRD techniques was performed using qualitative and quantitative TEM dislocation density results and semi-qualitative EBSD results. This study presents a consistent approach to determine the dislocation density using a benchtop laboratory based PXRD. The calculated dislocation density results analysed from the vast volumes of experimental data collected throughout the study highlighted important aspects to be undertaken. These include sample preparation, control of instrumentational parameters and the correct selection of instrument modelling standard. The Williamson-Hall plot and the whole pattern fitting methods are the two evaluation techniques utilised for size and micro-strain broadening of PXRD peaks. The results have proven to be repeatable owing to the systematic manner in the number of samples used per specimen as well as the stringent control of parameters used
The relationship between financial sector development and economic growth: the case of Zambia
Full text linkThis study examines the relationship between financial sector development and economic growth in Zambia, focusing on the roles of financial sector growth, bank efficiency, human capital, and institutional quality. Given Zambia's ongoing financial reforms, the research aims to fill the gap in understanding how these factors influence economic performance, particularly in the short and long term. The problem addressed by the study is the unclear impact of financial sector reforms on economic growth, despite substantial progress in financial sector development. The study's objectives were to estimate the short- and long-run relationships between financial sector development and economic growth, analyse the effect of bank efficiency on financial sector development, and explore the moderating influence of human capital and institutional quality. The results, derived from the ARDL model, indicate that financial sector development has a positive long-term relationship with economic growth, with no significant short-term effects. While improvements in bank efficiency were found to be positively associated with financial sector development in the long run, no substantial short-term impact was observed. Human capital and institutional quality did not show significant effects on economic growth or bank efficiency, suggesting that these areas need further development for full economic benefits. The study concludes that while financial sector development plays a critical role in driving long-term economic growth, improvements in human capital and institutional quality are necessary to enhance the sector's effectiveness. The findings offer valuable insights for policymakers seeking to strengthen Zambia's financial sector and achieve sustainable economic growth. Further research is recommended to explore the delayed effects of financial reforms, the role of financial technology, and the impact of institutional quality on economic outcomes
Investigation of circulatory and tissue-specific metabolomic biomarkers in valvular heart disease using mass spectrometry
Full text linkThe work presented in this thesis was based on an investigation of the circulatory and tissue specific metabolic biomarkers in patients with rheumatic heart disease (RHD) and degenerative aortic stenosis (AS), compared to matched, healthy controls. The study hypothesis was that cardiac tissue obtained from heart valve biopsies from RHD and degenerative AS patients would have distinct histological features. The second hypothesis was that severe RHD and degenerative AS patients have distinct serum and tissue specific metabolic profiles. The third hypothesis was that pathologic regions on heart valves would have distinct spatial metabolomic profiles compared to non-diseased regions of the valves. Whole blood samples were collected from matched participants with a diagnosis of RHD and degenerative AS, as well as matched controls recruited from the Cardiac Clinic at Groote Schuur Hospital. Valve tissue samples were collected from patients undergoing valve replacement surgery at Groote Schuur Hospital. Haematoxylin and eosin staining was used to assess the histopathological features of the heart valves. Untargeted metabolomics was performed on serum and valve tissues using ultra-performance liquid chromatography with quadrupole time-of-flight mass spectrometry. In-situ biomarker localisation was performed with matrix assisted laser desorption ionisation mass spectrometry imaging. Univariate and multivariate statistical analyses was used to explore covariation with the potential metabolomic biomarkers and bioinformatics tools used to explore the gene-metabolite interactions. The study had several key observations. First, though rare, we reported that chronic RHD may be admixed with features of acute rheumatic fever, within the same patient. Second, using an untargeted/discovery approach, we identified metabolites involved in the major energetic pathways, amino acids metabolism, and inflammation regulation which were altered in RHD and degenerative AS. The identified biomarkers were associated with cardiovascular imaging-based remodelling parameters. Third, RHD patients with single or double valve replacement, and degenerative AS patients demonstrated distinct tissue-specific metabolic signatures. Metabolites involved in amino acid, fatty acid, and crucial biomolecule metabolism were associated with histopathological and cardiovascular imaging-based parameters of valvular heart disease. Finally, tissue-specific metabolites could be localised on valve biopsies obtained from RHD and degenerative AS participants, though no differences were observed between the two group