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Evaluation of the operational Mercator Global Ocean analysis and forecast system modelled current vector product with in-situ ADCP data in the Southern Benguela upwelling system
Get PDFGlobal ocean current vector datasets are frequently used to force, or are assimilated into, local and regional particle tracking and pollutant dispersal models, metocean forecasting platforms, climate analyses, and natural resource management applications. The Operational Mercator global ocean analysis and forecast system (Mercator data product), made publicly available in 2022, provides near-real-time vector components of global ocean currents at 50 vertical levels (depths) in the water column with a horizontal resolution of 1/12 degree. Validation of ocean forecasting and simulation models is required to assess a modelled product's ability to represent the local environment. Validation is done using in-situ data such as those gathered by Acoustic Doppler Current Profilers (ADCP). In this study, an upward-facing Nortek Signature 250 ADCP was deployed at a depth of 123 m off the Southern Namibian coast for ten months. The resulting current profile data were used to validate the Mercator data product for the same area. Data collected by the ADCP and simulated data from the NEMO model were matched spatially (nearest-neighbour) and temporally (rolling average), and the similarity of current vector components was statistically investigated. Spearman Rank-Order Correlation, root-mean-square-error and bias were calculated for the full time series. The seasonal percent occurrence of current vector magnitude and direction were subsequently derived to assess the Mercator data product's ability to represent seasonal variability. The Mercator data product captured the seasonal variation in the magnitude of the nearshore southern Benguela Upwelling System for both the zonal and meridional components well. The Mercator data product represented much lower complexity in the direction of bulk flow GAMMON iii within the system but did contain the daily oscillation pattern measured by the ADCP. The Benguela Current is a physically complex eastern boundary current spanning three countries, used extensively for fishing, mining, maritime transit, and oil extraction. The ocean current outputs from the Mercator data product could allow for improved pollution modelling (oil dispersion or plume modelling), improved fuel optimisation models for maritime transit, and productivity prediction to support fisheries management without the cost of deploying devices to measure ocean currents in situ
Trajectories of Change in South Africa's Freshwater Fish Fauna
No full textIn South Africa, freshwaters are the most threatened ecosystems in the country, facing pressure from water abstraction, land-use change, pollution, invasive species and climate change. These anthropogenic pressures are directly impacting the diversity, abundance, and survival of freshwater fauna and flora across the country. Freshwater fishes are recognised as South Africa's most threatened species group, with one third of species classified as threatened (Vulnerable, Endangered, Critically Endangered) by the International Union for the Conservation of Nature (IUCN). Understanding patterns of diversity, threat, invasion, and protection status are vital for management. However, access to reliable and comprehensive long-term data on fish distributions, are limited. This thesis aims to collect, collate, and analyse historic and current freshwater fish records for all fish species (native and non-native) known to occur in South Africa, to better understand distribution, diversity, and threat patterns in space and time. A comprehensive freshwater fish occurrence dataset for South Africa was compiled and uploaded to the Freshwater Biodiversity Information System (FBIS, freshwaterbiodiversity.org). An 18-month historic-data collation effort resulted in the accrual of 35 955 records of freshwater fish from South Africa spanning 194 years (1828–2022), that have since also been uploaded to the Global Biodiversity Information Facility (GBIF). Together with pre-existing GBIF records (24 861), a total of 60 837 freshwater fish records are thus now available for South Africa. The data show a marked decline in the number of native fish occurrence records over the last decade relative to the previous five decades. Conversely, the number of occurrences for non-native fishes increased over the past three decades. A breakdown of the data is provided for all native (n = 105) and non-native (n = 24) species as well as for all endemic (n = 40) and threatened (n = 27) species. Using occurrence records collected for this thesis, spatial patterns in distribution, diversity, threat, invasion, and protection status of freshwater fishes in South Africa were analysed. Few studies have undertaken such analyses at ecologically and politically appropriate spatial scales, largely because of limited access to comprehensive biodiversity data sets. Results show that record density varies spatially, at both primary catchment and provincial scales. The diversity of freshwater fishes also varied spatially: native species hotspots were identified at provincial level in the Limpopo, Mpumalanga and KwaZulu-Natal provinces, endemic species hotspots were identified in the Western Cape, and threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Non-native species distributions mirrored threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Some 47% of threatened species records fell outside of protected areas, and 38% of non-native species records fell within protected areas. Concerningly, 58% of the distribution ranges of threatened species were invaded by non-native species. A data breakdown is provided for each of South Africa's nine provinces including total number of records, and the numbers of native, non-native, endemic and threatened species. These data provide a much-needed update of the known status and distribution of freshwater fishes in the country. To support future spatial modelling of South Africa's freshwater fish species distributions, a robust and repeatable method for applying Species Distribution Models (SDMs) to freshwater fishes was developed. Specifically, this thesis sought to investigate whether SDMs could be applied to a wide range of freshwater fishes in South Africa and whether the inclusion of invasive species spatial data would result in improved model accuracy and performance. Using a Bayesian Additive Regression Trees (BART) algorithm, the distributions of three black bass (Micropterus salmoides, M. dolomieu, and M. punctulatus) species and two native species (Clarias gariepinus and Pseudobarbus burgi) were modelled. A total of 148 hydrological and 16 biological predictor variables were specifically developed for this chapter, along with the collation of 75 environmental predictor variables. The results demonstrated that, with appropriate data cleaning and using a statistically robust method for selecting predictor variables, model outputs performed well, with the resulting modelled distributions congruent with known distributions and historic descriptions of the species' presence. All models for invasive, native, and threatened species performed well, with AUC values ranging from 0.923–0.994 and TSS ranging from 0.701–0.940. Furthermore, model performance for P. burgi was not improved by the inclusion of biological predictors (invasive species). The AUC for the original P. burgi model (including only climatic, environmental, and hydrological predictors) was 0.994, whereas the adapted model (including both climatic, environmental, and hydrological predictors as well as biological predictors) was marginally lower, with an AUC value of 0.993. This indicates that the inclusion of invasive species as biological predictors may not be necessary to produce accurate predicted species distributions. This thesis also presents a case study demonstrating how the FBIS system was used to provide freshwater fish spatial data products to a national conservation decision-support tool – The Department of Forestry, Fisheries, and the Environment (DFFE) National Environmental Screening Tool. The Tool uses empirical and modelled biodiversity data to guide Environmental Impact Assessments of proposed developments. Occurrence records for 34 threatened freshwater fishes occurring in South Africa were extracted from the FBIS and verified by taxon specialists, resulting in 6 660 records being used to generate modelled and empirical national distribution layers. This represents the first inclusion of freshwater biodiversity data in the Screening Tool, and future iterations of the Tool will incorporate additional freshwater taxa. This case study demonstrates how systems like the FBIS can play a pivotal role in the data-to-decision pipeline through supporting data-driven conservation and management decisions at a national level. The collective findings of the thesis are concluded in Chapter 6, which highlight the importance of collecting, collating, and consolidating biodiversity data at a national level. The dataset presents the largest (by number of records) collection of freshwater fish records in Africa to date, with data spanning 194 years. This thesis also presents an updated version of South Africa's Species List for Freshwater Fishes, which includes all known native (n = 107) and non-native (n = 27) species occurring in the country, and key species attributes like species origin, endemism, and threat status. By consolidating historical data for all known freshwater fishes, this thesis presents the first comprehensive assessment of the status of South Africa's freshwater fish fauna, providing valuable insights into spatial patterns of richness, endemism, threat status and non-native species, as well as assessing how effective the country's protected area network is for protecting freshwater fishes. This thesis addressed the critical need for a deeper, data-driven understanding of spatial and temporal variation in South Africa's freshwater fishes – an essential foundation for sound management of these species and their habitats into the future
ETD: Symptoms and Intraoperative findings in patients undergoing revision fundoplication
No full textApproximately 20% of patients who undergo anti-reflux surgery will report a recurrence of reflux symptoms or develop new symptoms, with 5% ultimately requiring revision fundoplication. The aim of this study is to document symptoms at representation, pre-operative work-up and intraoperative findings of patients presenting for revision fundoplication (RF). Methods: This is a single center descriptive retrospective review of 37 patients who required revision of a previous fundoplication for significant recurrent symptoms between January 2015 and December 2017 at Groote Schuur Hospital and UCT Private Academic Hospital. Patient data included demographics, body mass index (BMI), patient reported symptoms prompting initial fundoplication, interval to symptom recurrence and RF, technique of the first and subsequent revision surgery and perioperative morbidity. Recurrent symptoms at representation, results of pre-operative investigations and actual intraoperative assessment during RF were reviewed. Results: During the two-year study period 37 patients underwent RF. The mean age was 52.9 years (range 22 – 77 years, SD =13.3), with 25 (67.6%) females and 12 (32.4%) males included in the cohort. The most frequent patient-reported indication for index fundoplication was gastro- oesophageal reflux (GOR) (65%). Symptoms at representation prior to RF included dysphagia (51.4%) and heartburn (51.4%) equally, epigastric pain (48.6%), volume reflux (43.2%), atypical chest pain (24.3%), bloating (16.2%), nausea (13.5%) and early satiety (10.8%). The most observed endoscopic finding (available in 35 patients) was a recurrent sliding hiatus hernia (42.9%). All had a contrast swallow with evidence of delayed transit into the stomach present in 45.9%, recurrent sliding hernia and dilated distal oesophagus in 35.1% equally. The RF was performed at a median of 24 months (IQR 2.5 - 66 months) following prior fundoplication. Technique of RF included 17 (45.9%) conversions from full Nissen to partial anterior fundoplication (Dor), 10 (27.0%) re-do Nissen's, two (5.4%) conversions from full Nissen to partial posterior fundoplication's (Toupet), three (8.1%) complete reversal of fundoplication with oesophagogastric junction adhesiolysis, two (5.4%) Heller's myotomies with anterior fundoplication, two (5.4%) crural repairs only (intact wraps) and one (2.7%) opening of tight crura closure. The majority (83.8%) of revisions were completed laparoscopically. The most frequent intraoperative findings included significant oesophagogastric adhesions with wrap distortion (75.7%), recurrent crural defect (51.4%), slipped wrap (45.9%), distal oesophageal/crural fibrosis (37.8%), recurrent sliding hernia (35.1%), a tight crural inlet (24.3%), mixed herniation (10.8%) and three (8.1%) para-oesophageal hernias. Conclusion: This single-center review on revision fundoplication conforms with much of what is written in other studies. Dysphagia is the predominant symptom prompting repeat surgery and most patients present two years after their initial operation. Despite revision anti-reflux surgery remaining technically challenging, the vast majority of operations were completed laparoscopically with low associated morbidity. Larger, multi-center studies would allow for a bigger picture of revision anti-reflux surgery in the greater South African context
Mentorship expectations differences across generations: A study of South African black women
Get PDFThis research investigates the differing mentorship expectations among African-Black women across three generational cohorts: the Struggle Generation (ages 42–61), the Transition Generation (ages 29–41), and the Born Free Generation (ages 22–28). Recognizing mentorship as a vital coping strategy in workplace environments, the study employs qualitative research to explore how factors like historical context, technology, and intersectionality shape these expectations. The study employs a qualitative methodology to explore mentorship relationship expectations among different generational cohorts of African black women in South Africa. Through in- depth interviews with participants from the Struggle, Transition, and Born Free Generations, the research uncovers nuanced experiences and expectations surrounding mentorship. A semi-structured format facilitated open dialogue, allowing participants to share their beliefs and motivations. Data collection adhered to ethical guidelines, ensuring confidentiality, while thematic and narrative analysis identified key patterns and themes. This approach captures diverse perspectives, contributing to a deeper understanding of mentorship dynamics within this demographic. Findings reveal that while the cohorts share a common understanding of mentorship, they differ in preferred formats, key factors for effective relationships, and desired qualities in mentors and mentees. The Struggle Generation balances professional and familial roles, the Born Free Generation seeks digital and informal avenues, and the Transition Generation emphasises proactive engagement. Ultimately, this dissertation highlights that for mentorship to deliver on its promise of fostering both professional growth and personal empowerment, it needs to be dynamic and evolve with the changing needs of generations. The insights underscore the need for tailored mentorship programs that address the diverse needs of African-Black women
Performing the encounter; a practice-led inquiry
Get PDFThis dissertation explores the ethical and relational dimensions of verbatim theatre, focusing on how encounters between theatre-makers, participants, and audiences shape both the creative process and the final performance. Moving beyond traditional notions of representation, it argues that verbatim theatre is not merely a vehicle for reproducing real-life narratives but a dynamic practice of engagement, wit(h)nessing, and artistry. Through a practice-led inquiry, two key projects - Sense of Home and Company in the Gardens - are examined to consider how verbatim theatre can foster attentiveness to the complexities of lived experience while avoiding ethical paralysis in creative work with real-life narratives. By prioritising the process of encounter over fixed notions of truth or authenticity, these projects explore how the exchange between interviewer and interviewee, performer and audience, generates meaning and challenges pre-existing assumptions. The research situates verbatim theatre within broader discussions on ethics, presence, and relationality, considering how the form can resist simplification, create spaces for dialogue, and foster meaningful connections across difference. By weaving together autoethnographic reflections, theoretical analysis, and artistic practice, this study proposes a framework for an ethical and relational approach to verbatim theatre. Ultimately, it positions the form as a political act - an ongoing practice of presence, attentiveness, and shared meaning-making
“And then you go home having anger issues”: investigating Police-perpetrated domestic violence in South Africa
Get PDFAs those entrusted with the duties of safety, security, care and protection, police officers play a significant role in responding to the crisis of domestic violence in South Africa. Paradoxically, they are capable of perpetrating the very crime they are sworn to prevent and equally capable of failing to hold those who do accountable. Police-perpetrated domestic violence (PPDV) is a globally prevalent yet largely understudied phenomenon, particularly in the South African context. Drawing on literature, police oversight monitoring reports, quantitative data and interviews with South African Police Service (SAPS) Station Commanders and Domestic Violence coordinators, this dissertation sheds light on this largely underexplored phenomenon providing a more contextualised understanding of PPDV in South Africa with a more selective focus on the Western Cape where its rates are disproportionally high. Research findings illustrate the complexity of PPDV, revealing an interplay of multiple influences and factors that contribute to its emergence and undermine state efforts to address it. Its findings emphasise the need for targeted reforms to take the issue of PPDV and the wellness of police officers in South Africa far more seriously than is currently the case
The moral economy of Islamic philanthropy in Cape Town: the case of Mustadafin Foundation and the African Muslims Agency
Get PDFThis dissertation explores two Muslim philanthropy organisations in Cape Town, the Mustadafin Foundation and the Africa Muslims Agency (AMA). The aim of the thesis is twofold: one is to unpack the plurality of ethics that motivate their philanthropy, and the second is to explore the ways and extent to which they constitute a moral economy of donation and distribution. Established in 1986, the Mustadafin Foundation is a homegrown South African organisation with a legacy of community building and political activism driven by an Islamic social justice ethos. On the other hand, AMA was founded in 1981 as a transnational humanitarian organisation operating across Africa and Asia. Both organisations play a critical role in township development by providing food, water, education (secular and religious), disaster relief, and other essential services. Drawing on ethnographic fieldwork and theoretical analysis, this study illuminates the vast tapestry of engagement woven by faith, ethics of care, and community building in a post- apartheid dispensation. It argues that the motivations for giving are diverse, encompassing religious obligation, social solidarity, and community welfare. Anchored in Alhourani's (2024) conception of Islamic giving as constitutive of moral economy and Mona Atia's (2013) concept of pious neoliberalism, the dissertation examines the strategic objectives of Islamic philanthropy and its contributions to the social and economic growth of township communities in Cape Town. This dissertation contributes to the nascent field of Islamic philanthropy studies in Cape Town by providing a comparative account between local and transnational Muslim philanthropic organisations. The thesis argues that a plurality of ethics inspires both organisations and that they constitute a moral economy. It offers critical insights into its role in fostering social cohesion, social solidarity, conviviality, and Islamisation
DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea
No full textDichrostachys cinerea, commonly referred to as “sicklebush”, is a semideciduous nitrogen-fixing tree species belonging to the Fabaceae family and is native to parts of Africa, India and Northern Australia. In addition to propagation via seed dispersal, the species is capable of asexual reproduction via the process of root suckering. D. cinerea can aggressively colonize grasslands and quickly becomes problematic given its ability to persist through treatments such as fire, chemical treatment and mechanical removal. Due to its shrub-like physiology; propensity for root suckering; and the production of large amounts of seed, removal efforts often fail, especially in areas where D. cinerea has established dense thickets. African savannahs in particular have experienced a rapid rise in woody plant encroachment, with D. cinerea often one of the major species held responsible, and it is a species of concern to local ecologists. While previous studies have investigated the various factors which contribute to woody plant encroachment within Savanna ecosystems, it is still unclear as to what role asexual reproduction plays in this phenomenon and current methods to study this are laborious and time consuming. This study sought to develop a genetic based workflow to allow the detection of clonal individuals in D. cinerea. To facilitate this study, 225 D. cinerea samples were collected across the species range of D. cinerea in South Africa. DNA extracted from these samples allowed for the identification 39 299 SNP markers generated from ddRAD-seq libraries. These SNPs were then used to elucidate the phylogenetic relationships between individuals in order to ascertain whether clonality could be detected within the species, via the use of a genetic-distance-based threshold value which would discriminate between clonal and non-clonal individuals. Findings from this study revealed that across its species range, D. cinerea consisted of a mixed cytotype population, exhibiting a clear phylogenetic divide between diploid and tetraploid individuals. Identity-by-state analysis of the Kruger National Park diploid population confirmed that naturally occurring clonal individuals could be detected via ddRAD-seq generated SNP markers. This workflow will facilitate the study of clonality in D. cinerea in future studies which seek to answer ecologically relevant questions
Using single nucleus RNA-seq to determine the effect of immunosuppression on the transcriptional activity of resident CNS cells in a mouse model of CNS-TB
No full textTuberculosis (TB) is the leading infectious cause of death worldwide and is particularly prevalent in South Africa. Central Nervous System TB (CNS-TB), specifically TB Meningitis (TBM) is the deadliest complication of the disease. Given the high co-prevalence of HIV and CNS-TB, many transcriptional studies have examined the immunocompromised response to CNS-TB, but none have done so atsingle cell resolution. Single nucleus RNA Sequencing (snRNA-seq) was used to determine the effect of immunosuppression on the transcriptional activity of resident CNS cells in a mouse model of CNS-TB. The model consisted of two mouse genotypes, namely Wildtype and TNF knockout (TNF-/- ). Mycobacterium Tuberculosis was injected into the somatosensory cortex of the treatment groups, with control samples receiving a saline injection. Brains were harvested at 9- and 17-days post inoculation. Following library generation, removal of ambient RNA and data processing using Seurat, differential gene expression analysis was used to identify differentially expressed genes (DEGs). Oligodendrocytes had the most DEGs in the general TB response, whereas excitatory neurons had the highest DEGs in the immunocompromised TB response and with disease progression. Potential mechanisms by which these cell types contribute to the pathogenesis of CNS-TB were explored, such as excitotoxicity, demyelination and neurodegeneration. Pathways related to neurogenesis were identified in the immunocompromised TB response. The study adds to the body of knowledge by identifying cell type specific resident gene expression responses in the context of CNS-TB
Navigating equitable technological empowerment: Insights from Ghana and Rwanda on digital literacy and the fourth industrial revolution
No full textThe Fourth Industrial Revolution (4IR) is reshaping global economies and societies. Triggered by several factors including the COVID-19 pandemic, assuming its dynamics in developing countries will mirror those in wealthy economies is perilous. With its unique challenges and opportunities, Africa requires a tailored strategy for the 4IR. At the core of this strategy is achieving widespread digital literacy, a critical factor for technological empowerment and inclusive development. However, the urgent need for improved digital literacy in many parts of Africa poses a significant barrier to progress. This dissertation explores the key factors and strategies for fostering equitable technological empowerment across sub-Saharan Africa through digital literacy. For this purpose, Ghana and Rwanda have been chosen as case studies. To answer this question, we compared the experiences a sample of students in tertiary institutions in both countries before their enrolment. We uncovered several critical constraints on achieving adequate digital literacy, thereby highlighting the necessary policy changes and practice reforms required for Africa to thrive in the 4IR context. Through this comprehensive analysis, the dissertation seeks to contribute to developing an Africa-wide 4IR strategy that leverages digital literacy as a cornerstone for sustainable growth and development. The outcomes of this study have been conceptualized into a praxis model for 'Equitable Digital Literacy Community Centres.' This model, which offers a practical and actionable approach to implementing the required changes, aims to provide accessible, inclusive, and sustainable digital literacy training and resources to communities across sub-Saharan Africa