OpenUCT is the open access institutional repository of the University of Cape Town (UCT). It preserves and makes UCT scholarly outputs digitally and freely available, including theses and dissertations, journal articles, book chapters, technical and research reports, as well as open educational resources.
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Open Access
Generating mESC-derived cerebral organoids to study neurodevelopment and disorder
(2026) Andersen, Nathalie; Goolam, Mubeen
Background: The development of the human brain is a complex and regulated process that begins with the formation of the neural tube and continues into early adulthood. Disruptions at any stage of this process can lead to various neurological disorders. This is particularly relevant in Africa, which faces a considerable burden of neurological diseases such as tuberculous meningitis and epilepsy. Traditional models used to study neurodevelopment and neurological disorders include 2D cell cultures, animal models and human brain tissue, however, each of these model systems has limitations. The 2D cell cultures lack the complex cytoarchitecture and cellular diversity of the in vivo brain. Animal models exhibit species-specific differences and the ethical concerns surrounding the use of live animals limit their translatability and use. Human tissue is limited by availability, ethical considerations, short viability of live samples and absence of metabolic activity in post-mortem tissue. Together, these limitations highlight the need for biologically relevant and accessible model systems that more accurately represent brain development and disease. Advances in stem cell technology have led to the development of organoids, which are small, self-organizing 3D versions of organs that recapitulate tissue architecture, cell-cell interactions, cellular diversity and key early developmental processes of the in vivo organ. This research aims to develop a cerebral organoid model derived from mouse embryonic stem cells to study neurodevelopment and neurological disease. Methodologies: To generate cerebral organoids, mouse embryonic stem cells were grown in 2D culture and differentiated in 3D to form neural aggregates. Aggregates were collected on days 5 and 11 to assess their spatial and temporal protein and gene expression using immunocytochemistry and quantitative polymerase chain reaction, respectively. Key markers of neurological development were assessed, and statistical analysis of quantitative polymerase chain reaction data was performed using t-tests in Excel. Throughout an 18-day culture period, the aggregates were imaged daily at the same time using an EVOS light microscope to assess their morphological changes. ImageJ was used to quantify parameters such as area, perimeter, circularity, Feret diameter, aspect ratio, roundness and solidity. Results: This research showed that the aggregates expressed key markers of neural development at both the protein and gene levels, confirming successful neural differentiation. Additionally, the emergence of neural projections was observed, which started on day 5 and increased by day 11, further supporting the progression of neural development within the organoids. Morphologically, the aggregates initially increased in size and then decreased in size, likely due to the formation of a necrotic core as oxygen and nutrients were unable to di use into the centre of the organoid as it grew bigger. Circularity of the organoid progressively decreased as a result of neuroepithelial budding, a process that indicates neurogenesis and neural migration. The organoids also showed neural rosette formation, which reflects early neural tube organisation. Conclusion: This study successfully generated cerebral organoids from mouse embryonic stem cells that recapitulate key features of early neurodevelopment, as shown by the gene and protein expression patterns and by the formation of neuroepithelial buds, neural rosettes and neural projections. This shows that these models provide a reliable and biologically relevant platform for studying early neural development and the mechanisms that underlie neurological disorders.
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Open Access
Mirrors in frames: identity and belonging in the lives of second-generation Congolese immigrants in South Africa
(2026) Bashonga, Ragi; Chaturvedi, Ruchi; Garba, Muhammed Faisal
This thesis explores the experiences of identity and belonging among young, second-generation Congolese immigrants in South Africa. It arises within a global context where notions of belonging have become increasingly restrictive, including in South Africa, where xenophobic tensions and systemic inequalities prevail. Using the metaphor of a mirror in frames, this study examines how individual lives and everyday experiences illuminate questions of citizenship, national identity, and Africanity. It poses the question what is gained or lost in the process of intra-continent migration? Grounded in the historical and socio-political contexts that shape these experiences and employing a social constructivist framework, this thesis integrates portraiture and poetic inquiry as methodologies to center the voices of research participants. This approach reveals the nuances of their lived realities amid pervasive xenophobic sentiments and systemic inequalities. Through a series of poetic portraits, the study highlights how intersecting factors such as race, gender, and social class inform individual identities and experiences of belonging. The findings indicate that citizenship in South Africa is characterized by fragility, shaped by historical legacies of apartheid and ongoing socio-economic exclusions. For second-generation Congolese immigrants, this fragility extends to their national identity. However, expressions of national identity and Africanity—through race, language, and culture—reveal a more dynamic connection to Congolese and African identities. This thesis demonstrates the significance of storytelling in academic discourse, illustrating how personal narratives can illuminate broader themes related to migration, identity politics, and the quest for belonging. Ultimately, it contributes to an evolving dialogue on African identities by challenging monolithic representations and emphasizing the dynamic nature of belonging in a globalized world. The study calls for further exploration of these themes within the context of South-South migration and intra African migration.
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Open Access
Track matching using machine learning techniques in the ALICE Muon Forward Tracker
(2026) Barday, Salmaan; Horowitz, William; Buthelezi, Edith; Fortsch, Siegfried
Matching muon-arm tracks, reconstructed from the Muon Chambers (MCH) and Muon Identifier (MID), to Muon Forward Tracker (MFT) tracks is required to reconstruct global forward moun tracks in ALICE Run 3(2022- 2026). When the correct association is made, the MFT measurements close to the interaction point can be combined with the muon-arm track, yielding substantially improved pointing to the primary vertex. This is essential for separating prompt muons from displaced heavy-flavour decays, i.e. decays of particles containing charm or beauty quarks. For each muon-arm track, one selects the most compatible MFT candidate from a set of candidates, or rejects the match. The MFT reconstructs tracks very close to the interaction point, in a region of high track multiplicity. The muon-arm track, by contrast, is reconstructed further from the interaction point, only after the particle has traversed the hadron absorber. This transport distorts the trajectory through multiple scattering and energy loss. As a result, several MFT candidates can appear compatible with the same muon-arm track, and this ambiguity increases strongly in Pb–Pb collisions compared with pp. This thesis investigates supervised machine learning approaches to improve the MUON–MFT association decision while leaving other reconstruction steps unchanged. Training and validation use Run 3-style anchored Monte Carlo samples, which are simulated samples matched to realistic detector conditions and stored in the ALICE Analysis Object Data format (AO2D). These samples provide truth labels for candidate associations. Performance is evaluated with metrics designed for the best-candidate-or-no-match decision and studied in bins of transverse momentum to isolate the most difficult matching regions. In addition to track parameters from the AO2Ds, the models use engineered features that explicitly encode MUON–MFT compatibility. The study shows that retaining multiple candidate matches per muon-arm track is crucial for learning-based matching. Moving from a single saved candidate to five saved candidates substantially improves separability. For the stacked classifier, which combines the outputs of several base models, the ROC AUC increases from 0.916 to 0.968, corresponding to a 5.7% relative gain. In the multi-candidate setting, learning-based methods provide their most meaningful improvements at low pT. Across both proton–proton and Pb–Pb environments, the best-performing stacked configuration provides a robust balance between selecting correct pairings and maintaining matching efficiency in the most difficult kinematic region. Overall, the results demonstrate that supervised learning combined with multi-candidate information and physically motivated compatibility features can improve MUON–MFT association beyond the standard x2 baseline in both pp and Pb–Pb collisions. The largest impact is concentrated in the kinematic region where matching is intrinsically most challenging.
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Open Access
"Beyond the clash of civilizations" (Todorov)? The representation of the "sociorevolutionary" Islamist terrorism in contemporary Francophone literature (Philippe Lançon, Julien Suaudeau, Ousmane Diarra, and Bréhima Touré)
(2026) Bamupale, Kayembe Augustin; Arnold, Markus
Dans son essai La peur des barbares : Au-delà du choc des civilisations (2008), Tzvetan Todorov développe une théorie humaniste subdivisée en deux parties. « La peur des barbares », d'une part, identifie et dénonce le ressentiment que certains humains ont envers des populations issues des cultures différentes. L'idée de l'« au-delà du choc des civilisations » constitue, d'autre part, un appel à l'humanisme et à l'émancipation d'une grille de lecture identitaire réductrice pour lire les rapports culturels et géopolitiques globaux contemporains. En effet, Todorov conteste l'idée identitaire du « choc des civilisations » qui, selon Samuel Huntington, n'envisage la guerre qu'entre les populations issues des différentes aires culturelles. Dans le « monde nouveau » qui se dessine pour le politologue américain, « les conflits les plus étendues, les plus importants et les plus dangereux » dépasseront les clivages sociaux et économiques et auront lieu « entre peuples appartenant à différentes entités culturelles » (1997 : 20). La présente recherche s'appuiera sur ces deux pôles chez Todorov afin de comparer la représentation du terrorisme islamiste, dans sa forme « sociorévolutionnaire », dans quatre textes littéraires francophones contemporains, à savoir Dawa (2014) de Julien Suaudeau, Le lambeau (2018) de Philippe Lançon, La route des clameurs (2014) d'Ousmane Diarra et La guerre des influences (2019) de Bréhima Touré. Nous examinerons notamment comment ce corpus français-malien représente et investit la théorie huntingtonienne, qui est autant un reflet du terrorisme islamiste qu'il est susceptible de nourrir celui-ci. Mais nous nous intéresserons aussi à la question de savoir dans quelle mesure s'observent dans ces textes le postulat de l'« au-delà » civilisationnel selon Todorov ; une perspective qui complexifie et met à mal la lecture huntingtonienne ainsi qu'une lecture simpliste du terrorisme. En problématisant ces questions à travers ces quatre textes littéraires contemporains, cette recherche suggère que la perception du terrorisme islamiste doit évoluer d'une seule conception identitaire (soit civilisationnelle, culturaliste et religieuse) vers un cadre de lecture plus nuancé et complexe (soit historique et socio-politique). Cette ouverture des perspectives saura contribuer à une vision plus juste – plus émancipatrice et possiblement plus humaniste – quant à la représentation des violences historiques et contemporaines. Par ailleurs, le terrorisme islamo-politique mis en scène et analysé s'inscrit dans un prisme dit sociorévolutionnaire, dans la mesure où les personnages lient leurs motivations et actes djihadistes aux faits socio-politiques et (macro)économiques, y compris les défaillances étatiques, l'aire d'influence de la culture musulmane et les stratégies d'autodéfense. L'objectif principal de cette recherche est donc de montrer que l'engagement littéraire de Lançon, Suaudeau, Diarra et Touré repose également dans leur prise en compte critique de cette dimension sociorévolutionnaire afin de complexifier la représentation du terrorisme au-delà des visions idéologiques courantes.
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Open Access
Investigating how maternal HIV-1 infection and use of antiretroviral therapy impacts preterm birth using an in vitro model system
(2026) Andrews, Cameron; Woodman, Zenda
Preterm birth (PTB) remains a leading cause of neonatal morbidity and mortality, yet the mechanisms linking diverse maternal factors to premature labour are poorly understood. Women living with HIV, as well as those receiving antiretroviral therapy, have an elevated risk of preterm birth, but the underlying pathways remain unclear. This study investigated the effects of HIV pseudovirions (HIV-PSV), antiretroviral drugs, and immune cell interactions on human myometrial contractility using an in vitro model. HIV-PSV Env induced significant myometrial contraction, while ARVs had no effect. Viral entry assays confirmed that contraction occurs independently of productive infection. HIV-PSV exposure reduced ERK1/2 phosphorylation but triggered secretion of IL-1β, IL-6, IL-8, and MCP-1, with IL-1β and IL-6 directly promoting contraction. These findings support a model in which Env-dependent signalling activates myometrial cells and drives autocrine, cytokine-mediated contraction. This mechanism provides a biologically plausible explanation for PTB risk in women living with HIV and identifies potential targets for therapeutic intervention to mitigate HIV-associated preterm labour.