List of Titles

Search for acrylonitrile-based inhibitors of SAR-Cov-19 main and papain-like proteases through covalent docking and high-throughput virtual screening

- Ntantiso, Yamkela

Authors: Ntantiso, Yamkela
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/463941 , vital:76459
Description: The sudden outbreak of SARS-CoV-2 formerly known as the 2019 novel coronavirus (2019-nCoV) quickly turned into a pandemic of coronavirus disease 2019 (COVID-19), the scale of which has never been seen before. High infection rates and mortality from COVID-19 placed pressure on global health services, and this has been to the detriment of the global economy. However, treatment options for COVID-19 are still very limited; hence, it is now as important as ever that researchers explore searching for new compounds with pharmacokinetic properties that inhibit the two COVID proteases - the main protease (Mpro) and the papain-like protease (PLpro). The main protease is a cysteine protease; as such, it is susceptible to permanent inhibition by reactive species (warheads) that may covalently bind to cysteine residues. One such class of compounds is acrylonitriles, in which the reactive acrylonitrile is reactive towards cysteine through a Michael addition reaction. The resulting covalent interaction is permanent and inactivates the cysteine residue and hence the protease within the context of the COVID-19 life-cycle. In this context, this study seeks to utilize computational-based approaches to identify acrylonitrile-based inhibitors of coronavirus drug targets. To do this, the ZINC database has been screened for compounds containing acrylonitrile functionality, due to its known nature as a warhead that binds to cysteine residues. Pharmacokinetic properties are computed to evaluate the viability of identified inhibitors, and covalent and non-covalent molecular docking approaches to the Mpro enzyme crystal structure have also been used to assess the identified systems. To gather more information and evaluate the most promising systems, a subset of the most promising compounds have been subjected to molecular dynamics simulation (for both covalently bound and non-covalently bound systems). , Thesis (MSc) -- Faculty of Science, Biochemistry, Microbiology & Bioinformatics, 2024
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Date Issued: 2024-10-11

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Sediment and associated phosphorus dynamics in meandering floodplain wetlands in the Tsitsa River catchment

- Schlegel, Philippa Kirsten

Authors: Schlegel, Philippa Kirsten
Date: 2024-10-11
Subjects: Sediments (Geology) , Phosphorus , Sedimentation and deposition , Ecosystem services Law and legislation South Africa , Arid regions South Africa
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/466860 , vital:76793 , DOI https://doi.org/10.21504/10962/466860
Description: A key function of floodplain wetlands systems is their ability to remove and store sediments and associated particulates (such as nutrients, organic carbon, and contaminants) from water, thus improving water quality for downstream ecosystems and water users. Increases in sediment and nutrient inputs to drainage networks pose a serious challenge to integrated resource management. These issues can be partly mitigated through natural buffering solutions along drainage networks, such as preserving essential wetland systems like floodplains. However, their trapping efficiency and storage timescales are uncertain. Although a large body of international knowledge and literature has advanced our understanding of river-floodplain systems and the ecosystem services that they provide, the factors determining their likelihood and effectiveness in supplying those regulatory ecosystem services have not been extensively and scientifically tested in floodplain systems in South Africa. This research aimed to describe and quantify the regulatory ecosystem services related to sediment and phosphorus buffering dynamics of two meandering floodplain systems in the Eastern Cape, South Africa. The study examined the geomorphology, sedimentology, and historical rates of sediment and associated phosphorus accumulation and release in the two floodplain systems. These systems varied in their morphometric features, size, catchment location, and predominant land use, providing a diverse range of characteristics. A comparative analysis was conducted between the two systems to understand the influence of local and catchment-scale factors. Time-averaged suspended sediment samples from the two wetlands were used to compare suspended sediment and associated total phosphorous fluxes over annual scales. Although both floodplains were net depositional during the study period, contemporary suspended sediment mass balance calculations suggested that the relatively larger Minnehaha floodplain system (~1.5 km²) situated in a significantly smaller catchment (~40 km²) had notably higher sediment and associated phosphorus trapping efficiencies of 44 % and 49 % respectively, compared to 16 % and 8 % for the relatively small Gatberg floodplain system (~0.3 km2) situated in a much larger catchment (~135 km²). This variability is attributed to the interaction between annual rainfall regimes, sediment supply, sediment composition, relative wetland size to catchment area and wetland geomorphic character. To test the hypothesis that the suspended sediments and associated total phosphorus were retained by the adjacent floodplain system and to determine which parts of the two floodplains were most effective for retaining suspended sediments and phosphorus, concurrent measurements of sediment accretion were made at 6 sites in different geomorphic features in each of the floodplains. This was achieved using Cesium-137 and Lead-210 (Hereinafter referred to as ¹³⁷Cs and ²¹⁰Pb) dating techniques. In-field observations suggested that all geomorphic units are still active and are frequently inundated during overbank flood flows. The average overbank sediment deposition and total phosphorus accumulation rates were 9376.9 g-sediment m¯² yr¯¹, 0.8 g-TP m¯² yr¯¹ for the Gatberg floodplain and 11802.8 g-sediment m¯² yr¯¹, 1.0 g-TP m¯² yr¯¹ for the Minnehaha floodplain. Deposition rates were temporally and spatially highly variable and dependent on the sediment supply, microtopographic relief, sinuosity, distance from the channel, the mode of inundation, and the extent of retention pondage. Overall, high average deposition rates were associated closest to the channel within the proximal floodplain zone (9712.1 g-sediment m¯² yr¯¹, 1.0 g-TP m¯² yr¯¹ for the Gatberg floodplain; 13541.1 g-sediment m¯² yr¯¹, 1.0 g-TP m¯² yr¯¹ for the Minnehaha floodplain) where the highest D₅₀ particle sizes (25.4 μm for the Gatberg and 32.8 μm for the Minnehaha) and percentage sand fractions (15 % and 21 %, respectively) were found. This may reflect the coarse nature of the sediment and the frequent connectivity to the channel, suggesting rapid accumulation is linked to a larger particle size which was deposited more readily in this zone. In the Gatberg system, the backswamp zone had one of the highest sedimentation rates and second highest phosphorus accumulation rates (13806.8 g-sediment m¯² yr¯¹, 0.9 g-TP m¯² yr¯¹). This was attributed to the additional coarse sediment inputs from the uncapped gravel forestry road that runs adjacent to the floodplain margin. In contrast, the backswamp zone within the Minnehaha River floodplain system had the lowest sedimentation rates (2005.9 g-sediment m¯² yr¯¹, 0.1 g-TP m¯² yr¯¹, which is what would be expected for the zone furthest away from the channel. In both floodplains, oxbows were important fine-sediment and phosphorus retention features (7126.0 g-sediment m¯² yr¯¹, 0.6 g-TP m¯² yr¯¹ for the Gatberg floodplain; 10101.0 g-sediment m¯² yr¯¹, 1.1 g-TP m¯² yr¯¹). Phosphorus distribution patterns were mainly attributed to variations in organic matter content and iron concentrations in fine-grained sediment deposits, while particle size distributions were less important. Using a mass balance approach the trapping efficiencies of the two floodplain systems were estimated. The average trapping efficiency for the Gatberg River floodplain accounts for 16 % of the suspended sediment yield (1317.5 tonnes-sediment yr¯¹) and 8 % of the suspended sediment-associated total phosphorus yield (0.093 tonnes-TP yr¯¹). Deposition on the Minnehaha floodplain accounts for an average of 44 % (1073.6 tonnes-sediment yr¯¹) and 49 % of the suspended sediment-associated total phosphorus yield (0.098 tonnes-TP yr¯¹). Within the Gatberg and Minnehaha River floodplain systems, the sediment sinks (oxbow and backswamp geomorphic zones) accounted for 13 % and 6 % (1070.6 tonnes-sediment yr¯¹ and 0.069 tonnes-TP yr¯¹); and 28 % and 33 % (683.2 tonnes-sediment yr¯¹ and 0.066 tonnes-TP yr¯¹), respectively, of the mean proportion of the total sediment and associated phosphorus yield. The zone of potential exchange (the proximal floodplain geomorphic zone) within the Gatberg floodplain system was calculated to trap 3 % (247.1 tonnes-yr¯¹) of the mean proportion of the total sediment yield and 2 % (0.023-tonnes yr¯¹) of the mean proportion of the total associated-phosphorus yield. Within the Minnehaha floodplain, this zone was estimated to trap 16 % (390.4 tonnes-sediment yr¯¹ and 0.032 tonnes-TP yr¯¹) of the mean proportion of both the total sediment and associated total phosphorus yield. These results indicate the importance of the distal floodplain reaches and oxbows as sediment and phosphorus storage hotspots. While floodplains mainly result from the accumulation of sediment, they're often modified and altered by erosion processes. Channel erosion and avulsions (e.g. meander bend cutoff events) are natural dynamic processes and form two of the principal processes of meandering river migration. During two wet seasons, both Gatberg and Minnehaha River floodplain areas experienced a mix of deposition and erosion, with slightly higher erosion observed in the Gatberg River reach. Channel bed scouring was prevalent in most cross-sections, suggesting limited sediment accumulation within the main channel beds. Volumetric estimates of sediment loss from meander migration were calculated by analysing cross-sectional data from 2019 and 2021 surveys to determine median and maximum eroded volumes, which were then converted to mass and scaled to tonnes per year for each river's eroded meander bends. The eroded sediment volumes were estimated as 520 tonnes yr¯¹ for the Gatberg and 360 tonnes yr¯¹ for the Minnehaha. The time sequence analysis using historical aerial images (between 1958, 1966, 1993, and 2015) revealed a few channel planform changes due to meander bend cutoff events in both river reaches. These events influence river morphology, increasing local channel slope, reducing sinuosity, and limiting floodplain access while impacting sediment and phosphorus flux. In the Gatberg system, changes in land use, such as increased road density from commercial forestry activities, likely drove channel straightening to accommodate higher sediment and bed loads. In the Minnehaha system, agricultural practices and livestock tracks likely increased sediment loads and hillslope-channel connectivity, driving channel changes. The results from the geochronology of two nested oxbows on the Gatberg floodplain estimated lateral migration rates of ~0.03 m yr¯¹. The floodplain reworking rates of the Gatberg River floodplain are low compared to other systems in humid regions around the world, although, the Gatberg system compares well with migration rates of rivers in dryland regions. This study highlights the potential for floodplains undergoing regular flooding to be effective natural buffers along the sediment and phosphorus cascade in dryland landscapes. It enhances our comprehension of how sediment accumulates over time on floodplains within South African river systems, shedding light on both spatial and temporal patterns. These insights can contribute to better methodologies for evaluating the services provided by floodplain wetlands. These results can inform management decisions by offering a deeper understanding and allowing for the quantification of the cost-benefit of floodplain restoration and preservation actions in South Africa. , Thesis (PhD) -- Faculty of Science, Faculty of Science, Geography, 2024
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Date Issued: 2024-10-11

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Selective and sensitive electrochemical detection of the Human Epidermal Growth Receptor 2 breast cancer biomarker, using Co (II) phthalocyanine-nanoparticle based platforms

- Centane, Sixolile Sibongiseni

Authors: Centane, Sixolile Sibongiseni
Date: 2024-10-11
Subjects: Electrochemical sensors , HER-2 protein , Breast Cancer , Biochemical markers , Phthalocyanines , Nanoparticles
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/466569 , vital:76753 , DOI https://doi.org/10.21504/10962/466570
Description: Breast cancer is the world’s leading cause of cancer related deaths in women worldwide. The main reason lies in its late detection, mostly in the metastatic stage resulting in poor after-therapy prognosis, despite advances in methods of diagnosis and therapy. The reason for late-stage detection, is because breast cancer like any other cancers is asymptomatic in its early stages. Significant and characterizable features present in the later stages. Furthermore, conventional methods for breast cancer detection are more useful in the identification of the phenotypic features of cancer cells that arise at a later stage of the disease. Another issue with conventional methods where cancer diagnosis is concerned is that they tend to be specialist-dependent, time consuming and costly. Thus, easy, fast and inexpensive detection methods need to be developed urgently. Biomarker-based cancer diagnosis has emerged as one of the most promising strategies for early diagnosis, monitoring disease progression, and subsequent cancer treatment. This thesis focuses on the design and development of novel electrochemical biosensor platforms towards the low cost, efficient, sensitive and simple detection of early-stage breast cancer biomarker, human epidermal growth factor 2 (HER2). The electrochemical method is preferred because of its moderate cost, rapid response, ease of operation, readily quantifiable signal as well as high sensitivity and selectivity with lower detection limits. This thesis reports on two strategies towards signal amplification and sensitive detection of HER2, namely signal based amplification and target-based amplification. The former focuses on electrode or transducer modification techniques for improved signal to noise ratio. In which case; novel nanocomposites of phthalocyanines, graphene quantum dots, gold nanoparticles and cerium oxide nanoparticles are used for electrode modification for signal amplification and biorecognition element immobilization. The biorecognition elements of choice, are an aptamer and antibody known to be specific to the HER2 antigen for an enhanced sensor sensitivity and specificity. The second strategy focuses on increasing the number of detectable targets on the electrode surface towards enhanced sensitivity, precision and sensor accuracy. In which case; the performance of the aptamer and the antibody as recognition elements was explored. Furthermore, the effect of arrangement of these recognition elements on the electrode surface is investigated and reported upon. The strategies covered in this thesis are expected to result in novel biosensor platforms that can detect the HER2 biomarker with high precision, reproducibility, sensitivity and stability; towards low cost and effective early-stage breast cancer diagnostic tools. , Thesis (PhD) -- Faculty of Science, Chemistry, 2024
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Date Issued: 2024-10-11

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Shaping self through ceramic sculpture: representing anxiety in the rural black queer experience

- Phaliso, Phila Vuyiseka

Authors: Phaliso, Phila Vuyiseka
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/466082 , vital:76683
Description: I am a ceramic sculptor. I make use of clay that I have sourced from Joza, the Makhanda location, and Cofimvaba in a rural area called Magwala. I process this clay and then use it to create a visual and tangible representation of the anxiety I experience as a queer black woman living in South Africa. Unongayindoda is a word that has been used by isiXhosa speaking people in my village to call me ever since I was a child. This is a word that I have chosen to own, in much the same way that some people have chosen to own the word “queer.” My experience of being unongayindoda has had an impact on my mental health, and the process of digging clay, processing it for use and then using it to create my work has become very therapeutic for me. My work’s primary aim is to explore the use of clay as a representative embodiment of anxiety in my work as a rural black queer sculptor who identifies as unongayindoda. The thesis component of my work is a qualitative study informed by autoethnography, practice and art-based research. , Thesis (MA) -- Faculty of Humanities, Fine Art, 2024
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Date Issued: 2024-10-11

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Singing pretty: investigating female respectability in classical vocal performance in South Africa

- Van der Walt, Alida

Authors: Van der Walt, Alida
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/466102 , vital:76685
Description: In this thesis, I consider respectability in classical vocal performance in South Africa by presenting research on six women who hold prominent positions in this field intertwined with my own experiences in this arena. I introduce the context and background to my research across the fields of respectability politics, music studies, and intersectionality before investigating two main modes of gendered bodily respectability that featured in my singer-participants’ lives. These include first extra-bodily technologies in service of respectability, referring to anything that a singer may externally and visibly apply (on)to her body to enhance its physical appeal in specific ways, in line with respectability’s requirements. In thinking through the notion of extra-bodily technologies, I outline via cyborg theory how this first mode of respectability policing operates as an intersectionally oppressive force in my own and my singer-participants’ lives. The second form of bodily discipline emerges in what I call intra-bodily markers of respectability. In developing this term, I demonstrate, based on my singer-participants’ experiences and my own, how the policing of intra-bodily respectability markers may shift our understanding of identity performativity from the discursive realm into the physical. In doing so, I think critically about the importance of language in respectability’s shaping of women’s realities. With little subversive potential found in these themes, I explore the theme of play as a subversive strategy employed by the singers in my study, contrasting the playful subversion with my own mode of ‘serious’ rebellion. Play, with its ambiguous nature rooted in theories of psychology and self-realization, becomes a fundamental aspect of human development, allowing individuals to explore their capabilities and confront societal limitations. I explore the gendered aspects of subversive play in various arenas such as physical appearance, sexuality, musicianship, race, and class, emphasizing and questioning its potential as a political action within the constraints of societal structures. The final part of the thesis explores my own experiences of embodied unbecoming from respectability’s oppressions through vocal performance. Here, I tie together the three strands presented in the body of this thesis through my singing, transgressing body in reference to what I call a feminist musicianship practice as a way of singing beyond respectability. , Thesis (MA) -- Faculty of Humanities, Music and Musicology, 2024
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Date Issued: 2024-10-11

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SolarKAT: a solar imaging pipeline for MeerKAT

- Samboco, Victória da Graça Gilberto

Authors: Samboco, Victória da Graça Gilberto
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/465102 , vital:76573
Description: Solar interference poses a significant challenge in radio interferometric observations, particularly with the increasing sensitivity of modern new-generation telescopes. This thesis presents the SolarKAT pipeline, a novel approach designed to mitigate solar interference in MeerKAT observations. The pipeline incorporates a series of steps, including self-calibration (second generation calibration or 2GC), precise determination of the Sun’s position, phase centre adjustments, creation of region-based masks, deconvolution, prediction, solar model subtraction, and peeling. We applied the SolarKAT pipeline to three datasets that feature the Sun in different conditions (frequency band and angular distance from the Sun to the telescope pointing position). These observations were obtained from three MeerKAT telescope surveys: ThunderKAT, MIGHTEE and LADUMA. We compared the visual images, peak fluxes, flux density, RMS and pixel distribution to evaluate the pipeline. Our results showed a notable reduction in solar interference. This is evidenced by the improved image quality, reduction in RMS and pixel distribution values, and consistent peak flux measurements after applying the pipeline. SolarKAT has not only improved the data quality but also demonstrated to be a valuable tool in producing high-quality solar images, which can be a helpful resource for solar physics and space weather forecasts. This study showcases the potential of the SolarKAT pipeline in enabling high-quality radio interferometric observations, even in the presence of solar interference. Unlike conventional methods that often discard corrupted visibilities (e.g. flagging), our approach focuses on recovering them. Additionally, the SolarKAT pipeline naturally delivers detailed images of the Sun. Our findings contribute to advancing the field of radio interferometry, providing a valuable tool for researchers seeking to enhance the accuracy of their observations and conduct studies in solar physics and space weather. , Thesis (MSc) -- Faculty of Science, Physics and Electronics, 2024
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Date Issued: 2024-10-11

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South Africa’s financial services trade and trade potential under the African Continental Free Trade Area

- Gyan, Mawuko

Authors: Gyan, Mawuko
Date: 2024-10-11
Subjects: Trade finance , South Africa Commerce , African Continental Free Trade Area , Gravity model of international trade
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/462846 , vital:76340
Description: This study investigates the nature, importance and prospects for growth of South Africa’s trade in financial services and trade potential under the African Continental Free Trade Area (AfCFTA) Agreement. It does so by identifying and measuring the share, growth performance and some of the characteristics of South Africa’s financial services trade in the aggregate and with selected trading partners and regions. It also computes South Africa’s trade potential in financial and finance-related services trade with selected African trading partners amid the ongoing AfCFTA services trade negotiations, using trade complementarity indices (TCIs). Finally, the study estimates the effect of regional trade agreement participation on bilateral financial services trade involving African economies using a gravity model. The study employs the use of descriptive trade statistics to analyse the share and growth performance of South Africa’s services trade in the aggregate and at the sub-sector level, based on balance of payments (BOP) data for the years 2005 to 2022 from the ITC, UNCTAD and WTO Trade in Services Database. Bilateral trade data from the OECD and WTO BaTIS Database is also used in the analysis of intra-African trade. In order to investigate trade through Mode 3, information on FDI statistics is sourced from recent reports. Through analysing trade complementarity indices (TCIs), the study finds that South Africa has significant potential to increase exports of financial and finance-related services to Mauritius, Ghana and the SADC and non-TFTA regions. South Africa has significant import TCIs with the COMESA and non- TFTA regions as well as Egypt, Tunisia and Kenya. The gravity model estimation reveals that membership in African regional groupings like the AfCFTA, SADC, COMESA and the EAC have no significant positive impact as yet on intra-African financial services trade. , Thesis (MCom) -- Faculty of Commerce, Economics and Economic History, 2024
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Date Issued: 2024-10-11

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Spatial pattern analysis of thicket expansion in a semi-arid savanna

- Putzier, Rachel Rayne

Authors: Putzier, Rachel Rayne
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/464484 , vital:76515
Description: Woody thickening has negative economic and ecological impacts in savannas globally. While the increase of savanna trees as a form of bush encroachment has been well studied, less is known about the increase of thicket species in savannas, which is an important phenomenon resulting in the formation of closed-canopy clumps which may exclude the grass layer over time. The early stage of thicket expansion is often initiated by a nucleating savanna species which facilitates the establishment of woody thicket pioneer species, and as the thicket clump formation expands, bush clumps increase in dominance, thereby increasing the frequency of competitive interactions and leading to a possible switch from facilitative to competitive interactions. Spatial point pattern analysis provides a useful tool to elucidate these underlying patterns and ecological processes. I used high resolution LiDAR data combined with spatial point pattern analysis to understand tree-tree interactions in a semi-arid savanna in the Eastern Cape Province of South Africa. I conducted a cluster analysis based on vegetation structural variables to distinguish different stages of woody plant encroachment from open savanna to closed canopy thicket. Using the canopy height model, I quantified the change in the grass height from open savanna to closed canopy thicket clumps as an indicator of a possible biome shift. Additionally, I used spatial point pattern analyses to investigate the effect of thicket clump formation on the composition of savanna and thicket species, the overall patterns of trees, and the associations of small thicket species with large Vachellia karroo trees, which serve as clump initiators. Finally, I examined the mortality of savanna trees across increasing stages of thicket expansion using second order spatial statistics, namely the Mark- and Pair-Correlation Functions. Results confirmed that three vegetation states, influenced by elevation, are present at the study site, representing open canopy savanna (early-stage thicket encroachment), encroached savanna with low thicket dominance (intermediate-stage thicket encroachment), and highly encroached with dominant thicket clumps (late-stage thicket encroachment). These stages showed increasing tree height, canopy cover and canopy height density, as well as decreased (but not completely absent grass layer) as thicket encroachment progresses. Spatial point pattern analysis showed, as predicted, that there was an overall aggregation of trees at small-scales within early thicket clump formation, from which I inferred that facilitative relationships may exist between trees. Contrary to my predictions, at later stages of thicket clump formation I found dominant independent patterns between savanna adults and juvenile thicket species, which may result from a combination of facilitative and competitive effects. Lastly, as expected, I found that the density of V. karroo mortality increased as thicket encroachment increased, with an overall random spatial pattern of dead V. karroo across encroachment stages. As predicted, tree mortality was randomly distributed in space in the open savanna state, and as thicket clump formation increases, tree competitive mortality became more evident, as well as decreased tree performance. Overall, the study highlights the interplay between facilitation and competition in semiarid savanna where thicket clumps are expanding. Intervention strategies are suggested to target areas of intermediate thicket clump formation, as these areas provide an opportunity to remove V. karroo before the nucleation process has enabled the establishment and increase of thicket species and to ensure the grass layer is kept productive. I conclude that the use of remote sensing and LiDAR technology holds a wide range of possibilities for monitoring and managing woody encroachment in savanna systems, however these methods need to be further refined for effective use within African savanna and thicket context, which displays high spatial aggregation making typical segmentation methods difficult. , Thesis (MSc) -- Faculty of Science, Botany, 2024
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Date Issued: 2024-10-11

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Statistical classification, an application to credit default

- Sikhakhane, Anele Gcina

Authors: Sikhakhane, Anele Gcina
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/465069 , vital:76570
Description: Statistical learning has been used in both industry and academia to create credit scoring models. These models are used to predict who might default on their loan repayments, thus minimizing the risk financial institutions face. In this study six traditional and one more recent classifier, namely kNN, LDA, CART, RF, AdaBoost, XGBoost and SynBoost were used to predict who might default on their loans. The data set used in this study was imbalanced thus sampling and performance evaluation techniques were investigated and used to balance the class distribution and assess the classifiers performance. In addition to the standard variables and data set, new variables called synthetic variables and synthetic data sets were produced, investigated and used to predict who might default on their loans. This study found that the synthetic data set had strong predictive power and sampling methods negatively affected the classifiers performance. The best-performing classifier was XGBoost, with an AUC score of 0.7732. , Thesis (MSc) -- Faculty of Science, Statistics, 2024
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Date Issued: 2024-10-11

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Structural dynamic investigation of the mutation-induced resistance mechanisms of Mycobacterium tuberculosis DNA-directed RNA polymerase against Rifampicin

- Monama, Mokgerwa Zacharia

Authors: Monama, Mokgerwa Zacharia
Date: 2024-10-11
Subjects: Mycobacterium tuberculosis , Rifampin , Drug resistance , Molecular dynamics Simulation methods
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/466849 , vital:76792 , DOI https://doi.org/10.21504/10962/466849
Description: Emerging resistant strains of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB) disease, continue to plague mankind and reduce the efficacies of antitubercular therapies that have been an effective defence against TB for decades. More specifically, mutations located in the β subunit of the multisubunit Mtb RNA replicative machinery, RNA polymerase (RNAP), have been well established as the reason behind resistance to the first-line antitubercular drug rifampicin (RIF), which has resulted in therapeutic failure in several clinical cases. Additionally, elusive details pertaining to the underlying mechanisms associated with RIF resistance due to the presence of Mtb-RNAP-β mutations, have resulted in setbacks in the development of novel and effective drugs that might be able to curb the ongoing threat. Hence, in this investigation, we attempted to resolve the involved Mtb-RNAP structural events at the molecular level to discern potentially important details regarding the nine clinically relevant Mtb-RNAP-β missense mutations under investigation. Hence, for the first time, we conducted an in-silico RIF resistance investigation using the Mtb-RNAP complex. To accomplish the set-out task, we first employed the use of more traditional post-MD analytical approaches such as root mean square deviation, root mean square fluctuation, radius of gyration, center of mass distance analyses, hydrogen bond occupancies, and binding free energy calculations, to conduct a global analysis of the mutated Mtb-RNAP proteins referencing RIF efficacy. Our findings revealed that the mutations may have a perturbation effect resulting in the disruption of essential structural dynamics attributed to the protein’s catalytic functions. This was for instance observed for the βfork loop 2 domain, the β’zinc-binding domain, the β’ trigger loop domain, and the β’jaw domain, which happen to be in line with previously reported experiments detailing changes in RNAP processivity. Complementarily, some of the mutations more specifically perturbed the RIF binding pocket (RIF-BP) which observably led to the reorientation of RIF from the native or active orientation needed to obstruct the processive addition of nucleoside triphosphates to the growing RNA transcript. The mutation-induced repositioning from the active RIF orientation was also reflected through the loss of essential interactions between RIF and the RIF-BP along with the loss of binding affinities captured for a majority of the mutant proteins. In conjunction with traditional analytical approaches, we further employed computational alanine scanning, weighted contact map analyses, and dynamic residue network (DRN) analyses, a novel approach that delineates residue-residue communication pathways through several metrics, to further elucidate how a set of clinically relevant mutations affect Mtb-RNAP function. With that, we were able to observe several key changes in residue importance and interactions that may be instrumental in bringing about RIF resistance and the compensatory conformational changes we observed among the mt systems through global analysis. Furthermore, we identified persistent hubs that may be particularly important in maintaining transcriptional activities in the presence and absence of the investigated mutations and RIF that could serve as potential resistance markers for future therapeutic investigations. We believe these findings will significantly aid future efforts in the discovery of new treatment options with the potential to overcome antitubercular resistance. , Thesis (PhD) -- Faculty of Science, Biochemistry, Microbiology and Bioinformatics, 2024
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Date Issued: 2024-10-11

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Students' perception of pre-exposure prophylaxis as a prevention strategy for reducing HIV/AIDS incidences at Rhodes University

- Lepelesana, Mamorena Sylvia

Authors: Lepelesana, Mamorena Sylvia
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/466150 , vital:76701
Description: South Africa has the largest number of people living with HIV/AIDS compared to the rest of the world, with young people most at risk. The World Health Organisation (WHO) recommends the use of Pre-Exposure Prophylaxis (PrEP) in key populations at a higher risk of exposure to HIV/AIDS. The HIV/AIDS pandemic remains a pressing issue among higher education institutions, with a need for a comprehensive understanding of barriers and facilitators associated with the use of PrEP. The Higher Education AIDS (HEAIDS) plays a pivotal role in the mitigation of the spread of HIV/AIDS in Higher Education Institutions (HEIs). In this study, Rhodes University serves as a focal point for exploring PrEP implementation and acceptance. This qualitative study examines Rhodes University students' PrEP knowledge, perception, practice, and roll-out preference. More evidence is required to measure progress among students. A study was conducted involving sixteen (16) in-depth semi-structured interviews with students and health care workers, as well as a focus group consisting of three (3) students aged between 20-60 years. This study used the Socio-Ecological Model and Health Belief Model as theoretical frameworks. Participants in the study identified both the barriers and the facilitators to the use of PrEP. The findings show that there is a lack of knowledge and low perception among students about PrEP. The study found that lack of knowledge was the source of the stigma and misconception about PrEP. Most participants expressed the need for more information to differentiate between the ARVs in PrEP and the ARV medication for HIV-positive people. However, they further expressed a willingness to embrace PrEP if they had information about it. The study highlights that the use of PrEP is linked to individual and environmental factors, which are crucial for PrEP roll-out. These factors include access to PrEP in a friendly manner, supportive family and friends, and the reduction of stigma and misconception. Therefore, when addressed, the said factors can foster the use of PrEP and mitigate barriers. For students to fully realise the benefits of HIV/AIDS prevention strategies like PrEP, there is a need for informed educational efforts. A well-informed student body is important for the successful adoption and use of PrEP. The findings suggest that the health care workers were knowledgeable and conscious about the use of PrEP. However, there were inconsistencies in the information provided by the health care workers regarding the recommended period for taking PrEP before testing again and taking the three-month course. The inconsistencies raise questions regarding the accuracy and reliability of the information provided. , Thesis (MSocSci) -- Faculty of Humanities, Sociology, 2024
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Date Issued: 2024-10-11

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Suspicious sctivity reports: Enhancing the detection of terrorist financing and suspicious transactions in migrant remittances

- Mbiva, Stanley Munamato

Authors: Mbiva, Stanley Munamato
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/465058 , vital:76569
Description: Migrant remittances have become an important factor in poverty alleviation and microeconomic development in low-income nations. Global migrant remittances are expected to exceed US $630 billion by 2023, according to the World Bank. In addition to offering an alternate source of income that supplements the recipient’s household earnings, they are less likely to be affected by global economic downturns, ensuring stability and a consistent stream of revenue. However, the ease of global migrant remittance financial transfers has attracted the risk of being abused by terrorist organizations to quickly move and conceal operating cash, hence facilitating terrorist financing. This study aims to develop an unsupervised machine-learning model capable of detecting suspicious financial transactions associated with terrorist financing in migrant remittances. The data used in this study came from a World Bank survey of migrant remitters in Belgium. To understand the natural structures and grouping in the dataset, agglomerative hierarchical clustering and k-prototype clustering techniques were employed. This established the number of clusters present in the dataset making it possible to compare individual migrant remittances in the dataset with their peers. A Structural Equation Model (SEM) and an Local Outlier Factor - Isolation Forest (LOF-IF) algorithm were applied to analyze and detect suspicious transactions in the dataset. A traditional Rule-Based Method (RBM) was also created as a benchmark algorithm that evaluates model performance. The results show that the SEM model classifies a significantly high number of transactions as suspicious, making it prone to detecting false positives. Finally, the study applied the proposed ensemble outlier detection model to detect suspicious transactions in the same data set. The proposed ensemble model utilized an Isolation Forest (IF) for pruning and a Local Outlier Factor (LOF) to detect local outliers. The model performed exceptionally well, being able to detect over 90% of suspicious transactions in the testing data set during model cross-validation. , Thesis (MSc) -- Faculty of Science, Statistics, 2024
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Date Issued: 2024-10-11

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Taxonomy- and trait-based responses of chironomid assemblage structure to pollution in selected urban rivers, Eastern Cape, South Africa

- Osoh, Miracle Ogagaoghene

Authors: Osoh, Miracle Ogagaoghene
Date: 2024-10-11
Subjects: Environmental monitoring , Chironomidae , Water quality , Urbanization , Aquatic insects , Aquatic ecology , Urban pollution
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/466655 , vital:76764 , DOI https://doi.org/10.21504/10962/466655
Description: Urbanisation, occasioned by an increasing human population and the proliferation of industries, is a major threat to freshwater resources and has been implicated as a cause of stream water quality deterioration, habitat degradation, and the loss of aquatic biodiversity. Pollution of freshwater systems resulting from urban-related activities severely alters stream ecosystem structure and function. To effectively protect and sustainably manage freshwater resources, it is important to develop biomonitoring tools which are both sensitive to changes in water quality conditions and can provide an understanding of the mechanisms by which urban pollution impacts freshwater ecosystems. In South Africa, the macroinvertebrate-based South African Scoring System version 5 (SASS5) is routinely used for water quality assessment. This tool is developed at the family level of taxonomic resolution, with the exception of a few taxa. This raises the question as to whether a species-level taxonomic approach, complemented with a trait-based approach could add additional value. This question was addressed comparatively by developing and applying a taxonomy- and trait-based approach using the taxonomically and functionally diverse Chironomidae family. Fifteen sites across three urban river systems (Buffalo, Bloukrans and Swartkops River systems) in the Eastern Cape Province of South Africa were purposefully selected for this study. Based on the predominant land use within the catchment of the sites and water quality variables, the study sites were grouped into five site categories. The least-impacted sites (REF) had 78.53% mean forested area, 5.98% mean urban area and 13.49% mean agricultural land. Sites that received diffuse pollution but were upstream from the effluent discharge point of wastewater treatment works (DP) had 59.07% mean forested area, 32.53% mean urban area and 6.20% mean agricultural land. Sites that received point source pollution from wastewater treatment works (PP) had 63.66% mean forested area, 26.26% mean urban area and 7.39% mean agricultural land. Sites further downstream from the wastewater treatment works that received impacts from both point source and diffuse pollution (AG) had 65.95% mean forested area, 18.24% mean urban area and 12.5% mean agricultural land. Sites selected for exploring the potential system recovery of the study rivers (RECV) had 77.21% mean forested area, 9.12% mean urban area and 10.7% mean agricultural land. Macroinvertebrates and physicochemical variables were sampled at sites in the Bloukrans and Buffalo rivers over four sampling events (spring, summer, winter, and autumn) between November 2021 and June 2022 using the SASS5 protocol. Historical chironomid and physicochemical data from the Swartkops River collected between 2009 and 2012 were also used in this study. The SASS5 family-level biotic index classified the water quality condition at the least impacted site (REF) of the Swartkops River as minimally impaired 80% of the time, compared to the chironomid-based multimetric index (CUMMI), which indicated that the water quality condition at this site was near-natural 50% of the time. The chironomid-based multimetric index and the SASS5 were divergent in their classification of water quality conditions at the DP and AG sites but were 100% in agreement regarding water quality conditions at the PP site as critically/severely modified. The SASS5 scores classified the water quality condition at the AG site as critically/severely modified 100% of the time, whereas the CUMMI index classified the water quality condition at this site as critically/severely modified 90% of the time but moderately modified 10% of the time. The results indicate that species-level and family-level indices tend to be in agreement for heavily impacted sites, but the same was not true for least or moderately impacted sites. Traits such as the possession of tracheal gills, very large body size, burrowing, whole-body undulation, construction of rigid tubes, possession of three tracheae, completion of lifecycle in more than one year, production of more than 1000 eggs per egg mass, preferences for fine detritus, and bivoltinism were deemed tolerant of urban pollution. Traits such as cuticular respiration, medium body size, predator feeding mode, completion of lifecycle within one year, and a preference for stone biotope were deemed sensitive to urban pollution. An approach was developed to classify chironomids into those that are potentially vulnerable and those that are resilient to urban pollution. The abundances of vulnerable species correlated positively with increasing dissolved oxygen and negatively with increasing turbidity, electrical conductivity, nitrite-nitrogen, ammonium-nitrogen, and orthophosphate-phosphorus. The relative abundance of the highly vulnerable species and that of the highly tolerant species responded significantly to urban pollution and differentiated between the site categories. The relative abundance of the highly vulnerable species was significantly different between the DP and PP site categories. The richness of vulnerable and highly vulnerable species was significantly different between the REF sites and the impacted site categories (DP, PP, and AG). These results indicated that the developed approach successfully predicted chironomid responses to urban pollution. Overall, the study makes important contributions to the field of freshwater biomonitoring. First, the study highlighted that species-level identification is necessary to differentiate sites which may be considered moderately impacted. Both family and species-level tools were sensitive to water quality conditions for least impacted and highly impacted sites, but the differences between the family-level and species-level indices were pronounced for sites considered moderately impacted. Second, a trait-based approach provided a mechanism for developing predictive tools, and in the case of this study, the potential resilience or vulnerability of chironomids was reliably predicted. , Thesis (PhD) -- Faculty of Science, Institute for Water Research, 2024
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Date Issued: 2024-10-11

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Teachers’ use of authentic tasks through mathematics trails in a mobile learning environment to facilitate conceptual teaching

- Matengu, Given Kahale

Authors: Matengu, Given Kahale
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/466429 , vital:76727 , DOI https://doi.org/10.21504/10962/466429
Description: The teaching and learning of mathematics in Namibia is confronted by various forms of challenges that require continuous search for effective pedagogical strategies and approaches to enhance mathematical understanding. Some of the ways include using real and authentic outdoor activities and technological tools, such as smartphones, for teaching and learning purposes. The need to use authentic and realistic tasks in outdoor settings in the teaching of mathematics has strong support from the literature. Moreover, many recent reforms in education challenge teachers across all subjects to use modern and up-to-date technologies to complement and support existing approaches to teaching. Smartphones, in particular, offer new opportunities in the evolution of technology-enhanced learning by allowing teaching and learning to occur in authentic and realistic contexts that extend to real-life environments. This qualitative case study proposes a practical framework that can facilitate mathematical understanding in teaching through the implementation of authentic and realistic outdoor tasks by using the Math City Map (MCM) project on a smartphone. The study aims to analyse and understand how mathematics teachers can create and implement authentic and realistic tasks in an outdoor mathematics trail to facilitate the conceptual teaching of area, volume, ratio and proportion topics, within the context of the Realistic Mathematics Education theory (RME). The study is framed within the RME theory and the iPAC (personalisation, authenticity, collaboration) mobile pedagogical framework. The research process is underpinned by an interpretivist paradigm. Data was collected from eight selected teachers through observations and interviews and analysed using frameworks derived from the RME and iPAC mobile pedagogical theories and the emergence of common themes. The findings suggest that the integration of smartphones and mathematics trails have pedagogical benefits in mathematics teaching and can facilitate the use of outdoor tasks that are connected to learners’ realities. The study argues that while MCM mathematics trail tasks can be difficult to create, it was worthwhile for teachers using them to conceptually teach the selected topics. It is therefore hoped that the findings of this study contribute towards the use of outdoor mathematics trails and smartphones in the teaching of mathematics. , Thesis (PhD) -- Faculty of Education, Secondary and Post-School Education, 2024
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Date Issued: 2024-10-11

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Teaching problem solving: the "Ten Commandments" approach

- Matiwane, Noluvuyo

Authors: Matiwane, Noluvuyo
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/464897 , vital:76555
Description: The evident need for an intervention to help physics students, especially incoming university students, develop their problem-solving skills led to exploring possible curriculum structures to achieve the goal. A modified curriculum structure of the first-year physics course, including explicit teaching of physics problem solving, was developed and implemented at Rhodes University, South Africa, in 2017. First-year physics students learn to solve problems by implementing the "Ten Commandments" of physics problem solving in their solutions, following a three-stage problem-solving framework. Additionally, students attend whiteboard tutorial sessions where they actively practise using the problem-solving framework in their solutions to physics problems with peers in an environment where help is available. Students are explicitly prompted to use the \Ten Commandments" during the whiteboard tutorials and not prompted for other assessment tasks. Students' solutions to formative physics assessment tasks (problem sets and tests) in the first semester were examined, problem-solving scores were determined using a problem-solving rubric developed in the department, shifts in attitudes and beliefs about physics and solving problems in physics were measured, and relationships between their problem-solving scores and task performance were evaluated to investigate how students adopted the framework and its implications over one semester. The problems issued to students differed in context and difficulty level; as a result, not all of the "Ten Commandments" were applicable to solve all problems, and different combinations of the commandments were applied to different problems. The explicit use of the problem-solving rubric to mark student problem sets was an indirect prompt for students to use commandments when doing their problem sets. As a result, students attempted to implement more applicable "commandments" (mostly partially correct) in their solutions to problem sets than in tests. Moreover, students' solutions to problems show that they used more of the "commandments" they were familiar with from school and less of the new ones, such as drawing diagrams without being prompted, producing algebraic solutions before substituting numbers, and doing dimensional analysis. Problem sets are often assumed to help prepare students for tests; however, correlations between students' problem-solving scores and performance between the two assessments did not give clear indications of whether problem sets were helping to prepare students to solve problems. Lastly, students' attitudes and beliefs also show a negative shift in students' perceptions of problem-solving by the end of the first semester. Problem-solving is a skill that develops in stages and over time; therefore, a timeframe longer than one semester is needed to report on significant changes in students' problem-solving habits and perspectives about problem-solving in physics. The study results are also important in giving insights into the initial developments of problem-solving skills and teaching problem solving. , Thesis (MSc) -- Faculty of Science, Physics and Electronics, 2024
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Date Issued: 2024-10-11

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Technological pedagogical content knowledge: an examination of rural secondary school life sciences teachers’ integration of technology in Eastern Cape province

- Shambare, Brian

Authors: Shambare, Brian
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/466458 , vital:76730 , DOI https://doi.org/10.21504/10962/466458
Description: Rural education, particularly in the Global South, faces distinct challenges flowing from low socio-economic conditions, limited resources, and inadequate funding. These issues notably affect rural teachers’ abilities to deliver quality education. Although technology integration offers potential benefits and rural teachers have increased access to various technologies, they frequently adopt these tools spontaneously without guidelines. While many teachers in rural schools choose specific technologies to address teaching challenges, technology has to be integrated with a clear pedagogical intent. The rural teachers’ frequent adoption of technologies hints at technological pedagogical content knowledge (TPACK) development, consciously or unconsciously. However, the process of developing this expertise remains largely unknown. Furthermore, the development of TPACK among teachers in rural Global South schools, particularly those who did not receive formal or informal technology training during their initial teacher education or professional development, remains unclear. Therefore, this research delved into the practices, factors, and experiences influencing the development of TPACK, all from the perspective of Life Sciences teachers in rural schools. The voices of teachers in rural regions have been notably absent in the broader discourse of TPACK research, making the current study’s insights particularly significant. This qualitative and investigative study, located within the interpretivist paradigm, is grounded in Vygotsky’s (1978) socio-cultural theory and Koehler and Mishra’s (2006) Technological Pedagogical Content Knowledge framework. Seven Life Sciences teachers participated in the study. The teacher participants were purposively sampled from schools in the Joe Gqabi district in the Eastern Cape province of South Africa. Multiple data-generation instruments were employed. These included a questionnaire, semi-structured interviews, lesson observations, and sharing circle discussions. A thematic analysis approach, guided by the study’s dual theoretical perspective, was applied to dissect and analyse the data. The study’s findings challenged the prevailing assumption that rural schools lack access to technological resources, unveiling that rural Life Sciences teachers in this research had access to diverse educational technologies. Nevertheless, despite improved technology accessibility, these teachers predominantly employed ‘simple skill-based’ technologies for content delivery, resulting in limited learner engagement. Notwithstanding the challenges posed by inadequate school infrastructure, limited electricity access, and poor Internet connectivity, this investigation found that Life Sciences teachers in rural settings who lack formal technology integration training demonstrated enthusiasm for incorporating technology into their teaching methods. Furthermore, these teachers exhibited strength in non-technological TPACK domains, such as content knowledge (CK), pedagogical knowledge (PK), and pedagogical content knowledge (PCK), while demonstrating limited expertise in technology-related domains, such as technological knowledge (TK), technological pedagogical knowledge (TPK), and technological pedagogical content knowledge (TPACK). The study uncovered nuanced factors, practices, and experiences contributing to TPACK development among rural Life Sciences teachers. These include learning from their learners, collaborating with peers, and engaging in self-directed learning. The study also proposed a new theoretical perspective to the existing TPACK framework to cater for technology integration in rural school contexts. Overall, this research provided a unique perspective on TPACK development in rural schools, particularly in the Global South. The study recommended targeted investments in professional development, promoting peer collaboration, and fostering a culture of self-directed learning. Furthermore, the current research emphasised the importance of recognising the evolving educational landscape as a two-way knowledge exchange between teachers and learners to foster TPACK development in rural schools. , Thesis (PhD) -- Faculty of Education, Secondary and Post-School Education, 2024
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Date Issued: 2024-10-11

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The acceptability of Prolonged Exposure Therapy for Primary Care (PE-PC) for the treatment of PTSD in a low resourced community in the Eastern Cape

- Leboho, Lerato

Authors: Leboho, Lerato
Date: 2024-10-11
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/466191 , vital:76706
Description: Post-traumatic stress disorder (PTSD) is a global mental health concern, especially in low- resourced communities that are characterised by limited access to health professionals, limited healthcare infrastructure, and limited access to evidence-based mental healthcare at primary care level. Over the last decade, several psychological trauma-focused therapies (TFTs), such as prolonged exposure therapy (PE) have been developed to treat PTSD. In the context of the existing literature, studies done in HICs have explored the implementation and acceptability of prolonged exposure therapy at primary care level (PE-PC) as a first-line treatment for PTSD. Contrary to this, there is little to no implementation studies done to date that have examined the acceptability of empirically supported treatments (ESTs), such as PE in low-resourced countries, such as South Africa. Using the Implementation Science framework, ten participants were recruited to be interviewed, using semi-structured interviews, about their experiences and perceptions of PE-PC as a treatment for PTSD, and to also share their experiences of living with PTSD. The interview data was analysed using the reflexive thematic analysis (RTA) method to determine whether PE-PC is an acceptable treatment for PTSD that can be administered at community level and highlights the importance of integrating mental health within primary healthcare practice. Based on the analysis four superordinate themes were identified, namely, lack and absence of social support; factors preventing trauma survivors from accessing EBTs; lack of knowledge regarding mental health literacy, and adaptation of a brief trauma-focused therapy in a low-resource community. The evidence this study shows that some of the factors that hinder the acceptability of trauma-focused therapies (TFTs) at community level, include stigma and discrimination, the absence of social support, limited resources, and inadequate knowledge on mental health and illness. Therefore, it makes sense of the urgency to implement evidence-based treatments (EBTs) in LMICs. Findings of this thesis suggest that (a) PE-PC should be adopted at community level, and that (b) PE-PC is an acceptable treatment for PTSD in low-resourced communities. , Thesis (MSocSci) -- Faculty of Humanities, Psychology, 2024
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Date Issued: 2024-10-11

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