A descriptive study of lead arm muscle activation patterns during cricket batting
- Authors: McCarthy, Ryan Aidan
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/464754 , vital:76542
- Description: Introduction: Kinematic studies identify elbow extension and wrist flexion as key movements for bat swinging speed during cricket batting. Knowledge of lead arm muscle activation during cricket batting may provide a greater understanding of the mechanics leading to the generation of faster bat speed. Aim: The current investigation aimed to determine selected muscle activation of cricketer's lead arm, maximum bat swinging speed and angular separation of the pelvis and thorax in the transverse plane (known as the X-angle) during a distance-hitting batting protocol. Materials and Methods: 12 cricket players playing for a South African school 1st XI school team aged 16-19 years completed a distance-hitting batting protocol. Due to issues in data recording two participants' data was excluded leading to 10 participants being kept in the final analyses.Participants attempted to hit straight lofted drives while facing full-length deliveries at 80-100 km.h-1 from a bowling machine. Each participant faced 12-24 balls split into overs while lead arm muscle activation, bat speed, and angle of lead-elbow flexion were recorded. Each participant's elbow and wrist flexors and extensors were monitored by electromyography (EMG) units while they batted. The EMG units were placed on the wrist flexor and extensor origins and on Triceps and Biceps Brachii. Muscle activation for each muscle was recorded in millivolts (mv) and divided by the maximum measurement of voluntary muscle activation to determine the percentage of maximum voluntary contraction (%MVC) during each shot. Percentage MVC for batting phases of backlift, downswing, contact and follow-through were averaged to compare average %MVC per muscle across all batters and obtain inter-participant variability. Lead arm elbow angle and the %MVC of the elbow and wrist muscles will be compared between successful and unsuccessful shots for analysis. Each participant's lead arm elbow angle was monitored in degrees of flexion by a goniometer placed across the anterior aspect of the elbow joint. Due to the data not having a normal distribution, non-parametric tests were used to establish the variance between dependent variables. To determine the effect of multiple groups on the independent variables a Kruskal-Wallis test for ANOVA was used. Where significant differences were identified, multiple pairwise comparisons were completed to determine where the differences occurred. Results: Successful Lofted straight drives (32 shots) were compared to unsuccessful shots (101 shots) across all participants. Participants and batting phase were found to be significantly different for lead arm elbow angle and muscle activation however shot type was not found to be significantly different. Meaning that lead arm elbow angle and muscle activation differ based on the participant observed or based on the batting phase observed. The backswing phase recorded a higher amount of elbow flexion (155.25°) for Lofted straight drive compared to unsuccessful shots (157.86°) and lower activation across all muscles for Lofted straight drive. The lofted straight drive had a higher amount of elbow flexion (129.52°) compared to unsuccessful shots (149.24°) for the downswing phase and muscle activation was similar with greater variation for unsuccessful shots. At contact Lofted straight drive had a higher amount of elbow flexion (153.44° v 160.13°), and higher activation in the Biceps brachii (34.61% v 28.41%) and Triceps brachii (51.07% v 43.02%). For the follow-through phase Lofted straight drives had a higher amount of elbow flexion (144.87° v 149.59°) and greater Forearm extensor activation (37.13% v 31.28%). There was a large variation across all phases (coefitient of variation between 8.79%-70.28%) with backswing having the least variation and contact having the greatest. Meaning that the backswing phase is fairly predictable for batters and the contact phase is highly variable. Conclusion: Muscle activation increased in the last few milliseconds before contact. The Forearm extensor had the greatest activation during the backswing and follow-through phases. During the downswing phase, Forearm flexors had the greatest activation and at contact, the Triceps brachii had the greatest activation. This study emphasizes the importance of forearm and elbow muscle for batting. Appropriate strengthening of the muscles could also help a batter execute a powerful lofted drive. Future studies with objective measures linked to batting success in prior studies can build on the importance of these findings for batter success. This study provides insight into individual batter techniques and identifies important topics for future research. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: McCarthy, Ryan Aidan
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/464754 , vital:76542
- Description: Introduction: Kinematic studies identify elbow extension and wrist flexion as key movements for bat swinging speed during cricket batting. Knowledge of lead arm muscle activation during cricket batting may provide a greater understanding of the mechanics leading to the generation of faster bat speed. Aim: The current investigation aimed to determine selected muscle activation of cricketer's lead arm, maximum bat swinging speed and angular separation of the pelvis and thorax in the transverse plane (known as the X-angle) during a distance-hitting batting protocol. Materials and Methods: 12 cricket players playing for a South African school 1st XI school team aged 16-19 years completed a distance-hitting batting protocol. Due to issues in data recording two participants' data was excluded leading to 10 participants being kept in the final analyses.Participants attempted to hit straight lofted drives while facing full-length deliveries at 80-100 km.h-1 from a bowling machine. Each participant faced 12-24 balls split into overs while lead arm muscle activation, bat speed, and angle of lead-elbow flexion were recorded. Each participant's elbow and wrist flexors and extensors were monitored by electromyography (EMG) units while they batted. The EMG units were placed on the wrist flexor and extensor origins and on Triceps and Biceps Brachii. Muscle activation for each muscle was recorded in millivolts (mv) and divided by the maximum measurement of voluntary muscle activation to determine the percentage of maximum voluntary contraction (%MVC) during each shot. Percentage MVC for batting phases of backlift, downswing, contact and follow-through were averaged to compare average %MVC per muscle across all batters and obtain inter-participant variability. Lead arm elbow angle and the %MVC of the elbow and wrist muscles will be compared between successful and unsuccessful shots for analysis. Each participant's lead arm elbow angle was monitored in degrees of flexion by a goniometer placed across the anterior aspect of the elbow joint. Due to the data not having a normal distribution, non-parametric tests were used to establish the variance between dependent variables. To determine the effect of multiple groups on the independent variables a Kruskal-Wallis test for ANOVA was used. Where significant differences were identified, multiple pairwise comparisons were completed to determine where the differences occurred. Results: Successful Lofted straight drives (32 shots) were compared to unsuccessful shots (101 shots) across all participants. Participants and batting phase were found to be significantly different for lead arm elbow angle and muscle activation however shot type was not found to be significantly different. Meaning that lead arm elbow angle and muscle activation differ based on the participant observed or based on the batting phase observed. The backswing phase recorded a higher amount of elbow flexion (155.25°) for Lofted straight drive compared to unsuccessful shots (157.86°) and lower activation across all muscles for Lofted straight drive. The lofted straight drive had a higher amount of elbow flexion (129.52°) compared to unsuccessful shots (149.24°) for the downswing phase and muscle activation was similar with greater variation for unsuccessful shots. At contact Lofted straight drive had a higher amount of elbow flexion (153.44° v 160.13°), and higher activation in the Biceps brachii (34.61% v 28.41%) and Triceps brachii (51.07% v 43.02%). For the follow-through phase Lofted straight drives had a higher amount of elbow flexion (144.87° v 149.59°) and greater Forearm extensor activation (37.13% v 31.28%). There was a large variation across all phases (coefitient of variation between 8.79%-70.28%) with backswing having the least variation and contact having the greatest. Meaning that the backswing phase is fairly predictable for batters and the contact phase is highly variable. Conclusion: Muscle activation increased in the last few milliseconds before contact. The Forearm extensor had the greatest activation during the backswing and follow-through phases. During the downswing phase, Forearm flexors had the greatest activation and at contact, the Triceps brachii had the greatest activation. This study emphasizes the importance of forearm and elbow muscle for batting. Appropriate strengthening of the muscles could also help a batter execute a powerful lofted drive. Future studies with objective measures linked to batting success in prior studies can build on the importance of these findings for batter success. This study provides insight into individual batter techniques and identifies important topics for future research. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2024
- Full Text:
- Date Issued: 2024-10-11
Becoming a [COVID] student?: assessing the impact of COVID-19 on first-year students’ experiences of higher education in the Eastern Cape, South Africa
- Authors: Nebbe, Kelsey Ann
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/466295 , vital:76715
- Description: In 2020, the COVID-19 pandemic disrupted South African higher education which forced the shift to emergency distance learning to save the academic years of 2020-2022. The repercussions of this are still emerging, but current literature focuses on understanding the impact of first-year students is focused on the impact of academics caused by the emergency shift to online, the “double transition” as Nyar (2021) termed the adjustment to university and then again to the online emergency academics. There is also a niche for holistic research to be done regarding the student experience - pandemic times and elsewise. My thesis focuses on the journey of studenthood of three cohorts at a residential university in the Eastern Cape, South Africa, through the COVID-19 pandemic of 2020-2022. This research utilises ethnographic iterative mixed methods (questionnaire, interviews, focus groups and participant observation) and the theoretical lens of Rites of Passage to understand my research participant’s experiences. My findings are that due to the circumstances of an incomplete student experience of just online academics provided an continuous liminal period for first-year students of 2020-2021, with little to no opportunity for them to develop a connection to the university community. The opportunity for them to holistically become students arises at the end of the pandemic in 2022, with the restrictions lifting and the return to on-campus and in-person academic activities allowing them to have a first-year experienced that COVID-19 prohibited. , Thesis (MSocSci) -- Faculty of Humanities, Anthropology, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Nebbe, Kelsey Ann
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/466295 , vital:76715
- Description: In 2020, the COVID-19 pandemic disrupted South African higher education which forced the shift to emergency distance learning to save the academic years of 2020-2022. The repercussions of this are still emerging, but current literature focuses on understanding the impact of first-year students is focused on the impact of academics caused by the emergency shift to online, the “double transition” as Nyar (2021) termed the adjustment to university and then again to the online emergency academics. There is also a niche for holistic research to be done regarding the student experience - pandemic times and elsewise. My thesis focuses on the journey of studenthood of three cohorts at a residential university in the Eastern Cape, South Africa, through the COVID-19 pandemic of 2020-2022. This research utilises ethnographic iterative mixed methods (questionnaire, interviews, focus groups and participant observation) and the theoretical lens of Rites of Passage to understand my research participant’s experiences. My findings are that due to the circumstances of an incomplete student experience of just online academics provided an continuous liminal period for first-year students of 2020-2021, with little to no opportunity for them to develop a connection to the university community. The opportunity for them to holistically become students arises at the end of the pandemic in 2022, with the restrictions lifting and the return to on-campus and in-person academic activities allowing them to have a first-year experienced that COVID-19 prohibited. , Thesis (MSocSci) -- Faculty of Humanities, Anthropology, 2024
- Full Text:
- Date Issued: 2024-10-11
Biology and management of the fruit piercing moth Serrodes partita in citrus orchards
- Authors: Mushore, Tapiwa Gift
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/466792 , vital:76779 , DOI https://doi.org/10.21504/10962/466792
- Description: The fruit-piercing moth, Serrodes partita (Fabricius) (Lepidoptera: Erebidae), is a polyphagous, multivoltine pest of citrus. This insect has a distinct geographical separation between its larval and adult stages, each with different feeding patterns. During the larval stage, it primarily acts as a forest defoliator, feeding mostly on Jacket plum, Pappea capensis Eckl. & Zeyh. (Sapindaceae). In contrast, the adult stage of this moth feeds on both tropical and subtropical fruit, including citrus and can cause serious economic losses. The adult moth uses its sclerotised proboscis to pierce the skin of ripening or ripe fruit, from which it extracts the juice. This piercing action initiates a fermentation process within the fruit, attracting other secondary-feeding moths, commonly referred to as fruit-sucking moths. As a result of the feeding activity, the affected fruit eventually rot, drop to the ground, and become unsuitable for the market. Serrodes partita exhibits an outbreak life strategy, reoccurring every 5 to 10 years. In South Africa's Eastern Cape Province, specifically in the Upper Kat River Valley, citrus growers have expressed concerns about the impact of this moth on soft citrus (Satsumas and Clementines). This raises the possibility of a shift in the population dynamics of S. partita, where these occurrences become more frequent and less sporadic. Such a trend poses a significant threat to fruit arboriculture in the Eastern Cape region. Currently, there are limited management strategies available for managing fruit-piecing moths. The use of pesticides is not a feasible option for ripe or nearly ripe fruit, and is ineffective against the adult moth. Alternative control methods, such as orchard netting and light barriers, either come with high costs or are impractical for large-scale citrus production. Given the limited range of management options, combined with the moth's tendency for sudden outbreaks, citrus growers find themselves without effective means to manage this pest. The objective of this study was, therefore, to investigate the biology of S. partita and explore various control options to effectively manage this pest. Research focused on the biology and laboratory rearing of larval stages of S. partita. The flight behaviour, feeding patterns, and preferences of adult S. partita within citrus orchards were also explored. The aim was to elucidate key fundamental aspects, including whether the same population frequents a particular orchard, and if infestations within orchards exhibit a specific direction. Lure type and lure presentation method trials were conducted to determine the most effective lure and trap design. Seasonal monitoring of S. partita in soft citrus orchards was conducted over three years to determine its outbreak status in the Committee’s Drift area and the role of weather variables in the activity of the moth. Damage assessments were also conducted alongside monitoring to determine the level of damage inflicted by S. partita. Natural enemies associated with S. partita were explored to determine the prevalence and causes of mortality in late instars during laboratory rearing. Rearing S. partita on an artificial diet was unsuccessful despite several modifications. The moth, however, completed its entire life cycle on its natural host, P. capensis in the laboratory. The total life cycle from egg to adult took 80.7 ± 3.6 days, the larval stage lasted 52.3 ± 2.8 days, and the pupal stage lasted 25.8 ± 3.6 days at 21°C. The investigation into the biology of S. partita also brought attention to the most susceptible stages of its growth, with high mortality rates recorded among neonates and late instars. The findings of the study revealed directional patterns of moth infestations, with higher numbers observed at the orchard's periphery leading towards natural vegetation. This raises the prospect of using sacrificial rows on the edge of a citrus orchard to concentrate moth feeding damage during outbreak years. Using a mark and recapture technique, the study showed that a relatively small proportion (4.5 %) of moths tended to revisit the same orchard. The moths strongly preferred damaged fruit (85 %) over undamaged fruit. Visible damage (rotting symptoms) typically became apparent within 3 to 5 days. Satsumas had a higher number of feeding scars (2.1) than Clementines (1.08), highlighting their susceptibility. The study also established that, on average, pierced soft citrus fruit takes about four days to display symptoms of decay. Synthetic proprietary Australian lures were ineffective at attracting the moth, whereas fresh bananas proved to be a successful lure. Furthermore, the addition of both Agar and Super absorbent polymer showed promise as thickening agents to enhance the longevity of fresh bananas in traps. The effectiveness of various trap designs was compared, including the funnel trap, delta trap, bucket trap, and circular trap, in capturing fruit-feeding moths. The funnel trap performed best as it captured the most moths, followed by the delta trap, Lynfield trap and disc trap, respectively. Additionally, an electronic enhancement to the funnel trap, incorporating a zapper element, improved efficiency. However, efforts to exploit both visual and olfactory cues through the inclusion of an Ultraviolet (UV) light component did not improve its effectiveness. No extensive outbreaks were recorded during the study; however, population variations of S. partita populations were recorded. Annual trends showed two population peaks, with the first peak recorded from December to March, while the second peak was recorded from April to July. The activity of the moths also differed across different months, with the highest peaks recorded in May, while no moths were recorded from August to November. Both cultivar type and farm location did not influence the occurrence of the moth. Meanwhile cumulative weather parameters (rainfall, temperature and humidity) from the four months prior to occurrence influenced the activity of S. partita. Temperature determined the timing of the outbreak, while rainfall determined the magnitude of the outbreak. Damage assessment showed very low fruit damage by S. partita throughout the monitoring period. Varying levels of infestation by a tachinid fly, 4 % and 35 %, were recorded for 2021 and 2022, respectively. The tachinid parasitoid could not be identified at the species level. A novel baculovirus, tentatively classified as S. partita NPV (SepaNPV), was identified as the larval mortality causative agent. This study enhanced our understanding of S. partita's biology and population dynamics, providing valuable insights for developing effective management strategies against this economically impactful citrus pest. Future research should focus on refining control measures and addressing the challenges of the adult moth's elusive nature. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Mushore, Tapiwa Gift
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/466792 , vital:76779 , DOI https://doi.org/10.21504/10962/466792
- Description: The fruit-piercing moth, Serrodes partita (Fabricius) (Lepidoptera: Erebidae), is a polyphagous, multivoltine pest of citrus. This insect has a distinct geographical separation between its larval and adult stages, each with different feeding patterns. During the larval stage, it primarily acts as a forest defoliator, feeding mostly on Jacket plum, Pappea capensis Eckl. & Zeyh. (Sapindaceae). In contrast, the adult stage of this moth feeds on both tropical and subtropical fruit, including citrus and can cause serious economic losses. The adult moth uses its sclerotised proboscis to pierce the skin of ripening or ripe fruit, from which it extracts the juice. This piercing action initiates a fermentation process within the fruit, attracting other secondary-feeding moths, commonly referred to as fruit-sucking moths. As a result of the feeding activity, the affected fruit eventually rot, drop to the ground, and become unsuitable for the market. Serrodes partita exhibits an outbreak life strategy, reoccurring every 5 to 10 years. In South Africa's Eastern Cape Province, specifically in the Upper Kat River Valley, citrus growers have expressed concerns about the impact of this moth on soft citrus (Satsumas and Clementines). This raises the possibility of a shift in the population dynamics of S. partita, where these occurrences become more frequent and less sporadic. Such a trend poses a significant threat to fruit arboriculture in the Eastern Cape region. Currently, there are limited management strategies available for managing fruit-piecing moths. The use of pesticides is not a feasible option for ripe or nearly ripe fruit, and is ineffective against the adult moth. Alternative control methods, such as orchard netting and light barriers, either come with high costs or are impractical for large-scale citrus production. Given the limited range of management options, combined with the moth's tendency for sudden outbreaks, citrus growers find themselves without effective means to manage this pest. The objective of this study was, therefore, to investigate the biology of S. partita and explore various control options to effectively manage this pest. Research focused on the biology and laboratory rearing of larval stages of S. partita. The flight behaviour, feeding patterns, and preferences of adult S. partita within citrus orchards were also explored. The aim was to elucidate key fundamental aspects, including whether the same population frequents a particular orchard, and if infestations within orchards exhibit a specific direction. Lure type and lure presentation method trials were conducted to determine the most effective lure and trap design. Seasonal monitoring of S. partita in soft citrus orchards was conducted over three years to determine its outbreak status in the Committee’s Drift area and the role of weather variables in the activity of the moth. Damage assessments were also conducted alongside monitoring to determine the level of damage inflicted by S. partita. Natural enemies associated with S. partita were explored to determine the prevalence and causes of mortality in late instars during laboratory rearing. Rearing S. partita on an artificial diet was unsuccessful despite several modifications. The moth, however, completed its entire life cycle on its natural host, P. capensis in the laboratory. The total life cycle from egg to adult took 80.7 ± 3.6 days, the larval stage lasted 52.3 ± 2.8 days, and the pupal stage lasted 25.8 ± 3.6 days at 21°C. The investigation into the biology of S. partita also brought attention to the most susceptible stages of its growth, with high mortality rates recorded among neonates and late instars. The findings of the study revealed directional patterns of moth infestations, with higher numbers observed at the orchard's periphery leading towards natural vegetation. This raises the prospect of using sacrificial rows on the edge of a citrus orchard to concentrate moth feeding damage during outbreak years. Using a mark and recapture technique, the study showed that a relatively small proportion (4.5 %) of moths tended to revisit the same orchard. The moths strongly preferred damaged fruit (85 %) over undamaged fruit. Visible damage (rotting symptoms) typically became apparent within 3 to 5 days. Satsumas had a higher number of feeding scars (2.1) than Clementines (1.08), highlighting their susceptibility. The study also established that, on average, pierced soft citrus fruit takes about four days to display symptoms of decay. Synthetic proprietary Australian lures were ineffective at attracting the moth, whereas fresh bananas proved to be a successful lure. Furthermore, the addition of both Agar and Super absorbent polymer showed promise as thickening agents to enhance the longevity of fresh bananas in traps. The effectiveness of various trap designs was compared, including the funnel trap, delta trap, bucket trap, and circular trap, in capturing fruit-feeding moths. The funnel trap performed best as it captured the most moths, followed by the delta trap, Lynfield trap and disc trap, respectively. Additionally, an electronic enhancement to the funnel trap, incorporating a zapper element, improved efficiency. However, efforts to exploit both visual and olfactory cues through the inclusion of an Ultraviolet (UV) light component did not improve its effectiveness. No extensive outbreaks were recorded during the study; however, population variations of S. partita populations were recorded. Annual trends showed two population peaks, with the first peak recorded from December to March, while the second peak was recorded from April to July. The activity of the moths also differed across different months, with the highest peaks recorded in May, while no moths were recorded from August to November. Both cultivar type and farm location did not influence the occurrence of the moth. Meanwhile cumulative weather parameters (rainfall, temperature and humidity) from the four months prior to occurrence influenced the activity of S. partita. Temperature determined the timing of the outbreak, while rainfall determined the magnitude of the outbreak. Damage assessment showed very low fruit damage by S. partita throughout the monitoring period. Varying levels of infestation by a tachinid fly, 4 % and 35 %, were recorded for 2021 and 2022, respectively. The tachinid parasitoid could not be identified at the species level. A novel baculovirus, tentatively classified as S. partita NPV (SepaNPV), was identified as the larval mortality causative agent. This study enhanced our understanding of S. partita's biology and population dynamics, providing valuable insights for developing effective management strategies against this economically impactful citrus pest. Future research should focus on refining control measures and addressing the challenges of the adult moth's elusive nature. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2024
- Full Text:
- Date Issued: 2024-10-11
Computational search for nature-derived dual-action inhibitors of HIV-1 reverse transcriptase and integrase: a potential strategy to mitigate drug resistance progression
- Authors: Mwiinga, Luyando
- Date: 2024-10-11
- Subjects: HIV (Viruses) , Reverse transcriptase , Antiretroviral agents , RDKit , Drug resistance , Docking
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/463930 , vital:76458
- Description: Human immunodeficiency virus Type 1 (HIV-1) is a devastating viral infection affecting millions worldwide and presents significant challenges in treatment and management. In 2022, approximately 39 million people were living with HIV with Sub-Saharan Africa having two thirds of these infections. Devastatingly, there were approximately 300 000 HIV/AIDS related deaths in Sub-Saharan Africa alone in 2022 alone. Antiretroviral therapy (ART) which is fundamental for HIV treatment, comprises of a combination of drugs such as nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTs), protease inhibitors (PIs) and integrase strand transfer inhibitors (INSTIs). However, although 28.7 million people out of the estimated 38.4 million people living with HIV in 2021 were receiving ART, the emergence of drug-resistant strains further complicates treatment efforts, highlighting the need for novel therapeutic approaches. This study aimed to address the challenges raised by drug resistance and significant side effects by identifying potential dual inhibitors against HIV-1 Reverse Transcriptase (RT) and Integrase (IN) using in silico techniques. RT RNase H and IN were chosen as targets for their shared dependency on Mg2+ ions within their active sites, which are crucial for catalytic activity. The selection of dual inhibitors was motivated by the fact that the virus would need to replicate at two points simultaneously to develop resistance, making it less likely. The objectives of this study included the creation of a natural derivative compound library using RDKit with the aid of SciFinder, utilizing (-)-epigallocatechin-3-O-gallate (EGCG), because of its dual inhibitory effects against RT and IN, as indicated by a study conducted by Sanna et al. 2019. The natural derivatives were chosen to take advantage of their chemical diversity and to explore potential novel therapeutic options for combating HIV drug resistance. The compound library created comprised of 125 203 compounds. Then docking studies were conducted to assess proteinligand binding. After the correlation of the RT and IN docking studies, 288 compounds were filtered to have potential dual inhibitory activity. Then quantitative estimation of druggability (QED) analysis identified three compounds with superior properties compared to EGCG and FDAapproved drug raltegravir (RAL). Molecular docking simulations revealed interactions between the inhibitors and the key active site residues of RT and IN, along with the chelation of at least one 3 Mg2+, suggesting the potential for enzymatic disruption. Furthermore, molecular dynamic (MD) simulations were then conducted to assess protein-ligand system behavior, through RMSD and RMSF analysis. The RMSD analysis uncovered instability in the IN-Sci30703 complex, leading to its exclusion as a potential dual action inhibitor. RMSF analysis for IN showed that all the inhibitors had the ability to limit the flexibility of the catalytic loop which is essential for catalytic activity. Therefore, further in vitro studies are required to evaluate the effectiveness of the remaining two EGCG derivatives (Sci33211 and Sci48919) in inhibiting RT and IN through the chelation of at least one Mg2+ ion to determine if they have superior dual inhibitory effects compared to EGCG. This study adds to the ongoing efforts to develop effective strategies against HIV-1 drug resistance and emphasizes the importance of continued research in this field. , Thesis (MSc) -- Faculty of Science, Biochemistry, Microbiology & Bioinformatics, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Mwiinga, Luyando
- Date: 2024-10-11
- Subjects: HIV (Viruses) , Reverse transcriptase , Antiretroviral agents , RDKit , Drug resistance , Docking
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/463930 , vital:76458
- Description: Human immunodeficiency virus Type 1 (HIV-1) is a devastating viral infection affecting millions worldwide and presents significant challenges in treatment and management. In 2022, approximately 39 million people were living with HIV with Sub-Saharan Africa having two thirds of these infections. Devastatingly, there were approximately 300 000 HIV/AIDS related deaths in Sub-Saharan Africa alone in 2022 alone. Antiretroviral therapy (ART) which is fundamental for HIV treatment, comprises of a combination of drugs such as nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTs), protease inhibitors (PIs) and integrase strand transfer inhibitors (INSTIs). However, although 28.7 million people out of the estimated 38.4 million people living with HIV in 2021 were receiving ART, the emergence of drug-resistant strains further complicates treatment efforts, highlighting the need for novel therapeutic approaches. This study aimed to address the challenges raised by drug resistance and significant side effects by identifying potential dual inhibitors against HIV-1 Reverse Transcriptase (RT) and Integrase (IN) using in silico techniques. RT RNase H and IN were chosen as targets for their shared dependency on Mg2+ ions within their active sites, which are crucial for catalytic activity. The selection of dual inhibitors was motivated by the fact that the virus would need to replicate at two points simultaneously to develop resistance, making it less likely. The objectives of this study included the creation of a natural derivative compound library using RDKit with the aid of SciFinder, utilizing (-)-epigallocatechin-3-O-gallate (EGCG), because of its dual inhibitory effects against RT and IN, as indicated by a study conducted by Sanna et al. 2019. The natural derivatives were chosen to take advantage of their chemical diversity and to explore potential novel therapeutic options for combating HIV drug resistance. The compound library created comprised of 125 203 compounds. Then docking studies were conducted to assess proteinligand binding. After the correlation of the RT and IN docking studies, 288 compounds were filtered to have potential dual inhibitory activity. Then quantitative estimation of druggability (QED) analysis identified three compounds with superior properties compared to EGCG and FDAapproved drug raltegravir (RAL). Molecular docking simulations revealed interactions between the inhibitors and the key active site residues of RT and IN, along with the chelation of at least one 3 Mg2+, suggesting the potential for enzymatic disruption. Furthermore, molecular dynamic (MD) simulations were then conducted to assess protein-ligand system behavior, through RMSD and RMSF analysis. The RMSD analysis uncovered instability in the IN-Sci30703 complex, leading to its exclusion as a potential dual action inhibitor. RMSF analysis for IN showed that all the inhibitors had the ability to limit the flexibility of the catalytic loop which is essential for catalytic activity. Therefore, further in vitro studies are required to evaluate the effectiveness of the remaining two EGCG derivatives (Sci33211 and Sci48919) in inhibiting RT and IN through the chelation of at least one Mg2+ ion to determine if they have superior dual inhibitory effects compared to EGCG. This study adds to the ongoing efforts to develop effective strategies against HIV-1 drug resistance and emphasizes the importance of continued research in this field. , Thesis (MSc) -- Faculty of Science, Biochemistry, Microbiology & Bioinformatics, 2024
- Full Text:
- Date Issued: 2024-10-11
Eastern Cape jazz heritage: the jazz tradition and veteran musicians of East London and Zwelitsha
- Giyose, Thandikile Qhawekazi
- Authors: Giyose, Thandikile Qhawekazi
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/465964 , vital:76672
- Description: This thesis explores the memories of musicians and music collectors as evident in the performance of traditional jazz songs in East London and Zwelitsha. I ask, how may research on musicians and their songs develop new knowledge about the aesthetics of jazz in the Eastern Cape and contribute to transforming notions of memories and archives? I argue that these songs are repositories of collective memory about the musical pasts of Eastern Cape modernity. We commemorate cities such as Johannesburg and Cape Town for nurturing South African jazz but what is known of the jazz musicians who remained in the country, and those musicians whose musicality was nurtured in the Eastern Cape? Where are the stories of their musical journeys and compositions located? How did these musicians contribute to the development of a form of South African jazz, which now represents and forms a large part of our heritage and our various identities as musicians, fans and performers in South Africa? In-depth and semi-structured interviews were conducted with veteran jazz musicians, jazz music collectors and members of the younger generation of jazz musicians who are originally from or reside in East London and Zwelitsha, Eastern Cape. The research follows a qualitative methodology, using an exploratory case study with a focused ethnographic approach, to understand how these musicians’ songs have retained memories of their lived experiences. The research is derived from oral histories of musicians to understand how the songs survive in the collective memory of musicians and their fans, contributing to the preservation of Eastern Cape’s jazz heritage. , Thesis (MA) -- Faculty of Humanities, Music and Musicology, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Giyose, Thandikile Qhawekazi
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/465964 , vital:76672
- Description: This thesis explores the memories of musicians and music collectors as evident in the performance of traditional jazz songs in East London and Zwelitsha. I ask, how may research on musicians and their songs develop new knowledge about the aesthetics of jazz in the Eastern Cape and contribute to transforming notions of memories and archives? I argue that these songs are repositories of collective memory about the musical pasts of Eastern Cape modernity. We commemorate cities such as Johannesburg and Cape Town for nurturing South African jazz but what is known of the jazz musicians who remained in the country, and those musicians whose musicality was nurtured in the Eastern Cape? Where are the stories of their musical journeys and compositions located? How did these musicians contribute to the development of a form of South African jazz, which now represents and forms a large part of our heritage and our various identities as musicians, fans and performers in South Africa? In-depth and semi-structured interviews were conducted with veteran jazz musicians, jazz music collectors and members of the younger generation of jazz musicians who are originally from or reside in East London and Zwelitsha, Eastern Cape. The research follows a qualitative methodology, using an exploratory case study with a focused ethnographic approach, to understand how these musicians’ songs have retained memories of their lived experiences. The research is derived from oral histories of musicians to understand how the songs survive in the collective memory of musicians and their fans, contributing to the preservation of Eastern Cape’s jazz heritage. , Thesis (MA) -- Faculty of Humanities, Music and Musicology, 2024
- Full Text:
- Date Issued: 2024-10-11
Optimising Integrated Multitrophic Aquaculture (IMTA) on a South African abalone farm
- Authors: Falade, Abiodun Emmanuel
- Date: 2024-10-11
- Subjects: Aquaculture , Integrated multi-trophic aquaculture , Seaweed , Abalone culture South Africa , Abalones , Ingestion , Nutrient cycles
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/466712 , vital:76772 , DOI https://doi.org/10.21504/10962/466712
- Description: The efficiency of fed nutrient utilisation in integrated multitrophic aquaculture (IMTA) system was evaluated on a South African abalone farm. On many commercial abalone farms in South Africa, Haliotis midae are fed a combination of pelleted feed and live macroalgae cultured downstream in abalone effluent. This production technique reduces the discharge of dissolved nutrients into the environment and improves farm productivity as unquantified proportion of the waste metabolites is captured as macroalgal biomass. However, the solid waste from abalone culture tanks remains unutilised and discharged to the coastal environments. Thus, there is scope to improve the dissolved nutrients removal efficiency of the macroalgae and to reduce the discharge of particulate nutrients using detritus waste extractive organisms. The present study aimed at the production and environmental performance of a shore-based abalone/macroalgae IMTA improving farm in South Africa by improving the nutrient utilisation efficiency of farmed abalone and seaweed and testing the waste solids removal potential of a sea cucumber species. Monoculture systems, where abalone and seaweed were cultured separately, both in fresh seawater (salinity: 35 g/L), were compared with an integrated culture system where the seaweed (Ulva lacinulata) was cultured downstream in the wastewater flowing from abalone tanks that were up-channel. Based on the findings from quantifying the performance of these production systems, methods to improve the nutrient utilisation and production efficiencies of the production systems were explored. These assessed methods included (1) the removal of abalone biodeposits by detritus extractive sea cucumber production, (2) evaluating the potential of farmed macroalgae as supplement in formulated diet, and (3) replacing mineral fertilisers with eco-friendly live microbial fertilisers for seaweed farming. Furthermore, the overall environmental performance of the two farm systems was quantified using a life cycle analysis methodology. Monitoring of the nutrient flows through the monoculture and IMTA systems revealed that the highest inputs of nutrients (nitrogen and phosphorus) into the abalone and seaweed culture tanks of the two production systems were abalone feed pellet (70-81%) and mineral fertilisers respectively (63-93%). About 48-51% of the nitrogen supplied from the feed was utilised by abalone in the IMTA and monoculture systems, while the remaining portion was lost as organic waste nitrogen on the production tank floor (20-30%) and as dissolved nitrogen in post-abalone tank effluent (30-36%). In the seaweed tanks receiving abalone effluent (IMTA), 69% of the dissolved nitrogen input was absorbed by cultured Ulva while 25% of the nitrogen was lost to the post-seaweed effluent which returned to the environment. However, in the monoculture system, 52% of the nitrogen from supplemented inorganic fertiliser was absorbed by cultured Ulva while ca. 46% of the nutrient was lost to coastal waters through the post-seaweed effluent. Moreover, while the feed accounted for ca. 74-78% input of the phosphorus in abalone of the two production systems, not more than 19% and 13% of this phosphorus was utilised by H. midae in the IMTA and monoculture systems respectively, while the largest portions were lost as organic waste in the sediment (34-45%) and dissolved waste phosphorus in the effluent (33-54%). In the seaweed tanks, a small portion (11-15%) of supplied phosphorus was removed by farmed Ulva while 77-89% was lost in the post-seaweed effluent discharged to coastal environment. The substitution of 50% mineral fertilisers with live microbial fertilisers during seaweed production significantly reduced the discharge of dissolved nitrogen and phosphorus from macroalgae raceways to coastal environment by 55 and 45% respectively, without impacting their growth, yield and nutrient compositions. A life cycle analysis of the measured energy and nutrients utilisation efficiency of these production systems was compiled, and the impacts of the inputs and outputs from each production system on the environment was assessed. The electrical energy input to abalone and seaweed tanks constituted the highest contribution to all assessed environmental impact categories for the two production systems, followed by the contributions from the nutrients supplied to farmed abalone (formulated diet) and seaweed (mineral fertilisers). The impact of these inputs on the environment was most evident on marine aquatic ecotoxicity being 2.11E+03 kg 1.4-DB eq and 4.43E+03 kg 1.4-DB eq for IMTA and monoculture systems respectively. The measured impact of seaweed aquaculture on the environment was reduced by 50-52% when Ulva was cultured in abalone effluent (IMTA) compared to culture in fresh seawater (monoculture). However, the input of chemical fertilisers in the two systems of cultivation resulted in similar eutrophication potentials (8.09 - 8.41E-02 kg PO4--- eq). To reduce the solid waste discharge from abalone tanks, and create an additional high-value crop, an endemic sea cucumber species (Neostichopus grammatus) was introduced on the floor of the abalone culture tanks in a pilot abalone/detritivore/macroalgae IMTA system. The sea cucumber utilised the biodeposits in abalone tanks as food which reduced organic solid discharge to the environment by 11%. However, the sea cucumbers displayed poor nutrient utilisation, a negative growth rate (- 0.59% day-1) and 49% weight loss by the end of the trial that was probably due to sub-optimal habitat conditions (lack of a sand substrate). The potential of including farmed Ulva (IMTA and monoculture) meal in pelleted feed for H. midae was evaluated as a means of improving farming efficiency and reducing the levels of fishmeal and soya in the pellet. In an initial trial, Ulva was included at 12% dry weight in commercial diet and fed to farmed H. midae for 244 d. The 12% inclusion of IMTA and monoculture Ulva resulted in poor feed conversion and nutrient utilisation by H. midae. In a follow-up trial which tested graded inclusion levels of Ulva meal (0.75, 1.50, 3.00, 6.00 and 12.00%), the growth rate and feed utilisation of H. midae was enhanced at a 0.75-6.00% inclusion level of the seaweed in the diet, while at a 6.00-12.00% inclusion level growth rates and feed conversion efficiencies decreased. Therefore, it is recommended that for sub-adult South African abalone, up to 6.00% IMTA Ulva meal can be included in the diet formulation without impacting their growth performance and nutrient utilisation efficiency negatively. This present study contributes to the understanding of the nutrient utilisation dynamics on integrated abalone farms in South Africa. The evidence from the different trials suggests the IMTA techniques tested could be adopted to improve the production performance and reduce the impact of abalone farming on the environment. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Falade, Abiodun Emmanuel
- Date: 2024-10-11
- Subjects: Aquaculture , Integrated multi-trophic aquaculture , Seaweed , Abalone culture South Africa , Abalones , Ingestion , Nutrient cycles
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/466712 , vital:76772 , DOI https://doi.org/10.21504/10962/466712
- Description: The efficiency of fed nutrient utilisation in integrated multitrophic aquaculture (IMTA) system was evaluated on a South African abalone farm. On many commercial abalone farms in South Africa, Haliotis midae are fed a combination of pelleted feed and live macroalgae cultured downstream in abalone effluent. This production technique reduces the discharge of dissolved nutrients into the environment and improves farm productivity as unquantified proportion of the waste metabolites is captured as macroalgal biomass. However, the solid waste from abalone culture tanks remains unutilised and discharged to the coastal environments. Thus, there is scope to improve the dissolved nutrients removal efficiency of the macroalgae and to reduce the discharge of particulate nutrients using detritus waste extractive organisms. The present study aimed at the production and environmental performance of a shore-based abalone/macroalgae IMTA improving farm in South Africa by improving the nutrient utilisation efficiency of farmed abalone and seaweed and testing the waste solids removal potential of a sea cucumber species. Monoculture systems, where abalone and seaweed were cultured separately, both in fresh seawater (salinity: 35 g/L), were compared with an integrated culture system where the seaweed (Ulva lacinulata) was cultured downstream in the wastewater flowing from abalone tanks that were up-channel. Based on the findings from quantifying the performance of these production systems, methods to improve the nutrient utilisation and production efficiencies of the production systems were explored. These assessed methods included (1) the removal of abalone biodeposits by detritus extractive sea cucumber production, (2) evaluating the potential of farmed macroalgae as supplement in formulated diet, and (3) replacing mineral fertilisers with eco-friendly live microbial fertilisers for seaweed farming. Furthermore, the overall environmental performance of the two farm systems was quantified using a life cycle analysis methodology. Monitoring of the nutrient flows through the monoculture and IMTA systems revealed that the highest inputs of nutrients (nitrogen and phosphorus) into the abalone and seaweed culture tanks of the two production systems were abalone feed pellet (70-81%) and mineral fertilisers respectively (63-93%). About 48-51% of the nitrogen supplied from the feed was utilised by abalone in the IMTA and monoculture systems, while the remaining portion was lost as organic waste nitrogen on the production tank floor (20-30%) and as dissolved nitrogen in post-abalone tank effluent (30-36%). In the seaweed tanks receiving abalone effluent (IMTA), 69% of the dissolved nitrogen input was absorbed by cultured Ulva while 25% of the nitrogen was lost to the post-seaweed effluent which returned to the environment. However, in the monoculture system, 52% of the nitrogen from supplemented inorganic fertiliser was absorbed by cultured Ulva while ca. 46% of the nutrient was lost to coastal waters through the post-seaweed effluent. Moreover, while the feed accounted for ca. 74-78% input of the phosphorus in abalone of the two production systems, not more than 19% and 13% of this phosphorus was utilised by H. midae in the IMTA and monoculture systems respectively, while the largest portions were lost as organic waste in the sediment (34-45%) and dissolved waste phosphorus in the effluent (33-54%). In the seaweed tanks, a small portion (11-15%) of supplied phosphorus was removed by farmed Ulva while 77-89% was lost in the post-seaweed effluent discharged to coastal environment. The substitution of 50% mineral fertilisers with live microbial fertilisers during seaweed production significantly reduced the discharge of dissolved nitrogen and phosphorus from macroalgae raceways to coastal environment by 55 and 45% respectively, without impacting their growth, yield and nutrient compositions. A life cycle analysis of the measured energy and nutrients utilisation efficiency of these production systems was compiled, and the impacts of the inputs and outputs from each production system on the environment was assessed. The electrical energy input to abalone and seaweed tanks constituted the highest contribution to all assessed environmental impact categories for the two production systems, followed by the contributions from the nutrients supplied to farmed abalone (formulated diet) and seaweed (mineral fertilisers). The impact of these inputs on the environment was most evident on marine aquatic ecotoxicity being 2.11E+03 kg 1.4-DB eq and 4.43E+03 kg 1.4-DB eq for IMTA and monoculture systems respectively. The measured impact of seaweed aquaculture on the environment was reduced by 50-52% when Ulva was cultured in abalone effluent (IMTA) compared to culture in fresh seawater (monoculture). However, the input of chemical fertilisers in the two systems of cultivation resulted in similar eutrophication potentials (8.09 - 8.41E-02 kg PO4--- eq). To reduce the solid waste discharge from abalone tanks, and create an additional high-value crop, an endemic sea cucumber species (Neostichopus grammatus) was introduced on the floor of the abalone culture tanks in a pilot abalone/detritivore/macroalgae IMTA system. The sea cucumber utilised the biodeposits in abalone tanks as food which reduced organic solid discharge to the environment by 11%. However, the sea cucumbers displayed poor nutrient utilisation, a negative growth rate (- 0.59% day-1) and 49% weight loss by the end of the trial that was probably due to sub-optimal habitat conditions (lack of a sand substrate). The potential of including farmed Ulva (IMTA and monoculture) meal in pelleted feed for H. midae was evaluated as a means of improving farming efficiency and reducing the levels of fishmeal and soya in the pellet. In an initial trial, Ulva was included at 12% dry weight in commercial diet and fed to farmed H. midae for 244 d. The 12% inclusion of IMTA and monoculture Ulva resulted in poor feed conversion and nutrient utilisation by H. midae. In a follow-up trial which tested graded inclusion levels of Ulva meal (0.75, 1.50, 3.00, 6.00 and 12.00%), the growth rate and feed utilisation of H. midae was enhanced at a 0.75-6.00% inclusion level of the seaweed in the diet, while at a 6.00-12.00% inclusion level growth rates and feed conversion efficiencies decreased. Therefore, it is recommended that for sub-adult South African abalone, up to 6.00% IMTA Ulva meal can be included in the diet formulation without impacting their growth performance and nutrient utilisation efficiency negatively. This present study contributes to the understanding of the nutrient utilisation dynamics on integrated abalone farms in South Africa. The evidence from the different trials suggests the IMTA techniques tested could be adopted to improve the production performance and reduce the impact of abalone farming on the environment. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2024
- Full Text:
- Date Issued: 2024-10-11
Search for acrylonitrile-based inhibitors of SAR-Cov-19 main and papain-like proteases through covalent docking and high-throughput virtual screening
- 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
- Full Text:
- Date Issued: 2024-10-11
- 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
- Full Text:
- Date Issued: 2024-10-11
Ubomi ngamahla ndinyuka
- Authors: Snam-Dyani, Linda
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: Xhosa
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/465945 , vital:76670
- Description: Le thesisi yingqokelela yamabalana esiXhosa abalisa ngemeko yentlalo kwidolophana yaseMakhanda, eGqeberha nezinye iilali needolophana eziyingqongileyo. Ulwimi olusetyenziswayo lolwangoku noluthi luchaze iimeko zokuphila zangoku, luxuba namagama esiNgesi, lusongeza noburharha. Obu buncwane bolwimi buvela cacileyo kwindlela endibhale ngayo la mabalana - kwindlela abalinganiswa abalusebenzisa ngayo ulwimi kwiintetho neencoko zabo, kwimiba yobomi abajongene nayo, nakwindlela endithe ndazoba iingcinga ezidiza imivandedwa yabo, ngohlobo abakhetha ukuphila ubomi babo. Kuba incwadi yeBhayibhile inamabali athetha cacileyo ngexesha langoku, ekhuthaza inkululeko yomntu nangona yabhalwa kwiminyaka yakudala, le ngqokelela ikwajolisa kwinguqu ekhululayo eza kuncedisana nokujika kweelensi ezijongwa ngayo iBhayibhile. La mabali abonakalisa kwanendima edlalwa yiBhayibhile ekuphileni komntu ukunika ithemba kwimeko ezininzi zokuphila. Uncwadi olube nefuthe kum kuyilo lwale ngqokelela nasekusebenziseni kwam isandla sokubhala lolu: izicatshulwa eziphuma kwincwadi ebhalwe nguMxolisi Nyezwa ethi, ‘Bhlawa’s Inconsolable Spirits.’ Incwadi kaLukhanye E. Makhenyane ethi, ‘Kukhulu ukuthembeka kwakhe’, ‘Intsimbi’, ebhalwe nguP. T. Mtuze, ‘Umnxeba Wobomi’ ngokubhalwe ngu S.S.M. Mema kwanencwadi yeBhayibhile. , Thesis (MA) -- Faculty of Humanities, Languages and Literatures, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Snam-Dyani, Linda
- Date: 2024-10-11
- Subjects: Uncatalogued
- Language: Xhosa
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/465945 , vital:76670
- Description: Le thesisi yingqokelela yamabalana esiXhosa abalisa ngemeko yentlalo kwidolophana yaseMakhanda, eGqeberha nezinye iilali needolophana eziyingqongileyo. Ulwimi olusetyenziswayo lolwangoku noluthi luchaze iimeko zokuphila zangoku, luxuba namagama esiNgesi, lusongeza noburharha. Obu buncwane bolwimi buvela cacileyo kwindlela endibhale ngayo la mabalana - kwindlela abalinganiswa abalusebenzisa ngayo ulwimi kwiintetho neencoko zabo, kwimiba yobomi abajongene nayo, nakwindlela endithe ndazoba iingcinga ezidiza imivandedwa yabo, ngohlobo abakhetha ukuphila ubomi babo. Kuba incwadi yeBhayibhile inamabali athetha cacileyo ngexesha langoku, ekhuthaza inkululeko yomntu nangona yabhalwa kwiminyaka yakudala, le ngqokelela ikwajolisa kwinguqu ekhululayo eza kuncedisana nokujika kweelensi ezijongwa ngayo iBhayibhile. La mabali abonakalisa kwanendima edlalwa yiBhayibhile ekuphileni komntu ukunika ithemba kwimeko ezininzi zokuphila. Uncwadi olube nefuthe kum kuyilo lwale ngqokelela nasekusebenziseni kwam isandla sokubhala lolu: izicatshulwa eziphuma kwincwadi ebhalwe nguMxolisi Nyezwa ethi, ‘Bhlawa’s Inconsolable Spirits.’ Incwadi kaLukhanye E. Makhenyane ethi, ‘Kukhulu ukuthembeka kwakhe’, ‘Intsimbi’, ebhalwe nguP. T. Mtuze, ‘Umnxeba Wobomi’ ngokubhalwe ngu S.S.M. Mema kwanencwadi yeBhayibhile. , Thesis (MA) -- Faculty of Humanities, Languages and Literatures, 2024
- Full Text:
- Date Issued: 2024-10-11
What is remembered & what is forgotten: shipwrecks and social memory on South Africa’s Sunshine Coast
- Authors: Dickson-Bow, Emma Jane
- Date: 2024-10-11
- Subjects: Collective memory , Memorialization , Shipwrecks , Maritime heritage , Settler colonialism
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/465876 , vital:76664
- Description: Maritime heritage and its representation in South Africa, has been shaped by a settler colonial community heritage consciousness emphasising a heroic moral discourse legitimising local presence by settler communities. While much has been done to decolonise the representation of South African maritime heritage, at the local level small scale memorialisation continues to valorise maritime narratives that highlight the heroic aspects of historical settler colonial society, effectively concealing more fulsome of historical maritime events. Shipwrecks can function as potent tangible and intangible symbols of historical events, articulating a variety of perspectives on what constitutes social memory and history. This thesis examines the extension of public knowledge and representation of shipwreck maritime heritage on the Eastern Cape’s coastal belt, known in tourist branding vernacular as the ‘Sunshine Coast’ (East London to Port Elizabeth). The case study of ‘The Volo’, a Norwegian barge wrecked near present day Kenton-on-Sea and Bushman’s River Mouth (Boesmansriviermond) demonstrates how shipwreck narratives presented at the local public level can articulate a settler colonial community heritage consciousness that erases wider accounts of such stories. The reinterpretation and decentring of settler colonial maritime heritage stories allows for a more diverse and inclusive narrative that has the potential to promote social cohesion and social justice within restorative history work. , Thesis (MA) -- Faculty of Humanities, Anthropology, 2024
- Full Text:
- Date Issued: 2024-10-11
- Authors: Dickson-Bow, Emma Jane
- Date: 2024-10-11
- Subjects: Collective memory , Memorialization , Shipwrecks , Maritime heritage , Settler colonialism
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/465876 , vital:76664
- Description: Maritime heritage and its representation in South Africa, has been shaped by a settler colonial community heritage consciousness emphasising a heroic moral discourse legitimising local presence by settler communities. While much has been done to decolonise the representation of South African maritime heritage, at the local level small scale memorialisation continues to valorise maritime narratives that highlight the heroic aspects of historical settler colonial society, effectively concealing more fulsome of historical maritime events. Shipwrecks can function as potent tangible and intangible symbols of historical events, articulating a variety of perspectives on what constitutes social memory and history. This thesis examines the extension of public knowledge and representation of shipwreck maritime heritage on the Eastern Cape’s coastal belt, known in tourist branding vernacular as the ‘Sunshine Coast’ (East London to Port Elizabeth). The case study of ‘The Volo’, a Norwegian barge wrecked near present day Kenton-on-Sea and Bushman’s River Mouth (Boesmansriviermond) demonstrates how shipwreck narratives presented at the local public level can articulate a settler colonial community heritage consciousness that erases wider accounts of such stories. The reinterpretation and decentring of settler colonial maritime heritage stories allows for a more diverse and inclusive narrative that has the potential to promote social cohesion and social justice within restorative history work. , Thesis (MA) -- Faculty of Humanities, Anthropology, 2024
- Full Text:
- Date Issued: 2024-10-11
Co-occurrence of Sympatric Poroderma Species
- Authors: Watson, Ralph Gareth Andrew
- Date: 2024-04-05
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/436649 , vital:73289 , DOI 10.21504/10962/436649
- Description: Species exploiting similar ecological niches are expected to adapt their behaviour, which can either promote or hinder coexistence. This study examined the ecological (dis)similarity between the endemic Poroderma africanum (pyjama catshark) and Poroderma pantherinum (leopard catshark) in Mossel Bay, South Africa. The co-occurrence of these species was examined along the ecological axes of time, trophic position and space, between October 2015 and April 2018, through the use of Baited Remote Underwater Videos (BRUV), gastric lavage, and acoustic telemetry. Through the deployment of 197 BRUVs, P. africanum showed a seasonal, higher Relative Abundance (RA = 0.52), occurring more frequently during winter months, while showing an overall decline in RA over the course of the study period. Poroderma pantherinum on the other hand, showed a lower, unseasonal RA (0.20), remaining relatively stable throughout the study period. The BRUV deployments indicated that the two species showed a positive co-occurrence with one other, being sighted in BRUV deployments more frequently together as opposed to in isolation/at random. Acoustic telemetry indicated that the two species were active during different diel periods, influenced by a complex combination of tidal and diel rhythms, while P. pantherinum showed a higher residency compared to P. africanum (P. pantherinum: Continuous Residency Time (CRT)24 = 3.32 days (mean), 95% CI: 2.53–4.11 days; P. africanum: CRT24 = 2.01 days, 95% CI: 1.66–2.36 days). While the two species are sympatric in nature, and have an overlapping, endemic, distribution, acoustic telemetry indicated that 1 ABSTRACT P. africanum showed higher degrees of movement throughout the acoustic receiver array (P. africanum: edge density (ED) = 0.25; P. pantherinum: ED = 0.12); however, certain areas of the bay showed to be of high importance for both species. Both species revealed high levels of intra- and inter-specific variation in both residency and movement behaviour. Gastric lavage indicated partially overlapping trophic niches, between the two Poroderma spp. Poroderma africanum had a generalist diet, dominated by teleosts (Index of Relative Importance (IRI)% = 22.69), octopus (IRI% = 11.48) and discarded bait (IRI% = 64.54), while P. pantherinum showed indications of being a specialist predator, with a diet dominated by cephalopods (IRI% = 83.68). The two Poroderma spp. showed a partially overlapping, but separate trophic niches, while displaying spatial dissimilarity in diet. The study suggests that the two species are able to coexist within the same geographical area through niche differentiation across trophic and temporal ecological axes, with varying spatial use. The intra- and inter-specific differences between the two species may complicate elasmobranch management efforts for these co-occurring endemic catsharks, and as such, efforts should follow either an individual species approach, which is often not feasible, or an ecosystem-based approach, as opposed to considering the genus as a whole. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2024
- Full Text:
- Date Issued: 2024-04-05
- Authors: Watson, Ralph Gareth Andrew
- Date: 2024-04-05
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/436649 , vital:73289 , DOI 10.21504/10962/436649
- Description: Species exploiting similar ecological niches are expected to adapt their behaviour, which can either promote or hinder coexistence. This study examined the ecological (dis)similarity between the endemic Poroderma africanum (pyjama catshark) and Poroderma pantherinum (leopard catshark) in Mossel Bay, South Africa. The co-occurrence of these species was examined along the ecological axes of time, trophic position and space, between October 2015 and April 2018, through the use of Baited Remote Underwater Videos (BRUV), gastric lavage, and acoustic telemetry. Through the deployment of 197 BRUVs, P. africanum showed a seasonal, higher Relative Abundance (RA = 0.52), occurring more frequently during winter months, while showing an overall decline in RA over the course of the study period. Poroderma pantherinum on the other hand, showed a lower, unseasonal RA (0.20), remaining relatively stable throughout the study period. The BRUV deployments indicated that the two species showed a positive co-occurrence with one other, being sighted in BRUV deployments more frequently together as opposed to in isolation/at random. Acoustic telemetry indicated that the two species were active during different diel periods, influenced by a complex combination of tidal and diel rhythms, while P. pantherinum showed a higher residency compared to P. africanum (P. pantherinum: Continuous Residency Time (CRT)24 = 3.32 days (mean), 95% CI: 2.53–4.11 days; P. africanum: CRT24 = 2.01 days, 95% CI: 1.66–2.36 days). While the two species are sympatric in nature, and have an overlapping, endemic, distribution, acoustic telemetry indicated that 1 ABSTRACT P. africanum showed higher degrees of movement throughout the acoustic receiver array (P. africanum: edge density (ED) = 0.25; P. pantherinum: ED = 0.12); however, certain areas of the bay showed to be of high importance for both species. Both species revealed high levels of intra- and inter-specific variation in both residency and movement behaviour. Gastric lavage indicated partially overlapping trophic niches, between the two Poroderma spp. Poroderma africanum had a generalist diet, dominated by teleosts (Index of Relative Importance (IRI)% = 22.69), octopus (IRI% = 11.48) and discarded bait (IRI% = 64.54), while P. pantherinum showed indications of being a specialist predator, with a diet dominated by cephalopods (IRI% = 83.68). The two Poroderma spp. showed a partially overlapping, but separate trophic niches, while displaying spatial dissimilarity in diet. The study suggests that the two species are able to coexist within the same geographical area through niche differentiation across trophic and temporal ecological axes, with varying spatial use. The intra- and inter-specific differences between the two species may complicate elasmobranch management efforts for these co-occurring endemic catsharks, and as such, efforts should follow either an individual species approach, which is often not feasible, or an ecosystem-based approach, as opposed to considering the genus as a whole. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2024
- Full Text:
- Date Issued: 2024-04-05
Exploring grade 11 learners’ mathematical problem-solving skills using Polka’s model during the learning of Euclidean geometry
- Authors: Hlupeni, Ratham
- Date: 2024-04-05
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/436465 , vital:73274
- Description: The skill of Problem-solving in Mathematics is very imperative. Poor performance by most South African learners in schools and international tests such as the Trends in International Mathematics and Science, calls for emphasis to be placed on problem-solving in the teaching and learning of Mathematics. Euclidean Geometry is perceived, especially by learners, to be one of the difficult components of Mathematics. Thus, the aim of this study was to explore and develop the mathematical problem-solving and geometric skills of Grade 11 learners in Euclidean Geometry. Polya’s model of problem-solving was employed in geometric skills development as a tool for intervention. The concepts Geometry and problem-solving formed the conceptual framework of the study, while the social cognitive theory constituted the theoretical framework. A case study was used as the main research method following a mixed method approach within an interpretivist paradigm. Purposive and convenience sampling methods were used in the selection of both the Mathematics class and the six learners whose work was further observed and analysed. Data about the geometric skills displayed by the learners was gathered using a moderated pre-intervention test; observations; document analysis; a moderated post-intervention test; and focus group interviews. Data was analysed quantitatively using descriptive statistics and qualitatively using thematic analysis. In the pre-intervention test, learners did not bring with them expected geometric skills to the classroom before they were introduced to grade11 Geometry content and when doing problem-solving during intervention, the four stages of model used were not necessarily following each other in a linear sequence with most of the learners not applying the fourth stage “look back”. In the post intervention test, the frequency of use and application of most geometric skills improved in comparison to the pre-intervention test; the frequency of correct and inappropriate application of the skills increased at the expense of incorrect application. Learners appreciated the four stages model and gave their views related to the challenged faced during the use of the four stages model and the challenges revealed include: practice related challenges, challenges specific to certain learners, concept related challenges, curriculum-related challenges, model application challenge, and context related challenges. The study concludes that the effective use of Polyas’ four stages model can yield great results in developing learners’ geometric and problem-solving skills. The study recommends that teachers give more attention to prior geometric knowledge, teaching of geometric theorems, teaching of geometric problem-solving, and the learning environment. , Thesis (MEd) -- Faculty of Education, Secondary and Post School Education, 2024
- Full Text:
- Date Issued: 2024-04-05
- Authors: Hlupeni, Ratham
- Date: 2024-04-05
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/436465 , vital:73274
- Description: The skill of Problem-solving in Mathematics is very imperative. Poor performance by most South African learners in schools and international tests such as the Trends in International Mathematics and Science, calls for emphasis to be placed on problem-solving in the teaching and learning of Mathematics. Euclidean Geometry is perceived, especially by learners, to be one of the difficult components of Mathematics. Thus, the aim of this study was to explore and develop the mathematical problem-solving and geometric skills of Grade 11 learners in Euclidean Geometry. Polya’s model of problem-solving was employed in geometric skills development as a tool for intervention. The concepts Geometry and problem-solving formed the conceptual framework of the study, while the social cognitive theory constituted the theoretical framework. A case study was used as the main research method following a mixed method approach within an interpretivist paradigm. Purposive and convenience sampling methods were used in the selection of both the Mathematics class and the six learners whose work was further observed and analysed. Data about the geometric skills displayed by the learners was gathered using a moderated pre-intervention test; observations; document analysis; a moderated post-intervention test; and focus group interviews. Data was analysed quantitatively using descriptive statistics and qualitatively using thematic analysis. In the pre-intervention test, learners did not bring with them expected geometric skills to the classroom before they were introduced to grade11 Geometry content and when doing problem-solving during intervention, the four stages of model used were not necessarily following each other in a linear sequence with most of the learners not applying the fourth stage “look back”. In the post intervention test, the frequency of use and application of most geometric skills improved in comparison to the pre-intervention test; the frequency of correct and inappropriate application of the skills increased at the expense of incorrect application. Learners appreciated the four stages model and gave their views related to the challenged faced during the use of the four stages model and the challenges revealed include: practice related challenges, challenges specific to certain learners, concept related challenges, curriculum-related challenges, model application challenge, and context related challenges. The study concludes that the effective use of Polyas’ four stages model can yield great results in developing learners’ geometric and problem-solving skills. The study recommends that teachers give more attention to prior geometric knowledge, teaching of geometric theorems, teaching of geometric problem-solving, and the learning environment. , Thesis (MEd) -- Faculty of Education, Secondary and Post School Education, 2024
- Full Text:
- Date Issued: 2024-04-05
Insights: elucidation of squalene monooxygenase inhibitors for lowering cholesterol in cardiovascular diseases
- Authors: Leoma, Mofeli Benedict
- Date: 2024-04-04
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/434861 , vital:73111
- Description: Statins have been used to lower high cholesterol levels in the past few decades. However, several studies have shown that some people taking statins experience side effects over time, especially elderly patients, women of childbirth possibility, and children. Several studies have shown that the majority of people with underlying cardiovascular complications caused by high cholesterol are at a greater risk of fatality due to COVID-19, regardless of age and sex. The literature suggests that antimycotic squalene monooxygenase inhibitors, terbinafine and its derivatives, and anticholesterolemic squalene monooxygenase (SM) inhibitors could be another option and a safer remedy for lowering cholesterol in mammals. Molecular docking calculations, molecular dynamics (MD) simulations, molecular mechanics generalized born surface area (MM-GBSA) calculations, quantum mechanics/molecular mechanics calculations (QM/MM), and density functional theory (DFT) calculations were used in this study. An early stage in drug discovery, in which small molecular hits from high- throughput screening (HTS) are evaluated and undergo limited optimization to identify promising lead compounds, is referred to as lead generation. To address the first step of lead generation, the number of compounds to be tested was narrowed down, and the hit compounds that could be taken for further tests were obtained. Thus, the molecular docking technique was taken advantage of, which assisted us in identifying the antimycotic ligand SDZ 18, which had a good binding affinity of about -8,4 kcal mol−1. Another widely employed strategy, the molecular mechanics-generalized born surface area (MM-GBSA), was used to investigate the binding free energies of the protein-ligand complexes to validate the binding affinities obtained from molecular docking. Despite the excellent docking results, it must be emphasized that the stability of the ligand in the binding pocket must be investigated. To address this, the protein-ligand complexes were then taken through molecular dynamics for 100 ns simulations calculations which showed that the inhibitors stayed in the binding pocket with the RMSD values below 3.5 Å for most systems. This provided insight into a realistic model because the docked complexes were placed in conditions closer to the physiological environment at 300 K and 1.01325 bar, and in an explicitly solvated dynamic environment. Density functional theory (DFT) at the B3LPY level of theory using the standard 6-31G(d,p) basis set was used to assess the reactivity and other properties of the SM inhibitors. ONIOM calculations were performed to explain what was happening at the microscopic level by calculating the total energy of the complex. The aim of this project was to efficiently uncover the non-physical aspects of SM inhibitors with the help of computational techniques to identify new drugs that can lower high cholesterol levels. From a theoretical perspective, the results obtained from docking indicated that the antimycotic ligands SDZ SBA 586 18 and TNSA 84 (trisnor-squalene alcohol ) have good binding affinities, and the MM-GBSA method provided free energy calculations. MD results indicated that the stability of the ligand in the binding pocket was achieved during the 100 ns simulations. The HOMO-LUMO energy gaps obtained from DFT calculations provided information on the reactivity of the ligands. Other insights into the protein-ligand complexes were obtained from a hybrid ONIOM QM/MM study. , Thesis (MSc) -- Faculty of Science, Chemistry, 2024
- Full Text:
- Date Issued: 2024-04-04
- Authors: Leoma, Mofeli Benedict
- Date: 2024-04-04
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/434861 , vital:73111
- Description: Statins have been used to lower high cholesterol levels in the past few decades. However, several studies have shown that some people taking statins experience side effects over time, especially elderly patients, women of childbirth possibility, and children. Several studies have shown that the majority of people with underlying cardiovascular complications caused by high cholesterol are at a greater risk of fatality due to COVID-19, regardless of age and sex. The literature suggests that antimycotic squalene monooxygenase inhibitors, terbinafine and its derivatives, and anticholesterolemic squalene monooxygenase (SM) inhibitors could be another option and a safer remedy for lowering cholesterol in mammals. Molecular docking calculations, molecular dynamics (MD) simulations, molecular mechanics generalized born surface area (MM-GBSA) calculations, quantum mechanics/molecular mechanics calculations (QM/MM), and density functional theory (DFT) calculations were used in this study. An early stage in drug discovery, in which small molecular hits from high- throughput screening (HTS) are evaluated and undergo limited optimization to identify promising lead compounds, is referred to as lead generation. To address the first step of lead generation, the number of compounds to be tested was narrowed down, and the hit compounds that could be taken for further tests were obtained. Thus, the molecular docking technique was taken advantage of, which assisted us in identifying the antimycotic ligand SDZ 18, which had a good binding affinity of about -8,4 kcal mol−1. Another widely employed strategy, the molecular mechanics-generalized born surface area (MM-GBSA), was used to investigate the binding free energies of the protein-ligand complexes to validate the binding affinities obtained from molecular docking. Despite the excellent docking results, it must be emphasized that the stability of the ligand in the binding pocket must be investigated. To address this, the protein-ligand complexes were then taken through molecular dynamics for 100 ns simulations calculations which showed that the inhibitors stayed in the binding pocket with the RMSD values below 3.5 Å for most systems. This provided insight into a realistic model because the docked complexes were placed in conditions closer to the physiological environment at 300 K and 1.01325 bar, and in an explicitly solvated dynamic environment. Density functional theory (DFT) at the B3LPY level of theory using the standard 6-31G(d,p) basis set was used to assess the reactivity and other properties of the SM inhibitors. ONIOM calculations were performed to explain what was happening at the microscopic level by calculating the total energy of the complex. The aim of this project was to efficiently uncover the non-physical aspects of SM inhibitors with the help of computational techniques to identify new drugs that can lower high cholesterol levels. From a theoretical perspective, the results obtained from docking indicated that the antimycotic ligands SDZ SBA 586 18 and TNSA 84 (trisnor-squalene alcohol ) have good binding affinities, and the MM-GBSA method provided free energy calculations. MD results indicated that the stability of the ligand in the binding pocket was achieved during the 100 ns simulations. The HOMO-LUMO energy gaps obtained from DFT calculations provided information on the reactivity of the ligands. Other insights into the protein-ligand complexes were obtained from a hybrid ONIOM QM/MM study. , Thesis (MSc) -- Faculty of Science, Chemistry, 2024
- Full Text:
- Date Issued: 2024-04-04
Investigating playing-related musculoskeletal disorders in South African instrumental musicians
- Authors: Green, Erryn Mae
- Date: 2024-04-04
- Subjects: Musculoskeletal disorder , Musculoskeletal system Diseases , Musicians Wounds and injuries , Musicians Health and hygiene , Human engineering South Africa , Musicians Health risk assessment , Biomechanics , Musical instruments , Music genre
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435310 , vital:73146
- Description: This study, one of the first studies in SA to investigate PRMD in a wideranging sample of instrumental musicians using a validated self-report tool, shows that PRMDs are highly prevalent among a range of SA musicians and have a considerably negative effect on musicians’ performance ability and quality of life. However, making inferences about most affected genre or instrumental group was challenging due to the small sample sizes in some categories. The results from this study confirm that the nature of PRMD development is indeed multi-factorial, with factors numerous individual and playing-related factors playing a role in the development of PRMDs in SA musicians. Better support and education on health promotion for musicians, including awareness of and prevention strategies for PRMDs in the SA context are needed which may reduce the prevalence of PRMDs. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2024
- Full Text:
- Date Issued: 2024-04-04
- Authors: Green, Erryn Mae
- Date: 2024-04-04
- Subjects: Musculoskeletal disorder , Musculoskeletal system Diseases , Musicians Wounds and injuries , Musicians Health and hygiene , Human engineering South Africa , Musicians Health risk assessment , Biomechanics , Musical instruments , Music genre
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435310 , vital:73146
- Description: This study, one of the first studies in SA to investigate PRMD in a wideranging sample of instrumental musicians using a validated self-report tool, shows that PRMDs are highly prevalent among a range of SA musicians and have a considerably negative effect on musicians’ performance ability and quality of life. However, making inferences about most affected genre or instrumental group was challenging due to the small sample sizes in some categories. The results from this study confirm that the nature of PRMD development is indeed multi-factorial, with factors numerous individual and playing-related factors playing a role in the development of PRMDs in SA musicians. Better support and education on health promotion for musicians, including awareness of and prevention strategies for PRMDs in the SA context are needed which may reduce the prevalence of PRMDs. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2024
- Full Text:
- Date Issued: 2024-04-04
Perceptions of registered counselors’ ability to process clients’ narrated dreams during counselling
- Authors: Mpondo, Nontutuzelo
- Date: 2024-04-04
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435468 , vital:73160
- Description: Research related to South African registered counsellors (RCs) have yet to show how RCs incorporate dreamwork in their counselling sessions. Dreamwork has largely been relegated to the periphery of clinical psychological practice, posing a challenge as clients on other levels of counselling practice bring dream material to mental health practitioners often lacking confidence and competence to respond effectively to this material. Clients' discussion of dreams can be beneficial in the counselling process. However, there appears to be a gap in educational opportunities for practitioners to develop skills and competency in working with dreams. This study's objective was to contribute to the sparse research material in this area. A qualitative research approach with an exploratory design using semi-structured interviews was used to explore and understand the meaning RCs ascribed to their work with dreams and clients. Purposive sampling was used to recruit 5 participants. Social constructionism was used as a theoretical framework for understanding and interpreting the data, and the data was analysed using thematic analysis. This knowledge is geared towards providing insight into what extent university or college curriculum covered content related to dreams, dreamwork, dream theories, and dream models, and to what extent RC's training prepared them to provide essential primary psychological services related to distress arising from dreams. This research highlighted how RCs engaged and perceived their competency with dream material. This study also highlighted that RCs were interested in dreamwork training and believed it would enhance their confidence and effectiveness in working with dream material during their sessions. , Thesis (MA) -- Faculty of Humanities, Psychology, 2024
- Full Text:
- Date Issued: 2024-04-04
Perceptions of registered counselors’ ability to process clients’ narrated dreams during counselling
- Authors: Mpondo, Nontutuzelo
- Date: 2024-04-04
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435468 , vital:73160
- Description: Research related to South African registered counsellors (RCs) have yet to show how RCs incorporate dreamwork in their counselling sessions. Dreamwork has largely been relegated to the periphery of clinical psychological practice, posing a challenge as clients on other levels of counselling practice bring dream material to mental health practitioners often lacking confidence and competence to respond effectively to this material. Clients' discussion of dreams can be beneficial in the counselling process. However, there appears to be a gap in educational opportunities for practitioners to develop skills and competency in working with dreams. This study's objective was to contribute to the sparse research material in this area. A qualitative research approach with an exploratory design using semi-structured interviews was used to explore and understand the meaning RCs ascribed to their work with dreams and clients. Purposive sampling was used to recruit 5 participants. Social constructionism was used as a theoretical framework for understanding and interpreting the data, and the data was analysed using thematic analysis. This knowledge is geared towards providing insight into what extent university or college curriculum covered content related to dreams, dreamwork, dream theories, and dream models, and to what extent RC's training prepared them to provide essential primary psychological services related to distress arising from dreams. This research highlighted how RCs engaged and perceived their competency with dream material. This study also highlighted that RCs were interested in dreamwork training and believed it would enhance their confidence and effectiveness in working with dream material during their sessions. , Thesis (MA) -- Faculty of Humanities, Psychology, 2024
- Full Text:
- Date Issued: 2024-04-04
Towards a possible future solution against Multidrug Resistance: An in silico exploration of the Multidrug and Toxic compound Extrusion (MATE) transporter proteins as potential antimicrobial drug targets
- Authors: Damji, Amira Mahamood
- Date: 2024-04-04
- Subjects: Multidrug resistance , Multidrug and toxic compound extrusion family, eukaryotic , Docking , Molecular dynamics , Drug development , Transmembrane protein
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435009 , vital:73123
- Description: The rise of multidrug resistance (MDR) has become a pressing global issue, hindering the treatment of cancers and infectious diseases, and imposing a burden on healthcare systems and the economy. The Multidrug and Toxic compound Extrusion (MATE) superfamily of membrane efflux transporters is one of the key players contributing to MDR due to their ability to export a wide range of cationic and hydrophilic xenobiotics, including treatment drugs, from cells, diminishing their efficacy. Targeting MATE transporters holds great promise in achieving some cellular control over MDR, but first, a deeper understanding of their structure-function-dynamics link is required. This study aimed to explore the MATE transporters as potential antimicrobial drug targets using a two-fold in silico approach. First, virtual screening of compounds from the South African Natural Compounds Database (SANCDB) was performed to identify prospective lead inhibitory compounds against the MATE transporters using molecular docking, and top hits were selected based on their binding energy and interaction with the active site on the N-lobe of the protein. Second, to investigate the molecular-level dynamics of their extrusion mechanism, the MATE transporter structures were embedded in a POPC membrane bilayer using the CHARMM-GUI online tool and then subjected to MD simulations for 100 ns with the CHARMM 36m force field using GROMACS. The resulting trajectories were evaluated using three standard metrics – RMSD, RMSF, and Rg; significant global structural changes were observed and key functional regions in both membrane- and non-membrane transmembrane (TM) segments were identified, containing more dynamic and flexible residues than other regions. Furthermore, the MATE transporters showed more of a loosely-packed structure, providing flexibility to allow for conformational switching during their substrate-transport cycle, which is typical for proteins whose secondary structures are composed of all α-helices. The scope of this study lied in the preliminary stages of the computer-aided drug design process, and provided insights that can be used to guide the development of strategies aimed at regulating or inhibiting the function of the MATE transporters, offering a possible future solution to the growing challenge of MDR. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2024
- Full Text:
- Date Issued: 2024-04-04
- Authors: Damji, Amira Mahamood
- Date: 2024-04-04
- Subjects: Multidrug resistance , Multidrug and toxic compound extrusion family, eukaryotic , Docking , Molecular dynamics , Drug development , Transmembrane protein
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435009 , vital:73123
- Description: The rise of multidrug resistance (MDR) has become a pressing global issue, hindering the treatment of cancers and infectious diseases, and imposing a burden on healthcare systems and the economy. The Multidrug and Toxic compound Extrusion (MATE) superfamily of membrane efflux transporters is one of the key players contributing to MDR due to their ability to export a wide range of cationic and hydrophilic xenobiotics, including treatment drugs, from cells, diminishing their efficacy. Targeting MATE transporters holds great promise in achieving some cellular control over MDR, but first, a deeper understanding of their structure-function-dynamics link is required. This study aimed to explore the MATE transporters as potential antimicrobial drug targets using a two-fold in silico approach. First, virtual screening of compounds from the South African Natural Compounds Database (SANCDB) was performed to identify prospective lead inhibitory compounds against the MATE transporters using molecular docking, and top hits were selected based on their binding energy and interaction with the active site on the N-lobe of the protein. Second, to investigate the molecular-level dynamics of their extrusion mechanism, the MATE transporter structures were embedded in a POPC membrane bilayer using the CHARMM-GUI online tool and then subjected to MD simulations for 100 ns with the CHARMM 36m force field using GROMACS. The resulting trajectories were evaluated using three standard metrics – RMSD, RMSF, and Rg; significant global structural changes were observed and key functional regions in both membrane- and non-membrane transmembrane (TM) segments were identified, containing more dynamic and flexible residues than other regions. Furthermore, the MATE transporters showed more of a loosely-packed structure, providing flexibility to allow for conformational switching during their substrate-transport cycle, which is typical for proteins whose secondary structures are composed of all α-helices. The scope of this study lied in the preliminary stages of the computer-aided drug design process, and provided insights that can be used to guide the development of strategies aimed at regulating or inhibiting the function of the MATE transporters, offering a possible future solution to the growing challenge of MDR. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2024
- Full Text:
- Date Issued: 2024-04-04
Medication adherence: a review of policy and education in South Africa
- Authors: Nyoni, Cynthia Nomagugu
- Date: 2023-10-31
- Subjects: Patient compliance South Africa , Drugs Administration Study and teaching (Higher) , Pharmacist and patient South Africa , Pharmaceutical policy South Africa , Patient education South Africa , Medication adherence
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/419548 , vital:71653
- Description: Medication adherence is a patient's active and voluntary participation in following all the recommendations and instructions agreed upon with a health care provider such as a pharmacist. Adherence is a multidimensional phenomenon determined by the interplay of five factors: patient-related factors, socioeconomic factors, condition-related factors, health system-related factors, and therapy-related factors. Medication non-adherence is a problem in many countries, especially low to middle-income countries, including South Africa (SA). In low to middle-income countries, non-adherence is often worse due to insufficient health resources and inequities in access to health care. Medication adherence is a global problem and has raised the need for research and review. Many healthcare professionals, especially pharmacists, have an essential role in promoting medication adherence. This study described, explained and evaluated the policies in SA relating to the pharmacist's role in promoting medication adherence. Furthermore, it described medication adherence-related education at four universities in South Africa. The study was qualitative, and a two-phased approach was employed. In the first phase, a document analysis of the pharmacist’s role in supporting medication adherence was conducted as described in national policies and guidelines in SA. A total of 38 documents were analysed, including critical documents such as the South African Pharmacy Council Good Pharmacy Practice Manual and Associated SAPC rules (GPP) manual, National Drug Policy (NDP), Standard treatment guidelines (STGS) and Integrated Adherence Guidelines. The READ approach was used in conducting the document analysis and involved (1) preparing materials, (2) extracting data, (3) analysing data, and (4) distilling findings. The critical roles of pharmacists in medication adherence that were identified were in drug use, supply and management, dispensing, therapeutic drug monitoring, pharmacovigilance, pharmaceutical care, and special programmes like antimicrobial stewardship (AMS), multi-drug resistant tuberculosis (MDR-TB) care and antiretroviral treatment (ARV) and chronic conditions. In the second phase, in-depth interviews were conducted with lecturers to investigate and report on the inclusion of medication adherence and the teaching thereof in the curriculum of the Bachelor of Pharmacy Degree (BPharm) in pharmacy institutions in SA. Purposive sampling was used, and seven lecturers from four different institutions participated in the interviews. The interviews were conducted via Zoom® and were transcribed and analysed using thematic analysis. The teaching of medication adherence in the BPharm curriculum of the respective interviewed pharmacy institutions was explored. It was found that the topic of medication adherence was integrated into all subjects throughout the curriculum and not taught as a formal course. Although medication adherence is taught in many disciplines, it is predominantly in pharmacy practice in all institutions. The teaching methods identified included lectures, case studies, workshops, tutorials, practicals, readings, tasks, assignments and videos. The perceived effectiveness of the teaching methods was explored; also the time spent teaching medication adherence and the time efficiency. Student understanding, interest and engagement with the topic were explored and determined through their assessment performance and class attendance. In conclusion, from policies, the pharmacist's role concerning adherence is indirectly integrated into many other roles. It is often not distinguishable from that of other healthcare professionals and is often implied as part of a more generic role. Pharmacy students are educated on medication adherence and the skills and knowledge required to identify, monitor and support patient adherence to therapy. However, there is scope to increase the course content on medication adherence. There is a need to identify effective strategies for preparing pharmacists to assist patients in medication adherence. , Thesis (MPharm) -- Faculty of Pharmacy, 2023
- Full Text:
- Date Issued: 2023-10-31
- Authors: Nyoni, Cynthia Nomagugu
- Date: 2023-10-31
- Subjects: Patient compliance South Africa , Drugs Administration Study and teaching (Higher) , Pharmacist and patient South Africa , Pharmaceutical policy South Africa , Patient education South Africa , Medication adherence
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/419548 , vital:71653
- Description: Medication adherence is a patient's active and voluntary participation in following all the recommendations and instructions agreed upon with a health care provider such as a pharmacist. Adherence is a multidimensional phenomenon determined by the interplay of five factors: patient-related factors, socioeconomic factors, condition-related factors, health system-related factors, and therapy-related factors. Medication non-adherence is a problem in many countries, especially low to middle-income countries, including South Africa (SA). In low to middle-income countries, non-adherence is often worse due to insufficient health resources and inequities in access to health care. Medication adherence is a global problem and has raised the need for research and review. Many healthcare professionals, especially pharmacists, have an essential role in promoting medication adherence. This study described, explained and evaluated the policies in SA relating to the pharmacist's role in promoting medication adherence. Furthermore, it described medication adherence-related education at four universities in South Africa. The study was qualitative, and a two-phased approach was employed. In the first phase, a document analysis of the pharmacist’s role in supporting medication adherence was conducted as described in national policies and guidelines in SA. A total of 38 documents were analysed, including critical documents such as the South African Pharmacy Council Good Pharmacy Practice Manual and Associated SAPC rules (GPP) manual, National Drug Policy (NDP), Standard treatment guidelines (STGS) and Integrated Adherence Guidelines. The READ approach was used in conducting the document analysis and involved (1) preparing materials, (2) extracting data, (3) analysing data, and (4) distilling findings. The critical roles of pharmacists in medication adherence that were identified were in drug use, supply and management, dispensing, therapeutic drug monitoring, pharmacovigilance, pharmaceutical care, and special programmes like antimicrobial stewardship (AMS), multi-drug resistant tuberculosis (MDR-TB) care and antiretroviral treatment (ARV) and chronic conditions. In the second phase, in-depth interviews were conducted with lecturers to investigate and report on the inclusion of medication adherence and the teaching thereof in the curriculum of the Bachelor of Pharmacy Degree (BPharm) in pharmacy institutions in SA. Purposive sampling was used, and seven lecturers from four different institutions participated in the interviews. The interviews were conducted via Zoom® and were transcribed and analysed using thematic analysis. The teaching of medication adherence in the BPharm curriculum of the respective interviewed pharmacy institutions was explored. It was found that the topic of medication adherence was integrated into all subjects throughout the curriculum and not taught as a formal course. Although medication adherence is taught in many disciplines, it is predominantly in pharmacy practice in all institutions. The teaching methods identified included lectures, case studies, workshops, tutorials, practicals, readings, tasks, assignments and videos. The perceived effectiveness of the teaching methods was explored; also the time spent teaching medication adherence and the time efficiency. Student understanding, interest and engagement with the topic were explored and determined through their assessment performance and class attendance. In conclusion, from policies, the pharmacist's role concerning adherence is indirectly integrated into many other roles. It is often not distinguishable from that of other healthcare professionals and is often implied as part of a more generic role. Pharmacy students are educated on medication adherence and the skills and knowledge required to identify, monitor and support patient adherence to therapy. However, there is scope to increase the course content on medication adherence. There is a need to identify effective strategies for preparing pharmacists to assist patients in medication adherence. , Thesis (MPharm) -- Faculty of Pharmacy, 2023
- Full Text:
- Date Issued: 2023-10-31
A study on visual inspection of citrus sorters in a packhouse in the Eastern Cape of South Africa
- Authors: Maher, Christopher Richard
- Date: 2023-10-13
- Subjects: Citrus fruit industry South Africa Eastern Cape , Packing-house workers , Fatigue in the workplace , Drowsiness , Visual inspection , Employees Workload
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424256 , vital:72137
- Description: Background and Purpose. The South African citrus industry is a major global producer of citrus as well as the second largest exporter of citrus fruit in the world. This industry provides employment to an estimated 112 000 workers in South Africa and is vital in providing economic opportunities to communities such as those in the Sunday’s River Valley in the Eastern Cape province of South Africa due to the low employment and education levels within this province. Citrus sorting is a visual inspection task that requires workers to sustain attention and remain vigilant for the duration of a working shift. Their role in the packhouse is to ensure that no defective products are packed for export or the local market and that the fruit meets the customers’ expectations. Since the demands of sorting citrus are poorly understood, this study attempted to assess the effect that sorting citrus has on vigilance performance as well as attempt to quantify perceived workload while taking into account different contextual factors that affect perceptions of this working task. Methods. This study was conducted within a citrus packhouse in the Eastern Cape province of South Africa. The sample was comprised of individuals employed by the packhouse as citrus sorters. In addition to a recruitment and information session, testing was conducted at three intervals during a working shift on four consecutive days. Each time, indicators of vigilance, such as correct responses, sensitivity, reaction time, false alarms and misses, were collected during a 5-minute computerised version of the Mackworth Clock-test, while perceived workload was assessed with the NASA-TLX scale, and sleepiness was recording using the WITS Sleepiness Scale. Furthermore, an open-ended question was asked to further understand factors affecting the ability of participants to concentrate during their task of sorting. Results. 18 participants consented to participate in this study. 16 of these individuals identified as female with an average age of 30 years (± 7). 83% of participants were of Black African descent and were isiXhosa speakers, while 17% of participants were of Coloured descent and Afrikaans speakers. This study found that performance, as measured by the percentage of correct responses, sensitivity and reaction time on the 5-minute long Mackworth Clock Test was not significantly affected as time-on-task for sorting citrus increased during a working shift, neither did performance on the vigilance test change as days of the week proceeded. However, ‘misses’ during the vigilance test were found to significantly decrease over the course of a working shift, thus contradicting the expected outcomes of this study. Perceived workload of sorting citrus, as well as perceived sleepiness, significantly increased with time-on-task during the course of a working shift. The major contributions for this increase in perceived workload while sorting citrus were derived from the Mental Demand and Physical Demand sub-scale for the NASA-TLX. However, responses from the open-ended question indicated that participants generally enjoyed their work, although there were factors, such as the nature of fruit and social set-up of work, that negatively affected this perception. Discussion. The results from this study contradicted the researcher’s expectations. It was anticipated that measures of correct responses and sensitivity would decrease and misses, and reaction time would increase with time-on-task for sorting citrus, yet vigilance indicators from the Mackworth Clock Test generally indicated no change in vigilance, and, according to “misses” even improved with time-on-task. A likely explanation for this is that the use of a 5-minute Mackworth Clock-test was unsuitable in this context, or rather, the time of this test was not long enough to induce a ‘vigilance decrement’. Furthermore, in order to administer this vigilance test, participants were taken off the production line and led to a testing room which most likely increased their levels of arousal, thus affecting performance on the vigilance test. However, even though perceived sleepiness was found to significantly increase over the course of a working shift, these data correlated poorly with the vigilance results, thus contradicting the expected outcomes of the study. Mental demand significantly increased, possibly due to the demand of attentional informational processing required for sorting, as well as various environmental factors present within the packhouse. Physical demand, too, significantly increased as workers were required to remain standing throughout their working task as well as to make use of their upper extremities to remove defective fruit. Correlation analyses showed significantly weak correlation for Mackworth Clock Test variables and sleepiness ratings to all other variables. NASA-TLX variables, however, generally showed significantly moderate correlations with one another. Conclusion. It remains unclear how vigilance changes and sustained attention while sorting citrus, since the experiment did not show changes in performance. This is largely attributed to the methodological set-up which could have increased arousal and therefore affected vigilance. It is recommended that future studies research vigilance and sustained attention during the sorting itself, rather than attempting to infer vigilance results from a computerised vigilance test. Perceived workload of sorting, however, increased over the course of a working shift due to significant increases in perceptions of the physical and mental demands of sorting. Future studies should address concerns relating to the physical demand of sorting. Furthermore, it would be beneficial to compare responses of day and night shift sorters to further understand how the relationship between these variables may change. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Maher, Christopher Richard
- Date: 2023-10-13
- Subjects: Citrus fruit industry South Africa Eastern Cape , Packing-house workers , Fatigue in the workplace , Drowsiness , Visual inspection , Employees Workload
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424256 , vital:72137
- Description: Background and Purpose. The South African citrus industry is a major global producer of citrus as well as the second largest exporter of citrus fruit in the world. This industry provides employment to an estimated 112 000 workers in South Africa and is vital in providing economic opportunities to communities such as those in the Sunday’s River Valley in the Eastern Cape province of South Africa due to the low employment and education levels within this province. Citrus sorting is a visual inspection task that requires workers to sustain attention and remain vigilant for the duration of a working shift. Their role in the packhouse is to ensure that no defective products are packed for export or the local market and that the fruit meets the customers’ expectations. Since the demands of sorting citrus are poorly understood, this study attempted to assess the effect that sorting citrus has on vigilance performance as well as attempt to quantify perceived workload while taking into account different contextual factors that affect perceptions of this working task. Methods. This study was conducted within a citrus packhouse in the Eastern Cape province of South Africa. The sample was comprised of individuals employed by the packhouse as citrus sorters. In addition to a recruitment and information session, testing was conducted at three intervals during a working shift on four consecutive days. Each time, indicators of vigilance, such as correct responses, sensitivity, reaction time, false alarms and misses, were collected during a 5-minute computerised version of the Mackworth Clock-test, while perceived workload was assessed with the NASA-TLX scale, and sleepiness was recording using the WITS Sleepiness Scale. Furthermore, an open-ended question was asked to further understand factors affecting the ability of participants to concentrate during their task of sorting. Results. 18 participants consented to participate in this study. 16 of these individuals identified as female with an average age of 30 years (± 7). 83% of participants were of Black African descent and were isiXhosa speakers, while 17% of participants were of Coloured descent and Afrikaans speakers. This study found that performance, as measured by the percentage of correct responses, sensitivity and reaction time on the 5-minute long Mackworth Clock Test was not significantly affected as time-on-task for sorting citrus increased during a working shift, neither did performance on the vigilance test change as days of the week proceeded. However, ‘misses’ during the vigilance test were found to significantly decrease over the course of a working shift, thus contradicting the expected outcomes of this study. Perceived workload of sorting citrus, as well as perceived sleepiness, significantly increased with time-on-task during the course of a working shift. The major contributions for this increase in perceived workload while sorting citrus were derived from the Mental Demand and Physical Demand sub-scale for the NASA-TLX. However, responses from the open-ended question indicated that participants generally enjoyed their work, although there were factors, such as the nature of fruit and social set-up of work, that negatively affected this perception. Discussion. The results from this study contradicted the researcher’s expectations. It was anticipated that measures of correct responses and sensitivity would decrease and misses, and reaction time would increase with time-on-task for sorting citrus, yet vigilance indicators from the Mackworth Clock Test generally indicated no change in vigilance, and, according to “misses” even improved with time-on-task. A likely explanation for this is that the use of a 5-minute Mackworth Clock-test was unsuitable in this context, or rather, the time of this test was not long enough to induce a ‘vigilance decrement’. Furthermore, in order to administer this vigilance test, participants were taken off the production line and led to a testing room which most likely increased their levels of arousal, thus affecting performance on the vigilance test. However, even though perceived sleepiness was found to significantly increase over the course of a working shift, these data correlated poorly with the vigilance results, thus contradicting the expected outcomes of the study. Mental demand significantly increased, possibly due to the demand of attentional informational processing required for sorting, as well as various environmental factors present within the packhouse. Physical demand, too, significantly increased as workers were required to remain standing throughout their working task as well as to make use of their upper extremities to remove defective fruit. Correlation analyses showed significantly weak correlation for Mackworth Clock Test variables and sleepiness ratings to all other variables. NASA-TLX variables, however, generally showed significantly moderate correlations with one another. Conclusion. It remains unclear how vigilance changes and sustained attention while sorting citrus, since the experiment did not show changes in performance. This is largely attributed to the methodological set-up which could have increased arousal and therefore affected vigilance. It is recommended that future studies research vigilance and sustained attention during the sorting itself, rather than attempting to infer vigilance results from a computerised vigilance test. Perceived workload of sorting, however, increased over the course of a working shift due to significant increases in perceptions of the physical and mental demands of sorting. Future studies should address concerns relating to the physical demand of sorting. Furthermore, it would be beneficial to compare responses of day and night shift sorters to further understand how the relationship between these variables may change. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13
An investigation into fatigue prevalence amongst citrus packhouse sorters in the Eastern Cape province of South Africa
- Authors: Robinson, Harry Jack
- Date: 2023-10-13
- Subjects: Fatigue in the workplace , Packing-house workers South Africa Eastern Cape , Shift systems , Sleep-wake cycle , Drowsiness
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424312 , vital:72142
- Description: Background: South Africa is the second most influential exporter of citrus fruits internationally and holds a pivotal role in economic revenue for the country. Rural areas, such as the Sundays River Valley in the Eastern Cape province of South Africa, contribute to the country’s citrus production. Many women depend on citrus packhouses for employment as citrus sorters. As humans perceive certain defects in citrus fruits more accurately than machines, these sorters must identify and manually remove any fruit that does not conform with export requirements. Citrus sorters are exposed to numerous physical and cognitive stressors during the task while faced with organizational challenges, such as shift work and long working hours. Therefore, the potential for fatigue development is anticipated. Given the multifactorial nature of fatigue and the negative consequences it may have on workers, it also has the potential to impede the accuracy of the sorting performance. Stringent disciplinary action for the entire South African citrus industry may be of consequence if nonconforming or pest-infested fruit is missed by citrus sorters and exported to foreign countries. This study aimed to investigate the prevalence of fatigue among citrus sorters in a citrus packhouse in the Sundays River Valley of the Eastern Cape throughout a citrus harvesting season and to identify factors that may contribute towards fatigue development. Methods: The research design utilized a crosssectional, two-part approach that applied mixed methods. Part one was administered once-off, incorporating demographic, work-, and non-work-related questions. Part two was a self-developed repeated measures assessment comprising close-ended contextual questions, the Modified Fatigue Impact Scale, and the Karolinska Sleepiness Scale. Environmental and work output data were also recorded. Results: Citrus sorters (n= 35) recorded a mean MFIS score of 39.35 throughout the harvest season, which was above the prescribed fatigue threshold (38). However, there was no significant difference in fatigue ratings over time (p= 0.122). Day shift workers exceeded the fatigue threshold for the entire season compared to night shift workers, who only exceeded it in the last two weeks. The physical, cognitive, and psychosocial subscales found no significant difference in fatigue scores, although physical fatigue recorded the highest scores across all weeks and displayed a significant difference over time. Overall, participants, on average, perceived to be “neither sleepy nor alert” over the season. However, eight participants (22%) recorded sleepiness scores ii exceeding the excessive sleepiness threshold of seven. Educational levels, health status, work-pace, and the number of family dependents significantly contributed to fatigue development, albeit a weak correlation. Discussion: Sorters were perceived to be fatigued from week three till the end of the study; however, there was no variation in fatigue scores over time. An accumulation of physical fatigue over time was revealed where prolonged standing, repetitive work, and irregular working postures may have contributed. Night shift workers did not receive the recommended hours of sleep (7-8 hours); hence, they registered greater sleepiness scores over the season than day shift workers. Environmental and work output recordings did not prove to have a significant influence on fatigue development, and neither did work experience or physical exercise. Conclusion: An amalgamation of numerous contributing factors within the work situation, private situation, and the individual influenced the development of fatigue, where there was no primary causal factor. Future studies should consider recording the accuracy of the sorting performance to acquire rich, objective data. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Robinson, Harry Jack
- Date: 2023-10-13
- Subjects: Fatigue in the workplace , Packing-house workers South Africa Eastern Cape , Shift systems , Sleep-wake cycle , Drowsiness
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424312 , vital:72142
- Description: Background: South Africa is the second most influential exporter of citrus fruits internationally and holds a pivotal role in economic revenue for the country. Rural areas, such as the Sundays River Valley in the Eastern Cape province of South Africa, contribute to the country’s citrus production. Many women depend on citrus packhouses for employment as citrus sorters. As humans perceive certain defects in citrus fruits more accurately than machines, these sorters must identify and manually remove any fruit that does not conform with export requirements. Citrus sorters are exposed to numerous physical and cognitive stressors during the task while faced with organizational challenges, such as shift work and long working hours. Therefore, the potential for fatigue development is anticipated. Given the multifactorial nature of fatigue and the negative consequences it may have on workers, it also has the potential to impede the accuracy of the sorting performance. Stringent disciplinary action for the entire South African citrus industry may be of consequence if nonconforming or pest-infested fruit is missed by citrus sorters and exported to foreign countries. This study aimed to investigate the prevalence of fatigue among citrus sorters in a citrus packhouse in the Sundays River Valley of the Eastern Cape throughout a citrus harvesting season and to identify factors that may contribute towards fatigue development. Methods: The research design utilized a crosssectional, two-part approach that applied mixed methods. Part one was administered once-off, incorporating demographic, work-, and non-work-related questions. Part two was a self-developed repeated measures assessment comprising close-ended contextual questions, the Modified Fatigue Impact Scale, and the Karolinska Sleepiness Scale. Environmental and work output data were also recorded. Results: Citrus sorters (n= 35) recorded a mean MFIS score of 39.35 throughout the harvest season, which was above the prescribed fatigue threshold (38). However, there was no significant difference in fatigue ratings over time (p= 0.122). Day shift workers exceeded the fatigue threshold for the entire season compared to night shift workers, who only exceeded it in the last two weeks. The physical, cognitive, and psychosocial subscales found no significant difference in fatigue scores, although physical fatigue recorded the highest scores across all weeks and displayed a significant difference over time. Overall, participants, on average, perceived to be “neither sleepy nor alert” over the season. However, eight participants (22%) recorded sleepiness scores ii exceeding the excessive sleepiness threshold of seven. Educational levels, health status, work-pace, and the number of family dependents significantly contributed to fatigue development, albeit a weak correlation. Discussion: Sorters were perceived to be fatigued from week three till the end of the study; however, there was no variation in fatigue scores over time. An accumulation of physical fatigue over time was revealed where prolonged standing, repetitive work, and irregular working postures may have contributed. Night shift workers did not receive the recommended hours of sleep (7-8 hours); hence, they registered greater sleepiness scores over the season than day shift workers. Environmental and work output recordings did not prove to have a significant influence on fatigue development, and neither did work experience or physical exercise. Conclusion: An amalgamation of numerous contributing factors within the work situation, private situation, and the individual influenced the development of fatigue, where there was no primary causal factor. Future studies should consider recording the accuracy of the sorting performance to acquire rich, objective data. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13
Application of web design techniques and best practices in implementing web development, maintenance and enhancement of RUBi websites and web application systems
- Authors: Tshabalalala, Thulani
- Date: 2023-10-13
- Subjects: Web design , Web applications , Bioinformatics , Django , Web servers Computer programs
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424688 , vital:72175
- Description: The popularity of the web has seen various fields, such as the sciences taking advantage of this resource to further their scientific endeavours. This has seen science groups moving into developing websites and web applications, and such a group is the Research Unit in Bioinformative (RUBi). With the use of the web, the development and maintenance of whatever web-related tools become inevitable, given the continuous changes in the web space. This continuous evolution of web development and maintenance will come with techniques, principles and standards which will not only enable faster development of web entities but also ensure that modern hardware, fulfilment of the requirements to use such hardware and modern concepts are incorporated into forming web tools that enable such progression. Furthermore, introducing the previously mentioned progress of the web becomes an essential part of its development and maintenance. This paper did implement the processes of progressing the web using the technique of documentation and version control systems. The web development for the COVIDRUG website was done for the Covidrug-Africa Consortium (COVIDRUG) using the Django webdevelopment framework. The RUBi website and the MDM-Task we band the Job Management System (JMS) web applications were maintained for the maintenance aspect. Archives brought value regarding the traceability it provides of the various web-related aspects. The development showed a website’s potential value, particularly for research groups. The maintenance carried out showed how different techniques and approaches could be used in different maintenance prospects to achieve set objectives. The development and maintenance resulted in websites and web applications that have the features stated in their respective maintenance plans. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Tshabalalala, Thulani
- Date: 2023-10-13
- Subjects: Web design , Web applications , Bioinformatics , Django , Web servers Computer programs
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424688 , vital:72175
- Description: The popularity of the web has seen various fields, such as the sciences taking advantage of this resource to further their scientific endeavours. This has seen science groups moving into developing websites and web applications, and such a group is the Research Unit in Bioinformative (RUBi). With the use of the web, the development and maintenance of whatever web-related tools become inevitable, given the continuous changes in the web space. This continuous evolution of web development and maintenance will come with techniques, principles and standards which will not only enable faster development of web entities but also ensure that modern hardware, fulfilment of the requirements to use such hardware and modern concepts are incorporated into forming web tools that enable such progression. Furthermore, introducing the previously mentioned progress of the web becomes an essential part of its development and maintenance. This paper did implement the processes of progressing the web using the technique of documentation and version control systems. The web development for the COVIDRUG website was done for the Covidrug-Africa Consortium (COVIDRUG) using the Django webdevelopment framework. The RUBi website and the MDM-Task we band the Job Management System (JMS) web applications were maintained for the maintenance aspect. Archives brought value regarding the traceability it provides of the various web-related aspects. The development showed a website’s potential value, particularly for research groups. The maintenance carried out showed how different techniques and approaches could be used in different maintenance prospects to achieve set objectives. The development and maintenance resulted in websites and web applications that have the features stated in their respective maintenance plans. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2023
- Full Text:
- Date Issued: 2023-10-13
Applying human factors and ergonomics system analysis methods to the V5-NRS Cessna 441 Conquest II aviation accident
- Authors: Fischer, Jordan Daena
- Date: 2023-10-13
- Subjects: Ergonomics , Human engineering , Accident investigation , Aircraft accidents Investigation , AcciMap Approach , System theory , Study of complex systems
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424245 , vital:72136
- Description: Intro: Accidents are complex in nature with multiple contributing factors. The way in which accidents are investigated is important and using system-based analysis tools assists in understanding and mapping these contributing factors to learn from them. There has been an increase in the number of accidents that have occurred within the general aviation industry in South Africa and while accident investigations have been undertaken, these have not included the application of system-based analysis tools. This led to a collaboration between Rhodes University and the Accident and Incident Investigations Division (AIID) of the South African Civil Aviation Authority where it was agreed that two systems-based analysis tools will be applied to a previously investigated accident that occurred in 2015. Aims: The first aim of this thesis was to identify if, through the implementation of these systems-based tools, the systemic contributory factors could be determined using the existing report by the AIID. The second aim of this thesis was to identify if, using the two systems-based tools, the actors and levels involved in the accident could be identified and the third aim was to identify if the implementation of these tools generates the same or different recommendations to that of the AIID. Methods: The two systems-based analysis tools applied were AcciMap and Causal Analysis using Systems Theory (CAST). These tools were applied to the V5-NRS Cessna 441 Conquest II accident report which captured the details of how the aircraft flew into the Tygerberg mountain on its descent into the Cape Town International Airport in August 2015. Results: Through the application of these two systems-based analysis tools the major contributing factors elucidated throughout this analysis were: visual and lighting conditions, pilot experience, training, lack of terrain warning equipment, fatigue, inadequate oversight, and inadequate risk management. In line with these findings, the analysis revealed various actors across various levels (the crew; South African Air Traffic Control, the SACAA, WestAir (the operator) and the Namibian Civil Aviation Authority Through the elucidation of these factors at various levels, 14 to 15 different recommendations were generated which was more than the one recommendation that was generated by the AIID. Discussion: Even when applied to an existing report, both the CAST and Accimap tools were able to bring to light the systemic contributing factors to this accident and importantly, highlight the role that various actors and levels within the system had in this unfortunate event. Consistent with previous literature, most of the contributing factors were found at the lowest level (the crew in this case) and fewer, but key factors were identified at higher levels (management and regulator level). Importantly, the application of the systems tools facilitated a systematic and systemic analysis of this accident, which allowed for the generation of recommendations at all levels, not just at the operator level. Conclusion: This study demonstrates the benefits and importance behind implementing a systems-based analysis method to an accident as these tools generate more useful recommendations which allows for important lessons to be learned following accidents, with the intention of re-designing systems to prevent them from happening again. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Fischer, Jordan Daena
- Date: 2023-10-13
- Subjects: Ergonomics , Human engineering , Accident investigation , Aircraft accidents Investigation , AcciMap Approach , System theory , Study of complex systems
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424245 , vital:72136
- Description: Intro: Accidents are complex in nature with multiple contributing factors. The way in which accidents are investigated is important and using system-based analysis tools assists in understanding and mapping these contributing factors to learn from them. There has been an increase in the number of accidents that have occurred within the general aviation industry in South Africa and while accident investigations have been undertaken, these have not included the application of system-based analysis tools. This led to a collaboration between Rhodes University and the Accident and Incident Investigations Division (AIID) of the South African Civil Aviation Authority where it was agreed that two systems-based analysis tools will be applied to a previously investigated accident that occurred in 2015. Aims: The first aim of this thesis was to identify if, through the implementation of these systems-based tools, the systemic contributory factors could be determined using the existing report by the AIID. The second aim of this thesis was to identify if, using the two systems-based tools, the actors and levels involved in the accident could be identified and the third aim was to identify if the implementation of these tools generates the same or different recommendations to that of the AIID. Methods: The two systems-based analysis tools applied were AcciMap and Causal Analysis using Systems Theory (CAST). These tools were applied to the V5-NRS Cessna 441 Conquest II accident report which captured the details of how the aircraft flew into the Tygerberg mountain on its descent into the Cape Town International Airport in August 2015. Results: Through the application of these two systems-based analysis tools the major contributing factors elucidated throughout this analysis were: visual and lighting conditions, pilot experience, training, lack of terrain warning equipment, fatigue, inadequate oversight, and inadequate risk management. In line with these findings, the analysis revealed various actors across various levels (the crew; South African Air Traffic Control, the SACAA, WestAir (the operator) and the Namibian Civil Aviation Authority Through the elucidation of these factors at various levels, 14 to 15 different recommendations were generated which was more than the one recommendation that was generated by the AIID. Discussion: Even when applied to an existing report, both the CAST and Accimap tools were able to bring to light the systemic contributing factors to this accident and importantly, highlight the role that various actors and levels within the system had in this unfortunate event. Consistent with previous literature, most of the contributing factors were found at the lowest level (the crew in this case) and fewer, but key factors were identified at higher levels (management and regulator level). Importantly, the application of the systems tools facilitated a systematic and systemic analysis of this accident, which allowed for the generation of recommendations at all levels, not just at the operator level. Conclusion: This study demonstrates the benefits and importance behind implementing a systems-based analysis method to an accident as these tools generate more useful recommendations which allows for important lessons to be learned following accidents, with the intention of re-designing systems to prevent them from happening again. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13