Observations of cosmic re-ionisation with the Hydrogen Epoch of Reionization Array: simulations of closure phase spectra
- Authors: Charles, Ntsikelelo
- Date: 2021-04
- Subjects: Epoch of reionization , Space interferometry , Astronomy -- Observations , Closure phase spectra
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/174470 , vital:42480
- Description: The 21 cm transition from neutral Hydrogen promises to be the best observational probe of the Epoch of Reionisation. It has driven the construction of the new generation of low frequency radio interferometric arrays, including the Hydrogen Epoch of Reionization Array (HERA). The main difficulty in measuring the 21 cm signal is the presence of bright foregrounds that require very accurate interferometric calibration. Thyagarajan et al. (2018) proposed the use of closure phase quantities as a means to detect the 21 cm signal, which has the advantage of being independent (to first order) from calibration errors and therefore, bypasses the need for accurate calibration. Closure phases are, however, affected by so-called direction dependent effects, e.g. the fact that the dishes - or antennas - of an interferometric array are not identical to each other and , therefore, yield different antenna primary beam responses. In this thesis, we investigate the impact of direction dependent effects on closure quantities and simulate the impact that primary antenna beams affected by mutual coupling have on the foreground closure phase and its power spectrum i.e. the power spectrum of the bispectrum phase (Thyagarajan et al., 2020). Our simulations show that primary beams affected by mutual coupling lead to an overall leakage of foreground power in the so-called EoR window, i.e. power from smooth-spectrum foregrounds is confined to low k modes. We quantified this effect and found that the leakage is up to ~ 8 orders magnitude higher than the case of an ideal beam at kǁ > 0:5 h Mpc-1. We also found that the foreground leakage is worse when edge antennas are included, as they have a more different primary beam compared to antennas at the centre of the array. The leakage magnitude is worse when bright foregrounds appear in the antenna sidelobes, as expected. Our simulations provide a useful framework to interpret observations and assess which power spectrum region is expected to be most contaminated by foreground power leakage.
- Full Text:
- Authors: Charles, Ntsikelelo
- Date: 2021-04
- Subjects: Epoch of reionization , Space interferometry , Astronomy -- Observations , Closure phase spectra
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/174470 , vital:42480
- Description: The 21 cm transition from neutral Hydrogen promises to be the best observational probe of the Epoch of Reionisation. It has driven the construction of the new generation of low frequency radio interferometric arrays, including the Hydrogen Epoch of Reionization Array (HERA). The main difficulty in measuring the 21 cm signal is the presence of bright foregrounds that require very accurate interferometric calibration. Thyagarajan et al. (2018) proposed the use of closure phase quantities as a means to detect the 21 cm signal, which has the advantage of being independent (to first order) from calibration errors and therefore, bypasses the need for accurate calibration. Closure phases are, however, affected by so-called direction dependent effects, e.g. the fact that the dishes - or antennas - of an interferometric array are not identical to each other and , therefore, yield different antenna primary beam responses. In this thesis, we investigate the impact of direction dependent effects on closure quantities and simulate the impact that primary antenna beams affected by mutual coupling have on the foreground closure phase and its power spectrum i.e. the power spectrum of the bispectrum phase (Thyagarajan et al., 2020). Our simulations show that primary beams affected by mutual coupling lead to an overall leakage of foreground power in the so-called EoR window, i.e. power from smooth-spectrum foregrounds is confined to low k modes. We quantified this effect and found that the leakage is up to ~ 8 orders magnitude higher than the case of an ideal beam at kǁ > 0:5 h Mpc-1. We also found that the foreground leakage is worse when edge antennas are included, as they have a more different primary beam compared to antennas at the centre of the array. The leakage magnitude is worse when bright foregrounds appear in the antenna sidelobes, as expected. Our simulations provide a useful framework to interpret observations and assess which power spectrum region is expected to be most contaminated by foreground power leakage.
- Full Text:
Perceptions of the role of Lantana camara on human well-being and rural livelihoods in Vhembe Biosphere Reserve, South Africa
- Authors: Mhlongo, Edward Swazi
- Date: 2021-04
- Subjects: Lantana camara -- South Africa -- Vhembe District Municipality , Introduced organisms -- South Africa -- Vhembe District Municipality , Biological invasions -- South Africa -- Vhembe District Municipality , Plant invasions -- South Africa -- Vhembe District Municipality , Lantana camara -- Control -- South Africa -- Vhembe District Municipality , South Africa -- Rural conditions , Ethnoscience -- South Africa -- Vhembe District Municipality
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177952 , vital:42893
- Description: In the past, social aspects on biological invasions were less documented, this hindered the development of sound and effective management of Invasive Alien Species (IAS). However, there has been a shift in trends with more studies on biological invasions integrating local knowledge together with ecological studies to develop effective management interventions. Invasive Alien Species are widespread throughout Southern Africa and are usually prevalent in the rural areas. Limpopo province consists of large rural areas where people depend on natural resources, wild and exotic species for their livelihoods. Lantana camara is one of the major invaders that is problematic worldwide having detrimental impacts on biodiversity, ecosystem functions, and economies. This study assessed the perceptions of the role of L. camara on the well-being and rural livelihoods of local communities in the Vhembe Biosphere Reserve using household surveys. A total of 300 surveys were administered in six villages. The study further used a two-pronged approach to examine invasion extent and management options. The two-pronged approach included (i) detailed vegetation surveys in 50 household yards within each village, and (ii) focus group to solicit local knowledge of invasion extent and managing L. camara by the rural communities. The results of the study showed that almost all the respondents knew L. camara and could describe it. Most of the respondents were of the view that L. camara had no negative impacts on their livelihoods. Other respondents stated costs associated with L. camara were more than benefits and wanted a reduction in L. camara densities in the area. Most respondents wanted more government intervention to help in managing L. camara, this is because of the perceived future impacts of L. camara. Vegetation survey results showed no significant difference in L. camara abundances and plant heights among the six study villages. The average number of L. camara counted per household yard in all villages was (2.41 ± 0.20) plants, with average plant basal diameter of (0.94 ± 0.02 cm). There were significant differences in canopy width of L. camara among the six study villages. Plant basal diameter was high in Tshakhuma (1.05 ± 0.04 m) and Duthuni (1.00 ± 0.04 m) villages, and low in Ha Mutsha village (0.82 ± 0.03 m). Lantana camara canopy width at household level across all villages averaged 1.34 ± 0.03 m. Canopy cover was high in Tshakhuma village (1.70 ± 0.09 m) and low at Ha Mutsha village (1.03 ± 0.03 m). In all six village focus group discussions, it was noted that mechanical clearing of L. camara was the most used method, but they reported minimum help from the government particularly Working for Water (WfW). The study concludes that L. camara has no substantial adverse impacts to most of the respondents. The study further noted that L. camara is dominant in most household yards ii and that management is taking place however current control options are not enough on their own. Suggestions for further research are to explore more alternative indigenous species present or easily accessible to the community members which may offer the same benefits as IAS. Furthermore, additional research at local level is required for implementing management techniques best suited for the area. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2021
- Full Text:
- Authors: Mhlongo, Edward Swazi
- Date: 2021-04
- Subjects: Lantana camara -- South Africa -- Vhembe District Municipality , Introduced organisms -- South Africa -- Vhembe District Municipality , Biological invasions -- South Africa -- Vhembe District Municipality , Plant invasions -- South Africa -- Vhembe District Municipality , Lantana camara -- Control -- South Africa -- Vhembe District Municipality , South Africa -- Rural conditions , Ethnoscience -- South Africa -- Vhembe District Municipality
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177952 , vital:42893
- Description: In the past, social aspects on biological invasions were less documented, this hindered the development of sound and effective management of Invasive Alien Species (IAS). However, there has been a shift in trends with more studies on biological invasions integrating local knowledge together with ecological studies to develop effective management interventions. Invasive Alien Species are widespread throughout Southern Africa and are usually prevalent in the rural areas. Limpopo province consists of large rural areas where people depend on natural resources, wild and exotic species for their livelihoods. Lantana camara is one of the major invaders that is problematic worldwide having detrimental impacts on biodiversity, ecosystem functions, and economies. This study assessed the perceptions of the role of L. camara on the well-being and rural livelihoods of local communities in the Vhembe Biosphere Reserve using household surveys. A total of 300 surveys were administered in six villages. The study further used a two-pronged approach to examine invasion extent and management options. The two-pronged approach included (i) detailed vegetation surveys in 50 household yards within each village, and (ii) focus group to solicit local knowledge of invasion extent and managing L. camara by the rural communities. The results of the study showed that almost all the respondents knew L. camara and could describe it. Most of the respondents were of the view that L. camara had no negative impacts on their livelihoods. Other respondents stated costs associated with L. camara were more than benefits and wanted a reduction in L. camara densities in the area. Most respondents wanted more government intervention to help in managing L. camara, this is because of the perceived future impacts of L. camara. Vegetation survey results showed no significant difference in L. camara abundances and plant heights among the six study villages. The average number of L. camara counted per household yard in all villages was (2.41 ± 0.20) plants, with average plant basal diameter of (0.94 ± 0.02 cm). There were significant differences in canopy width of L. camara among the six study villages. Plant basal diameter was high in Tshakhuma (1.05 ± 0.04 m) and Duthuni (1.00 ± 0.04 m) villages, and low in Ha Mutsha village (0.82 ± 0.03 m). Lantana camara canopy width at household level across all villages averaged 1.34 ± 0.03 m. Canopy cover was high in Tshakhuma village (1.70 ± 0.09 m) and low at Ha Mutsha village (1.03 ± 0.03 m). In all six village focus group discussions, it was noted that mechanical clearing of L. camara was the most used method, but they reported minimum help from the government particularly Working for Water (WfW). The study concludes that L. camara has no substantial adverse impacts to most of the respondents. The study further noted that L. camara is dominant in most household yards ii and that management is taking place however current control options are not enough on their own. Suggestions for further research are to explore more alternative indigenous species present or easily accessible to the community members which may offer the same benefits as IAS. Furthermore, additional research at local level is required for implementing management techniques best suited for the area. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2021
- Full Text:
Photodynamic antimicrobial chemotherapy against Staphylococcus aureus and Escherichia coli sensitized using indium (III) cationic porphyrins linked to core-shell magnetic nanoparticles
- Authors: Makola, Lekgowa Collen
- Date: 2021-04
- Subjects: Photochemotherapy , Photosensitizing compounds , Staphylococcus aureus , Escherichia coli , Indium , Porphyrins , Magnetic nanoparticles , Quaternize
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177225 , vital:42801
- Description: Photodynamic antimicrobial chemotherapy (PACT) is a well-known antimicrobial therapy technique used against multi-drug resistant pathogens. In this study, the syntheses, characterization, photophysicochemical properties, and the applications of symmetrically and asymmetrically substituted cationic indium (III) porphyrins linked to silver/copper ferrite core-shell (Ag/CuFe2O4) magnetic nanoparticles (MNPs) as potential photosensitizers for PACT are reported. The synthesized complexes include axially modified porphyrins quaternized through an axial ligand. All the asymmetrically substituted porphyrins were linked to the NPs via an ester bond and the symmetrically substituted porphyrins were linked (peripherally and /or axially) via self-assembly (Ag-S and/or Ag-N). The impact of axial modification, peripheral substituents, conjugation to the NPs, the number of positive charges, and the chain length of the alkyl halides quaternizing agents on PACT efficacy and photophysicochemical properties of porphyrins were studied. High singlet oxygen quantum yields and antimicrobial log reductions were observed. Lipophilicity and hydrophilicity of the porphyrins were also studies, where the complexes quaternized with methyl iodide showed relatively high hydrophilicity character. Upon in vitro PACT studies, the quaternized complexes were observed to have 0% viable colony, signifying their effectiveness. Moreover, the highest log reductions of 9.27 were observed against S. aureus and 9.58 were observed against E. coli. The findings from this work delineate that singlet oxygen generation alone is not a distinct factor on the PACT efficacy of the porphyrin complexes, since some of the complexes have practically the same singlet oxygen quantum but different PACT activity. However, other contributing factors including water solubility play a significant role. , Thesis (MSc) -- Faculty of Science, Department of Chemistry, 2021
- Full Text:
- Authors: Makola, Lekgowa Collen
- Date: 2021-04
- Subjects: Photochemotherapy , Photosensitizing compounds , Staphylococcus aureus , Escherichia coli , Indium , Porphyrins , Magnetic nanoparticles , Quaternize
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177225 , vital:42801
- Description: Photodynamic antimicrobial chemotherapy (PACT) is a well-known antimicrobial therapy technique used against multi-drug resistant pathogens. In this study, the syntheses, characterization, photophysicochemical properties, and the applications of symmetrically and asymmetrically substituted cationic indium (III) porphyrins linked to silver/copper ferrite core-shell (Ag/CuFe2O4) magnetic nanoparticles (MNPs) as potential photosensitizers for PACT are reported. The synthesized complexes include axially modified porphyrins quaternized through an axial ligand. All the asymmetrically substituted porphyrins were linked to the NPs via an ester bond and the symmetrically substituted porphyrins were linked (peripherally and /or axially) via self-assembly (Ag-S and/or Ag-N). The impact of axial modification, peripheral substituents, conjugation to the NPs, the number of positive charges, and the chain length of the alkyl halides quaternizing agents on PACT efficacy and photophysicochemical properties of porphyrins were studied. High singlet oxygen quantum yields and antimicrobial log reductions were observed. Lipophilicity and hydrophilicity of the porphyrins were also studies, where the complexes quaternized with methyl iodide showed relatively high hydrophilicity character. Upon in vitro PACT studies, the quaternized complexes were observed to have 0% viable colony, signifying their effectiveness. Moreover, the highest log reductions of 9.27 were observed against S. aureus and 9.58 were observed against E. coli. The findings from this work delineate that singlet oxygen generation alone is not a distinct factor on the PACT efficacy of the porphyrin complexes, since some of the complexes have practically the same singlet oxygen quantum but different PACT activity. However, other contributing factors including water solubility play a significant role. , Thesis (MSc) -- Faculty of Science, Department of Chemistry, 2021
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Physical activity, physical fitness, sedentary behaviour and screen time profiles of primary school children in a school within the Makana Municipality, Eastern Cape, South Africa
- Authors: Kade, Andréa Gaby
- Date: 2021-04
- Subjects: Sedentary behavior in children -- South Africa -- Makana Municipality , Physical fitness for children -- South Africa -- Makana Municipality , Exercise -- Physiological aspects , Exercise -- Health aspects , Diabetes -- Risk factors , Heart -- Diseases -- Risk factors
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177282 , vital:42806
- Description: There is a lack of data on the physical activity, physical fitness and sedentary behaviour of children in South Africa. Furthermore chronic diseases such as type II diabetes and coronary heart disease have been linked to childhood inactivity, and improving cardiorespiratory fitness and increasing levels of physical activity has been shown to be beneficial in reducing the risk of such diseases. In South Africa more broadly there is a lack of information on levels of physical activity and sedentary behaviour as well as physical fitness measures particularly in children. Objective: The purpose of this study was to enhance the existing body of knowledge on this, by measuring the prevalence of physical inactivity, sedentary behaviour and screen time of primary school children in a private school from the Makana Municipal region in the Eastern Cape Province of South Africa, where the evidence is most sparse. A secondary aim was to assess levels of physical fitness in this cohort, as well as to compare across grades and sexes. Method: After ethical approval was granted, stature and body mass measurements were taken and body mass index was computed for primary school children (Grade one to seven) from a private school in the Makana Municipality. Sitting stature was measured in order to determine each child’s peak height velocity and maturity offset. Five different physical fitness tests were conducted on the children and blood pressure and heart rate values were measured at rest. Physical activity and screen time questionnaires were completed by the children’s parents for a seven day period. Results: Females were found to mature faster than males. In addition females were more physically active (Females= 916 min/week; Males= 669 min/week) while also accumulating more sedentary time (Females= 1241 min/week; Males= 970 min/week) as compared to males, although no significant differences were found between males and females for these variables. The sample participated in more than 60 minutes of moderate-to-vigorous physical activity and less than two hours of screen time daily, which is in accordance with guidelines. No differences were found between grades and sexes for accumulated screen time. Strength increased significantly with grade and age, and there were also statistical differences between the sexes for all three strength measures with males being stronger than females. Females were more flexible than males and no statistical differences were found between sexes for the shuttle run test. Blood pressure correlated positively with mass, as did all the strength measures as well as maturity offset. No correlations were found between screen time and all other variables. A negative relationship was recorded between screen time and physical activity, although not significant. For females a strong positive correlation was found between sedentary behaviour and physical activity. Conclusion: The study was successful in adding to the body of knowledge regarding the prevalence of physical inactivity, sedentary behaviour and screen time within school children from the Makana Municipality in the Eastern Cape Province of South Africa. The sample was considered physically active as they accumulated on average more than 60 minutes of moderate-to-vigorous physical activity daily (Males= 96 min/day; Females 130 min/day), which is in accordance with guidelines recommended by the World Health Organization (World Health Organization, 2018). The sample accumulated more sedentary behaviour than physical activity, although not significant. Screen time was below regulations of two hours daily, indicating this population participated in more non screen related sedentary behaviour. More research is needed into the risks presented with different forms of sedentary behaviour. Physical fitness increased with increasing grade and age and males were considerably more fit. The current study did not present any concern with regards to the effects of increased physical activity and fitness levels within school aged children. More research into the current levels of physical activity, physical fitness and sedentary behaviour of school aged children in South Africa in general, and in the Eastern Cape Province, is needed. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
- Authors: Kade, Andréa Gaby
- Date: 2021-04
- Subjects: Sedentary behavior in children -- South Africa -- Makana Municipality , Physical fitness for children -- South Africa -- Makana Municipality , Exercise -- Physiological aspects , Exercise -- Health aspects , Diabetes -- Risk factors , Heart -- Diseases -- Risk factors
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177282 , vital:42806
- Description: There is a lack of data on the physical activity, physical fitness and sedentary behaviour of children in South Africa. Furthermore chronic diseases such as type II diabetes and coronary heart disease have been linked to childhood inactivity, and improving cardiorespiratory fitness and increasing levels of physical activity has been shown to be beneficial in reducing the risk of such diseases. In South Africa more broadly there is a lack of information on levels of physical activity and sedentary behaviour as well as physical fitness measures particularly in children. Objective: The purpose of this study was to enhance the existing body of knowledge on this, by measuring the prevalence of physical inactivity, sedentary behaviour and screen time of primary school children in a private school from the Makana Municipal region in the Eastern Cape Province of South Africa, where the evidence is most sparse. A secondary aim was to assess levels of physical fitness in this cohort, as well as to compare across grades and sexes. Method: After ethical approval was granted, stature and body mass measurements were taken and body mass index was computed for primary school children (Grade one to seven) from a private school in the Makana Municipality. Sitting stature was measured in order to determine each child’s peak height velocity and maturity offset. Five different physical fitness tests were conducted on the children and blood pressure and heart rate values were measured at rest. Physical activity and screen time questionnaires were completed by the children’s parents for a seven day period. Results: Females were found to mature faster than males. In addition females were more physically active (Females= 916 min/week; Males= 669 min/week) while also accumulating more sedentary time (Females= 1241 min/week; Males= 970 min/week) as compared to males, although no significant differences were found between males and females for these variables. The sample participated in more than 60 minutes of moderate-to-vigorous physical activity and less than two hours of screen time daily, which is in accordance with guidelines. No differences were found between grades and sexes for accumulated screen time. Strength increased significantly with grade and age, and there were also statistical differences between the sexes for all three strength measures with males being stronger than females. Females were more flexible than males and no statistical differences were found between sexes for the shuttle run test. Blood pressure correlated positively with mass, as did all the strength measures as well as maturity offset. No correlations were found between screen time and all other variables. A negative relationship was recorded between screen time and physical activity, although not significant. For females a strong positive correlation was found between sedentary behaviour and physical activity. Conclusion: The study was successful in adding to the body of knowledge regarding the prevalence of physical inactivity, sedentary behaviour and screen time within school children from the Makana Municipality in the Eastern Cape Province of South Africa. The sample was considered physically active as they accumulated on average more than 60 minutes of moderate-to-vigorous physical activity daily (Males= 96 min/day; Females 130 min/day), which is in accordance with guidelines recommended by the World Health Organization (World Health Organization, 2018). The sample accumulated more sedentary behaviour than physical activity, although not significant. Screen time was below regulations of two hours daily, indicating this population participated in more non screen related sedentary behaviour. More research is needed into the risks presented with different forms of sedentary behaviour. Physical fitness increased with increasing grade and age and males were considerably more fit. The current study did not present any concern with regards to the effects of increased physical activity and fitness levels within school aged children. More research into the current levels of physical activity, physical fitness and sedentary behaviour of school aged children in South Africa in general, and in the Eastern Cape Province, is needed. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
Selection for improved virulence of Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV) to False Codling Moth, Thaumatotibia leucotreta, by serial passage through a heterologous host
- Authors: Iita, Petrus Paulus
- Date: 2021-04
- Subjects: Cryptophlebia leucotreta -- Biological control , Biological pest control agents , Citrus -- Diseases and pests , Baculoviruses , Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178180 , vital:42918
- Description: The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is endemic to southern Africa, and strongly associated with citrus. As South African citrus production is mainly for export to foreign markets, the market access risk due to the phytosanitary status of this pest is considerable and its control is therefore imperative. Various control measures as part of a rigorous integrated pest management (IPM) programme targeted against T. leucotreta have been effective at suppressing the pest in citrus, but there is still a growing need for continued improvement of the programme and augmentation of the available control options. Of these control options, biological control, particularly the use of Cryptophlebia leucotreta granulovirus (CrleGV-SA), is a key component of IPM in citrus orchards and it has been very successful at reducing T. leucotreta populations in the field for almost two decades. There is however, a growing need for more baculovirus variants with an improved virulence against T. leucotreta for a more efficient pest management system. The newly identified insect virus, Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV) offers a unique opportunity for an additional biopesticide in IPM for control of T. leucotreta in the field. This study aimed to conduct serial passaging of CrpeNPV through a heterologous host, T. leucotreta, in order to determine the potential for improved virulence or speed of kill against it. In order to select for a variant of CrpeNPV with improved virulence against T. leucotreta, a high dose (LC90) of the virus OBs was used to perform 12 serial passages through T. leucotreta larvae in surface-dose bioassays. Whole genome sequencing and analysis of the passaged virus, along with restriction endonuclease profiling in silico was performed to determine if the genetic identity of the virus had changed during serial passage, in relation to the original virus. These analyses indicated that the dominant genotype of CrpeNPV was maintained following 12 serial passages through the heterologous host. The biological activity of the passaged virus, along with the original virus was evaluated against neonate T. leucotreta in surface-dose bioassays and compared. Results from dose-response bioassays showed that the virulence of CrpeNPV did not improve after 12 serial passages. The LC50 values of the passaged virus and the original virus were estimated at 1.96 × 104 and 1.58 × 104 OBs/ml, respectively, whereas the LC90 values were estimated at 3.46 × 104 OBs/ml for the passaged virus and 3.68 × 104 for the original virus. Similarly, the results from time-response bioassays showed that the speed of kill of CrpeNPV did not improve after 12 serial passages. The LT50 values of the passaged virus and the original virus were 88.44 hours (3 days and 16 hours) and 83.74 hours (3 days and 12 hours), respectively, whereas the LT90 values were 115 hours (4 days 19 hours) for the passaged virus and 102 hours (4 days 6 hours) for the original virus. The virulence and speed of kill of the passaged virus decreased significantly, in relation to the original virus. When the full genome of the passaged virus was sequenced and analysed, only a few SNPs were detected in the viral genome, in comparison to the original virus. No detectable difference in REN digestion patterns were observed following REN analysis of gDNA of the passaged virus with several restriction enzymes in silico. The results for this study suggest that CrpeNPV may already be optimally suited to the heterologous host as it persists under these conditions without significant changes to the genome. These results have positive implications for the genetic integrity of CrpeNPV as a potential biocontrol agent in the field. This study is the first to report the virulence selection of CrpeNPV by serial passage through a heterologous host, and also the first to record bioassay data in terms of dose response (or lethal concentration) against T. leucotreta second instars. The data obtained have added to the knowledge about interactions between CrpeNPV and its heterologous host, and may be fundamental to continued investigation into the effect of serial passage on pathogenicity and genetic diversity of CrpeNPV. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Authors: Iita, Petrus Paulus
- Date: 2021-04
- Subjects: Cryptophlebia leucotreta -- Biological control , Biological pest control agents , Citrus -- Diseases and pests , Baculoviruses , Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178180 , vital:42918
- Description: The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is endemic to southern Africa, and strongly associated with citrus. As South African citrus production is mainly for export to foreign markets, the market access risk due to the phytosanitary status of this pest is considerable and its control is therefore imperative. Various control measures as part of a rigorous integrated pest management (IPM) programme targeted against T. leucotreta have been effective at suppressing the pest in citrus, but there is still a growing need for continued improvement of the programme and augmentation of the available control options. Of these control options, biological control, particularly the use of Cryptophlebia leucotreta granulovirus (CrleGV-SA), is a key component of IPM in citrus orchards and it has been very successful at reducing T. leucotreta populations in the field for almost two decades. There is however, a growing need for more baculovirus variants with an improved virulence against T. leucotreta for a more efficient pest management system. The newly identified insect virus, Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV) offers a unique opportunity for an additional biopesticide in IPM for control of T. leucotreta in the field. This study aimed to conduct serial passaging of CrpeNPV through a heterologous host, T. leucotreta, in order to determine the potential for improved virulence or speed of kill against it. In order to select for a variant of CrpeNPV with improved virulence against T. leucotreta, a high dose (LC90) of the virus OBs was used to perform 12 serial passages through T. leucotreta larvae in surface-dose bioassays. Whole genome sequencing and analysis of the passaged virus, along with restriction endonuclease profiling in silico was performed to determine if the genetic identity of the virus had changed during serial passage, in relation to the original virus. These analyses indicated that the dominant genotype of CrpeNPV was maintained following 12 serial passages through the heterologous host. The biological activity of the passaged virus, along with the original virus was evaluated against neonate T. leucotreta in surface-dose bioassays and compared. Results from dose-response bioassays showed that the virulence of CrpeNPV did not improve after 12 serial passages. The LC50 values of the passaged virus and the original virus were estimated at 1.96 × 104 and 1.58 × 104 OBs/ml, respectively, whereas the LC90 values were estimated at 3.46 × 104 OBs/ml for the passaged virus and 3.68 × 104 for the original virus. Similarly, the results from time-response bioassays showed that the speed of kill of CrpeNPV did not improve after 12 serial passages. The LT50 values of the passaged virus and the original virus were 88.44 hours (3 days and 16 hours) and 83.74 hours (3 days and 12 hours), respectively, whereas the LT90 values were 115 hours (4 days 19 hours) for the passaged virus and 102 hours (4 days 6 hours) for the original virus. The virulence and speed of kill of the passaged virus decreased significantly, in relation to the original virus. When the full genome of the passaged virus was sequenced and analysed, only a few SNPs were detected in the viral genome, in comparison to the original virus. No detectable difference in REN digestion patterns were observed following REN analysis of gDNA of the passaged virus with several restriction enzymes in silico. The results for this study suggest that CrpeNPV may already be optimally suited to the heterologous host as it persists under these conditions without significant changes to the genome. These results have positive implications for the genetic integrity of CrpeNPV as a potential biocontrol agent in the field. This study is the first to report the virulence selection of CrpeNPV by serial passage through a heterologous host, and also the first to record bioassay data in terms of dose response (or lethal concentration) against T. leucotreta second instars. The data obtained have added to the knowledge about interactions between CrpeNPV and its heterologous host, and may be fundamental to continued investigation into the effect of serial passage on pathogenicity and genetic diversity of CrpeNPV. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
The application of Classification Trees in the Banking Sector
- Authors: Mtwa, Sithayanda
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178514 , vital:42946
- Description: Access restricted until April 2026. , Thesis (MSc) -- Faculty of Science, Statistics, 2021
- Full Text:
- Authors: Mtwa, Sithayanda
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/178514 , vital:42946
- Description: Access restricted until April 2026. , Thesis (MSc) -- Faculty of Science, Statistics, 2021
- Full Text:
The effect of plant-derived dietary protein sources on cultured abalone Haliotis midae (L. 1758) digestive physiology
- Authors: Wright, Jason Geoffrey
- Date: 2021-04
- Subjects: Haliotis midae -- South Africa , Haliotis midae -- Nutrition -- South Africa , Haliotis midae -- Physiology -- South Africa , Haliotis midae -- South Africa -- Growth , Haliotis midae -- Digestive organs , Abalone culture -- South Africa , Plant proteins as feed
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176803 , vital:42760
- Description: The growth and feed conversion ratio of farmed abalone Haliotis midae (L. 1758) fed a formulated diet varies in feeds with different protein sources. To better understand this, the effect that various combinations of dietary soybean meal (SBM), sunflower meal (SFM) and fishmeal (FM) had on the digestive efficiency of farmed H. midae when included in a formulated feed, were assessed. The aim of this study was to investigate the effect that plant-based proteins had on abalone digestion and gut-bacterial profile of cultured adult abalone when combined with fishmeal. This was done by analysing the chymotrypsin (protease) and cellulase (carbohydrase) digestive enzyme activities from whole-gut sections of farmed abalone that were fed one of four diets for 12 months: FM-only, SBM-only, fishmeal and soybean meal (FM-SBM), and fishmeal and sunflower meal (FM-SFM). There were significant interactions between the diets, sampling date, and sex of the abalone, which had an influence on the cellulase activities in the digestive tracts of the animals. Those fed the SBM diet had the highest cellulase activity by the end of the sampling period (ANOVA; df = 9; F = 2.9; P = 0.005). The significant interactions between diet and sampling date influenced the chymotrypsin activities of abalone. Animals fed the FM diet had the highest activity of chymotrypsin for most of the sampling period (ANOVA; df = 9; F = 2.5; P = 0.01). Therefore, diet did have an impact on the cellulase and chymotrypsin activities of abalone fed either combination diets (FM-SBM; FM-SFM) or single protein diets (FM; SBM). The presence of plant material such as cellulose fibres in the diets containing plant proteins may have influenced the cellulase activity levels of each treatment as it would have stimulated endogenous and exogenous cellulase production. However, treatments with the highest crude fibre content, SBM and FM-SFM, resulted in differing activities. The activity levels of chymotrypsin may have been impacted by the protein type, presence of protein inhibitors and temporal changes in utilisation. Abalone fed the FM diet exhibited the highest chymotrypsin activities on sampling day 182, which was in summer. Animals fed the treatment diets containing fishmeal also developed their reproductive tissues, and may explain the low chymotrypsin activities in abalone fed SBM-only. Additionally, the presence of allergenic compounds would have influenced enzyme activity, as they would have negatively affected the nutrient utilisation and absorptive capacity. Fluctuations in water temperature may have had an effect on enzyme activity, as activities were highest during summer, when seawater temperatures are most variable. A change to lowered water temperatures are known to trigger the growth of digestive epithelial tissue in abalone to allow for increased enzyme secretions and nutrient absorption (Schaeffer et al. 2013). The effect that plant protein inclusion in abalone diets had on the gut-microbiota was revealed by analysing the differences in gut-bacterial community profiles, through the use of metagenomic sequencing. The relative abundance of the phylum Verrucomicrobia, class Verrcomicrobiae and the genus Rubritalea were highest in the SBM diet. These bacterial groups were also influenced by the plant material from soybean meal, as hydrolysed cellulose is broken down by cellulases, and allowed for the proliferation of Rubritalea bacteria due to them using cellobiose as an energy source. The presence of Bacteroidetes was due to the phyla having bacterial species that can breakdown proteins and species that can break down carbohydrates. The animal protein present in the composition of the FM diet had a positive influence on proteolytic Bacteroidetes growth. The high levels of cellulose from the plant fibres in the soybean meal-only diet (SBM) promoted growth of saccharolytic Bacteroidetes. Tenericutes bacteria’s prominence was due to the higher plant fibres from the soybean meal as some Mycoplasma are known to degrade polysaccharides. Therefore, exposure to formulated feeds with high levels of these plant materials would allow for high proliferation. The thesis established that plant-derived dietary proteins in formulated feeds result in an effect on digestive enzyme activity and a difference in the community structure of gut bacteria in H. midae abalone. The results from the current research highlight the importance of studying abalone gut physiology when investigating the impacts of formulated feed composition, and can be used as an additional factor when determining the efficacy of a dietary component. Further research on the gut-bacterial groups and different digestive enzymes of H. midae abalone is encouraged, in order to create a holistic view on their response to dietary plant proteins inclusion in formulated feeds, thus reducing the need for fishmeal protein. , Thesis (MSc)-- Rhodes University, Faculty of Science, Department of Ichthyology and Fisheries Science, 2021
- Full Text:
- Authors: Wright, Jason Geoffrey
- Date: 2021-04
- Subjects: Haliotis midae -- South Africa , Haliotis midae -- Nutrition -- South Africa , Haliotis midae -- Physiology -- South Africa , Haliotis midae -- South Africa -- Growth , Haliotis midae -- Digestive organs , Abalone culture -- South Africa , Plant proteins as feed
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/176803 , vital:42760
- Description: The growth and feed conversion ratio of farmed abalone Haliotis midae (L. 1758) fed a formulated diet varies in feeds with different protein sources. To better understand this, the effect that various combinations of dietary soybean meal (SBM), sunflower meal (SFM) and fishmeal (FM) had on the digestive efficiency of farmed H. midae when included in a formulated feed, were assessed. The aim of this study was to investigate the effect that plant-based proteins had on abalone digestion and gut-bacterial profile of cultured adult abalone when combined with fishmeal. This was done by analysing the chymotrypsin (protease) and cellulase (carbohydrase) digestive enzyme activities from whole-gut sections of farmed abalone that were fed one of four diets for 12 months: FM-only, SBM-only, fishmeal and soybean meal (FM-SBM), and fishmeal and sunflower meal (FM-SFM). There were significant interactions between the diets, sampling date, and sex of the abalone, which had an influence on the cellulase activities in the digestive tracts of the animals. Those fed the SBM diet had the highest cellulase activity by the end of the sampling period (ANOVA; df = 9; F = 2.9; P = 0.005). The significant interactions between diet and sampling date influenced the chymotrypsin activities of abalone. Animals fed the FM diet had the highest activity of chymotrypsin for most of the sampling period (ANOVA; df = 9; F = 2.5; P = 0.01). Therefore, diet did have an impact on the cellulase and chymotrypsin activities of abalone fed either combination diets (FM-SBM; FM-SFM) or single protein diets (FM; SBM). The presence of plant material such as cellulose fibres in the diets containing plant proteins may have influenced the cellulase activity levels of each treatment as it would have stimulated endogenous and exogenous cellulase production. However, treatments with the highest crude fibre content, SBM and FM-SFM, resulted in differing activities. The activity levels of chymotrypsin may have been impacted by the protein type, presence of protein inhibitors and temporal changes in utilisation. Abalone fed the FM diet exhibited the highest chymotrypsin activities on sampling day 182, which was in summer. Animals fed the treatment diets containing fishmeal also developed their reproductive tissues, and may explain the low chymotrypsin activities in abalone fed SBM-only. Additionally, the presence of allergenic compounds would have influenced enzyme activity, as they would have negatively affected the nutrient utilisation and absorptive capacity. Fluctuations in water temperature may have had an effect on enzyme activity, as activities were highest during summer, when seawater temperatures are most variable. A change to lowered water temperatures are known to trigger the growth of digestive epithelial tissue in abalone to allow for increased enzyme secretions and nutrient absorption (Schaeffer et al. 2013). The effect that plant protein inclusion in abalone diets had on the gut-microbiota was revealed by analysing the differences in gut-bacterial community profiles, through the use of metagenomic sequencing. The relative abundance of the phylum Verrucomicrobia, class Verrcomicrobiae and the genus Rubritalea were highest in the SBM diet. These bacterial groups were also influenced by the plant material from soybean meal, as hydrolysed cellulose is broken down by cellulases, and allowed for the proliferation of Rubritalea bacteria due to them using cellobiose as an energy source. The presence of Bacteroidetes was due to the phyla having bacterial species that can breakdown proteins and species that can break down carbohydrates. The animal protein present in the composition of the FM diet had a positive influence on proteolytic Bacteroidetes growth. The high levels of cellulose from the plant fibres in the soybean meal-only diet (SBM) promoted growth of saccharolytic Bacteroidetes. Tenericutes bacteria’s prominence was due to the higher plant fibres from the soybean meal as some Mycoplasma are known to degrade polysaccharides. Therefore, exposure to formulated feeds with high levels of these plant materials would allow for high proliferation. The thesis established that plant-derived dietary proteins in formulated feeds result in an effect on digestive enzyme activity and a difference in the community structure of gut bacteria in H. midae abalone. The results from the current research highlight the importance of studying abalone gut physiology when investigating the impacts of formulated feed composition, and can be used as an additional factor when determining the efficacy of a dietary component. Further research on the gut-bacterial groups and different digestive enzymes of H. midae abalone is encouraged, in order to create a holistic view on their response to dietary plant proteins inclusion in formulated feeds, thus reducing the need for fishmeal protein. , Thesis (MSc)-- Rhodes University, Faculty of Science, Department of Ichthyology and Fisheries Science, 2021
- Full Text:
The physical activity levels and preferences of South African breast cancer survivors : a pilot study
- Authors: Campbell, Belinda Claire
- Date: 2021-04
- Subjects: Breast -- Cancer , Cancer -- Patients -- South Africa , Cancer -- Patients -- Rehabilitation , Exercise -- Health aspects , Godin leisure-time activity questionnaire (GLTPAQ) , International Physical Activity Questionnaire (IPAQ)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177748 , vital:42855
- Description: Introduction: Breast cancer is currently the most commonly diagnosed cancer in South African women. Physical activity has proven to have preventative, treatment and management benefits for breast cancer and other cancers and exercise has been found as both viable and safe during cancer treatment and recovery. However, there is limited research on breast cancer and the levels and preferences of physical activity and sedentary behaviour in a South African context. Therefore, the purpose of this study was to identify levels of physical activity and sedentary behaviour of South African breast cancer survivors and to investigate the physical activity advice and participation preferences of these participants. Methods: A cross-sectional research design was implemented to identify the physical activity, sedentary behaviour levels and exercise preferences of 48 South African breast cancer survivors (age range 45 years). An online survey comprising demographic and anthropometric questions, the Godin leisure-time activity questionnaire (GLTPAQ), the International Physical Activity Questionnaire (IPAQ) and an exercise preference questionnaire was presented to participating breast cancer survivors in order to i) identify the levels of physical activity and sedentary behaviour engaged in, ii) obtain demographic and anthropometric information and iii) identify exercise preferences. A linear mixed model regression was used to examine potential associations between demographic and anthropometric variables and physical activity levels. Chi-squared and Pearson’s Product-Moment correlation tests were used to identify relationships between categorical and numerical variables. A correlation matrix was generated to further explore any correlations. Statistical significance for all measures was set at p<0.05. Results: The mean age of the group was 49 ± 9.87 years. The most common time since diagnosis was <5 years ago and the most common stage of breast cancer was stage I. The mean BMI was 27.87 ± 5.53kg/m2. The most common treatment combination was surgery with either chemotherapy or radiation. According to the leisure score index (LSI) the majority of the group (56%) was active and according to IPAQ data 60% were meeting physical activity guidelines. The highest physical activity levels were seen in the average weekly minutes of moderate-intensity activity, and there was a strong, non-significant positive correlation (p>0.05, R2 = 0.95) between moderate-intensity physical activity and total physical activity levels. High levels of weekly sedentary behaviour and sitting time (302.60 ± 169.96 minutes) were reported. A weak, non-significant, positive correlation was found between total sedentary time and BMI (p>0.05, R2 = 0.1). A weak, non-significant, negative correlation was found between age and sedentary time (p>0.05, R2 = 0.002). More participants below 50 years were insufficiently active compared to above the age of 50 years. 1.7 to 2.6 years since diagnosis saw the greatest number of insufficiently active survivors and the category over 2.6 years since diagnosis saw the most active survivors. Most breast cancer survivors (71.10% & 82.05%) indicated being interested in and feeling capable of participating in an exercise programme (p>0.05, R2 = 0.72). The favoured preference for receiving physical activity advice was face-to-face with an exercise specialist at a cancer centre before treatment. Participation preferences included starting a programme immediately after treatment, in a home-based setting with one or two other people, where walking and a moderate exercise intensity were the preferred exercise type and level of intensity. Data collection occurred both immediately prior to (42% of participants) and during (56% of participants) the South African Covid-19 lockdown, so the results should be seen in light of this context. Conclusion: The current study is one of the first to explore physical activity rates and preferences of South African breast cancer survivors. As a group and individually these survivors were meeting public physical activity guidelines and engaging in the recommended weekly minutes. The high sitting time coupled with the high overweight and obesity levels highlight the need for positive behavioural changes including improved levels of physical activity and reduced sedentary behaviour. These changes need involvement from the numerous levels of society that affect health. Broad physical activity guidelines need to be developed not only to improve physical activity levels in breast cancer survivors but to work as a preventative measure by facilitating physical activity promotion in the general population. The findings of this study demonstrate that this group of South African breast cancer survivors is open to physical activity advice, to programmes and to improving physical activity levels. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
- Authors: Campbell, Belinda Claire
- Date: 2021-04
- Subjects: Breast -- Cancer , Cancer -- Patients -- South Africa , Cancer -- Patients -- Rehabilitation , Exercise -- Health aspects , Godin leisure-time activity questionnaire (GLTPAQ) , International Physical Activity Questionnaire (IPAQ)
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177748 , vital:42855
- Description: Introduction: Breast cancer is currently the most commonly diagnosed cancer in South African women. Physical activity has proven to have preventative, treatment and management benefits for breast cancer and other cancers and exercise has been found as both viable and safe during cancer treatment and recovery. However, there is limited research on breast cancer and the levels and preferences of physical activity and sedentary behaviour in a South African context. Therefore, the purpose of this study was to identify levels of physical activity and sedentary behaviour of South African breast cancer survivors and to investigate the physical activity advice and participation preferences of these participants. Methods: A cross-sectional research design was implemented to identify the physical activity, sedentary behaviour levels and exercise preferences of 48 South African breast cancer survivors (age range 45 years). An online survey comprising demographic and anthropometric questions, the Godin leisure-time activity questionnaire (GLTPAQ), the International Physical Activity Questionnaire (IPAQ) and an exercise preference questionnaire was presented to participating breast cancer survivors in order to i) identify the levels of physical activity and sedentary behaviour engaged in, ii) obtain demographic and anthropometric information and iii) identify exercise preferences. A linear mixed model regression was used to examine potential associations between demographic and anthropometric variables and physical activity levels. Chi-squared and Pearson’s Product-Moment correlation tests were used to identify relationships between categorical and numerical variables. A correlation matrix was generated to further explore any correlations. Statistical significance for all measures was set at p<0.05. Results: The mean age of the group was 49 ± 9.87 years. The most common time since diagnosis was <5 years ago and the most common stage of breast cancer was stage I. The mean BMI was 27.87 ± 5.53kg/m2. The most common treatment combination was surgery with either chemotherapy or radiation. According to the leisure score index (LSI) the majority of the group (56%) was active and according to IPAQ data 60% were meeting physical activity guidelines. The highest physical activity levels were seen in the average weekly minutes of moderate-intensity activity, and there was a strong, non-significant positive correlation (p>0.05, R2 = 0.95) between moderate-intensity physical activity and total physical activity levels. High levels of weekly sedentary behaviour and sitting time (302.60 ± 169.96 minutes) were reported. A weak, non-significant, positive correlation was found between total sedentary time and BMI (p>0.05, R2 = 0.1). A weak, non-significant, negative correlation was found between age and sedentary time (p>0.05, R2 = 0.002). More participants below 50 years were insufficiently active compared to above the age of 50 years. 1.7 to 2.6 years since diagnosis saw the greatest number of insufficiently active survivors and the category over 2.6 years since diagnosis saw the most active survivors. Most breast cancer survivors (71.10% & 82.05%) indicated being interested in and feeling capable of participating in an exercise programme (p>0.05, R2 = 0.72). The favoured preference for receiving physical activity advice was face-to-face with an exercise specialist at a cancer centre before treatment. Participation preferences included starting a programme immediately after treatment, in a home-based setting with one or two other people, where walking and a moderate exercise intensity were the preferred exercise type and level of intensity. Data collection occurred both immediately prior to (42% of participants) and during (56% of participants) the South African Covid-19 lockdown, so the results should be seen in light of this context. Conclusion: The current study is one of the first to explore physical activity rates and preferences of South African breast cancer survivors. As a group and individually these survivors were meeting public physical activity guidelines and engaging in the recommended weekly minutes. The high sitting time coupled with the high overweight and obesity levels highlight the need for positive behavioural changes including improved levels of physical activity and reduced sedentary behaviour. These changes need involvement from the numerous levels of society that affect health. Broad physical activity guidelines need to be developed not only to improve physical activity levels in breast cancer survivors but to work as a preventative measure by facilitating physical activity promotion in the general population. The findings of this study demonstrate that this group of South African breast cancer survivors is open to physical activity advice, to programmes and to improving physical activity levels. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
Accelerated implementations of the RIME for DDE calibration and source modelling
- Authors: Van Staden, Joshua
- Date: 2021
- Subjects: Radio astronomy , Radio inferometers , Radio inferometers -- Calibration , Radio astronomy -- Data processing , Radio inferometers -- Data processing , Radio inferometers -- Calibration -- Data processing
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172422 , vital:42199
- Description: Second- and third-generation calibration methods filter out subtle effects in interferometer data, and therefore yield significantly higher dynamic ranges. The basis of these calibration techniques relies on building a model of the sky and corrupting it with models of the effects acting on the sources. The sensitivities of modern instruments call for more elaborate models to capture the level of detail that is required to achieve accurate calibration. This thesis implements two types of models to be used in for second- and third-generation calibration. The first model implemented is shapelets, which can be used to model radio source morphologies directly in uv space. The second model implemented is Zernike polynomials, which can be used to represent the primary beam of the antenna. We implement these models in the CODEX-AFRICANUS package and provide a set of unit tests for each model. Additionally, we compare our implementations against other methods of representing these objects and instrumental effects, namely NIFTY-GRIDDER against shapelets and a FITS-interpolation method against the Zernike polynomials. We find that to achieve sufficient accuracy, our implementation of the shapelet model has a higher runtime to that of the NIFTY-GRIDDER. However, the NIFTY-GRIDDER cannot simulate a component-based sky model while the shapelet model can. Additionally, the shapelet model is fully parametric, which allows for integration into a parameterised solver. We find that, while having a smaller memory footprint, our Zernike model has a greater computational complexity than that of the FITS-interpolated method. However, we find that the Zernike implementation has floating-point accuracy in its modelling, while the FITS-interpolated model loses some accuracy through the discretisation of the beam.
- Full Text:
- Authors: Van Staden, Joshua
- Date: 2021
- Subjects: Radio astronomy , Radio inferometers , Radio inferometers -- Calibration , Radio astronomy -- Data processing , Radio inferometers -- Data processing , Radio inferometers -- Calibration -- Data processing
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172422 , vital:42199
- Description: Second- and third-generation calibration methods filter out subtle effects in interferometer data, and therefore yield significantly higher dynamic ranges. The basis of these calibration techniques relies on building a model of the sky and corrupting it with models of the effects acting on the sources. The sensitivities of modern instruments call for more elaborate models to capture the level of detail that is required to achieve accurate calibration. This thesis implements two types of models to be used in for second- and third-generation calibration. The first model implemented is shapelets, which can be used to model radio source morphologies directly in uv space. The second model implemented is Zernike polynomials, which can be used to represent the primary beam of the antenna. We implement these models in the CODEX-AFRICANUS package and provide a set of unit tests for each model. Additionally, we compare our implementations against other methods of representing these objects and instrumental effects, namely NIFTY-GRIDDER against shapelets and a FITS-interpolation method against the Zernike polynomials. We find that to achieve sufficient accuracy, our implementation of the shapelet model has a higher runtime to that of the NIFTY-GRIDDER. However, the NIFTY-GRIDDER cannot simulate a component-based sky model while the shapelet model can. Additionally, the shapelet model is fully parametric, which allows for integration into a parameterised solver. We find that, while having a smaller memory footprint, our Zernike model has a greater computational complexity than that of the FITS-interpolated method. However, we find that the Zernike implementation has floating-point accuracy in its modelling, while the FITS-interpolated model loses some accuracy through the discretisation of the beam.
- Full Text:
Evaluating the cyber security skills gap relating to penetration testing
- Authors: Beukes, Dirk Johannes
- Date: 2021
- Subjects: Computer networks -- Security measures , Computer networks -- Monitoring , Computer networks -- Management , Data protection , Information technology -- Security measures , Professionals -- Supply and demand , Electronic data personnel -- Supply and demand
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171120 , vital:42021
- Description: Information Technology (IT) is growing rapidly and has become an integral part of daily life. It provides a boundless list of services and opportunities, generating boundless sources of information, which could be abused or exploited. Due to this growth, there are thousands of new users added to the grid using computer systems in a static and mobile environment; this fact alone creates endless volumes of data to be exploited and hardware devices to be abused by the wrong people. The growth in the IT environment adds challenges that may affect users in their personal, professional, and business lives. There are constant threats on corporate and private computer networks and computer systems. In the corporate environment companies try to eliminate the threat by testing networks making use of penetration tests and by implementing cyber awareness programs to make employees more aware of the cyber threat. Penetration tests and vulnerability assessments are undervalued; are seen as a formality and are not used to increase system security. If used regularly the computer system will be more secure and attacks minimized. With the growth in technology, industries all over the globe become fully dependent on information systems in doing their day-to-day business. As technology evolves and new technology becomes available, the bigger the risk becomes to protect against the dangers which come with this new technology. For industry to protect itself against this growth in technology, personnel with a certain skill set is needed. This is where cyber security plays a very important role in the protection of information systems to ensure the confidentiality, integrity and availability of the information system itself and the data on the system. Due to this drive to secure information systems, the need for cyber security by professionals is on the rise as well. It is estimated that there is a shortage of one million cyber security professionals globally. What is the reason for this skills shortage? Will it be possible to close this skills shortage gap? This study is about identifying the skills gap and identifying possible ways to close this skills gap. In this study, research was conducted on the cyber security international standards, cyber security training at universities and international certification focusing specifically on penetration testing, the evaluation of the need of industry while recruiting new penetration testers, finishing with suggestions on how to fill possible gaps in the skills market with a conclusion.
- Full Text:
- Authors: Beukes, Dirk Johannes
- Date: 2021
- Subjects: Computer networks -- Security measures , Computer networks -- Monitoring , Computer networks -- Management , Data protection , Information technology -- Security measures , Professionals -- Supply and demand , Electronic data personnel -- Supply and demand
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171120 , vital:42021
- Description: Information Technology (IT) is growing rapidly and has become an integral part of daily life. It provides a boundless list of services and opportunities, generating boundless sources of information, which could be abused or exploited. Due to this growth, there are thousands of new users added to the grid using computer systems in a static and mobile environment; this fact alone creates endless volumes of data to be exploited and hardware devices to be abused by the wrong people. The growth in the IT environment adds challenges that may affect users in their personal, professional, and business lives. There are constant threats on corporate and private computer networks and computer systems. In the corporate environment companies try to eliminate the threat by testing networks making use of penetration tests and by implementing cyber awareness programs to make employees more aware of the cyber threat. Penetration tests and vulnerability assessments are undervalued; are seen as a formality and are not used to increase system security. If used regularly the computer system will be more secure and attacks minimized. With the growth in technology, industries all over the globe become fully dependent on information systems in doing their day-to-day business. As technology evolves and new technology becomes available, the bigger the risk becomes to protect against the dangers which come with this new technology. For industry to protect itself against this growth in technology, personnel with a certain skill set is needed. This is where cyber security plays a very important role in the protection of information systems to ensure the confidentiality, integrity and availability of the information system itself and the data on the system. Due to this drive to secure information systems, the need for cyber security by professionals is on the rise as well. It is estimated that there is a shortage of one million cyber security professionals globally. What is the reason for this skills shortage? Will it be possible to close this skills shortage gap? This study is about identifying the skills gap and identifying possible ways to close this skills gap. In this study, research was conducted on the cyber security international standards, cyber security training at universities and international certification focusing specifically on penetration testing, the evaluation of the need of industry while recruiting new penetration testers, finishing with suggestions on how to fill possible gaps in the skills market with a conclusion.
- Full Text:
High-resolution geological, petrological and geochemical investigation of the mid mid-lower c. 3.3 Ga Kromberg type type-section, Barberton greenstone belt, South Africa Africa
- Authors: Ndlela, Sibusisiwe
- Date: 2021
- Subjects: Petrology -- Eswatini and South Africa -- Barberton Greenstone Belt , Geology -- Eswatini and South Africa -- Barberton Greenstone Belt , Geochemistry -- Eswatini and South Africa -- Barberton Greenstone Belt , Onverwacht Group (South Africa) , Barberton Greenstone Belt (Eswatini and South Africa) , Groups (Stratigraph) -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172241 , vital:42179
- Description: The geology of the SE limb of the Kromberg type-section, its origin and its evolution has remained controversial for more than five decades since its discovery by Viljoen and Viljoen (1969). Different lithostratigraphy and geodynamic models have been proposed that were centred around two end-member models, a continuous layer-cake stratigraphy model (Viljoen and Viljoen, 1969c, Lowe et al., 1999) or a tectono-stratigraphic model (de Wit et al., 2011, Furnes et al., 2012). Additionally, the Kromberg type-section mafic-ultramafic sequence represents a relatively thin, dismembered sequence compared to other formations or ‘complexes’ in the Onverwacht Group. Previous geology workers relied on the field interpretations for the construction of the geological architecture of the Kromberg type-section; but no petrographic analyses were conducted for accurate, integrated geological characterization of different rock compositions. To address controversies centred around the Kromberg type-section geology and geodynamic setting, this study is aimed at testing previously proposed stratigraphic and geodynamic models by integrating high-resolution geological mapping, petrography, mineral chemistry and whole-rock geochemistry to verify rock characterization. The aim is to accurately reconstruct the volcano-sedimentary architecture of the Kromberg type-section and to compare this to the results of previous fieldwork. Moreover, the manner in which the Kromberg sequence may relate to current Archean geodynamic models is evaluated, and a new model explaining the origin and evolution of the Kromberg type sequence is proposed. The integration of high-resolution field mapping, petrography and geochemistry has allowed for a high precision study and that has resulted in the construction of a new geological architecture for the SE limb of the Kromberg type-section. The stratigraphic thickness of the SE limb of the Kromberg sequence comprises dominant c. 80% volcanic rocks and minor c. 15% intrusive rocks, intercalated by 7 volcano-sedimentary chert horizons (c. 5%). Four main rock types (groups) are present in the Kromberg type-section with two sub-types of komatiitic basalts (the Badplaas-type and Geluk-types), Fe-rich tholeiitic basalt, cumulate peridotite, and a metadunite. Although the Kromberg type-section records sub-greenschist to lower greenschist facies, more than 50% of the rock samples classify as altered with parts of the stratigraphy recording extensive chloritization and severe ocean-floor silicification. Geochemical data revealed an enrichment in SiO2, K2O, Ba, Rb and variation in HREE for highly silicified samples whereas, chloritized samples are enriched in FeO and have concave upward LREE patterns. Partially chloritized tholeiites and komatiitic basalts have overlapping SiO2 signatures, relatively flat REE patterns and a small negative Nb anomaly in the primitive mantle-normalized spider diagrams. This thesis provides the first Lu-Hf isotope data on whole rock samples from the Kromberg type-section. The εHf values at t=3.33 Ga range between -0.62 to +4.18 and Hf model ages range between 3.43 - 4.27 Ga. The rock compositions are compared to the geochemistry of other greenstone belt rocks, which are considered to provide insight onto the geodynamic setting under which the Kromberg mafic-ultramafic sequence formed. The rock compositions reveal plume-related processes where a primitive mantle melt interacts with recycled mafic crust or mafic lower crust of older units of the Onverwacht Group. Only a small Nb anomaly is found in some samples and the data plots outside the subduction zone (forearc and back-arc) field. Rare-Earth element profiles are flat and not consistent with a subduction zone signature, as proposed in previous studies. Rifting of an oceanic floor in a juvenile basin is proposed for the formation of the Kromberg type-section rocks, prior to being tectonically accreted during regional transpressional deformation at c. 3.23 Ga.
- Full Text:
- Authors: Ndlela, Sibusisiwe
- Date: 2021
- Subjects: Petrology -- Eswatini and South Africa -- Barberton Greenstone Belt , Geology -- Eswatini and South Africa -- Barberton Greenstone Belt , Geochemistry -- Eswatini and South Africa -- Barberton Greenstone Belt , Onverwacht Group (South Africa) , Barberton Greenstone Belt (Eswatini and South Africa) , Groups (Stratigraph) -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172241 , vital:42179
- Description: The geology of the SE limb of the Kromberg type-section, its origin and its evolution has remained controversial for more than five decades since its discovery by Viljoen and Viljoen (1969). Different lithostratigraphy and geodynamic models have been proposed that were centred around two end-member models, a continuous layer-cake stratigraphy model (Viljoen and Viljoen, 1969c, Lowe et al., 1999) or a tectono-stratigraphic model (de Wit et al., 2011, Furnes et al., 2012). Additionally, the Kromberg type-section mafic-ultramafic sequence represents a relatively thin, dismembered sequence compared to other formations or ‘complexes’ in the Onverwacht Group. Previous geology workers relied on the field interpretations for the construction of the geological architecture of the Kromberg type-section; but no petrographic analyses were conducted for accurate, integrated geological characterization of different rock compositions. To address controversies centred around the Kromberg type-section geology and geodynamic setting, this study is aimed at testing previously proposed stratigraphic and geodynamic models by integrating high-resolution geological mapping, petrography, mineral chemistry and whole-rock geochemistry to verify rock characterization. The aim is to accurately reconstruct the volcano-sedimentary architecture of the Kromberg type-section and to compare this to the results of previous fieldwork. Moreover, the manner in which the Kromberg sequence may relate to current Archean geodynamic models is evaluated, and a new model explaining the origin and evolution of the Kromberg type sequence is proposed. The integration of high-resolution field mapping, petrography and geochemistry has allowed for a high precision study and that has resulted in the construction of a new geological architecture for the SE limb of the Kromberg type-section. The stratigraphic thickness of the SE limb of the Kromberg sequence comprises dominant c. 80% volcanic rocks and minor c. 15% intrusive rocks, intercalated by 7 volcano-sedimentary chert horizons (c. 5%). Four main rock types (groups) are present in the Kromberg type-section with two sub-types of komatiitic basalts (the Badplaas-type and Geluk-types), Fe-rich tholeiitic basalt, cumulate peridotite, and a metadunite. Although the Kromberg type-section records sub-greenschist to lower greenschist facies, more than 50% of the rock samples classify as altered with parts of the stratigraphy recording extensive chloritization and severe ocean-floor silicification. Geochemical data revealed an enrichment in SiO2, K2O, Ba, Rb and variation in HREE for highly silicified samples whereas, chloritized samples are enriched in FeO and have concave upward LREE patterns. Partially chloritized tholeiites and komatiitic basalts have overlapping SiO2 signatures, relatively flat REE patterns and a small negative Nb anomaly in the primitive mantle-normalized spider diagrams. This thesis provides the first Lu-Hf isotope data on whole rock samples from the Kromberg type-section. The εHf values at t=3.33 Ga range between -0.62 to +4.18 and Hf model ages range between 3.43 - 4.27 Ga. The rock compositions are compared to the geochemistry of other greenstone belt rocks, which are considered to provide insight onto the geodynamic setting under which the Kromberg mafic-ultramafic sequence formed. The rock compositions reveal plume-related processes where a primitive mantle melt interacts with recycled mafic crust or mafic lower crust of older units of the Onverwacht Group. Only a small Nb anomaly is found in some samples and the data plots outside the subduction zone (forearc and back-arc) field. Rare-Earth element profiles are flat and not consistent with a subduction zone signature, as proposed in previous studies. Rifting of an oceanic floor in a juvenile basin is proposed for the formation of the Kromberg type-section rocks, prior to being tectonically accreted during regional transpressional deformation at c. 3.23 Ga.
- Full Text:
Parametrised gains for direction-dependent calibration
- Authors: Russeeaeon, Cyndie
- Date: 2021
- Subjects: Radio astronomy , Radio inferometers , Radio inferometers -- Calibration
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172400 , vital:42196
- Description: Calibration in radio interferometry describes the process of estimating and correcting for instrumental errors from data. Direction-Dependent (DD) calibration entails correcting for corruptions which vary across the sky. For small field of view observations, DD corruptions can be ignored but for wide fild observations, it is crucial to account for them. Traditional maximum likelihood calibration is not necessarily efficient in low signal-to-noise ratio (SNR) scenarios and this can lead to ovefitting. This can bias continuum subtraction and hence, restrict the spectral line studies. Since DD effects are expected to vary smoothly across the sky, the gains can be parametrised as a smooth function of the sky coordinates. Hence, we implement a solver where the atmosphere is modelled using a time-variant 2-dimensional phase screen with an arbitrary known frequency dependence. We assume arbitrary linear basis functions for the gains over the phase screen. The implemented solver is ptimised using the diagonal approximation of the Hessian as shown in previous studies. We present a few simulations to illustrate the performance of the solver.
- Full Text:
- Authors: Russeeaeon, Cyndie
- Date: 2021
- Subjects: Radio astronomy , Radio inferometers , Radio inferometers -- Calibration
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172400 , vital:42196
- Description: Calibration in radio interferometry describes the process of estimating and correcting for instrumental errors from data. Direction-Dependent (DD) calibration entails correcting for corruptions which vary across the sky. For small field of view observations, DD corruptions can be ignored but for wide fild observations, it is crucial to account for them. Traditional maximum likelihood calibration is not necessarily efficient in low signal-to-noise ratio (SNR) scenarios and this can lead to ovefitting. This can bias continuum subtraction and hence, restrict the spectral line studies. Since DD effects are expected to vary smoothly across the sky, the gains can be parametrised as a smooth function of the sky coordinates. Hence, we implement a solver where the atmosphere is modelled using a time-variant 2-dimensional phase screen with an arbitrary known frequency dependence. We assume arbitrary linear basis functions for the gains over the phase screen. The implemented solver is ptimised using the diagonal approximation of the Hessian as shown in previous studies. We present a few simulations to illustrate the performance of the solver.
- Full Text:
Synthesis, spectroscopic and nonlinear optical properties of asymmetric A3B type phthalocyanine complexes
- Authors: Mugeza, Rhulani Donney
- Date: 2021
- Subjects: Spectrum analysis , Mass spectrometry , Phthalocyanines
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171667 , vital:42108
- Description: This work reports on the synthesis of symmetrical and asymmetrical A 3 B type metal free, cobalt and zinc Phthalocyanines (Pc) .A wide range of spectroscopic techniques such as Uv - visible absorption (UV), magnetic circular dichroism (MCD), mass spectrometry, elemental analysis, IR spectroscopy and time correlated single photo n counting spectroscopy (TCSPC) have been used to study the spectroscopic properties of the phthalocyanine complexes. The Z - scan technique was used to comparatively investigate the nonlinear absorption coefficient ( 휷 ) and the nonlinear refraction index ( 풏 ퟐ ) of the synthesized complexes. The following trend was obtained for the synthesized Pc’s in terms of the 휷 values 7.25 × 10 − 10 ( 4b ) > 3.76 × 10 − 10 ( 4a ) > 3.52 × 10 − 10 ( 4c ) > 2.29 × 10 − 10 ( 3c ) > 1.68 × 10 − 10 ( 3a ) > 1.65 × 10 − 10 ( 3b ) mW - 1 . The 휷 values trend of synthesized Pc complexes show that the asymmetrical A 3 B type metal free, cobalt and zinc Pc complexes ( 4a , 4b and 4c ) have larger 휷 values as compared to the octa - substituted symmetrical metal free, cobalt and zinc Pc complexes ( 3a , 3b and 3c ) which is attributed to the low symmetry of the Pc complexes. The five - level model rate equations were used to determine the two photon absorption, excited state absorption and ground state absorption cross sections of the synthesized complexes. The z inc A 3 B type asymmetrical Pc complexes gave the largest two photon absorption and 휎 푒 / 휎 푔 ratio values. This Pc complex could be used in future work to enhance the nonlinear response further by introducing nanomaterials and converting the Pc complex to a binuclear Pc. This work also reports on the density functional theory (DFT) calculations o f dipolar/octupolar contributions in order to study the first order hyperpolarizability of the synthesized Pc complexes.
- Full Text:
- Authors: Mugeza, Rhulani Donney
- Date: 2021
- Subjects: Spectrum analysis , Mass spectrometry , Phthalocyanines
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171667 , vital:42108
- Description: This work reports on the synthesis of symmetrical and asymmetrical A 3 B type metal free, cobalt and zinc Phthalocyanines (Pc) .A wide range of spectroscopic techniques such as Uv - visible absorption (UV), magnetic circular dichroism (MCD), mass spectrometry, elemental analysis, IR spectroscopy and time correlated single photo n counting spectroscopy (TCSPC) have been used to study the spectroscopic properties of the phthalocyanine complexes. The Z - scan technique was used to comparatively investigate the nonlinear absorption coefficient ( 휷 ) and the nonlinear refraction index ( 풏 ퟐ ) of the synthesized complexes. The following trend was obtained for the synthesized Pc’s in terms of the 휷 values 7.25 × 10 − 10 ( 4b ) > 3.76 × 10 − 10 ( 4a ) > 3.52 × 10 − 10 ( 4c ) > 2.29 × 10 − 10 ( 3c ) > 1.68 × 10 − 10 ( 3a ) > 1.65 × 10 − 10 ( 3b ) mW - 1 . The 휷 values trend of synthesized Pc complexes show that the asymmetrical A 3 B type metal free, cobalt and zinc Pc complexes ( 4a , 4b and 4c ) have larger 휷 values as compared to the octa - substituted symmetrical metal free, cobalt and zinc Pc complexes ( 3a , 3b and 3c ) which is attributed to the low symmetry of the Pc complexes. The five - level model rate equations were used to determine the two photon absorption, excited state absorption and ground state absorption cross sections of the synthesized complexes. The z inc A 3 B type asymmetrical Pc complexes gave the largest two photon absorption and 휎 푒 / 휎 푔 ratio values. This Pc complex could be used in future work to enhance the nonlinear response further by introducing nanomaterials and converting the Pc complex to a binuclear Pc. This work also reports on the density functional theory (DFT) calculations o f dipolar/octupolar contributions in order to study the first order hyperpolarizability of the synthesized Pc complexes.
- Full Text:
The effect of habitat and spatial management on reef fish in an established marine protected area
- Authors: Dames, Vivienne Abigail
- Date: 2021
- Subjects: iSimangaliso Wetland Park (South Africa) -- Management , Reef fishes -- South Africa -- KwaZulu-Natal , Baited remote underwater stereo-video systems (stereo-BRUVs) , Marine parks and reserves -- Monitoring -- South Africa -- KwaZulu-Natal , Fish populations -- Measurement
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171150 , vital:42024
- Description: The persistence of harvested fish populations in the Anthropocene will be determined, above all, by how they respond to the interacting effects of climate change and fisheries exploitation. Predicting how populations will respond to both these threats is essential for any adaptive and sustainable management strategy. The response of fish populations to climate change is underpinned by physiological rates and tolerances, and emerging evidence suggests there may be physiological-based selection in capture fisheries. By quantifying important physiological rates of a model species, the endemic seabream, Chrysoblephus laticeps, across ecologically relevant thermal gradients and from populations subjected to varying intensities of commercial exploitation, this thesis aimed to 1) provide the first physiologically grounded climate resilience assessment for a South African linefish species, and 2) elucidate whether exploitation can drive populations to less physiologically resilient states in response to climate change. To identify physiologically limiting sea temperatures and to determine if exploitation alters physiological trait distributions, an intermittent flow respirometry experiment was used to test the metabolic response of spatially protected and exploited populations of C. laticeps to acute thermal variability. Exploited populations showed reduced metabolic phenotype diversity, fewer high-performance aerobic scope phenotypes, and a significantly lower aerobic scope curve across all test temperatures. Although both populations maintained a relatively high aerobic scope across a wide thermal range, their metabolic rates were compromised when extreme cold events were simulated (8 °C), suggesting that predicted future increases in upwelling frequency and intensity may be the primary limiting factor in a more thermally variable future ocean. The increment widths of annuli in the otoliths of C. laticeps from contemporary and historic collections were measured, as a proxy for the annual growth rate of exploited and protected populations. Hierarchical mixed models were used to partition growth variation within and among individuals and ascribe growth to intrinsic and extrinsic effects. The best model for the protected population indicated that the growth response of C. laticeps was poorer during years characterised by a high cumulative upwelling intensity, and better during years characterised by higher mean autumn sea surface temperatures. The exploited population growth chronology was too short to identify an extrinsic growth driver. The growth results again highlight the role of thermal variability in modulating the response of C. laticeps to its ambient environment and indicate that the predicted increases in upwelling frequency and intensity may constrain future growth rates of this species. A metabolic index (ϕ), representing the ratio of O2 supply to demand at various temperatures and oxygen concentrations, was estimated for exploited and protected populations of C. laticeps and used to predict future distribution responses. There was no difference in the laboratory calibrations of ϕ between populations, and all data was subsequently combined into a single piecewise (12 °C) calibrated ϕ model. To predict the distribution of C. laticeps, ϕ was projected across a high-resolution ocean model of the South African coastal zone, and a species distribution model implemented using the random forest algorithm and C. laticeps occurrence points. The future distribution of C. laticeps was estimated by predicting trained models across ocean model projections up to 2100. The best predictor of C. laticeps’ current distribution was minimum monthly ϕ and future predictions indicated only a slight range contraction on either edge of C. laticeps’ distribution by 2100. In order to provide policy makers, currently developing climate change management frameworks for South Africa’s ocean, with a usable output, the results of all research chapters were combined into a marine spatial model. The spatial model identified areas where C. laticeps is predicted to be resilient to climate change in terms of physiology, growth and distribution responses, which can then be prioritised for adaptation measures, such as spatial protection from exploitation. While these results are specific to C. laticeps, the methodology developed to identify areas of climate resilience has broad applications across taxa. From a global perspective, perhaps the most salient points to consider from this case study are the evidence of selective exploitation on physiological traits and the importance of environmental variability, rather than long-term mean climate changes, in affecting organism performance. These ideas are congruent with the current paradigm shift in how we think of the ocean, selective fisheries, and how they relate to organism climate resilience.
- Full Text:
- Authors: Dames, Vivienne Abigail
- Date: 2021
- Subjects: iSimangaliso Wetland Park (South Africa) -- Management , Reef fishes -- South Africa -- KwaZulu-Natal , Baited remote underwater stereo-video systems (stereo-BRUVs) , Marine parks and reserves -- Monitoring -- South Africa -- KwaZulu-Natal , Fish populations -- Measurement
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171150 , vital:42024
- Description: The persistence of harvested fish populations in the Anthropocene will be determined, above all, by how they respond to the interacting effects of climate change and fisheries exploitation. Predicting how populations will respond to both these threats is essential for any adaptive and sustainable management strategy. The response of fish populations to climate change is underpinned by physiological rates and tolerances, and emerging evidence suggests there may be physiological-based selection in capture fisheries. By quantifying important physiological rates of a model species, the endemic seabream, Chrysoblephus laticeps, across ecologically relevant thermal gradients and from populations subjected to varying intensities of commercial exploitation, this thesis aimed to 1) provide the first physiologically grounded climate resilience assessment for a South African linefish species, and 2) elucidate whether exploitation can drive populations to less physiologically resilient states in response to climate change. To identify physiologically limiting sea temperatures and to determine if exploitation alters physiological trait distributions, an intermittent flow respirometry experiment was used to test the metabolic response of spatially protected and exploited populations of C. laticeps to acute thermal variability. Exploited populations showed reduced metabolic phenotype diversity, fewer high-performance aerobic scope phenotypes, and a significantly lower aerobic scope curve across all test temperatures. Although both populations maintained a relatively high aerobic scope across a wide thermal range, their metabolic rates were compromised when extreme cold events were simulated (8 °C), suggesting that predicted future increases in upwelling frequency and intensity may be the primary limiting factor in a more thermally variable future ocean. The increment widths of annuli in the otoliths of C. laticeps from contemporary and historic collections were measured, as a proxy for the annual growth rate of exploited and protected populations. Hierarchical mixed models were used to partition growth variation within and among individuals and ascribe growth to intrinsic and extrinsic effects. The best model for the protected population indicated that the growth response of C. laticeps was poorer during years characterised by a high cumulative upwelling intensity, and better during years characterised by higher mean autumn sea surface temperatures. The exploited population growth chronology was too short to identify an extrinsic growth driver. The growth results again highlight the role of thermal variability in modulating the response of C. laticeps to its ambient environment and indicate that the predicted increases in upwelling frequency and intensity may constrain future growth rates of this species. A metabolic index (ϕ), representing the ratio of O2 supply to demand at various temperatures and oxygen concentrations, was estimated for exploited and protected populations of C. laticeps and used to predict future distribution responses. There was no difference in the laboratory calibrations of ϕ between populations, and all data was subsequently combined into a single piecewise (12 °C) calibrated ϕ model. To predict the distribution of C. laticeps, ϕ was projected across a high-resolution ocean model of the South African coastal zone, and a species distribution model implemented using the random forest algorithm and C. laticeps occurrence points. The future distribution of C. laticeps was estimated by predicting trained models across ocean model projections up to 2100. The best predictor of C. laticeps’ current distribution was minimum monthly ϕ and future predictions indicated only a slight range contraction on either edge of C. laticeps’ distribution by 2100. In order to provide policy makers, currently developing climate change management frameworks for South Africa’s ocean, with a usable output, the results of all research chapters were combined into a marine spatial model. The spatial model identified areas where C. laticeps is predicted to be resilient to climate change in terms of physiology, growth and distribution responses, which can then be prioritised for adaptation measures, such as spatial protection from exploitation. While these results are specific to C. laticeps, the methodology developed to identify areas of climate resilience has broad applications across taxa. From a global perspective, perhaps the most salient points to consider from this case study are the evidence of selective exploitation on physiological traits and the importance of environmental variability, rather than long-term mean climate changes, in affecting organism performance. These ideas are congruent with the current paradigm shift in how we think of the ocean, selective fisheries, and how they relate to organism climate resilience.
- Full Text:
The invasion ecology of Pontederia cordata L. (Pontederiaceae) in South Africa
- Authors: Wansell, Sage Nora-Lee
- Date: 2021
- Subjects: Plant invsions -- South AFrica , Invasive plants -- Ecology -- South Africa , Pontederiaceae -- South AFrica
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172433 , vital:42200
- Description: Pontederia cordata L. (Pontederiaceae) is a tristylous invasive macrophyte – originating from North and South America – that has caused detrimental environmental, agricultural and socio-economic impacts in South Africa (SA). This novel study investigates the invasive ecology of P. cordata in SA by determining population genetics, pollination ecology and floral traits. Preliminary field surveys suggest that only one of three tristylous forms of P. cordata is invading SA and no seeds have been observed in any invasive populations. This study therefore determined the population genetics, mode of spread of P. cordata in SA and possible reasons for the lack of seed production, as well as providing suggestions for future control and management strategies. Inter Simple Sequence Repeats of leaf samples from invasive populations in SA and the native range of the United States of America (USA) were performed to determine the population genetics of P. cordata. The clarification of population structure of an alien invasive plant can provide insight into founder effects, introduction events and modes of spread and is important for the development of management plans such as biological control. Results from the genetic analyses indicated that P. cordata populations have low genetic diversity within and amongst invasive populations in comparison to native populations. This suggests that high gene flow and sexual reproduction is not present in invasive populations, and that only a single or very few introductory events have occurred in SA. Furthermore, invasive P. cordata populations shared the highest genetic similarity with native samples from Belle Haven, Virginia, USA, and thus further sampling and future genetic surveys should be conducted in this area to identify source populations to survey for potential biological control agents. Following these findings, I investigated whether sexual reproduction and seed production is absent from invasive P. cordata populations in SA as speculated. Floral traits from populations throughout all the invaded provinces were measured and, along with pollen grain measurements, it was determined that only short-morphed plants are present in SA. It was speculated that the absence of native pollinators in the invasive range may be responsible for the absence of sexual reproduction. However, a pollination study confirmed the presence of generalist insect pollinators. Thereafter, artificial pollination experiments on 8 865 flowers were conducted to determine whether an incompatibility system was present which prevented seed production. No seeds were produced and it was concluded that illegitimate pollination of the short-morphed plants prevented seed production and rhizomes are responsible for the invasion of P. cordata throughout SA. The implications of these findings and possible management strategies such as biological control is discussed in Chapter 4. These findings suggest that control programmes should target the plants rhizomes to prevent and reduce spread. Preventing the introduction of medium- and long-morphed plants into SA is crucial to prevent P. cordata from producing seeds and intensifying invasion further through both asexual and sexual spread.
- Full Text:
- Authors: Wansell, Sage Nora-Lee
- Date: 2021
- Subjects: Plant invsions -- South AFrica , Invasive plants -- Ecology -- South Africa , Pontederiaceae -- South AFrica
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172433 , vital:42200
- Description: Pontederia cordata L. (Pontederiaceae) is a tristylous invasive macrophyte – originating from North and South America – that has caused detrimental environmental, agricultural and socio-economic impacts in South Africa (SA). This novel study investigates the invasive ecology of P. cordata in SA by determining population genetics, pollination ecology and floral traits. Preliminary field surveys suggest that only one of three tristylous forms of P. cordata is invading SA and no seeds have been observed in any invasive populations. This study therefore determined the population genetics, mode of spread of P. cordata in SA and possible reasons for the lack of seed production, as well as providing suggestions for future control and management strategies. Inter Simple Sequence Repeats of leaf samples from invasive populations in SA and the native range of the United States of America (USA) were performed to determine the population genetics of P. cordata. The clarification of population structure of an alien invasive plant can provide insight into founder effects, introduction events and modes of spread and is important for the development of management plans such as biological control. Results from the genetic analyses indicated that P. cordata populations have low genetic diversity within and amongst invasive populations in comparison to native populations. This suggests that high gene flow and sexual reproduction is not present in invasive populations, and that only a single or very few introductory events have occurred in SA. Furthermore, invasive P. cordata populations shared the highest genetic similarity with native samples from Belle Haven, Virginia, USA, and thus further sampling and future genetic surveys should be conducted in this area to identify source populations to survey for potential biological control agents. Following these findings, I investigated whether sexual reproduction and seed production is absent from invasive P. cordata populations in SA as speculated. Floral traits from populations throughout all the invaded provinces were measured and, along with pollen grain measurements, it was determined that only short-morphed plants are present in SA. It was speculated that the absence of native pollinators in the invasive range may be responsible for the absence of sexual reproduction. However, a pollination study confirmed the presence of generalist insect pollinators. Thereafter, artificial pollination experiments on 8 865 flowers were conducted to determine whether an incompatibility system was present which prevented seed production. No seeds were produced and it was concluded that illegitimate pollination of the short-morphed plants prevented seed production and rhizomes are responsible for the invasion of P. cordata throughout SA. The implications of these findings and possible management strategies such as biological control is discussed in Chapter 4. These findings suggest that control programmes should target the plants rhizomes to prevent and reduce spread. Preventing the introduction of medium- and long-morphed plants into SA is crucial to prevent P. cordata from producing seeds and intensifying invasion further through both asexual and sexual spread.
- Full Text:
Towards the development of a pro-environmental strategy for improving catch-and-release behaviour in recreational fisheries – a case study on a competitive South African angling body
- Authors: Mannheim, Samantha L
- Date: 2021
- Subjects: Fishing -- Environmental aspects -- South Africa , Fishing -- South Africa , Fishers -- Attitudes -- South Africa , Fishers -- Attitudes -- South Africa -- Cast studies , Fishes -- Conservation -- South Africa , Rock and Surf Super Pro League , Southern African Fisheries Ecology Research Lab
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171862 , vital:42133
- Description: Catch-and-release (C&R) is becoming increasingly popular in recreational fisheries with the potential to contribute towards conserving the oceans limited fish stocks. Several studies have highlighted high rates of mortality and many sub-lethal effects which ultimately have a negative impact on fish population viability. With poorly developed handling practices, the fish that are released suffer the consequences of physical and physiological stress and do not always survive, thus making the ethics of C&R fishing questionable. Many studies have contributed to our understanding of the factors that influence the fate of fish released by anglers. Despite this, few interventions have been able to improve angler C&R behaviour. Pro-environmental behavioural strategies however hold some potential for improving angler C&R behaviour. To test their potential, we partnered with the South African Rock and Surf Super Pro League (RASSPL Africa), the biggest exclusively C&R competitive shore-based angling league in South Africa. The first two years (2013 and 2014) of the partnership were purely focused on building trust and relationships and making observations on angler behaviour. In 2015, we collected baseline data on angler behaviour and fish health during the RASSPL national fishing competition. This was followed by comparable data collection at the following two national competitions in 2016 and 2017 after the introduction of a combination of pro- environmental behaviour interventions, including rule changes, improving angler knowledge, behavioural modelling, rewards, penalties and feedback to improve C&R behaviour. There were significant improvements in angler behaviour, including a decline in total air exposure from 101.93s ± 64.34 in 2015 to 77.37s ± 60.52 in 2017 (F(2,618) = 9.27, P < 0.01), and the time taken for an angler to place their fish into a bucket declined from 105.86s ± 69.47 in 2015 to 23.05s ± 24.13 in 2017 (F(2,556) = 158.71, P < 0.01). There were also improvements in the health of the fish, with a decline in the blood lactate concentration and mean reflex action mortality predictor (RAMP’s) scores for the dominant species, Diplodus capensis (lactate – 9.46 ± 3.80 mmol.l-1 in 2015 and 6.69 ± 2.99 mmol.l-1 in 2017, RAMP – 0.28 ± 0.22 in 2015 and 0.19 ± 0.17 in 2017), and Haploblapharus fuscus (lactate – 4.25 ± 1.89 mmol.l-1 in 2015 and 1.76 ± 0.78 mmol.l-1in 2017, RAMP – 0.15 ± 0.18 in 2015 and 0 ± 0 in 2017). In 2018, surveys were conducted to gain insight into angler demographics and external (social, economic, cultural and institutional) and internal factors (knowledge and awareness, motivations, attitudes and perceptions) associated with the RASSPL anglers. Surveys were also designed to assist in identifying what components were key drivers behind the angler’s behavioural changes. The demographic characteristics of RASSPL anglers were not dissimilar from the general recreational angling public in South Africa, suggesting that this kind of intervention may have potential at a broader scale. In terms of the drivers of behavioural change, the surveys revealed that 68% of respondents strongly agreed that the structural rule changes contributed to their improved behaviour. This was followed by the educational presentations (66% of the respondents) and modelling / demonstrative videos (59% of the respondents). The conservation prizes were considered less effective, with only 27% of anglers strongly agreeing that this intervention improved their C&R behaviour. Overall this study has demonstrated that it is possible to improve the C&R behaviour of anglers in a competitive setting, with the most effective component of the intervention being the use of rule changes (structural approach). These findings suggest that proenvironmental strategies hold potential for improving the C&R behaviour of anglers and the health of released fishes. It is suggested that interventions to improve C&R behaviour should aim to develop long-term relationships, and implement a broad range of well communicated strategies based on reliable data and sound rationality. Key words: marine shore-based fisheries; community engagement; pro- environmental behaviour; behavioural intervention.
- Full Text:
- Authors: Mannheim, Samantha L
- Date: 2021
- Subjects: Fishing -- Environmental aspects -- South Africa , Fishing -- South Africa , Fishers -- Attitudes -- South Africa , Fishers -- Attitudes -- South Africa -- Cast studies , Fishes -- Conservation -- South Africa , Rock and Surf Super Pro League , Southern African Fisheries Ecology Research Lab
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/171862 , vital:42133
- Description: Catch-and-release (C&R) is becoming increasingly popular in recreational fisheries with the potential to contribute towards conserving the oceans limited fish stocks. Several studies have highlighted high rates of mortality and many sub-lethal effects which ultimately have a negative impact on fish population viability. With poorly developed handling practices, the fish that are released suffer the consequences of physical and physiological stress and do not always survive, thus making the ethics of C&R fishing questionable. Many studies have contributed to our understanding of the factors that influence the fate of fish released by anglers. Despite this, few interventions have been able to improve angler C&R behaviour. Pro-environmental behavioural strategies however hold some potential for improving angler C&R behaviour. To test their potential, we partnered with the South African Rock and Surf Super Pro League (RASSPL Africa), the biggest exclusively C&R competitive shore-based angling league in South Africa. The first two years (2013 and 2014) of the partnership were purely focused on building trust and relationships and making observations on angler behaviour. In 2015, we collected baseline data on angler behaviour and fish health during the RASSPL national fishing competition. This was followed by comparable data collection at the following two national competitions in 2016 and 2017 after the introduction of a combination of pro- environmental behaviour interventions, including rule changes, improving angler knowledge, behavioural modelling, rewards, penalties and feedback to improve C&R behaviour. There were significant improvements in angler behaviour, including a decline in total air exposure from 101.93s ± 64.34 in 2015 to 77.37s ± 60.52 in 2017 (F(2,618) = 9.27, P < 0.01), and the time taken for an angler to place their fish into a bucket declined from 105.86s ± 69.47 in 2015 to 23.05s ± 24.13 in 2017 (F(2,556) = 158.71, P < 0.01). There were also improvements in the health of the fish, with a decline in the blood lactate concentration and mean reflex action mortality predictor (RAMP’s) scores for the dominant species, Diplodus capensis (lactate – 9.46 ± 3.80 mmol.l-1 in 2015 and 6.69 ± 2.99 mmol.l-1 in 2017, RAMP – 0.28 ± 0.22 in 2015 and 0.19 ± 0.17 in 2017), and Haploblapharus fuscus (lactate – 4.25 ± 1.89 mmol.l-1 in 2015 and 1.76 ± 0.78 mmol.l-1in 2017, RAMP – 0.15 ± 0.18 in 2015 and 0 ± 0 in 2017). In 2018, surveys were conducted to gain insight into angler demographics and external (social, economic, cultural and institutional) and internal factors (knowledge and awareness, motivations, attitudes and perceptions) associated with the RASSPL anglers. Surveys were also designed to assist in identifying what components were key drivers behind the angler’s behavioural changes. The demographic characteristics of RASSPL anglers were not dissimilar from the general recreational angling public in South Africa, suggesting that this kind of intervention may have potential at a broader scale. In terms of the drivers of behavioural change, the surveys revealed that 68% of respondents strongly agreed that the structural rule changes contributed to their improved behaviour. This was followed by the educational presentations (66% of the respondents) and modelling / demonstrative videos (59% of the respondents). The conservation prizes were considered less effective, with only 27% of anglers strongly agreeing that this intervention improved their C&R behaviour. Overall this study has demonstrated that it is possible to improve the C&R behaviour of anglers in a competitive setting, with the most effective component of the intervention being the use of rule changes (structural approach). These findings suggest that proenvironmental strategies hold potential for improving the C&R behaviour of anglers and the health of released fishes. It is suggested that interventions to improve C&R behaviour should aim to develop long-term relationships, and implement a broad range of well communicated strategies based on reliable data and sound rationality. Key words: marine shore-based fisheries; community engagement; pro- environmental behaviour; behavioural intervention.
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A 150 MHz all sky survey with the Precision Array to Probe the Epoch of Reionization
- Authors: Chege, James Kariuki
- Date: 2020
- Subjects: Epoch of reionization -- Research , Astronomy -- Observations , Radio interferometers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117733 , vital:34556
- Description: The Precision Array to Probe the Epoch of Reionization (PAPER) was built to measure the redshifted 21 cm line of hydrogen from cosmic reionization. Such low frequency observations promise to be the best means of understanding the cosmic dawn; when the first galaxies in the universe formed, and also the Epoch of Reionization; when the intergalactic medium changed from neutral to ionized. The major challenges to these observations is the presence of astrophysical foregrounds that are much brighter than the cosmological signal. Here, I present an all-sky survey at 150 MHz obtained from the analysis of 300 hours of PAPER observations. Particular focus is given to the calibration and imaging techniques that need to deal with the wide field of view of a non-tracking instrument. The survey covers ~ 7000 square degrees of the southern sky. From a sky area of 4400 square degrees out of the total survey area, I extract a catalogue of sources brighter than 4 Jy whose accuracy was tested against the published GLEAM catalogue, leading to a fractional difference rms better than 20%. The catalogue provides an all-sky accurate model of the extragalactic foreground to be used for the calibration of future Epoch of Reionization observations and to be subtracted from the PAPER observations themselves in order to mitigate the foreground contamination.
- Full Text:
- Authors: Chege, James Kariuki
- Date: 2020
- Subjects: Epoch of reionization -- Research , Astronomy -- Observations , Radio interferometers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117733 , vital:34556
- Description: The Precision Array to Probe the Epoch of Reionization (PAPER) was built to measure the redshifted 21 cm line of hydrogen from cosmic reionization. Such low frequency observations promise to be the best means of understanding the cosmic dawn; when the first galaxies in the universe formed, and also the Epoch of Reionization; when the intergalactic medium changed from neutral to ionized. The major challenges to these observations is the presence of astrophysical foregrounds that are much brighter than the cosmological signal. Here, I present an all-sky survey at 150 MHz obtained from the analysis of 300 hours of PAPER observations. Particular focus is given to the calibration and imaging techniques that need to deal with the wide field of view of a non-tracking instrument. The survey covers ~ 7000 square degrees of the southern sky. From a sky area of 4400 square degrees out of the total survey area, I extract a catalogue of sources brighter than 4 Jy whose accuracy was tested against the published GLEAM catalogue, leading to a fractional difference rms better than 20%. The catalogue provides an all-sky accurate model of the extragalactic foreground to be used for the calibration of future Epoch of Reionization observations and to be subtracted from the PAPER observations themselves in order to mitigate the foreground contamination.
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A Bayesian approach to tilted-ring modelling of galaxies
- Authors: Maina, Eric Kamau
- Date: 2020
- Subjects: Bayesian statistical decision theory , Galaxies , Radio astronomy , TiRiFiC (Tilted Ring Fitting Code) , Neutral hydrogen , Spectroscopic data cubes , Galaxy parametrisation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145783 , vital:38466
- Description: The orbits of neutral hydrogen (H I) gas found in most disk galaxies are circular and also exhibit long-lived warps at large radii where the restoring gravitational forces of the inner disk become weak (Spekkens and Giovanelli 2006). These warps make the tilted-ring model an ideal choice for galaxy parametrisation. Analysis software utilizing the tilted-ring-model can be grouped into two and three-dimensional based software. Józsa et al. (2007b) demonstrated that three dimensional based software is better suited for galaxy parametrisation because it is affected by the effect of beam smearing only by increasing the uncertainty of parameters but not with the notorious systematic effects observed for two-dimensional fitting techniques. TiRiFiC, The Tilted Ring Fitting Code (Józsa et al. 2007b), is a software to construct parameterised models of high-resolution data cubes of rotating galaxies. It uses the tilted-ring model, and with that, a combination of some parameters such as surface brightness, position angle, rotation velocity and inclination, to describe galaxies. TiRiFiC works by directly fitting tilted-ring models to spectroscopic data cubes and hence is not affected by beam smearing or line-of-site-effects, e.g. strong warps. Because of that, the method is unavoidable as an analytic method in future Hi surveys. In the current implementation, though, there are several drawbacks. The implemented optimisers search for local solutions in parameter space only, do not quantify correlations between parameters and cannot find errors of single parameters. In theory, these drawbacks can be overcome by using Bayesian statistics, implemented in Multinest (Feroz et al. 2008), as it allows for sampling a posterior distribution irrespective of its multimodal nature resulting in parameter samples that correspond to the maximum in the posterior distribution. These parameter samples can be used as well to quantify correlations and find errors of single parameters. Since this method employs Bayesian statistics, it also allows the user to leverage any prior information they may have on parameter values.
- Full Text:
- Authors: Maina, Eric Kamau
- Date: 2020
- Subjects: Bayesian statistical decision theory , Galaxies , Radio astronomy , TiRiFiC (Tilted Ring Fitting Code) , Neutral hydrogen , Spectroscopic data cubes , Galaxy parametrisation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145783 , vital:38466
- Description: The orbits of neutral hydrogen (H I) gas found in most disk galaxies are circular and also exhibit long-lived warps at large radii where the restoring gravitational forces of the inner disk become weak (Spekkens and Giovanelli 2006). These warps make the tilted-ring model an ideal choice for galaxy parametrisation. Analysis software utilizing the tilted-ring-model can be grouped into two and three-dimensional based software. Józsa et al. (2007b) demonstrated that three dimensional based software is better suited for galaxy parametrisation because it is affected by the effect of beam smearing only by increasing the uncertainty of parameters but not with the notorious systematic effects observed for two-dimensional fitting techniques. TiRiFiC, The Tilted Ring Fitting Code (Józsa et al. 2007b), is a software to construct parameterised models of high-resolution data cubes of rotating galaxies. It uses the tilted-ring model, and with that, a combination of some parameters such as surface brightness, position angle, rotation velocity and inclination, to describe galaxies. TiRiFiC works by directly fitting tilted-ring models to spectroscopic data cubes and hence is not affected by beam smearing or line-of-site-effects, e.g. strong warps. Because of that, the method is unavoidable as an analytic method in future Hi surveys. In the current implementation, though, there are several drawbacks. The implemented optimisers search for local solutions in parameter space only, do not quantify correlations between parameters and cannot find errors of single parameters. In theory, these drawbacks can be overcome by using Bayesian statistics, implemented in Multinest (Feroz et al. 2008), as it allows for sampling a posterior distribution irrespective of its multimodal nature resulting in parameter samples that correspond to the maximum in the posterior distribution. These parameter samples can be used as well to quantify correlations and find errors of single parameters. Since this method employs Bayesian statistics, it also allows the user to leverage any prior information they may have on parameter values.
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A comparative mineralogical and geochemical study of manganese deposits in the Postmasburg Manganese Field, South Africa
- Authors: Thokoa, Mamello
- Date: 2020
- Subjects: Manganese ores -- South Africa -- Postmasburg , Geology -- South Africa -- Postmasburg
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167609 , vital:41496
- Description: The Postmasburg Manganese Field (PMF), located in the Northern Cape Province of South Africa, is host to some of the largest deposits of iron and manganese metal in the world. These deposits are restricted to a geographical area known as the Maremane Dome, an anticlinal structure defined by folded dolostones of the Campbellrand Subgroup and overlying ironformations of the Asbestos Hills Subgroup of the Neoarchaean-Palaeproterozoic Transvaal Supergroup. Manganese ores associated with the Maremane Dome have been divided into two major classes in the literature: the Wolhaarkop breccia-hosted massive ores of the Eastern Belt, as well as the shale-associated ores of the Western Belt. The Eastern Belt ores have been classed as siliceous in nature, while the Western Belt deposits are reported to be typically ferruginous. These divisions were made based on their varying bulk chemical and mineralogical compositions in conjunction with their different stratigraphic sub-settings. Presently, both deposit types are explained as variants of supergene mineralisation that would have formed through a combination of intense ancient lateritic weathering in the presence of oxygen, extreme residual enrichments in Mn (and Fe), and accumulations in karstic depressions at the expense of underlying manganiferous dolostones. This study revisits these deposits and their origins by sampling representative end-member examples of both Eastern Belt and Western Belt manganese ores in both drillcore (localities Khumani, McCarthy and Leeuwfontein), and outcrop sections (locality Bishop). In an attempt to provide new insights into the processes responsible for the genesis of these deposits, the possibility of hydrothermal influences and associated metasomatic replacement processes is explored in this thesis. This was achieved using standard petrographic and mineralogical techniques (transmitted and reflected light microscopy, XRD , SEM-EDS and EMPA), coupled with bulk-rock geochemical analysis of the same samples using a combination of XRF and LAICP- MS analyses. Combination of field observations, petrographic and mineralogical results, and geochemical data allowed for the re-assessment of the different ore types encountered in the field. Comparative considerations made between the bulk geochemistry of the different end-member ore types revealed no clear-cut compositional distinctions and therefore do not support existing classifications between siliceous (Eastern Belt) and ferruginous (Western Belt) ores. This is supported by trace and REE element data as well, when normalised against average shale. The geochemistry reflects the bulk mineralogy of the ores which is broadly comparable, whereby braunite and hematite appear to be dominant co-existing minerals in both Eastern Belt (Khumani) and Western Belt (Bishop) ore. In the case of the McCarthy locality, manganese ore is cryptomelane-rich and appears to have involved recent supergene overprint over Eastern Belt type ore, whereas the Leeuwfontein ores are far more ferruginous than at any other locality studied and therefore represent a more complex, hybrid type of oxide-rich Mn mineralisation (mainly bixbyitic) within massive hematite iron ore. In terms of gangue mineralogy, the ores share some close similarities through the omnipresence of barite, and the abundance of alkalirich silicate minerals. Eastern Belt ores contain abundant albite and serandite whereas the main alkali-rich phase in Western Belt ores is the mineral ephesite. In both cases, Na contents are therefore high at several wt% levels registered in selected samples. The afore-mentioned alkali enrichments have been variously reported for both these deposit types. The occurrence of high alkalis cannot be explained through classic residual or aqueous supergene systems of ore formation, as proposed in prevailing genetic models in the literature. Together with the detection of halogens such as F and Br through SEM-EDS analyses of ore from both belts, the alkali enrichments suggest possible hydrothermal processes of ore formation involving circulation of metalliferous sodic brines. Selected textural evidence from samples from both ore belts lends support to fluid-related models and allow the proposal for a common hydrothermal-replacement model to have been responsible for ore formation across the broader Maremane Dome region.
- Full Text:
- Authors: Thokoa, Mamello
- Date: 2020
- Subjects: Manganese ores -- South Africa -- Postmasburg , Geology -- South Africa -- Postmasburg
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167609 , vital:41496
- Description: The Postmasburg Manganese Field (PMF), located in the Northern Cape Province of South Africa, is host to some of the largest deposits of iron and manganese metal in the world. These deposits are restricted to a geographical area known as the Maremane Dome, an anticlinal structure defined by folded dolostones of the Campbellrand Subgroup and overlying ironformations of the Asbestos Hills Subgroup of the Neoarchaean-Palaeproterozoic Transvaal Supergroup. Manganese ores associated with the Maremane Dome have been divided into two major classes in the literature: the Wolhaarkop breccia-hosted massive ores of the Eastern Belt, as well as the shale-associated ores of the Western Belt. The Eastern Belt ores have been classed as siliceous in nature, while the Western Belt deposits are reported to be typically ferruginous. These divisions were made based on their varying bulk chemical and mineralogical compositions in conjunction with their different stratigraphic sub-settings. Presently, both deposit types are explained as variants of supergene mineralisation that would have formed through a combination of intense ancient lateritic weathering in the presence of oxygen, extreme residual enrichments in Mn (and Fe), and accumulations in karstic depressions at the expense of underlying manganiferous dolostones. This study revisits these deposits and their origins by sampling representative end-member examples of both Eastern Belt and Western Belt manganese ores in both drillcore (localities Khumani, McCarthy and Leeuwfontein), and outcrop sections (locality Bishop). In an attempt to provide new insights into the processes responsible for the genesis of these deposits, the possibility of hydrothermal influences and associated metasomatic replacement processes is explored in this thesis. This was achieved using standard petrographic and mineralogical techniques (transmitted and reflected light microscopy, XRD , SEM-EDS and EMPA), coupled with bulk-rock geochemical analysis of the same samples using a combination of XRF and LAICP- MS analyses. Combination of field observations, petrographic and mineralogical results, and geochemical data allowed for the re-assessment of the different ore types encountered in the field. Comparative considerations made between the bulk geochemistry of the different end-member ore types revealed no clear-cut compositional distinctions and therefore do not support existing classifications between siliceous (Eastern Belt) and ferruginous (Western Belt) ores. This is supported by trace and REE element data as well, when normalised against average shale. The geochemistry reflects the bulk mineralogy of the ores which is broadly comparable, whereby braunite and hematite appear to be dominant co-existing minerals in both Eastern Belt (Khumani) and Western Belt (Bishop) ore. In the case of the McCarthy locality, manganese ore is cryptomelane-rich and appears to have involved recent supergene overprint over Eastern Belt type ore, whereas the Leeuwfontein ores are far more ferruginous than at any other locality studied and therefore represent a more complex, hybrid type of oxide-rich Mn mineralisation (mainly bixbyitic) within massive hematite iron ore. In terms of gangue mineralogy, the ores share some close similarities through the omnipresence of barite, and the abundance of alkalirich silicate minerals. Eastern Belt ores contain abundant albite and serandite whereas the main alkali-rich phase in Western Belt ores is the mineral ephesite. In both cases, Na contents are therefore high at several wt% levels registered in selected samples. The afore-mentioned alkali enrichments have been variously reported for both these deposit types. The occurrence of high alkalis cannot be explained through classic residual or aqueous supergene systems of ore formation, as proposed in prevailing genetic models in the literature. Together with the detection of halogens such as F and Br through SEM-EDS analyses of ore from both belts, the alkali enrichments suggest possible hydrothermal processes of ore formation involving circulation of metalliferous sodic brines. Selected textural evidence from samples from both ore belts lends support to fluid-related models and allow the proposal for a common hydrothermal-replacement model to have been responsible for ore formation across the broader Maremane Dome region.
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A comparison between the responsiveness of selected physiological and subjective mental workload indicators during real-world driving scenarios
- Authors: Schmidtke, Nadia-Jasmine
- Date: 2020
- Subjects: Automobile driving -- Physiological aspects , Automobile driving -- Psychological aspects , Automobile drivers -- Health and hygiene , Mental fatigue , Mental work -- Case studies
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/148115 , vital:38711
- Description: Sub-optimal levels of mental workload in automobile drivers is a risk factor for road accidents. However, mental workload as a construct cannot be directly measured. Common indicators of mental workload include heart rate frequency and variability, eye motion and subjective rating tools. Namely, the National Aeronautics and Space Administration Task Load Index (NASA-TLX), its modified, unweighted version called the Raw-TLX, and the Rating Scale of Mental Effort (RSME). Comparisons between the suitability and responsiveness of these mental workload indicators have been almost exclusively examined in driving simulators. However, real-world driving research is important as even high-fidelity simulators cannot capture the complexity of driving scenarios. Hence, this research aimed to compare the suitability and responsiveness of these mental workload indicators in response to real-world driving scenarios. Six participants drove along a set route for an hour while wearing a heart rate monitor and eye tracker. A dashcam was used to capture footage of the different driving scenarios encountered. The set route comprised of driving through the industrial, residential, provincial main road and Rhodes University campus areas. RSME scores were taken during brief stops after driving though each zone. The NASA-TLX questionnaire was administered on completion of the drive and analysed later as the modified Raw-TLX version. The data collected in response to the encountered driving scenarios were sorted into three meta-groupings. (1) Data was segmented according to the different areas that participants drove through. This was termed Area Events and were long duration scenarios of between five and thirty minutes. These driving scenarios were further segmented into two meta-groups with short duration driving scenarios (< 90 seconds). (2) The Common Events meta-group consisted of driving scenarios that were encountered by all participants. These were scenarios were anticipated by drivers. (3) The All Events meta-group was grouped according to all the driving scenarios that were encountered by participants. It consisted of both anticipated and unanticipated driving scenarios of short durations. Data were further analysed using a method of systematically selecting a threshold value for each mental workload indicator. Responses to driving scenarios which surpassed the threshold were considered indicative of an increase in mental workload. The total frequency of higher mental workload events was used as a determiner responsiveness (or ‘sensitivity’) for each mental workload indicator. Mental workload indicators were evaluated for their responsiveness and suitability for assessing mental workload. Results found blink frequency to be a responsive mental workload indicator for all categories of driving scenarios. Blink frequency and duration were the most responsive short duration mental workload indicators. Furthermore, the indicators were able to distinguish between higher and lower mental workload driving scenarios. However, blink parameters are also sensitive to driver fatigue and drowsiness. Further research on distinguishing mental workload from that of fatigue in response to real-world driving was recommended. Pupil diameter, fixation duration, saccade saccade duration and saccade amplitude were found to be responsive short duration mental workload indicators. However, these measures were not determined to be suitable for real-world driving applications. Pupil diameter was confounded by changing illumination levels. Fixation and saccade responses were confounded by the driving task itself as gaze could not be accounted for. For long duration driving scenarios heart rate frequency, heart rate variability: high-frequency power, blink frequency and RSME were found to be responsive and suitable MWL indicators. The Raw-TLX results could not be assessed for responsiveness as it was administered once. However, it was confirmed as a suitable cumulative mental workload indicator in the application of real-world driving. The moderate levels of workload reported by participants agreed with the experimental protocol that prevented inducing sub-optimal mental workload. Blink frequency shows promise as a responsive and suitable mental workload indicator for different types of driving scenarios. More research is needed regarding the assessment of mental workload during short durations using blink frequency and blink duration. For driving durations between five and thirty minutes long, further research into heart rate frequency, heart rate variability: high frequency power, and the RSME was recommended.
- Full Text:
- Authors: Schmidtke, Nadia-Jasmine
- Date: 2020
- Subjects: Automobile driving -- Physiological aspects , Automobile driving -- Psychological aspects , Automobile drivers -- Health and hygiene , Mental fatigue , Mental work -- Case studies
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/148115 , vital:38711
- Description: Sub-optimal levels of mental workload in automobile drivers is a risk factor for road accidents. However, mental workload as a construct cannot be directly measured. Common indicators of mental workload include heart rate frequency and variability, eye motion and subjective rating tools. Namely, the National Aeronautics and Space Administration Task Load Index (NASA-TLX), its modified, unweighted version called the Raw-TLX, and the Rating Scale of Mental Effort (RSME). Comparisons between the suitability and responsiveness of these mental workload indicators have been almost exclusively examined in driving simulators. However, real-world driving research is important as even high-fidelity simulators cannot capture the complexity of driving scenarios. Hence, this research aimed to compare the suitability and responsiveness of these mental workload indicators in response to real-world driving scenarios. Six participants drove along a set route for an hour while wearing a heart rate monitor and eye tracker. A dashcam was used to capture footage of the different driving scenarios encountered. The set route comprised of driving through the industrial, residential, provincial main road and Rhodes University campus areas. RSME scores were taken during brief stops after driving though each zone. The NASA-TLX questionnaire was administered on completion of the drive and analysed later as the modified Raw-TLX version. The data collected in response to the encountered driving scenarios were sorted into three meta-groupings. (1) Data was segmented according to the different areas that participants drove through. This was termed Area Events and were long duration scenarios of between five and thirty minutes. These driving scenarios were further segmented into two meta-groups with short duration driving scenarios (< 90 seconds). (2) The Common Events meta-group consisted of driving scenarios that were encountered by all participants. These were scenarios were anticipated by drivers. (3) The All Events meta-group was grouped according to all the driving scenarios that were encountered by participants. It consisted of both anticipated and unanticipated driving scenarios of short durations. Data were further analysed using a method of systematically selecting a threshold value for each mental workload indicator. Responses to driving scenarios which surpassed the threshold were considered indicative of an increase in mental workload. The total frequency of higher mental workload events was used as a determiner responsiveness (or ‘sensitivity’) for each mental workload indicator. Mental workload indicators were evaluated for their responsiveness and suitability for assessing mental workload. Results found blink frequency to be a responsive mental workload indicator for all categories of driving scenarios. Blink frequency and duration were the most responsive short duration mental workload indicators. Furthermore, the indicators were able to distinguish between higher and lower mental workload driving scenarios. However, blink parameters are also sensitive to driver fatigue and drowsiness. Further research on distinguishing mental workload from that of fatigue in response to real-world driving was recommended. Pupil diameter, fixation duration, saccade saccade duration and saccade amplitude were found to be responsive short duration mental workload indicators. However, these measures were not determined to be suitable for real-world driving applications. Pupil diameter was confounded by changing illumination levels. Fixation and saccade responses were confounded by the driving task itself as gaze could not be accounted for. For long duration driving scenarios heart rate frequency, heart rate variability: high-frequency power, blink frequency and RSME were found to be responsive and suitable MWL indicators. The Raw-TLX results could not be assessed for responsiveness as it was administered once. However, it was confirmed as a suitable cumulative mental workload indicator in the application of real-world driving. The moderate levels of workload reported by participants agreed with the experimental protocol that prevented inducing sub-optimal mental workload. Blink frequency shows promise as a responsive and suitable mental workload indicator for different types of driving scenarios. More research is needed regarding the assessment of mental workload during short durations using blink frequency and blink duration. For driving durations between five and thirty minutes long, further research into heart rate frequency, heart rate variability: high frequency power, and the RSME was recommended.
- Full Text: