Joint Modelling Inference for Longitudinal and Time To Event Data with Application to Biomarkers in Medical and Clinical Studies
- Authors: Azeez, Adeboye Nurudeen
- Date: 2020
- Subjects: Biochemical markers Bayesian statistical decision theory
- Language: English
- Type: Thesis , Doctoral , PhD (Biostatistics)
- Identifier: http://hdl.handle.net/10353/18476 , vital:42543
- Description: In the past couple of decades, longitudinal and survival data analysis have emerged as important and popular concepts of biostatistics and statistics for disease modelling. In recent years, these two statistics concepts have been combined to develop a joint model for longitudinal and survival data analysis. The Joint model is a simultaneous modelling application of longitudinal and survival data while taking into account a possible association between them. In this thesis, three sub-topics (Conditional score approach, estimating equation approach, and modified Cholesky decomposition approach) are utilised to model the association if the independence assumption is violated. Using the conditional score approach, the study investigated the association between longitudinal covariates and the time-to-event process to examine the within-subject measurement error that could influence estimation when the assumption of normality and mutual independence is violated. Given the assumption violation, I proposed an estimating equation approach based on the conditional score to relax parametric distributional assumptions for repeated measures of random effects. I jointly modelled the time-dependent biomarkers and event times using the Cox model with intermittent time-dependent covariates measure, in which the longitudinal model was used to characterize the biomarker underlying (unobservable) trajectory and incorporated as a latent time-dependent covariate in the survival model to predict failure times. Estimates of the parameters were obtained by a restricted maximum likelihood estimate (REML). A modified Cholesky decomposition method was used to capture the within-subject covariance for a positive definite and symmetric matrix, with the assumption that the observed data from different subjects are independent. I illustrated the proposed method by a real data set from a lung study and simulation. An extension to the joint model of longitudinal-survival data was also proposed, in which the longitudinal data has a cumulative and weighted effect on the hazard event function. Using a Bayesian parametric method, I proposed a skewed weighted probability density function to estimate the parameters. The weighted cumulative effect used enabled different longitudinal profiles to be incorporated over time in calculating the hazard ratio between the subjects. The proposed functions provide greater flexibility for modelling the association structure of different longitudinal and survival sub-model. The focus was on the association between the biomarker (serum creatinine, sCr) and the development of end-stage renal disease (ESRD). Since the effect of sCr biomarker is anticipated to be a cumulative effect, with the development of sCr biomarker over time leading to progressively higher damage of the kidney. The approach was applied a simulation for validation of the proposed method
- Full Text:
- Date Issued: 2020
- Authors: Azeez, Adeboye Nurudeen
- Date: 2020
- Subjects: Biochemical markers Bayesian statistical decision theory
- Language: English
- Type: Thesis , Doctoral , PhD (Biostatistics)
- Identifier: http://hdl.handle.net/10353/18476 , vital:42543
- Description: In the past couple of decades, longitudinal and survival data analysis have emerged as important and popular concepts of biostatistics and statistics for disease modelling. In recent years, these two statistics concepts have been combined to develop a joint model for longitudinal and survival data analysis. The Joint model is a simultaneous modelling application of longitudinal and survival data while taking into account a possible association between them. In this thesis, three sub-topics (Conditional score approach, estimating equation approach, and modified Cholesky decomposition approach) are utilised to model the association if the independence assumption is violated. Using the conditional score approach, the study investigated the association between longitudinal covariates and the time-to-event process to examine the within-subject measurement error that could influence estimation when the assumption of normality and mutual independence is violated. Given the assumption violation, I proposed an estimating equation approach based on the conditional score to relax parametric distributional assumptions for repeated measures of random effects. I jointly modelled the time-dependent biomarkers and event times using the Cox model with intermittent time-dependent covariates measure, in which the longitudinal model was used to characterize the biomarker underlying (unobservable) trajectory and incorporated as a latent time-dependent covariate in the survival model to predict failure times. Estimates of the parameters were obtained by a restricted maximum likelihood estimate (REML). A modified Cholesky decomposition method was used to capture the within-subject covariance for a positive definite and symmetric matrix, with the assumption that the observed data from different subjects are independent. I illustrated the proposed method by a real data set from a lung study and simulation. An extension to the joint model of longitudinal-survival data was also proposed, in which the longitudinal data has a cumulative and weighted effect on the hazard event function. Using a Bayesian parametric method, I proposed a skewed weighted probability density function to estimate the parameters. The weighted cumulative effect used enabled different longitudinal profiles to be incorporated over time in calculating the hazard ratio between the subjects. The proposed functions provide greater flexibility for modelling the association structure of different longitudinal and survival sub-model. The focus was on the association between the biomarker (serum creatinine, sCr) and the development of end-stage renal disease (ESRD). Since the effect of sCr biomarker is anticipated to be a cumulative effect, with the development of sCr biomarker over time leading to progressively higher damage of the kidney. The approach was applied a simulation for validation of the proposed method
- Full Text:
- Date Issued: 2020
Zoning the Southwestern Indian Ocean to mitigate impacts from ocean-based hydrocarbon exploration and production on sea turtles
- Authors: Pretorius, Dirk
- Date: 2019
- Subjects: Ocean zoning , Marine ecology -- Indian Ocean Sea turtles -- Indian Ocean Marine animals -- Ecology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43303 , vital:36787
- Description: The conflict between sea turtles and the numerous socio-economic developments in the Southwestern Indian Ocean (SWIO) are set to intensify as countries are looking to develop their ocean-based economies. The Hydrocarbon Exploration and Production (HEP) industry is of particular importance, since many of the SWIO governments view it as catalyst for development. This has raised concerns about potentially significant environmental impacts from the HEP industry, to sea turtles and their habitats, based on international examples where sea turtles have been severely negatively impacted upon, like the Deepwater Horizon spill in the Gulf of Mexico. Given that the four sea turtles species in the SWIO are listed on the IUCN Red List of threatened species, the aim of this study was to derive priority areas for sea turtles in the face of HEP, that could be used in an ocean zoning strategy for sustainable economic development of HEP in the SWIO region. To achieve this, the study spatially represented the main life-history stages of sea turtles, i.e. the breeding, migrating and foraging areas of Caretta caretta (loggerhead turtles), Dermochelys coriacea (leatherback turtles), Chelonia mydas (green turtles) and Eretmochelys imbricata (hawksbill turtles), within a telemetry derived distribution for each species. This spatial representation was used to quantify the extent of Marine Protected Areas (MPAs) conserving sea turtles in the SWIO, which revealed that sea turtle breeding areas were well represented in MPAs, including C. caretta (~40 %), C. mydas (~53 %), E. imbricata (~59 %) and D. coriacea (~22 %), the latter being least protected by MPAs during breeding, possibly due to a far greater extent of their internesting areas than the other three species. MPA coverage of breeding areas could be positively correlated to the increasing population trends of C. caretta and C. mydas in the SWIO, and therefore the assumption was made that increasing population trends of sea turtles are in part related to MPA protection of their breeding areas. In addition, the potential impacts on sea turtles from existing and proposed HEP developments were assessed and mapped by using a novel, species-specific rating index. The results revealed the extensive nature of potential water pollution impacts on sea turtles, constituting 16 of the top 28 most significant impacts from HEP on sea turtles. Other significant impacts on sea turtles associated with the HEP industry, included habitat destruction, light pollution and noise pollution. Importantly, this study found that ~70 % of all potential HEP impacts (irrespective of significance) on adult nesting sea turtles could be avoided if seasonal sea turtle movement during critical life stages are included as species-specific HEP mitigation measures. The data and maps on the main life-history stages of sea turtles, and the potential cumulative impacts from the HEP industry, were used in a Systematic Conservation Planning process, to derive a concept ocean zoning. As final outcome of this study, the concept ocean zoning highlighted areas where increased protection to sea turtles, and management of the conflict between sea turtles and the HEP industry, will be required if the HEP industry is to develop in a sustainable manner in the SWIO.
- Full Text:
- Date Issued: 2019
- Authors: Pretorius, Dirk
- Date: 2019
- Subjects: Ocean zoning , Marine ecology -- Indian Ocean Sea turtles -- Indian Ocean Marine animals -- Ecology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/43303 , vital:36787
- Description: The conflict between sea turtles and the numerous socio-economic developments in the Southwestern Indian Ocean (SWIO) are set to intensify as countries are looking to develop their ocean-based economies. The Hydrocarbon Exploration and Production (HEP) industry is of particular importance, since many of the SWIO governments view it as catalyst for development. This has raised concerns about potentially significant environmental impacts from the HEP industry, to sea turtles and their habitats, based on international examples where sea turtles have been severely negatively impacted upon, like the Deepwater Horizon spill in the Gulf of Mexico. Given that the four sea turtles species in the SWIO are listed on the IUCN Red List of threatened species, the aim of this study was to derive priority areas for sea turtles in the face of HEP, that could be used in an ocean zoning strategy for sustainable economic development of HEP in the SWIO region. To achieve this, the study spatially represented the main life-history stages of sea turtles, i.e. the breeding, migrating and foraging areas of Caretta caretta (loggerhead turtles), Dermochelys coriacea (leatherback turtles), Chelonia mydas (green turtles) and Eretmochelys imbricata (hawksbill turtles), within a telemetry derived distribution for each species. This spatial representation was used to quantify the extent of Marine Protected Areas (MPAs) conserving sea turtles in the SWIO, which revealed that sea turtle breeding areas were well represented in MPAs, including C. caretta (~40 %), C. mydas (~53 %), E. imbricata (~59 %) and D. coriacea (~22 %), the latter being least protected by MPAs during breeding, possibly due to a far greater extent of their internesting areas than the other three species. MPA coverage of breeding areas could be positively correlated to the increasing population trends of C. caretta and C. mydas in the SWIO, and therefore the assumption was made that increasing population trends of sea turtles are in part related to MPA protection of their breeding areas. In addition, the potential impacts on sea turtles from existing and proposed HEP developments were assessed and mapped by using a novel, species-specific rating index. The results revealed the extensive nature of potential water pollution impacts on sea turtles, constituting 16 of the top 28 most significant impacts from HEP on sea turtles. Other significant impacts on sea turtles associated with the HEP industry, included habitat destruction, light pollution and noise pollution. Importantly, this study found that ~70 % of all potential HEP impacts (irrespective of significance) on adult nesting sea turtles could be avoided if seasonal sea turtle movement during critical life stages are included as species-specific HEP mitigation measures. The data and maps on the main life-history stages of sea turtles, and the potential cumulative impacts from the HEP industry, were used in a Systematic Conservation Planning process, to derive a concept ocean zoning. As final outcome of this study, the concept ocean zoning highlighted areas where increased protection to sea turtles, and management of the conflict between sea turtles and the HEP industry, will be required if the HEP industry is to develop in a sustainable manner in the SWIO.
- Full Text:
- Date Issued: 2019
Assessing the perceptions of academic staff towards an academic staff development programme in a selected university in the Eastern Cape province
- Authors: Mankayi, Mandisa
- Date: 2018
- Subjects: College teachers -- In-service training -- South Africa -- Eastern Cape Education, Higher -- South Africa -- Eastern Cape Universities and colleges -- Employees -- Training of. -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10353/8530 , vital:32869
- Description: Institutions of higher education offer diverse staff development programmes to all staff members as a means of improving their educational quality and standards. The current study investigated using interviews, if whether the academic staff perceived staff development as a means of skills development; what factors motivated academic staff to attend the skills development programmes offered by their organisation; and which staff development programmes are perceived to be contributing much to academic skills development in a selected university in the Eastern Cape Province in South Africa. Utilising a purposive sampling technique, the number of academic staff interviewed was 15 from five faculties. A structured interview guide was used to solicit responses from the selected participants. Questions in the interview schedule ranged from issues pertaining to their registration on the skills development programme and how their personal skills have improved due to the programme. Upon completing the interview with an audio recorder, it was then transcribed and a thematic analysis method was used. It was found that participants were not satisfied with the academic skills development programmes offered by the university. While most respondents seemed to be aware of the skills programme, many were adamant to provide conclusive evidence on the impact of the programmes. The major disjoint among the participants rested on the performance tools used by the university to promote staff, which was mainly based on research output. This view meant that teaching and learning were not recognized as a tool that can be used to improve staff skills development, and as such, the perception was that there was bias in the education system in terms of rewarding employees who participate in certain programmes. The majority of the participants stated that they do apply what they learn to their teaching approaches, although they felt they were not rewarded by the education system as a whole. The major implication coming from this study is that the duality of the education system in South Africa makes it harder to achieve an equilibrium were both academic staffs practicing teaching and learning, and researchers are seen as equals.
- Full Text:
- Date Issued: 2018
- Authors: Mankayi, Mandisa
- Date: 2018
- Subjects: College teachers -- In-service training -- South Africa -- Eastern Cape Education, Higher -- South Africa -- Eastern Cape Universities and colleges -- Employees -- Training of. -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10353/8530 , vital:32869
- Description: Institutions of higher education offer diverse staff development programmes to all staff members as a means of improving their educational quality and standards. The current study investigated using interviews, if whether the academic staff perceived staff development as a means of skills development; what factors motivated academic staff to attend the skills development programmes offered by their organisation; and which staff development programmes are perceived to be contributing much to academic skills development in a selected university in the Eastern Cape Province in South Africa. Utilising a purposive sampling technique, the number of academic staff interviewed was 15 from five faculties. A structured interview guide was used to solicit responses from the selected participants. Questions in the interview schedule ranged from issues pertaining to their registration on the skills development programme and how their personal skills have improved due to the programme. Upon completing the interview with an audio recorder, it was then transcribed and a thematic analysis method was used. It was found that participants were not satisfied with the academic skills development programmes offered by the university. While most respondents seemed to be aware of the skills programme, many were adamant to provide conclusive evidence on the impact of the programmes. The major disjoint among the participants rested on the performance tools used by the university to promote staff, which was mainly based on research output. This view meant that teaching and learning were not recognized as a tool that can be used to improve staff skills development, and as such, the perception was that there was bias in the education system in terms of rewarding employees who participate in certain programmes. The majority of the participants stated that they do apply what they learn to their teaching approaches, although they felt they were not rewarded by the education system as a whole. The major implication coming from this study is that the duality of the education system in South Africa makes it harder to achieve an equilibrium were both academic staffs practicing teaching and learning, and researchers are seen as equals.
- Full Text:
- Date Issued: 2018
Distribution of virulence determinants in Plesiomonas shigelloides and Vibrio species isolated from selected hospital wastewater effluents in the Eastern Cape Province, South Africa
- Authors: Mashudu, Mavhungu
- Date: 2018
- Subjects: Vibrio
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: http://hdl.handle.net/10353/14505 , vital:39996
- Description: Plesiomonas shigelloides and some Vibrio species are amongst the bacteria species classified into the emerging pathogenic bacteria grouping, and they portend increasing virulence and high resistance to some of the most potent antimicrobial agents used as most important and critical lines of defence against pathogenic infectious agents. Hospital wastewater has attracted significant attention as a pool for the regurgitation of pathogens into the environment which eventually becomes a problem to public health. It has been variously reported that hospital wastewater critically serves also as a puddle for microbial genetic interaction with outcomes including the development of resistance to antimicrobial agents among other pathogenic traits. And, in the same vein, exchanges and gene recombination may have been leading to the emergence of virulence determinants not previously known owing to the capacity of hospital wastewater to encompass a vast diversity of pathogenic bacteria and antimicrobial agents at the same material time. Hence, this research aimed at the evaluation of the prevalence of virulence and antibiotic resistance in Plesiomonas shigelloides and some human pathogenic Vibrio species isolated from selected hospital wastewater in the Eastern Cape Province of South Africa. Wastewater samples were collected at two weeks intervals throughout three months sampling duration from hospital wastewater facility in the Eastern Cape Province. The wastewater samples were from the secondary hospital and, tertiary hospital along with Limbede community wastewater facilities based in the Eastern Cape Province of South Africa. The wastewater samples were aseptically screened for the presence of presumptive Plesiomonas shigelloides and selected Vibrio species using the culture-based method. The identity of the presumptive Plesiomonas shigelloides and Vibrio species (Vibrio cholerae, V. fluvialis, V. parahaemolyticus, and V. vulnificus) isolates were confirmed using species specific primers. After that, the presence 14 of virulence determinants and the antimicrobial susceptibility profiles of the positive strains as well as the antimicrobial resistance factors were all determined. The distribution of the presumptive isolates was as follows; 322 Plesiomans shigelloides and 378 Vibrio species respectively. However, upon molecular confirmation studies, 85 out of 322; 26% of the total presumptive isolates, were confirmed as positive for Plesiomans shigelloides and, on the other hand, from the 378 presumptive Vibrio species, 71% (270) was as positive to Vibrio genus, and upon speciation of the positive isolates; 27% (73) was confirmed as Vibrio cholerae, 9% (24) as Vibrio parahaemolyticus, 4% (12) as Vibrio vulnificus and 3% (8) as Vibrio fluvialis. The remaining 57% (153) which was unaccounted for may belong to other Vibrio species not included in this studies. Various virulence determinants were shown to be present in the Vibrio species identified and the degree varied in line with the species. P. shigelloides showed high levels of resistance to impregnated antibiotics (18 different types). The antibiogram characteristics showed P. shigelloides to possess 100% resistance to Ciprofloxacin, Nalidixic acid, Trimethoprim, Ampicillin, Penicillin, Tetracycline, Doxycycline, Erythromycin, and Cephalothin. These findings are of crucial importance to public health and the science of infectology as it gives insight into the role of the hospital wastewater as a puddle for the recombination of antibiotic resistance determinants and virulence emergence in bacteria. On the strength of the finding of this research, it is essential to indicate that there is a need for an immediate review of hospital wastewater disposal process. Some form of treatment or pretreatment of the hospital wastewater is required before discharge into municipal wastewater treatment facilities. And, perhaps, continuous monitoring of hospital wastewater to reduce the risk posed to public health.
- Full Text:
- Date Issued: 2018
- Authors: Mashudu, Mavhungu
- Date: 2018
- Subjects: Vibrio
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: http://hdl.handle.net/10353/14505 , vital:39996
- Description: Plesiomonas shigelloides and some Vibrio species are amongst the bacteria species classified into the emerging pathogenic bacteria grouping, and they portend increasing virulence and high resistance to some of the most potent antimicrobial agents used as most important and critical lines of defence against pathogenic infectious agents. Hospital wastewater has attracted significant attention as a pool for the regurgitation of pathogens into the environment which eventually becomes a problem to public health. It has been variously reported that hospital wastewater critically serves also as a puddle for microbial genetic interaction with outcomes including the development of resistance to antimicrobial agents among other pathogenic traits. And, in the same vein, exchanges and gene recombination may have been leading to the emergence of virulence determinants not previously known owing to the capacity of hospital wastewater to encompass a vast diversity of pathogenic bacteria and antimicrobial agents at the same material time. Hence, this research aimed at the evaluation of the prevalence of virulence and antibiotic resistance in Plesiomonas shigelloides and some human pathogenic Vibrio species isolated from selected hospital wastewater in the Eastern Cape Province of South Africa. Wastewater samples were collected at two weeks intervals throughout three months sampling duration from hospital wastewater facility in the Eastern Cape Province. The wastewater samples were from the secondary hospital and, tertiary hospital along with Limbede community wastewater facilities based in the Eastern Cape Province of South Africa. The wastewater samples were aseptically screened for the presence of presumptive Plesiomonas shigelloides and selected Vibrio species using the culture-based method. The identity of the presumptive Plesiomonas shigelloides and Vibrio species (Vibrio cholerae, V. fluvialis, V. parahaemolyticus, and V. vulnificus) isolates were confirmed using species specific primers. After that, the presence 14 of virulence determinants and the antimicrobial susceptibility profiles of the positive strains as well as the antimicrobial resistance factors were all determined. The distribution of the presumptive isolates was as follows; 322 Plesiomans shigelloides and 378 Vibrio species respectively. However, upon molecular confirmation studies, 85 out of 322; 26% of the total presumptive isolates, were confirmed as positive for Plesiomans shigelloides and, on the other hand, from the 378 presumptive Vibrio species, 71% (270) was as positive to Vibrio genus, and upon speciation of the positive isolates; 27% (73) was confirmed as Vibrio cholerae, 9% (24) as Vibrio parahaemolyticus, 4% (12) as Vibrio vulnificus and 3% (8) as Vibrio fluvialis. The remaining 57% (153) which was unaccounted for may belong to other Vibrio species not included in this studies. Various virulence determinants were shown to be present in the Vibrio species identified and the degree varied in line with the species. P. shigelloides showed high levels of resistance to impregnated antibiotics (18 different types). The antibiogram characteristics showed P. shigelloides to possess 100% resistance to Ciprofloxacin, Nalidixic acid, Trimethoprim, Ampicillin, Penicillin, Tetracycline, Doxycycline, Erythromycin, and Cephalothin. These findings are of crucial importance to public health and the science of infectology as it gives insight into the role of the hospital wastewater as a puddle for the recombination of antibiotic resistance determinants and virulence emergence in bacteria. On the strength of the finding of this research, it is essential to indicate that there is a need for an immediate review of hospital wastewater disposal process. Some form of treatment or pretreatment of the hospital wastewater is required before discharge into municipal wastewater treatment facilities. And, perhaps, continuous monitoring of hospital wastewater to reduce the risk posed to public health.
- Full Text:
- Date Issued: 2018
Evaluation and identification of microbial contaminants in polyherbal medicines used for the treatment of tuberculosis in Amathole District Municipality, Eastern Cape Province, South Africa
- Authors: Famewo, Elizabeth Bosede
- Date: 2018
- Subjects: Tuberculosis -- Treatment -- South Africa Mycobacterial diseases -- South Africa -- Eastern Cape Medicinal plants -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/9680 , vital:34818
- Description: Tuberculosis is caused by Mycobacterium tuberculosis. The emergence of drug-resistant strains of this organism has become a global public health problem. In the continuing search for effective treatment, polyherbal medicines offer a great hope in the development of alternative drugs for the treatment of tuberculosis. The use of herbal formulations for therapeutic purposes has significantly increased in the developed and developing countries because of their curative property, less toxicity and minimal side effects. However, there is little information on their safety and effectiveness in the literature. To address this, polyherbal medicines used for the treatment of tuberculosis in the Eastern Cape Province of South Africa were evaluated. Ethno-medicinal survey was conducted through semi-structured questionnaires coupled with informal conversations with the herbal sellers in five communities in the study area. Bacterial and fungal DNA was extracted from the polyherbal medicines purchased. A fragment of the bacterial 16S rRNA gene and internal transcribed spacer region of the fungal rRNA operon were amplified with universal primers 27F and 518R, and ITS1 and ITS4 respectively. Following standard procedures, the amplicons were finally run on Illumina’s MiSeq platform. Furthermore, the remedies were screened against Mycobacterium tuberculosis H37Rv using Middlebrook 7H9 media and MGIT BACTEC 960 system. Agar dilution method was used to determine the minimum inhibitory concentration (MIC) of the remedies against eight bacteria and three fungi isolates. The herbal preparations were assayed for their toxicity using hatchability success and larval mortality of Artemia salina Leach. Finally, their nutritive properties were analysed using an inductively coupled plasma optical emission spectrometer for mineral analysis while the vitamins were determined using standardized methods A total of nine polyherbal preparations were collected. The herbs used for the preparation of these remedies belong to 20 families. Apiaceae [5(25 percent)] was the most prominent plant family used, followed by Liliaceae [4(20 percent)], Strychnaceae [4(20 percent)], Rutaceae [4(20 percent)] and Hypoxidaceae [3(15 percent)]. The two most frequently used plants were Allium sativum L. (Liliaceae) and Strychnos decussata (Pappe) Gilg. (Strychnaceae). Rhizomes was the most common parts used, followed by the roots and barks. The herbal medicines were prepared mainly by infusion and decoction. The presences of pathogenic and non-pathogenic bacteria were identified in the polyherbal medicines. Generally, the most common bacteria identified from the samples were Bacillus sp., Enterobacter sp., Klebsiella sp., Rahnella sp., Paenibacillus sp., Clostridium sp. and Pantoea sp. The predominant mycoflora obtained belongs to different genera or species of fungi; these include Alternaria, Candida, Ramularia, Cladosporium, Penicillium, Aspergillus and Malassezia. The susceptibility testing revealed that all the remedies contain anti-tubercular activity against M. tuberculosis H37Rv at concentrations below 50 ug/ml. Seven of the polyherbal preparations showed activity at concentrations below 25 ug/ml. The MIC values exhibited inhibitory activity at 1.562 μg/ml. However, isoniazid showed more inhibitory activity against M. tuberculosis at 0.05 μg/ml when compared to the polyherbal remedies. The inhibitory activity of the polyherbal medicines based on the overall MIC revealed that Hogsback first site (HBfs) and Fort Beaufort (FB) remedies were the most active remedies against the bacterial isolates at the concentration of 2.5 mg/mL. Among the nine herbal formulations, only King Williams Town site A (KWTa) remedy showed activity against Aspergillus niger and Aspergillus fumigatus with the MIC valve of 2.5 mg/mL. While King Williams Town site C (KWTc) and Hogsback third site (HBts) had the highest activity at 1.25 mg/mL against Candida albicans, the remaining remedies were active at 2.5 mg/mL. The percentage hatchability of 44.42 percent, 42.96 percent and 39.70 percent were observed in A. salina cysts incubated with herbal preparations from KWTa, HBfs and HBts respectively. The hatching success of the cysts in these remedies was significantly higher than the positive control (nystatin) and the negative control (sea water) at p < 0.05. The mortality of A. salina nauplii incubated in Alice (AL), King Williams Town site B (KWTb) and KWTc remedies were significantly higher than when larvae were incubated in both controls. Based on Meyer’s index, the LD50 of each polyherbal medicine was between 2.9 and 4.0 mg/ml, the LD50 values greater than 1 mg/ml, an indication that they are not toxic. The polyherbal preparations were found to be rich in vitamins and mineral nutrients. Calcium was the highest macronutrient detected while the lowest nutrient was phosphorus. Iron was the highest micronutrient in the majority of the polyherbal preparations while the lowest value was recorded for copper. Vitamin C was absent in the herbal preparations while vitamin A and E were detected. This study provides significant ethno-medicinal information on polyherbal medicines used for the treatment of TB in the study area. The presence of the identified bacteria and fungi in the herbal formulations is a cause for concern. However, the ability of the remedies to possess activity against Mycobacterium tuberculosis and other pathogenic microorganisms associated with tuberculosis infection makes them potential sources of new antimycobacterial agents. Also, they are rich sources of mineral nutrients, and are as well non-toxic, thus, they are safe for consumption. In view of their anti-tubercular properties, this study has provided a better understanding of the reasons why TB-patients make use of these polyherbal formulations. Also, the study supports the folkloric use of polyherbal medicines in the treatment of tuberculosis in the Eastern Cape Province, South Africa.
- Full Text:
- Date Issued: 2018
- Authors: Famewo, Elizabeth Bosede
- Date: 2018
- Subjects: Tuberculosis -- Treatment -- South Africa Mycobacterial diseases -- South Africa -- Eastern Cape Medicinal plants -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/9680 , vital:34818
- Description: Tuberculosis is caused by Mycobacterium tuberculosis. The emergence of drug-resistant strains of this organism has become a global public health problem. In the continuing search for effective treatment, polyherbal medicines offer a great hope in the development of alternative drugs for the treatment of tuberculosis. The use of herbal formulations for therapeutic purposes has significantly increased in the developed and developing countries because of their curative property, less toxicity and minimal side effects. However, there is little information on their safety and effectiveness in the literature. To address this, polyherbal medicines used for the treatment of tuberculosis in the Eastern Cape Province of South Africa were evaluated. Ethno-medicinal survey was conducted through semi-structured questionnaires coupled with informal conversations with the herbal sellers in five communities in the study area. Bacterial and fungal DNA was extracted from the polyherbal medicines purchased. A fragment of the bacterial 16S rRNA gene and internal transcribed spacer region of the fungal rRNA operon were amplified with universal primers 27F and 518R, and ITS1 and ITS4 respectively. Following standard procedures, the amplicons were finally run on Illumina’s MiSeq platform. Furthermore, the remedies were screened against Mycobacterium tuberculosis H37Rv using Middlebrook 7H9 media and MGIT BACTEC 960 system. Agar dilution method was used to determine the minimum inhibitory concentration (MIC) of the remedies against eight bacteria and three fungi isolates. The herbal preparations were assayed for their toxicity using hatchability success and larval mortality of Artemia salina Leach. Finally, their nutritive properties were analysed using an inductively coupled plasma optical emission spectrometer for mineral analysis while the vitamins were determined using standardized methods A total of nine polyherbal preparations were collected. The herbs used for the preparation of these remedies belong to 20 families. Apiaceae [5(25 percent)] was the most prominent plant family used, followed by Liliaceae [4(20 percent)], Strychnaceae [4(20 percent)], Rutaceae [4(20 percent)] and Hypoxidaceae [3(15 percent)]. The two most frequently used plants were Allium sativum L. (Liliaceae) and Strychnos decussata (Pappe) Gilg. (Strychnaceae). Rhizomes was the most common parts used, followed by the roots and barks. The herbal medicines were prepared mainly by infusion and decoction. The presences of pathogenic and non-pathogenic bacteria were identified in the polyherbal medicines. Generally, the most common bacteria identified from the samples were Bacillus sp., Enterobacter sp., Klebsiella sp., Rahnella sp., Paenibacillus sp., Clostridium sp. and Pantoea sp. The predominant mycoflora obtained belongs to different genera or species of fungi; these include Alternaria, Candida, Ramularia, Cladosporium, Penicillium, Aspergillus and Malassezia. The susceptibility testing revealed that all the remedies contain anti-tubercular activity against M. tuberculosis H37Rv at concentrations below 50 ug/ml. Seven of the polyherbal preparations showed activity at concentrations below 25 ug/ml. The MIC values exhibited inhibitory activity at 1.562 μg/ml. However, isoniazid showed more inhibitory activity against M. tuberculosis at 0.05 μg/ml when compared to the polyherbal remedies. The inhibitory activity of the polyherbal medicines based on the overall MIC revealed that Hogsback first site (HBfs) and Fort Beaufort (FB) remedies were the most active remedies against the bacterial isolates at the concentration of 2.5 mg/mL. Among the nine herbal formulations, only King Williams Town site A (KWTa) remedy showed activity against Aspergillus niger and Aspergillus fumigatus with the MIC valve of 2.5 mg/mL. While King Williams Town site C (KWTc) and Hogsback third site (HBts) had the highest activity at 1.25 mg/mL against Candida albicans, the remaining remedies were active at 2.5 mg/mL. The percentage hatchability of 44.42 percent, 42.96 percent and 39.70 percent were observed in A. salina cysts incubated with herbal preparations from KWTa, HBfs and HBts respectively. The hatching success of the cysts in these remedies was significantly higher than the positive control (nystatin) and the negative control (sea water) at p < 0.05. The mortality of A. salina nauplii incubated in Alice (AL), King Williams Town site B (KWTb) and KWTc remedies were significantly higher than when larvae were incubated in both controls. Based on Meyer’s index, the LD50 of each polyherbal medicine was between 2.9 and 4.0 mg/ml, the LD50 values greater than 1 mg/ml, an indication that they are not toxic. The polyherbal preparations were found to be rich in vitamins and mineral nutrients. Calcium was the highest macronutrient detected while the lowest nutrient was phosphorus. Iron was the highest micronutrient in the majority of the polyherbal preparations while the lowest value was recorded for copper. Vitamin C was absent in the herbal preparations while vitamin A and E were detected. This study provides significant ethno-medicinal information on polyherbal medicines used for the treatment of TB in the study area. The presence of the identified bacteria and fungi in the herbal formulations is a cause for concern. However, the ability of the remedies to possess activity against Mycobacterium tuberculosis and other pathogenic microorganisms associated with tuberculosis infection makes them potential sources of new antimycobacterial agents. Also, they are rich sources of mineral nutrients, and are as well non-toxic, thus, they are safe for consumption. In view of their anti-tubercular properties, this study has provided a better understanding of the reasons why TB-patients make use of these polyherbal formulations. Also, the study supports the folkloric use of polyherbal medicines in the treatment of tuberculosis in the Eastern Cape Province, South Africa.
- Full Text:
- Date Issued: 2018
Protected area expansion and conservation stewardship in the Olifants Catchment: mechanisms, patterns and benefits
- Authors: Coetzer, Crystal Jeanne
- Date: 2018
- Subjects: Biodiversity conservation -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30006 , vital:30808
- Description: State Conservation Areas (SCAs), as state-owned and -run parks, form the foundation of recognised conservation actions. However, park expansion on the scale required to meet urgent conservation targets is limited by state budgets and parks are increasingly framed in the context of advancing broader societal needs. Motivating for the need to assess the efficacy of alternative conservation strategies, as both contrasting governance and legal mechanisms, this study aimed to rapidly assess the role of private land conservation (PLC) strategies in expanding protection. In particular, this included the role of emerging stewardship approaches, by using semi-structured interviews with park implementers on a national scale. Evaluating the biodiversity and ecosystem service representation and complementarity of contrasting conservation strategies on a catchment scale, using open-source spatial data was employed. Questionnaires tested park managers’ perceptions of benefits across different strategies in a conservation-oriented landscape. Results indicate a strategic shift toward PLC strategies to expand parks in the form of formalised, well-planned and supported contractual and stewardship agreements. SCAs are vital baselines for biodiversity and ecosystem service representation in the catchment with a variety of private mechanisms supplementing protection, especially in highly contested areas. The perceived benefits rated by managers revealed interesting links between benefits and contrasting governance types, legal mechanisms, legal status, size and age of reserves. State parks may be more relevant for generating socio-cultural benefits, while private parks, through the need to remain economically viable, valued a diverse range of socio-economic benefits. Informal conservation areas formed integral parts of the conservation-orientated landscape, rating benefits equally to more secure mechanisms. Private land must be incorporated into conservation through diverse mechanisms to meet the range of mutually exclusive conservation objectives of the 21st century.
- Full Text:
- Date Issued: 2018
- Authors: Coetzer, Crystal Jeanne
- Date: 2018
- Subjects: Biodiversity conservation -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30006 , vital:30808
- Description: State Conservation Areas (SCAs), as state-owned and -run parks, form the foundation of recognised conservation actions. However, park expansion on the scale required to meet urgent conservation targets is limited by state budgets and parks are increasingly framed in the context of advancing broader societal needs. Motivating for the need to assess the efficacy of alternative conservation strategies, as both contrasting governance and legal mechanisms, this study aimed to rapidly assess the role of private land conservation (PLC) strategies in expanding protection. In particular, this included the role of emerging stewardship approaches, by using semi-structured interviews with park implementers on a national scale. Evaluating the biodiversity and ecosystem service representation and complementarity of contrasting conservation strategies on a catchment scale, using open-source spatial data was employed. Questionnaires tested park managers’ perceptions of benefits across different strategies in a conservation-oriented landscape. Results indicate a strategic shift toward PLC strategies to expand parks in the form of formalised, well-planned and supported contractual and stewardship agreements. SCAs are vital baselines for biodiversity and ecosystem service representation in the catchment with a variety of private mechanisms supplementing protection, especially in highly contested areas. The perceived benefits rated by managers revealed interesting links between benefits and contrasting governance types, legal mechanisms, legal status, size and age of reserves. State parks may be more relevant for generating socio-cultural benefits, while private parks, through the need to remain economically viable, valued a diverse range of socio-economic benefits. Informal conservation areas formed integral parts of the conservation-orientated landscape, rating benefits equally to more secure mechanisms. Private land must be incorporated into conservation through diverse mechanisms to meet the range of mutually exclusive conservation objectives of the 21st century.
- Full Text:
- Date Issued: 2018
The management of records for accountability by municipalities in the Eastern Cape Province, South Africa : a case study of Mbizana Local Municipality
- Authors: Tseku, Zintle
- Date: 2018
- Subjects: Records--Management Information organization Public records--Management
- Language: English
- Type: Thesis , Masters , Library and Information Science
- Identifier: http://hdl.handle.net/10353/15254 , vital:40331
- Description: Records management is a major element for accountability in the municipality. The research topic was “the management of records for accountability by the municipalities in the Eastern Cape Province, South Africa: A case study of Mbizana Local Municipality”. The objectives of the study were: to find out the types of records management programme maintained by Bizana Local Municipality, to describe available infrastructure that supports the records management programme in Mbizana Local Municipality, to find out the extent to which the management of records in Mbizana Local Municipality complies with statutory and legislative requirements, and to find out the possible constraints that affects the records management programme in Mbizana Local Municipality. The study was conducted in Mbizana Local Municipality which is under Alfred Ndzo District Municipality in Eastern Cape, South Africa. The sample was municipality staff and the residents of the municipality. The study used both qualitative and quantitative research methods. The findings were that Mbizana Local Municipality has a records management programme which is important for accountability, however, there is a need for security maintenance. In addition, the findings were that the municipality need to train its registry staff about records management or hire new people who are capable of managing records. The researcher recommended that Mbizana Local Municipality should provide more training to registry staff on the management of records. The municipality should introduce electronic records management system since nowadays records are created electronically. Electronic records can be easily retrieved when needed for accountability. Also the municipality should allow the public to have access to records.
- Full Text:
- Date Issued: 2018
- Authors: Tseku, Zintle
- Date: 2018
- Subjects: Records--Management Information organization Public records--Management
- Language: English
- Type: Thesis , Masters , Library and Information Science
- Identifier: http://hdl.handle.net/10353/15254 , vital:40331
- Description: Records management is a major element for accountability in the municipality. The research topic was “the management of records for accountability by the municipalities in the Eastern Cape Province, South Africa: A case study of Mbizana Local Municipality”. The objectives of the study were: to find out the types of records management programme maintained by Bizana Local Municipality, to describe available infrastructure that supports the records management programme in Mbizana Local Municipality, to find out the extent to which the management of records in Mbizana Local Municipality complies with statutory and legislative requirements, and to find out the possible constraints that affects the records management programme in Mbizana Local Municipality. The study was conducted in Mbizana Local Municipality which is under Alfred Ndzo District Municipality in Eastern Cape, South Africa. The sample was municipality staff and the residents of the municipality. The study used both qualitative and quantitative research methods. The findings were that Mbizana Local Municipality has a records management programme which is important for accountability, however, there is a need for security maintenance. In addition, the findings were that the municipality need to train its registry staff about records management or hire new people who are capable of managing records. The researcher recommended that Mbizana Local Municipality should provide more training to registry staff on the management of records. The municipality should introduce electronic records management system since nowadays records are created electronically. Electronic records can be easily retrieved when needed for accountability. Also the municipality should allow the public to have access to records.
- Full Text:
- Date Issued: 2018
An investigation of the Sowetan “enough is enough-take back your dignity” campaign to challenge violence against women and children
- Ndabezitha, Nomthandazo Sibusisiwe Mary-Angel
- Authors: Ndabezitha, Nomthandazo Sibusisiwe Mary-Angel
- Date: 2017
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/4521 , vital:20685
- Description: This investigation of the Sowetan “Enough is Enough - take back your dignity” campaign to challenge sexual violence explores whether the South African daily newspaper’s sustained anti-rape coverage challenges or reinforces the social order. It locates the Sowetan campaign’s response within two troubling contradictions. First, while South Africa is a democracy with arguably the most liberally progressive constitution in the world, the epidemically high rape statistics indicate that South African women and children inhabit an environment in which they are effectively denied the same freedoms and rights as men. The Sowetan anti-rape campaign responds to this paradox. Second, heightened exposure and coverage in the news media of rape incidents do not seem to correlate directly with a decrease in incidents of sexual violence. My observation of these contradictions leads me to question whether the anti-rape campaign can be socially transformative. Informed by the Foucauldian insights that the meaning of things is not inherent but exists in discourse, which has the power to make itself true, this study investigates what discourses are articulated in the representation of masculinities and femininities. In this regard, my investigation is informed by cultural studies and gender studies theories. Recognising rape as an enactment of a particular type of masculinity makes it clear that rapists are not deviant monsters, but are men embodying a discourse of male sexual entitlement legitimated by the social order. As the campaign coverage largely represents rape in historically black locations such as townships and villages, I argue that rape is an enactment of a particular violent masculinity within a particular socio-economically marginalised postcolonial context. Hence I also use postcolonial studies and gender studies to inform my theory. This qualitative research takes the form of a case study which entails a critical discourse analysis of 19 texts purposively sampled in order to identify whether the campaign challenges or reinforces the social order. I argue that rehearsing the narratives of prevalent rape and horror at this epidemic without addressing the social order of gender inequality that enables rape is inadequate. The findings indicate that the campaign has limited socially transformative potential, as, while it sometimes challenges the discourse of female passivity, it does not go so far as to critically engage with masculinities and questioning how violent ones are produced in the social order.
- Full Text:
- Date Issued: 2017
- Authors: Ndabezitha, Nomthandazo Sibusisiwe Mary-Angel
- Date: 2017
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/4521 , vital:20685
- Description: This investigation of the Sowetan “Enough is Enough - take back your dignity” campaign to challenge sexual violence explores whether the South African daily newspaper’s sustained anti-rape coverage challenges or reinforces the social order. It locates the Sowetan campaign’s response within two troubling contradictions. First, while South Africa is a democracy with arguably the most liberally progressive constitution in the world, the epidemically high rape statistics indicate that South African women and children inhabit an environment in which they are effectively denied the same freedoms and rights as men. The Sowetan anti-rape campaign responds to this paradox. Second, heightened exposure and coverage in the news media of rape incidents do not seem to correlate directly with a decrease in incidents of sexual violence. My observation of these contradictions leads me to question whether the anti-rape campaign can be socially transformative. Informed by the Foucauldian insights that the meaning of things is not inherent but exists in discourse, which has the power to make itself true, this study investigates what discourses are articulated in the representation of masculinities and femininities. In this regard, my investigation is informed by cultural studies and gender studies theories. Recognising rape as an enactment of a particular type of masculinity makes it clear that rapists are not deviant monsters, but are men embodying a discourse of male sexual entitlement legitimated by the social order. As the campaign coverage largely represents rape in historically black locations such as townships and villages, I argue that rape is an enactment of a particular violent masculinity within a particular socio-economically marginalised postcolonial context. Hence I also use postcolonial studies and gender studies to inform my theory. This qualitative research takes the form of a case study which entails a critical discourse analysis of 19 texts purposively sampled in order to identify whether the campaign challenges or reinforces the social order. I argue that rehearsing the narratives of prevalent rape and horror at this epidemic without addressing the social order of gender inequality that enables rape is inadequate. The findings indicate that the campaign has limited socially transformative potential, as, while it sometimes challenges the discourse of female passivity, it does not go so far as to critically engage with masculinities and questioning how violent ones are produced in the social order.
- Full Text:
- Date Issued: 2017
Rights as trumps in African communitarian ethics
- Authors: Nwogbo, Johnbosco
- Date: 2017
- Subjects: Communitarianism Human rights Social values
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10353/12282 , vital:39249
- Description: The notion of rights is among the most basic ideas of contemporary political philosophy on the continent and elsewhere. Although rights are common-place in political philosophy it is fair to say that the discussion around it has been nothing short of contested. On the whole, there have been two kinds of questions to which most of the discussion about rights in political philosophy have been answers, namely, (i) what are rights?, and (ii) to what do people have rights? The first has to do with the nature of rights, while the second has to the nature of that to which people may be said to have rights. This research falls neatly within the parlance of the first kind of questions (i.e., the question of what rights are). Specifically, in this research, I am concerned with the question of whether the radical and moderate African communitarian rights theses of Ifeanyi Menkiti and Kwame Gyekye measure up to what rights are commonly understood to be. I argue that if rights are trumps, which override competing societal and communal considerations, then Menkiti’s and Gyekye’s theories of rights fall short of this fairly standard and typical conception of rights.
- Full Text:
- Date Issued: 2017
- Authors: Nwogbo, Johnbosco
- Date: 2017
- Subjects: Communitarianism Human rights Social values
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10353/12282 , vital:39249
- Description: The notion of rights is among the most basic ideas of contemporary political philosophy on the continent and elsewhere. Although rights are common-place in political philosophy it is fair to say that the discussion around it has been nothing short of contested. On the whole, there have been two kinds of questions to which most of the discussion about rights in political philosophy have been answers, namely, (i) what are rights?, and (ii) to what do people have rights? The first has to do with the nature of rights, while the second has to the nature of that to which people may be said to have rights. This research falls neatly within the parlance of the first kind of questions (i.e., the question of what rights are). Specifically, in this research, I am concerned with the question of whether the radical and moderate African communitarian rights theses of Ifeanyi Menkiti and Kwame Gyekye measure up to what rights are commonly understood to be. I argue that if rights are trumps, which override competing societal and communal considerations, then Menkiti’s and Gyekye’s theories of rights fall short of this fairly standard and typical conception of rights.
- Full Text:
- Date Issued: 2017
Detecting derivative malware samples using deobfuscation-assisted similarity analysis
- Authors: Wrench, Peter Mark
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/383 , vital:19954
- Description: The overwhelming popularity of PHP as a hosting platform has made it the language of choice for developers of Remote Access Trojans (RATs or web shells) and other malicious software. These shells are typically used to compromise and monetise web platforms by providing the attacker with basic remote access to the system, including _le transfer, command execution, network reconnaissance, and database connectivity. Once infected, compromised systems can be used to defraud users by hosting phishing sites, performing Distributed Denial of Service attacks, or serving as anonymous platforms for sending spam or other malfeasance. The vast majority of these threats are largely derivative, incorporating core capabilities found in more established RATs such as c99 and r57. Authors of malicious software routinely produce new shell variants by modifying the behaviours of these ubiquitous RATs, either to add desired functionality or to avoid detection by signature-based detection systems. Once these modified shells are eventually identified (or additional functionality is required), the process of shell adaptation begins again. The end result of this iterative process is a web of separate but related shell variants, many of which are at least partially derived from one of the more popular and influential RATs. In response to the problem outlined above, the author set out to design and implement a system capable of circumventing common obfuscation techniques and identifying derivative malware samples in a given collection. To begin with, a decoder component was developed to syntactically deobfuscate and normalise PHP code by detecting and reversing idiomatic obfuscation constructs, and to apply uniform formatting conventions to all system inputs. A unified malware analysis framework, called Viper, was then extended to create a modular similarity analysis system comprised of individual feature extraction modules, modules responsible for batch processing, a matrix module for comparing sample features, and two visualisation modules capable of generating visual representations of shell similarity. The principal conclusion of the research was that the deobfuscation performed by the decoder component prior to analysis dramatically improved the observed levels of similarity between test samples. This in turn allowed the modular similarity analysis system to identify derivative clusters (or families) within a large collection of shells more accurately. Techniques for isolating and re-rendering these clusters were also developed and demonstrated to be effective at increasing the amount of detail available for evaluating the relative magnitudes of the relationships within each cluster.
- Full Text:
- Date Issued: 2016
- Authors: Wrench, Peter Mark
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/383 , vital:19954
- Description: The overwhelming popularity of PHP as a hosting platform has made it the language of choice for developers of Remote Access Trojans (RATs or web shells) and other malicious software. These shells are typically used to compromise and monetise web platforms by providing the attacker with basic remote access to the system, including _le transfer, command execution, network reconnaissance, and database connectivity. Once infected, compromised systems can be used to defraud users by hosting phishing sites, performing Distributed Denial of Service attacks, or serving as anonymous platforms for sending spam or other malfeasance. The vast majority of these threats are largely derivative, incorporating core capabilities found in more established RATs such as c99 and r57. Authors of malicious software routinely produce new shell variants by modifying the behaviours of these ubiquitous RATs, either to add desired functionality or to avoid detection by signature-based detection systems. Once these modified shells are eventually identified (or additional functionality is required), the process of shell adaptation begins again. The end result of this iterative process is a web of separate but related shell variants, many of which are at least partially derived from one of the more popular and influential RATs. In response to the problem outlined above, the author set out to design and implement a system capable of circumventing common obfuscation techniques and identifying derivative malware samples in a given collection. To begin with, a decoder component was developed to syntactically deobfuscate and normalise PHP code by detecting and reversing idiomatic obfuscation constructs, and to apply uniform formatting conventions to all system inputs. A unified malware analysis framework, called Viper, was then extended to create a modular similarity analysis system comprised of individual feature extraction modules, modules responsible for batch processing, a matrix module for comparing sample features, and two visualisation modules capable of generating visual representations of shell similarity. The principal conclusion of the research was that the deobfuscation performed by the decoder component prior to analysis dramatically improved the observed levels of similarity between test samples. This in turn allowed the modular similarity analysis system to identify derivative clusters (or families) within a large collection of shells more accurately. Techniques for isolating and re-rendering these clusters were also developed and demonstrated to be effective at increasing the amount of detail available for evaluating the relative magnitudes of the relationships within each cluster.
- Full Text:
- Date Issued: 2016
Terrorism as a contributory factor to state failure in Somalia: a case study of Al- Shabaab
- Authors: Ndlovu, Sitembiso Irene
- Date: 2016
- Subjects: Terrorism -- Somalia Terrorism -- Government policy -- Somalia
- Language: English
- Type: Thesis , Masters , M Soc Sci
- Identifier: http://hdl.handle.net/10353/2458 , vital:27843
- Description: This study is an investigation of terrorism as a contributory factor to state failure in Somalia with specific reference to Al-Shabaab, using Huntington‟s Clash of Civilizations theory. It utilises both primary and secondary sources of data. The study found out that Somalia had been a failed state even before the birth of Al-Shabaab. However, the activities of Al-Shabaab perpetuated state failure in Somalia. These activities included bombings, small arms attacks, executions, siege, kidnappings, hijackings and looting. The study also found out that Al-Shabaab regularly conducted incursions in neighbouring countries and all these activities destabilised Somalia politically and perpetuated state failure. However, the study also found out that there were other factors that contributed to Somalia‟s state failure some of which were clan rivalry, civil war, warlordism, piracy, poverty and religion. Despite all these, the study noted that there were various actors involved in containing the terrorist activities of Al-Shabaab. These actors included the Transitional Federal Government, Kenya, the African Union, the United Nations and the United States. The study recommends that dialogue between the TFG, the clan structures and Al-Shabaab is the most viable path to sustainable peace in Somalia.
- Full Text:
- Date Issued: 2016
- Authors: Ndlovu, Sitembiso Irene
- Date: 2016
- Subjects: Terrorism -- Somalia Terrorism -- Government policy -- Somalia
- Language: English
- Type: Thesis , Masters , M Soc Sci
- Identifier: http://hdl.handle.net/10353/2458 , vital:27843
- Description: This study is an investigation of terrorism as a contributory factor to state failure in Somalia with specific reference to Al-Shabaab, using Huntington‟s Clash of Civilizations theory. It utilises both primary and secondary sources of data. The study found out that Somalia had been a failed state even before the birth of Al-Shabaab. However, the activities of Al-Shabaab perpetuated state failure in Somalia. These activities included bombings, small arms attacks, executions, siege, kidnappings, hijackings and looting. The study also found out that Al-Shabaab regularly conducted incursions in neighbouring countries and all these activities destabilised Somalia politically and perpetuated state failure. However, the study also found out that there were other factors that contributed to Somalia‟s state failure some of which were clan rivalry, civil war, warlordism, piracy, poverty and religion. Despite all these, the study noted that there were various actors involved in containing the terrorist activities of Al-Shabaab. These actors included the Transitional Federal Government, Kenya, the African Union, the United Nations and the United States. The study recommends that dialogue between the TFG, the clan structures and Al-Shabaab is the most viable path to sustainable peace in Somalia.
- Full Text:
- Date Issued: 2016
The beat
- Authors: Masheane, Napo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:6014 , http://hdl.handle.net/10962/d1021234
- Description: My play script is a docu-drama inspired by the 1950s Drum journalists: Can Themba, Bloke Modisane, Nat Nakasa, Henry Nxumalo, Lewis Nkosi, Peter Magubane, Casey Motsitsi and Todd Matshikiza. The setting is a Sophiatown shebeen through which the characters move in and out. The central dramatic exploration hinges on female characters’ experiences rather than the perspectives of the male journalists connected to them. I dramatise documented events such as Modisane’s wife leaving him and taking their daughter with her, or a woman who buried her lover’s body after he was beaten and stabbed to death. There are other twists and turns based on the Drum journalists writings. I play with the seriousness of politics, love affairs, and the comedy of their daily lives. My influences come from plays such as Nongogo (1959) and Sophiatown (1986). The Beat is dedicated to all the women who have been silenced and as a result became products of their consequences. Their voices remind me as a theatre maker that my poems and plays might arrive in me as pure SONGS (Dipina) or a CRY (Kodiyamalla). Sometimes their inspiration will spring from my traditional family rituals, as a PRAISE song/s (Dithoko/ Thoko), or from a simple memory of a childhood church song, a HYMN (Difela/ Sefela). At times these words will present themselves as a source of where one comes from, CLAN NAMES (Seboko/ Poko). These stories will find me in the dusty streets of my village and township HERSTORY… they will touch, move, provoke, push and force me to vomit on page words that are subjects of that which we are even when silence seems inevitable. , My poetry collection fuses Sesotho and English, often within the same poem, as a way of showing how I live within and between two cultures. I write to celebrate these two tongues without compromising either language and allow each poem, to express its own musical component, tone, rhythm, and pace as it moves between stage and page. My poems converse about difficult subjects from a feminine voice. They look at family structures and dynamics, using everyday household things as metaphors. They take on deep family narratives of generational curses, births, deaths and love. There are also some more political poems about community outrage, the exploitation caused by outmoded culture and tradition, and about the nightmare that constantly wants to come out of the township.
- Full Text:
- Date Issued: 2016
- Authors: Masheane, Napo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:6014 , http://hdl.handle.net/10962/d1021234
- Description: My play script is a docu-drama inspired by the 1950s Drum journalists: Can Themba, Bloke Modisane, Nat Nakasa, Henry Nxumalo, Lewis Nkosi, Peter Magubane, Casey Motsitsi and Todd Matshikiza. The setting is a Sophiatown shebeen through which the characters move in and out. The central dramatic exploration hinges on female characters’ experiences rather than the perspectives of the male journalists connected to them. I dramatise documented events such as Modisane’s wife leaving him and taking their daughter with her, or a woman who buried her lover’s body after he was beaten and stabbed to death. There are other twists and turns based on the Drum journalists writings. I play with the seriousness of politics, love affairs, and the comedy of their daily lives. My influences come from plays such as Nongogo (1959) and Sophiatown (1986). The Beat is dedicated to all the women who have been silenced and as a result became products of their consequences. Their voices remind me as a theatre maker that my poems and plays might arrive in me as pure SONGS (Dipina) or a CRY (Kodiyamalla). Sometimes their inspiration will spring from my traditional family rituals, as a PRAISE song/s (Dithoko/ Thoko), or from a simple memory of a childhood church song, a HYMN (Difela/ Sefela). At times these words will present themselves as a source of where one comes from, CLAN NAMES (Seboko/ Poko). These stories will find me in the dusty streets of my village and township HERSTORY… they will touch, move, provoke, push and force me to vomit on page words that are subjects of that which we are even when silence seems inevitable. , My poetry collection fuses Sesotho and English, often within the same poem, as a way of showing how I live within and between two cultures. I write to celebrate these two tongues without compromising either language and allow each poem, to express its own musical component, tone, rhythm, and pace as it moves between stage and page. My poems converse about difficult subjects from a feminine voice. They look at family structures and dynamics, using everyday household things as metaphors. They take on deep family narratives of generational curses, births, deaths and love. There are also some more political poems about community outrage, the exploitation caused by outmoded culture and tradition, and about the nightmare that constantly wants to come out of the township.
- Full Text:
- Date Issued: 2016
Using data mining techniques for the prediction of student dropouts from university science programs
- Authors: Vambe, William Tichaona
- Date: 2016
- Subjects: Data mining Dropout behavior, Prediction of
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/12314 , vital:39252
- Description: Data Mining has taken a center stage in education for addressing student dropout challenges as it has become one of the major threat affecting Higher Educational Institutes (HEIs). Being able to predict students who are likely to dropout helps the university to assist those facing challenges early. This will results in producing more graduates with the intellectual capital who will provide skills in the industries, hence addressing the major challenge of skill shortage being faced in South Africa. Studies and researches as purported in literature have been done to address this major threat of dropout challenge by using the theoretical approach which banked on Tinto’s model, followed by the traditional and statistical approach. However, the two lacked accuracy and the automation aspect which makes them difficult and time-consuming to use as they require to be tested periodically for them to be validated. Recently data mining has become a vital tool for predicting non-linear phenomenon including where there is missing data and bringing about accuracy and automation aspect. Data mining usefulness and reliability assessment in education made it possible to be used for prediction by different researchers. As such this research used data mining approach that integrates classification and prediction techniques to analyze student academic data at the University of Fort Hare to create a model for student dropout using preentry data and university academic performance of each student. Following Knowledge Discovery from Database (KDD) framework, data for the students enrolled in the Bachelor of Science programs between 2003 and 2014 was selected. It went through preprocessing and transformation as to deal with the missing data and noise data. Classification algorithms were then used for student characterization. Decision trees (J48) which are found in Weka software were used to build the model for data mining and prediction. The reason for choosing decision trees was it’s ability to deal with textual, nominal and numeric data as was the case with our input data and because they have good precision.The model was then trained using a train data set, validated and evaluated with another data set. Experimental results demonstrations that data mining is useful in predicting students who have chances to drop out. A critical analysis of correctly classifying instances, the confusion matrix and ROC area shows that the model can correctly classify and predict those who are likely to dropout. The model accuracy was 66percent which is a good percentage as supported in literature which means the results produced can be reliably used for assessment and make strategic decisions. Furthermore, the model took a matter of seconds to compute the results when supplied with 400 instances which prove that it is effective and efficient. Grounding our conclusion from these experimental results, this research proved that Data Mining is useful for bringing about automation, accuracy in prediction of student dropouts and the results can be reliably depended on for decision making by faculty managers who are the decision makers.
- Full Text:
- Date Issued: 2016
Using data mining techniques for the prediction of student dropouts from university science programs
- Authors: Vambe, William Tichaona
- Date: 2016
- Subjects: Data mining Dropout behavior, Prediction of
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/12314 , vital:39252
- Description: Data Mining has taken a center stage in education for addressing student dropout challenges as it has become one of the major threat affecting Higher Educational Institutes (HEIs). Being able to predict students who are likely to dropout helps the university to assist those facing challenges early. This will results in producing more graduates with the intellectual capital who will provide skills in the industries, hence addressing the major challenge of skill shortage being faced in South Africa. Studies and researches as purported in literature have been done to address this major threat of dropout challenge by using the theoretical approach which banked on Tinto’s model, followed by the traditional and statistical approach. However, the two lacked accuracy and the automation aspect which makes them difficult and time-consuming to use as they require to be tested periodically for them to be validated. Recently data mining has become a vital tool for predicting non-linear phenomenon including where there is missing data and bringing about accuracy and automation aspect. Data mining usefulness and reliability assessment in education made it possible to be used for prediction by different researchers. As such this research used data mining approach that integrates classification and prediction techniques to analyze student academic data at the University of Fort Hare to create a model for student dropout using preentry data and university academic performance of each student. Following Knowledge Discovery from Database (KDD) framework, data for the students enrolled in the Bachelor of Science programs between 2003 and 2014 was selected. It went through preprocessing and transformation as to deal with the missing data and noise data. Classification algorithms were then used for student characterization. Decision trees (J48) which are found in Weka software were used to build the model for data mining and prediction. The reason for choosing decision trees was it’s ability to deal with textual, nominal and numeric data as was the case with our input data and because they have good precision.The model was then trained using a train data set, validated and evaluated with another data set. Experimental results demonstrations that data mining is useful in predicting students who have chances to drop out. A critical analysis of correctly classifying instances, the confusion matrix and ROC area shows that the model can correctly classify and predict those who are likely to dropout. The model accuracy was 66percent which is a good percentage as supported in literature which means the results produced can be reliably used for assessment and make strategic decisions. Furthermore, the model took a matter of seconds to compute the results when supplied with 400 instances which prove that it is effective and efficient. Grounding our conclusion from these experimental results, this research proved that Data Mining is useful for bringing about automation, accuracy in prediction of student dropouts and the results can be reliably depended on for decision making by faculty managers who are the decision makers.
- Full Text:
- Date Issued: 2016
Evaluation of incidence of Mycobacterium tuberculosis complex associated with soil, hayfeed and water in three agricultural facilities in Amathole District Municipality in the Eastern Cape Province, South Africa
- Authors: Ntloko, Athini
- Date: 2015
- Subjects: Mycobacterium tuberculosis -- South Africa -- Eastern Cape Drug resistance in microorganisms Mycobacterial diseases
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/2689 , vital:27993
- Description: Mycobacterium bovis and other species of Mycobacterium tuberculosis complex (MTBC) can result to a zoonotic infection known as Bovine tuberculosis (bTB). MTBC has members that may contaminate an extensive range of hosts, including wildlife. Diverse wild species are known to cause disease in domestic livestock and are acknowledged as TB reservoirs. It has been a main study worldwide to deliberate on bTB risk factors as a result some studies focused on particular parts of risk factors such as wildlife and herd management. The objectives of this study were to design questionnaires from commercial farms and smallholding farms; isolate and identify MTBC from collected samples using culture and PCR assays recovered from Fort Hare, Middledrift and Seven star dairy farms; and assessing genotypic drug resistance through detection of mutations conferring resistance to INH and RMP associated with first line treatment for MTBC infection. Questionnaires were administered to thirty (30) smallholding farm owners in the two villages (kwaMasele and Qungqwala) and three (3) three commercial farms (Fort Hare dairy farm, Middledrift dairy farm and Seven-star dairy farm). Detection of M. tuberculosis complex was achieved by Polymerase Chain Reaction using primers for IS6110; whereas a genotypic drug resistance mutation was detected using Genotype MTBDRplus assays. Nine percent (9 percent) of respondents had more than 40 cows in their herd, while 60 percent reported between 10 and 20 cows in their herd. Relationship between farm size and vaccination for TB differed from forty-one percent (41 percent) being the highest to the least five percent (5 percent). The highest number of respondents who knew about relationship between TB cases and cattle location was ninety-one percent (91 percent). Approximately fifty-one percent (51 percent) of respondents had knowledge about wild life access to the farms. Relationship between import of cattle and farm size ranged from nine percent (9 percent) to thirty-five percent (35 percent). Cattle sickness in relation to farm size differed from forty-three (43 percent) being the highest to the least three percent (3 percent); while thirty-three percent (33 percent) of respondents had knowledge about health management. Respondents with knowledge about the occurrence of TB infections in farms were forty-eight percent (48 percent). The frequency of DNA isolation from samples ranged from the highest forty-five percent (45 percent) from water to the least twenty-two percent (22 percent) from soil. Fort Hare dairy farm had the highest number of positive samples forty-four percent (44 percent) from water samples; whereas Middledrift dairy farm had the lowest positive from water, seventeen percent (17 percent). Twelve (22 percent) out of 55 isolates showed resistance to INH and RMP that is, multi-drug resistance (MDR) and nine percent (9 percent) were sensitive to either INH or RMP. The mutations at rpoB gene differed from 58 percent being the highest to the least (23 percent). Fifty-seven percent (57 percent) of samples showed a S315T1 mutation while only 14 percent possessed a S531L in the katG gene. The highest inhA mutations were detected in T8A (80 percent) eighty percent and the least was observed in A16G (17 percent). The results of this study reveals that risk factors for bTB in cattle and dairy farm workers is a serious issue abound in the Eastern Cape of South Africa; with the possibility of widespread dissemination of multidrug resistant determinants in MTBC from the environment.
- Full Text:
- Date Issued: 2015
- Authors: Ntloko, Athini
- Date: 2015
- Subjects: Mycobacterium tuberculosis -- South Africa -- Eastern Cape Drug resistance in microorganisms Mycobacterial diseases
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/2689 , vital:27993
- Description: Mycobacterium bovis and other species of Mycobacterium tuberculosis complex (MTBC) can result to a zoonotic infection known as Bovine tuberculosis (bTB). MTBC has members that may contaminate an extensive range of hosts, including wildlife. Diverse wild species are known to cause disease in domestic livestock and are acknowledged as TB reservoirs. It has been a main study worldwide to deliberate on bTB risk factors as a result some studies focused on particular parts of risk factors such as wildlife and herd management. The objectives of this study were to design questionnaires from commercial farms and smallholding farms; isolate and identify MTBC from collected samples using culture and PCR assays recovered from Fort Hare, Middledrift and Seven star dairy farms; and assessing genotypic drug resistance through detection of mutations conferring resistance to INH and RMP associated with first line treatment for MTBC infection. Questionnaires were administered to thirty (30) smallholding farm owners in the two villages (kwaMasele and Qungqwala) and three (3) three commercial farms (Fort Hare dairy farm, Middledrift dairy farm and Seven-star dairy farm). Detection of M. tuberculosis complex was achieved by Polymerase Chain Reaction using primers for IS6110; whereas a genotypic drug resistance mutation was detected using Genotype MTBDRplus assays. Nine percent (9 percent) of respondents had more than 40 cows in their herd, while 60 percent reported between 10 and 20 cows in their herd. Relationship between farm size and vaccination for TB differed from forty-one percent (41 percent) being the highest to the least five percent (5 percent). The highest number of respondents who knew about relationship between TB cases and cattle location was ninety-one percent (91 percent). Approximately fifty-one percent (51 percent) of respondents had knowledge about wild life access to the farms. Relationship between import of cattle and farm size ranged from nine percent (9 percent) to thirty-five percent (35 percent). Cattle sickness in relation to farm size differed from forty-three (43 percent) being the highest to the least three percent (3 percent); while thirty-three percent (33 percent) of respondents had knowledge about health management. Respondents with knowledge about the occurrence of TB infections in farms were forty-eight percent (48 percent). The frequency of DNA isolation from samples ranged from the highest forty-five percent (45 percent) from water to the least twenty-two percent (22 percent) from soil. Fort Hare dairy farm had the highest number of positive samples forty-four percent (44 percent) from water samples; whereas Middledrift dairy farm had the lowest positive from water, seventeen percent (17 percent). Twelve (22 percent) out of 55 isolates showed resistance to INH and RMP that is, multi-drug resistance (MDR) and nine percent (9 percent) were sensitive to either INH or RMP. The mutations at rpoB gene differed from 58 percent being the highest to the least (23 percent). Fifty-seven percent (57 percent) of samples showed a S315T1 mutation while only 14 percent possessed a S531L in the katG gene. The highest inhA mutations were detected in T8A (80 percent) eighty percent and the least was observed in A16G (17 percent). The results of this study reveals that risk factors for bTB in cattle and dairy farm workers is a serious issue abound in the Eastern Cape of South Africa; with the possibility of widespread dissemination of multidrug resistant determinants in MTBC from the environment.
- Full Text:
- Date Issued: 2015
The diversity of root fungi associated with Erica species occurring in the Albany Centre of Endemism
- Authors: Bizabani, Christine
- Date: 2015
- Subjects: Ericaceae , Ericas , Roots (Botany) -- Diseases and pests , Mycorrhizal fungi , Polymerase chain reaction , Fungi -- Classification
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4160 , http://hdl.handle.net/10962/d1018575
- Description: South Africa has the highest species diversity of ericaceous plants belonging to the Erica genus. There are over 850 identified species in the Cape Floral Region. The Albany Centre of Endemism (ACOE) is located within this region and is a hotspot of diversity consisting of various plant genera. The success of Erica plants is ubiquitously attributed to mycorrhizal relationships they engage in with a diverse group of fungi. This symbiosis is known as the ericoid mycorrhizal (ERM) association. The overall aim of this study was to establish the diversity of root fungi associated with Erica plants using morphological, molecular and 454 pyrosequencing techniques. Six Erica species were identified using leaf and flower morphology according to taxonomic keys. The identified plants were Erica cerinthoides, Erica demissa, Erica chamissonis, Erica glumiflora, Erica caffra and Erica nemorosa. Roots from sampled plants were stained and examined microscopically to determine their mycorrhizal status. Ericoid mycorrhizal associations together with dark septate endophyte (DSE) structures and hyphae that did not form any specific structure were observed in all the roots. In addition arbuscular mycorrhizal (AM) structures in the form of vesicles were detected in E. glumiflora and E. cerinthoides. In order to identify the culturable fungi associated with the respective hosts, sterilised roots were placed on various culture media for cultivation. Thereafter isolated fungi were morphologically classified into 67 morphotypes. These were mostly sterile and darkly pigmented. Non-sporulating mycelia of variable colouration such as white, cream-yellowish, beige, green and brown were also observed. Further identification was carried out using molecular techniques. DNA was extracted separately from pure cultures and amplified using ITS1 and ITS4 primers in a polymerase chain reaction (PCR). Thereafter sequencing and Basic Local Alignment Search Tool (BLAST) were used to identify the isolates to generic level. The fungi were taxonomically classified into 54 operational taxonomic units and 94 percent were Ascomycetes and Helotiales was the dominant order. Unclassified Helotiales with affinities to fungi currently identified as Epacrid root fungus was common in all hosts. Other isolates that were identified included Oidiodendron, Meliniomyces, Phialocephala, Cadophora, Lachnum, Leohumicola Cryptosporiopsis, Chaetomium, Acremonium and Epicoccum species. Basidiomycetes were represented by two OTUs belonging to the genus Mycena. Four OTUs comprised fungi that had no significant alignments in the reference databases. Direct root DNA extraction together with 454 pyrosequencing was used to detect the diversity of culturable and unculturable fungi associated with the identified hosts. The ITS2 region was targeted for sequencing. Although Ascomycetes remained the dominant phyla, Basidiomycetes were also detected in all host plants. Glomeromycota was present in E. caffra and E. cerinthoides. Helotiales was dominant in all Erica plants with the exception of E. cerinthoides and E. chamissonis which were dominated by the order Chaetothyriales. The OTUs identified to genus level included Epacris pulchella root fungus, Oidiodendron cf. maius, Acremonium implicatum, Leohumicola, Lachnum, Capronia and Mycena species. Culture-based techniques and pyrosequencing detected similar fungal composition comprising Ascomycetes, while, pyrosequencing was able to detect Glomeromycetes and Basidiomycetes.
- Full Text:
- Date Issued: 2015
The diversity of root fungi associated with Erica species occurring in the Albany Centre of Endemism
- Authors: Bizabani, Christine
- Date: 2015
- Subjects: Ericaceae , Ericas , Roots (Botany) -- Diseases and pests , Mycorrhizal fungi , Polymerase chain reaction , Fungi -- Classification
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4160 , http://hdl.handle.net/10962/d1018575
- Description: South Africa has the highest species diversity of ericaceous plants belonging to the Erica genus. There are over 850 identified species in the Cape Floral Region. The Albany Centre of Endemism (ACOE) is located within this region and is a hotspot of diversity consisting of various plant genera. The success of Erica plants is ubiquitously attributed to mycorrhizal relationships they engage in with a diverse group of fungi. This symbiosis is known as the ericoid mycorrhizal (ERM) association. The overall aim of this study was to establish the diversity of root fungi associated with Erica plants using morphological, molecular and 454 pyrosequencing techniques. Six Erica species were identified using leaf and flower morphology according to taxonomic keys. The identified plants were Erica cerinthoides, Erica demissa, Erica chamissonis, Erica glumiflora, Erica caffra and Erica nemorosa. Roots from sampled plants were stained and examined microscopically to determine their mycorrhizal status. Ericoid mycorrhizal associations together with dark septate endophyte (DSE) structures and hyphae that did not form any specific structure were observed in all the roots. In addition arbuscular mycorrhizal (AM) structures in the form of vesicles were detected in E. glumiflora and E. cerinthoides. In order to identify the culturable fungi associated with the respective hosts, sterilised roots were placed on various culture media for cultivation. Thereafter isolated fungi were morphologically classified into 67 morphotypes. These were mostly sterile and darkly pigmented. Non-sporulating mycelia of variable colouration such as white, cream-yellowish, beige, green and brown were also observed. Further identification was carried out using molecular techniques. DNA was extracted separately from pure cultures and amplified using ITS1 and ITS4 primers in a polymerase chain reaction (PCR). Thereafter sequencing and Basic Local Alignment Search Tool (BLAST) were used to identify the isolates to generic level. The fungi were taxonomically classified into 54 operational taxonomic units and 94 percent were Ascomycetes and Helotiales was the dominant order. Unclassified Helotiales with affinities to fungi currently identified as Epacrid root fungus was common in all hosts. Other isolates that were identified included Oidiodendron, Meliniomyces, Phialocephala, Cadophora, Lachnum, Leohumicola Cryptosporiopsis, Chaetomium, Acremonium and Epicoccum species. Basidiomycetes were represented by two OTUs belonging to the genus Mycena. Four OTUs comprised fungi that had no significant alignments in the reference databases. Direct root DNA extraction together with 454 pyrosequencing was used to detect the diversity of culturable and unculturable fungi associated with the identified hosts. The ITS2 region was targeted for sequencing. Although Ascomycetes remained the dominant phyla, Basidiomycetes were also detected in all host plants. Glomeromycota was present in E. caffra and E. cerinthoides. Helotiales was dominant in all Erica plants with the exception of E. cerinthoides and E. chamissonis which were dominated by the order Chaetothyriales. The OTUs identified to genus level included Epacris pulchella root fungus, Oidiodendron cf. maius, Acremonium implicatum, Leohumicola, Lachnum, Capronia and Mycena species. Culture-based techniques and pyrosequencing detected similar fungal composition comprising Ascomycetes, while, pyrosequencing was able to detect Glomeromycetes and Basidiomycetes.
- Full Text:
- Date Issued: 2015
Identifying appropriate paths for establishing sustainable irrigated crop based farming business on smallholder irrigation schemes: a case of Ncora Irrigation Scheme
- Authors: Mbizana, Nandipha
- Date: 2014
- Subjects: Crops -- Irrigation -- South Africa -- Eastern Cape , Crops -- Water requirements -- South Africa -- Eastern Cape , Agricultural extension work -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc Agric (Agricultural Economics)
- Identifier: vital:11213 , http://hdl.handle.net/10353/d1016205 , Crops -- Irrigation -- South Africa -- Eastern Cape , Crops -- Water requirements -- South Africa -- Eastern Cape , Agricultural extension work -- South Africa -- Eastern Cape
- Description: The study examined the impact of small scale irrigation technology in crop production under Ncora areas of Cofimvaba. To achieve the objective of the study, data were collected from 212 farmers engaged in various crop enterprises under the Ncora. The farmers were randomly selected. Descriptive Statistics, DEA model, linear regression model and gross margin analysis were used to analyse the results obtained from the survey. The descriptive results showed that Ncora farmers are small-scale farmers cultivating small hectare of land and using simple farm tools, mainly using furrow irrigation. Furthermore, they produce more than one crop enterprises. The gross margin Analysis shows that Ncora cultivation is profitable. The most profitable crop was found to be maize than potatoes. Farm production function revealed that land, labour and purchased inputs had a positive relationship with the output of the enterprises. SPSS was used to run data for linear regression model (OLS). It was suggested that extension services and private organizations assist farmers especially the emerging ones via provision of training, processing and storage facilities. Furthermore, continuous monitoring of soil and water quality as well as ground water table was recommended, in order to ensure sustainability of Ncora irrigation in the area.
- Full Text:
- Date Issued: 2014
- Authors: Mbizana, Nandipha
- Date: 2014
- Subjects: Crops -- Irrigation -- South Africa -- Eastern Cape , Crops -- Water requirements -- South Africa -- Eastern Cape , Agricultural extension work -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc Agric (Agricultural Economics)
- Identifier: vital:11213 , http://hdl.handle.net/10353/d1016205 , Crops -- Irrigation -- South Africa -- Eastern Cape , Crops -- Water requirements -- South Africa -- Eastern Cape , Agricultural extension work -- South Africa -- Eastern Cape
- Description: The study examined the impact of small scale irrigation technology in crop production under Ncora areas of Cofimvaba. To achieve the objective of the study, data were collected from 212 farmers engaged in various crop enterprises under the Ncora. The farmers were randomly selected. Descriptive Statistics, DEA model, linear regression model and gross margin analysis were used to analyse the results obtained from the survey. The descriptive results showed that Ncora farmers are small-scale farmers cultivating small hectare of land and using simple farm tools, mainly using furrow irrigation. Furthermore, they produce more than one crop enterprises. The gross margin Analysis shows that Ncora cultivation is profitable. The most profitable crop was found to be maize than potatoes. Farm production function revealed that land, labour and purchased inputs had a positive relationship with the output of the enterprises. SPSS was used to run data for linear regression model (OLS). It was suggested that extension services and private organizations assist farmers especially the emerging ones via provision of training, processing and storage facilities. Furthermore, continuous monitoring of soil and water quality as well as ground water table was recommended, in order to ensure sustainability of Ncora irrigation in the area.
- Full Text:
- Date Issued: 2014
South African women's literature and the ecofeminist perspective
- Authors: Ewing, Maureen Colleen
- Date: 2013-05-24
- Subjects: Ecofeminism in literature Ecology in literature Nature in literature South African fiction -- History and criticism Smith, Pauline, 1883-1959 Schreiner, Olive, 1855-1920 Matthee, Dalene, 1938-2005 Poland, Marguerite
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2287 , http://hdl.handle.net/10962/d1007808
- Description: A social-constructionist ecofeminist perspective argues that patriarchal society separates the human (or culture) from nature, which causes a false assumption that humanity possesses the right, as a superior species, to dominate nature. This perspective integrates the domination of nature with social conflicts, including but not limited to racial discrimination, gender oppression, and class hierarchies. Understanding how these various forms of oppression interrelate forms the main goal of an ecofeminist perspective. Since the nature-culture, female-male, and whitenonwhite conflicts resonate and interlock throughout South Africa's history, socialconstructionist ecofeminism is an indispensable perspective for analysing South African literature. This thesis takes a social-constructionist ecofeminist approach and applies it to four women authors that write about South African society between the years 1860-1900. This thesis includes the following authors and their works: Olive Schreiner (1855-1920) and two of her novels, The Story of an African Farm (1883) and From Man to Man (published posthumously in 1927); Pauline Smith (1882-1959) and her novel The Beadle (1926); Dalene Matthee (1938- ) and three of her novels, Circles in a Forest (1984), Fiela's Child (1986), and The Mulberry Forest (1987); and Marguerite Poland (1950- ) and one of her novels, Shades (1993). This thesis investigates two women from the time period (Schreiner and Smith) and two women from a late twentieth century perspective (Matthee and Poland) and compares how they depict the natural environment, how they construct gender, and how they interpret class and race power struggles. This thesis concludes that the social-constructionist perspective offers unique insights into these four authors. Schreiner's novels reveal her concerns about gender and racial conflicts in South Africa and her understanding of the nature-culture dichotomy as sustained by Social Darwinism. Smith offers insights into the complex power structures in a rural Afrikaans society that keep women and nonwhite races silent. Matthee writes nature as an active participant in her novels; the social and ecological conflicts emphasise the transformation of the Knysna area. Poland explores the racial tensions, gender conflicts, and environmental concerns that preceded the South African War. Schreiner, Smith, Matthee, and Poland make up a small cross-section of South African literature, but they provide a basis for further discussing the ecofeminist perspective within a South African context. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Authors: Ewing, Maureen Colleen
- Date: 2013-05-24
- Subjects: Ecofeminism in literature Ecology in literature Nature in literature South African fiction -- History and criticism Smith, Pauline, 1883-1959 Schreiner, Olive, 1855-1920 Matthee, Dalene, 1938-2005 Poland, Marguerite
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2287 , http://hdl.handle.net/10962/d1007808
- Description: A social-constructionist ecofeminist perspective argues that patriarchal society separates the human (or culture) from nature, which causes a false assumption that humanity possesses the right, as a superior species, to dominate nature. This perspective integrates the domination of nature with social conflicts, including but not limited to racial discrimination, gender oppression, and class hierarchies. Understanding how these various forms of oppression interrelate forms the main goal of an ecofeminist perspective. Since the nature-culture, female-male, and whitenonwhite conflicts resonate and interlock throughout South Africa's history, socialconstructionist ecofeminism is an indispensable perspective for analysing South African literature. This thesis takes a social-constructionist ecofeminist approach and applies it to four women authors that write about South African society between the years 1860-1900. This thesis includes the following authors and their works: Olive Schreiner (1855-1920) and two of her novels, The Story of an African Farm (1883) and From Man to Man (published posthumously in 1927); Pauline Smith (1882-1959) and her novel The Beadle (1926); Dalene Matthee (1938- ) and three of her novels, Circles in a Forest (1984), Fiela's Child (1986), and The Mulberry Forest (1987); and Marguerite Poland (1950- ) and one of her novels, Shades (1993). This thesis investigates two women from the time period (Schreiner and Smith) and two women from a late twentieth century perspective (Matthee and Poland) and compares how they depict the natural environment, how they construct gender, and how they interpret class and race power struggles. This thesis concludes that the social-constructionist perspective offers unique insights into these four authors. Schreiner's novels reveal her concerns about gender and racial conflicts in South Africa and her understanding of the nature-culture dichotomy as sustained by Social Darwinism. Smith offers insights into the complex power structures in a rural Afrikaans society that keep women and nonwhite races silent. Matthee writes nature as an active participant in her novels; the social and ecological conflicts emphasise the transformation of the Knysna area. Poland explores the racial tensions, gender conflicts, and environmental concerns that preceded the South African War. Schreiner, Smith, Matthee, and Poland make up a small cross-section of South African literature, but they provide a basis for further discussing the ecofeminist perspective within a South African context. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
An investigation into how grade 10 learners make meaning during the teaching and learning of the topic on nutrition in Life Science: a case study
- Mwiikeni, Helena Twiihaleni, Shimwafeni-Mwiikeni, Helena Twiihaleni
- Authors: Mwiikeni, Helena Twiihaleni , Shimwafeni-Mwiikeni, Helena Twiihaleni
- Date: 2013
- Subjects: Nutrition -- Study and teaching (Secondary) -- Namibia -- Oshana -- Case studies Environmental sciences -- Study and teaching (Secondary) -- Namibia -- Oshana -- Case studies Experiential learning -- Namibia -- Oshana -- Case studies Education, Secondary -- Namibia -- Oshana
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: vital:1403 , http://hdl.handle.net/10962/d1001876
- Description: The integration of learners’ prior everyday knowledge and experiences during teaching and learning is a pre-requisite in the Namibian curriculum. The curriculum states that if learners are taught in a way which builds on what they already know and they relate new knowledge to the reality around them, their learning in school can be made more meaningful. Thus, learners’ meaning making in the topic on nutrition was researched to find out whether elicitation and integration of learners’ prior everyday knowledge and experience in the nutrition topic enhanced or constrained their learning. This study was conducted with my grade10 learners at the school where I am currently teaching. The school is located in a rural area in Oshana region in Northern Namibia. This study is situated within an interpretive paradigm. Within the interpretive paradigm a qualitative case study approach was adopted. I considered this methodological orientation appropriate in this study as it allowed me to use the following methods: document analysis, brainstorming and discussion, semi-structured interviews and a focus group interview, practical activities with worksheets and observation and reflection. Multiple methods to gather data were used for triangulation and validation purposes. For data analysis purposes, the data sets were colour coded to derive themes and analytical statements. Ethical consideration was also taken seriously in this study. The findings from this study revealed that integration of learners’ prior everyday knowledge and experience enabled learners to understand science better particularly in the topic of nutrition. The study also revealed that learners possess a lot of prior everyday knowledge and experience about food they eat in their homes. However, data from the community members revealed that there are some contradictions between learners’ prior everyday knowledge and the science content of the topic. Nonetheless, engaging learners in practical activities in the testing of food (local and conventional western type foods) helped them to make meaning of the content learned. I therefore, recommend that learners’ prior everyday knowledge and experiences should be incorporated during teaching and learning of the topic on nutrition. The study also recommends that the Department of Education should ensure that teachers get the necessary support and training on how to integrate learners’ prior everyday knowledge and experiences.
- Full Text:
- Date Issued: 2013
- Authors: Mwiikeni, Helena Twiihaleni , Shimwafeni-Mwiikeni, Helena Twiihaleni
- Date: 2013
- Subjects: Nutrition -- Study and teaching (Secondary) -- Namibia -- Oshana -- Case studies Environmental sciences -- Study and teaching (Secondary) -- Namibia -- Oshana -- Case studies Experiential learning -- Namibia -- Oshana -- Case studies Education, Secondary -- Namibia -- Oshana
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: vital:1403 , http://hdl.handle.net/10962/d1001876
- Description: The integration of learners’ prior everyday knowledge and experiences during teaching and learning is a pre-requisite in the Namibian curriculum. The curriculum states that if learners are taught in a way which builds on what they already know and they relate new knowledge to the reality around them, their learning in school can be made more meaningful. Thus, learners’ meaning making in the topic on nutrition was researched to find out whether elicitation and integration of learners’ prior everyday knowledge and experience in the nutrition topic enhanced or constrained their learning. This study was conducted with my grade10 learners at the school where I am currently teaching. The school is located in a rural area in Oshana region in Northern Namibia. This study is situated within an interpretive paradigm. Within the interpretive paradigm a qualitative case study approach was adopted. I considered this methodological orientation appropriate in this study as it allowed me to use the following methods: document analysis, brainstorming and discussion, semi-structured interviews and a focus group interview, practical activities with worksheets and observation and reflection. Multiple methods to gather data were used for triangulation and validation purposes. For data analysis purposes, the data sets were colour coded to derive themes and analytical statements. Ethical consideration was also taken seriously in this study. The findings from this study revealed that integration of learners’ prior everyday knowledge and experience enabled learners to understand science better particularly in the topic of nutrition. The study also revealed that learners possess a lot of prior everyday knowledge and experience about food they eat in their homes. However, data from the community members revealed that there are some contradictions between learners’ prior everyday knowledge and the science content of the topic. Nonetheless, engaging learners in practical activities in the testing of food (local and conventional western type foods) helped them to make meaning of the content learned. I therefore, recommend that learners’ prior everyday knowledge and experiences should be incorporated during teaching and learning of the topic on nutrition. The study also recommends that the Department of Education should ensure that teachers get the necessary support and training on how to integrate learners’ prior everyday knowledge and experiences.
- Full Text:
- Date Issued: 2013
The use of English and isiXhosa in teaching and learning Physical Sciences in four schools in King Williams Town education district of the Eastern Cape: a case study
- Authors: Sibanda, Busani
- Date: 2013
- Language: English
- Type: Thesis , Masters , M Ed
- Identifier: vital:16222 , http://hdl.handle.net/10353/d1019733
- Description: The present study investigates the use of English and isiXhosa in teaching and learning Physical Sciences in four King Williams Town schools. Physical Sciences educators and Grade 11 Physical Sciences learners were interviewed to find out about their perceptions with regard to the language(s) used in the learning and teaching of the subject Physical Sciences. The same educators and learners were also observed to find out their actual language practices in class. The findings revealed that English was the preferred medium of instruction in the learning and teaching of Physical Sciences, even though the majority of learners had low proficiency in English. Both teachers and learners extensively use code-switching to bridge this language gap in order to improve the learning of content. The choice to use isiXhosa to bridge the English second language barrier was influenced by the language profile of the learners. However, even in lessons in which teachers used code-switching, the participation of learners in class discussions was very low because the delivery of the lessons was still teacher-centred. The National Department of Education assessment policy seems to limit schools toward adopting English as the LoLT even though learners in these schools were isiXhosa first language speakers. The fact that all assessment are done in English leads to school adopting English on LoLT. Schools adopted the English only policy as way of promoting learners’ learning and understanding of English, so that the learners are not disadvantaged by the English language factor when writing examinations.
- Full Text:
- Date Issued: 2013
- Authors: Sibanda, Busani
- Date: 2013
- Language: English
- Type: Thesis , Masters , M Ed
- Identifier: vital:16222 , http://hdl.handle.net/10353/d1019733
- Description: The present study investigates the use of English and isiXhosa in teaching and learning Physical Sciences in four King Williams Town schools. Physical Sciences educators and Grade 11 Physical Sciences learners were interviewed to find out about their perceptions with regard to the language(s) used in the learning and teaching of the subject Physical Sciences. The same educators and learners were also observed to find out their actual language practices in class. The findings revealed that English was the preferred medium of instruction in the learning and teaching of Physical Sciences, even though the majority of learners had low proficiency in English. Both teachers and learners extensively use code-switching to bridge this language gap in order to improve the learning of content. The choice to use isiXhosa to bridge the English second language barrier was influenced by the language profile of the learners. However, even in lessons in which teachers used code-switching, the participation of learners in class discussions was very low because the delivery of the lessons was still teacher-centred. The National Department of Education assessment policy seems to limit schools toward adopting English as the LoLT even though learners in these schools were isiXhosa first language speakers. The fact that all assessment are done in English leads to school adopting English on LoLT. Schools adopted the English only policy as way of promoting learners’ learning and understanding of English, so that the learners are not disadvantaged by the English language factor when writing examinations.
- Full Text:
- Date Issued: 2013
Evaluating the sustainable management of the State indigenous forests in the Eastern Cape Province
- Authors: Quvile, Nkosipendule
- Date: 2012
- Subjects: Forests and forestry -- South Africa -- Eastern Cape Forest conservation -- South Africa -- Eastern Cape Forest ecology -- South Africa -- Eastern Cape Sustainable forestry -- South Africa -- Eastern Cape Forest management -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MBA
- Identifier: vital:775 , http://hdl.handle.net/10962/d1003896
- Description: This research assesses the state of sustainability of State indigenous forests in the Eastern Cape and provides recommendations to improve their sustainability. The Eastern Cape Indigenous Forest Management Audit (ECIFMA) report of 2009 provided the primary data for this assessment (DAFF, 2009). The research was inspired by the fact that the global challenge of forestry destruction and degradation where the extent of forests is being reduced at an alarming rate of 6% annually. It became essential for global leaders to develop policies and strategies that sought to promote sustainable forest management. The monitoring of sustainability of forests was only possible through use of globally and nationally developed sets of criteria and indicators. Eleven forest estates responsible for the management of State indigenous forests in the Eastern Cape were selected for this research. The choice was influenced by the availability of audit data from the ECIFMA report of 2009. This report contained performance information of 41 indicators under 18 criteria for monitoring sustainable forest management as extracted from the PCI&S assessment checklist developed for monitoring the sustainability of indigenous forests in South Africa (DWAF, 2005). The data was refined using the MCA methods (ranking and scoring) as described by Mendoza and Prabhu (2000). These methods yielded to the determination of the performance of indicators of forest sustainability. It was thus important to conclude the research by responding to the following questions: • What is the state of sustainability of the State indigenous forests in the Eastern Cape? • What recommendations could be made to improve the sustainability of State indigenous forests? It was found that the State indigenous forests were not managed in a sustainable manner. The research report is concluded by providing concrete recommendations to improve forest sustainability.
- Full Text:
- Date Issued: 2012
- Authors: Quvile, Nkosipendule
- Date: 2012
- Subjects: Forests and forestry -- South Africa -- Eastern Cape Forest conservation -- South Africa -- Eastern Cape Forest ecology -- South Africa -- Eastern Cape Sustainable forestry -- South Africa -- Eastern Cape Forest management -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MBA
- Identifier: vital:775 , http://hdl.handle.net/10962/d1003896
- Description: This research assesses the state of sustainability of State indigenous forests in the Eastern Cape and provides recommendations to improve their sustainability. The Eastern Cape Indigenous Forest Management Audit (ECIFMA) report of 2009 provided the primary data for this assessment (DAFF, 2009). The research was inspired by the fact that the global challenge of forestry destruction and degradation where the extent of forests is being reduced at an alarming rate of 6% annually. It became essential for global leaders to develop policies and strategies that sought to promote sustainable forest management. The monitoring of sustainability of forests was only possible through use of globally and nationally developed sets of criteria and indicators. Eleven forest estates responsible for the management of State indigenous forests in the Eastern Cape were selected for this research. The choice was influenced by the availability of audit data from the ECIFMA report of 2009. This report contained performance information of 41 indicators under 18 criteria for monitoring sustainable forest management as extracted from the PCI&S assessment checklist developed for monitoring the sustainability of indigenous forests in South Africa (DWAF, 2005). The data was refined using the MCA methods (ranking and scoring) as described by Mendoza and Prabhu (2000). These methods yielded to the determination of the performance of indicators of forest sustainability. It was thus important to conclude the research by responding to the following questions: • What is the state of sustainability of the State indigenous forests in the Eastern Cape? • What recommendations could be made to improve the sustainability of State indigenous forests? It was found that the State indigenous forests were not managed in a sustainable manner. The research report is concluded by providing concrete recommendations to improve forest sustainability.
- Full Text:
- Date Issued: 2012