List of Titles

De-identification of personal information for use in software testing to ensure compliance with the Protection of Personal Information Act

- Mark, Stephen John

Authors: Mark, Stephen John
Date: 2018
Subjects: Data processing , Information technology -- Security measures , Computer security -- South Africa , Data protection -- Law and legislation -- South Africa , Data encryption (Computer science) , Python (Computer program language) , SQL (Computer program language) , Protection of Personal Information Act (POPI)
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/63888 , vital:28503
Description: Encryption of Personally Identifiable Information stored in a Structured Query Language Database has been difficult for a long time. This is owing to block-cipher encryption algorithms changing the length and type of the input data when encrypted, which cannot subsequently be stored in the database without altering its structure. As the enactment of the South African Protection of Personal Information Act, No 4 of 2013 (POPI), was set in motion with the appointment of the Information Regulators Office in December 2016, South African companies are intensely focused on implementing compliance strategies and processes. The legislation, promulgated in 2013, encompasses the processing and storage of personally identifiable information (PII), ensuring that corporations act responsibly when collecting, storing and using individuals’ personal data. The Act comprises eight broad conditions that will become legislation once the new Information Regulator’s office is fully equipped to carry out their duties. POPI requires that individuals’ data should be kept confidential from all but those who specifically have permission to access the data. This means that not all members of IT teams should have access to the data unless it has been de-identified. This study tests an implementation of the Fixed Feistel 1 algorithm from the National Institute of Standards and Technology (NIST) “Special Publication 800-38G: Recommendation for Block Cipher Modes of Operation : Methods for Format-Preserving Encryption” using the LibFFX Python library. The Python scripting language was used for the experiments. The research shows that it is indeed possible to encrypt data in a Structured Query Language Database without changing the database schema using the new Format-Preserving encryption technique from NIST800-38G. Quality Assurance software testers can then run their full set of tests on the encrypted database. There is no reduction of encryption strength when using the FF1 encryption technique, compared to the underlying AES-128 encryption algorithm. It further shows that the utility of the data is not lost once it is encrypted.
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Demographic change in the Upper Tsitsa Catchment: the integration of census and land cover data for 2001 and 2011

- Hodgson, Danuta Lorina

Authors: Hodgson, Danuta Lorina
Date: 2018
Subjects: Land use -- South Africa -- Eastern Cape , Watersheds -- South Africa -- Eastern Cape , Thematic maps -- South Africa -- Eastern Cape , Population density -- South Africa -- Eastern Cape , Mzimvubu River Watershed (South Africa) -- Census , Upper Tsitsa Catchment (South Africa)
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/57296 , vital:26870
Description: The purpose of this research was to determine if the integration of census and land cover data could provide evidence of spatial patterns and temporal change for the Upper Tsitsa Catchment. This thesis contributed to academic literature with regards to dasymetric mapping and provided a database for the Ntabelanga and Laleni Ecological Infrastructure Project. The study took place in the Upper Tsitsa Catchment which is located in the north-eastern region of the Eastern Cape and falls within the uMzimvubu Catchment. South Africa National Population Censuses for 2001 and 2011 and the National Land Cover data sets for 2000 and 2013/14 were used to create dasymetric maps depicting demographic changes over time for the catchment area. Spatial statistics were performed on the dasymetric and choropleth map to determine the accuracy of the data that was created. From the results, it was found that although the statistics were skewed, the method was more accurate in displaying the population densities, which was noted during the sampling process of the spatial analysis. It was found that there had been a decrease in the population density within the catchment. This affected the density of several other variables such as population race group, language and employment status statistics as decreases in these values could be due to individuals migrating out of the catchment as well as socio-economic upliftment, such as having better access to services. The use of dasymetric mapping allowed an accurate representation of the population density from the census data to be created. The results of the dasymetric mapping were more accurate as they depicted where the population within the enumeration areas were located, and recognised that some areas were populated while some areas were not. To conclude, it was found that using dasymetric mapping provided reliable and useful data about population density and enables comparison over time.
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Designing and prototyping WebRTC and IMS integration using open source tools

- Motsumi, Tebagano Valerie

Authors: Motsumi, Tebagano Valerie
Date: 2018
Subjects: Internet Protocol multimedia subsystem , Session Initiation Protocol (Computer network protocol) , Computer software -- Development , Web Real-time Communications (WebRTC)
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/63245 , vital:28386
Description: WebRTC, or Web Real-time Communications, is a collection of web standards that detail the mechanisms, architectures and protocols that work together to deliver real-time multimedia services to the web browser. It represents a significant shift from the historical approach of using browser plugins, which over time, have proven cumbersome and problematic. Furthermore, it adopts various Internet standards in areas such as identity management, peer-to-peer connectivity, data exchange and media encoding, to provide a system that is truly open and interoperable. Given that WebRTC enables the delivery of multimedia content to any Internet Protocol (IP)-enabled device capable of hosting a web browser, this technology could potentially be used and deployed over millions of smartphones, tablets and personal computers worldwide. This service and device convergence remains an important goal of telecommunication network operators who seek to enable it through a converged network that is based on the IP Multimedia Subsystem (IMS). IMS is an IP-based subsystem that sits at the core of a modern telecommunication network and acts as the main routing substrate for media services and applications such as those that WebRTC realises. The combination of WebRTC and IMS represents an attractive coupling, and as such, a protracted investigation could help to answer important questions around the technical challenges that are involved in their integration, and the merits of various design alternatives that present themselves. This thesis is the result of such an investigation and culminates in the presentation of a detailed architectural model that is validated with a prototypical implementation in an open source testbed. The model is built on six requirements which emerge from an analysis of the literature, including previous interventions in IMS networks and a key technical report on design alternatives. Furthermore, this thesis argues that the client architecture requires support for web-oriented signalling, identity and call handling techniques leading to a potential for IMS networks to natively support these techniques as operator networks continue to grow and develop. The proposed model advocates the use of SIP over WebSockets for signalling and DTLS-SRTP for media to enable one-to-one communication and can be extended through additional functions resulting in a modular architecture. The model was implemented using open source tools which were assembled to create an experimental network testbed, and tests were conducted demonstrating successful cross domain communications under various conditions. The thesis has a strong focus on enabling ordinary software developers to assemble a prototypical network such as the one that was assembled and aims to enable experimentation in application use cases for integrated environments.
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Developing a citizen technician based approach to suspended sediment monitoring in the Tsitsa River catchment, Eastern Cape, South Africa

- Bannatyne, Laura Joan

Authors: Bannatyne, Laura Joan
Date: 2018
Subjects: Sediments (Geology) -- Management , Sediments (Geology) -- South Africa -- Eastern Cape , Watersheds -- South Africa -- Eastern Cape , Suspended sediments -- South Africa -- Eastern Cape , Suspended sediments -- Monitoring -- Citizen participation , Tsitsa River
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/62593 , vital:28211
Description: Suspended sediment (SS) in channels is spatiotemporally heterogeneous and, over the long term, is known to be moved predominantly by flood flows with return periods of ~1 - 1.5 years. Flood flows in the Tsitsa catchment (Eastern Cape Province, South Africa) are unpredictable, and display a wide range of discharges. Direct, flood-focused SS sampling at sub-catchment scale was required to provide a SS baseline against which to monitor the impact on SS of catchment rehabilitation interventions, to determine the relative contributions of sub-catchments to SS loads and yields at the site of the proposed Ntabelanga Dam wall, and to verify modelled SS baselines, loads and yields. Approaches to SS sampling relying on researcher presence and/or installed equipment to adequately monitor SS through flood flows were precluded by cost, and the physical and socioeconomic conditions in the project area. A citizen technician (CT)-based flood-focused approach to direct SS sampling was developed and implemented. It was assessed in terms of its efficiency and effectiveness, the proficiency of the laboratory analysis methods, and the accuracy of the resulting SS data. A basic laboratory protocol for SSC analysis was developed, but is not the focus of this thesis. Using basic sampling equipment and smartphone-based reporting protocols, local residents at eleven points on the Tsitsa River and its major tributaries were employed as CTs. They were paid to take water samples during daylight hours at sub-daily timestep, with the emphasis on sampling through flood flows. The method was innovative in that it opted for manual sampling against a global trend towards instrumentation. Whilst the management of CTs formed a significant project component, the CTs benefitted directly through remuneration and work experience opportunities. The sampling method was evaluated at four sites from December 2015 - May 2016. The CTs were found to have efficiently and effectively sampled SS through a range of water levels, particularly in the main Tsitsa channel. An acceptable level of proficiency and accuracy was achieved, and many flood events were successfully defined by multiple data points. The method was chiefly limited by the inability of CTs to sample overnight rises and peaks occurring as a result of afternoon thunderstorms, particularly in small tributaries. The laboratory process was responsible for some losses in proficiency and accuracy. Improved laboratory quality control was therefore recommended. The CT-based approach can be adapted to other spatial and temporal scales in other areas, and to other environmental monitoring applications.
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Developing and testing the congruency of selected biological indicators and an existing tool designed to assess wetland health in agricultural settings in the KZN Midlands

- Kubheka, Patrick Skhumbuzo

Authors: Kubheka, Patrick Skhumbuzo
Date: 2018
Subjects: Wetland conservation -- South Africa -- KwaZulu-Natal , Wetland management -- South Africa -- KwaZulu-Natal , Wetland ecology -- South Africa -- KwaZulu-Natal , Ecosystem services -- South Africa -- KwaZulu-Natal , Environmental monitoring -- South Africa -- KwaZulu-Natal , Water quality biological assessment -- South Africa -- KwaZulu-Natal
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/58310 , vital:27211
Description: Despite the fact that wetlands have been understood to be important for a wide range of ecosystem services, wetlands continue to be degraded globally. There has been a growing need to develop biomonitoring tools that reflect the present ecological state of wetlands, but very few attempts have been made in South Africa to achieve this, and those that have attempted this have generally achieved limited success. This study was conducted to develop and test the congruency of four selected biological indicators (dragonflies, frogs, macroinveterbrates and plants) in relation to the assessment of present ecological state using an existing method in South Africa, "WET-Health". WET-Health assessments rely primarily on transformations to a wetland that result from human impacts in both the catchment and the wetland itself. Using the tool, a health score is obtained that is consistent with the Department of Water Affairs (DWA) current "present ecological state” as applied to river health assessment. The study was conducted in agricultural settings of the Midlands of KwaZulu-Natal based on 13 wetlands. The selected wetlands were scored using WET - Health and grouped in four different ecological condition classes (A, B, C and D). Physical characteristics (wetland area, mean depth), biological characteristics (species cover/abundance, presence and species richness), and chemical characteristics (ammonia, pH, sulphate, nitrogen and phosphate) were also recorded in the selected wetlands. Nineteen different species of dragonfly were recorded in this study. The study demonstrated that dragonflies are a promising bioindicator of wetland present ecological state as the dragonfly index was found to be closely correlated with WET- Health scores. Open water bodies within the selected wetlands were the focus of dragonfly sampling, as male dragonflies are territorial and they will patrol or be found around this habitat. Emergent vegetation dominated by sedges formed the focus of macroinvertebrate sampling in this study because greater numbers of macroinvertebrate families were found in this biotope in comparison to open water areas with no emergent vegetation. A total of 47 macroinvertebrate families were recorded in this study, but SASS5 scores based on macroinvetebrates showed no correlation with WET-Health scores. A total of 10 different frog species were recorded in this study. All the species were common frog species found in most parts of the country. Frog species richness and occurrence showed no correlation with WET- Health scores. A total of twenty samples of two meter radius were measured per wetland and sampled for plant species and estimation of cover-abundance of each species per sample. Over 50 different plant species were recorded in this study, and both species accumulation and species richness showed a degree of correlation with WET-Health scores. All the wetlands in class A had generally higher species accumulation rate and species richness compared to the other wetland classes. In addition to testing the congruency of four selected biological indicators with WET- Health, water quality was measured in all the wetlands. Wetlands in class A were associated with improved water quality as the water passes through the wetland. However, wetlands in class C and D did not show consistently improved water quality between the apex and the toe of these wetlands. In some cases the water quality deteriorated as it passed through wetlands in these two classes.
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Development and optimisation of a novel Plasmodium falciparum Hsp90-Hop interaction assay

- Wambua, Lynn

Authors: Wambua, Lynn
Date: 2018
Subjects: Plasmodium falciparum , Molecular chaperones , Heat shock proteins , Protein-protein interactions , Antimalarials
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/62626 , vital:28216
Description: Protein-protein interactions are involved in a range of disease processes and thus have become the focus of many drug discovery programs. Widespread drug resistance to all currently used antimalarial drugs drives the search for alternative drug targets with novel mechanisms of action that offer new therapeutic options. Molecular chaperones such as heat shock proteins facilitate protein folding, play a role in protein trafficking and prevent protein misfolding in cells under stress. Heat shock protein 90 (Hsp90) is a well-studied chaperone that has been the focus of cancer drug development with moderate success. In Plasmodium falciparum (P. falciparum), heat shock proteins are thought to play a vital role in parasite survival of the physiologically diverse habitats of the parasite lifecycle and because Hsp90 is prominently expressed in P. falciparum, the chaperone is considered a potentially ideal drug target. Hsp90 function in cells is regulated by interactions with co-chaperones, which includes Heat shock protein 70-Heat shock protein 90 organising protein (Hop). As opposed to directly inhibiting Hsp90 activity, targeting Hsp90 interaction with Hop has recently been suggested as an alternative method of Hsp90 inhibition that has not been explored in P. falciparum. The aim of this research project was to demonstrate PfHsp90 and PfHop robustly interact in vitro and to facilitate high-throughput screening of PfHsp90-PfHop inhibitors by developing and optimising a novel plate capture Hsp90-Hop interaction assay. To establish the assay, the respective domains of the proteins that mediate Hsp90-Hop interaction were used (Hsp90 C- terminal domain and Hop TPR2A domain). The human Hsp90 C-terminal domain and glutathione-S-transferase (GST) coding sequences were cloned into pET-28a(+) and murine and P. falciparum TPR2A sequences into pGEX-4T-1 plasmids to enable expression of histidine-tagged and GST fusion proteins, respectively, in Escherichia coli. The P. falciparum Hsp90 C-terminal domain sequence cloned into pET-28a(+) was supplied by GenScript. The constructs were transformed into T7 Express lysYcompetent E. coli cells and subsequent small- scale expression studies showed the recombinant proteins were expressed in a soluble form allowing for subsequent protein purification. Purification of the recombinant proteins was achieved using nickel-NTA and glutathione affinity chromatography for the His-tagged (Hsp90 C-terminal domains and GST) and GST fusion proteins (TPR2A domains), respectively. The purified proteins were used to establish and optimise mammalian and P. falciparum Hsp90- Hop interaction assays on nickel-coated plates by immobilising the His-tagged C-terminal domains on the plates and detecting the binding of the GST-TPR2A domains using a colorimetric GST enzyme assay. Z’-factor values above 0.5 were observed for both assays indicating good separation between the protein interaction signals and negative control background signals, although relatively high background signals were observed for the mammalian interaction due to non-specific binding of murine TPR2A to the plate. Designed human and P. falciparum TPR peptides were observed to be effective inhibitors of the mammalian and P. falciparum interactions, demonstrating the assay’s ability to respond to inhibitor compounds. Comparison of assay performance using GST assay kit reagents and lab- prepared reagents showed the assay was more efficient using lab-prepared reagents, however, lower GST signals were observed when comparing assay performance using a custom prepared Ni-NTA plate to a purchased Ni-NTA plate. The Hsp90-Hop interaction assays were also performed using an alternative assay format in which the GST-TPR2A fusion proteins were immobilised on glutathione-coated plates and binding of the His-tagged C-terminal domains detected with a nickel-horseradish peroxidase (HRP) conjugate and a colorimetric HRP substrate. The assay showed higher interaction signals for the P. falciparum proteins but comparatively low signals for the mammalian proteins. Z’-factor values for the assay were above 0.8 for both protein sets, suggesting this assay format is superior to the GST assay. However, further optimisation of this assay format is required. This study demonstrated direct binding of PfHsp90-PfHop in vitro and established a novel and robust PfHsp90-PfHop interaction assay format that can be used in future screening campaigns.
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Development of a computational chemistry scheme for testing the utility of synthetic bacteriochlorin in dye-sensitized solar cells

- Kota, Ntsika

Authors: Kota, Ntsika
Date: 2018
Subjects: Dye-sensitized solar cells , Computational chemistry , Density functionals , Electronic excitation , Molecular orbitals , Oscillator strengths , Bacteriochlorin
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/62327 , vital:28155
Description: A computational chemistry scheme, based on density functional theory, was developed for in silico testing of a few bacteriochlorin properties relevant to dye-sensitized solar cells. These properties included electronic excitation wavelengths, molecular orbital energy levels, and oscillator strengths among others. Comparisons were made among four species, using computational proxies for electron injection quantum yield and photo-induced current production. The proxy measures for current production (frontier orbital energy level and short circuit current) made consistent, though qualitative, predictions about the ranking of the four dyes. The proxy measures for electron injection quantum yield (change in planar dipole moment and density of states) made less categorical predictions about the ranking. Overall, the scheme singled out one dye as the worst, but made no conclusive predictions about the relative ranking of the other three. There was insufficient data for comparison of the ranking predictions with experiment.
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Development of a low-cost bioprinting system for the fabrication of cell-laden sodium alginate hydrogels

- Honiball, John Robert

Authors: Honiball, John Robert
Date: 2018
Subjects: Regenerative medicine , Tissue engineering , Alginates , Colloids , Three-dimensional printing
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/59204 , vital:27470
Description: Bioprinting is a rapidly expanding technology with the ability to fabricate in vitro 3D tissues in a layer-by-layer manner to ultimately produce a living tissue which physiologically resembles native in vivo tissue functionality. Unfortunately, large costs associated with commercially available bioprinters severely limit the amount of people/research groups with access to the technology. Here, we investigated the potential for modifying a commercially available RepRap Prusa iteration 3 (i3) three-dimensional (3D) printer, by replacing the traditional plastic-based print-head with various open-source syringe-housed microextrusion print-head units, such that deposition of composite bioinks consisting of cells, biopolymer scaffolds and/or biomolecules may be achieved at a relatively low cost. Using adipose-derived human mesenchymal stromal stem cells (ad-HMSC) induced for adipogenic differentiation, as well as human umbilical vein endothelial cells (HUVEC), the potential for fabricating vascularised adipose tissue was investigated. The non-toxic, inexpensive algal polysaccharide, sodium alginate, was used to test the printability of the system, as well as for investigating the functionality unmodified sodium alginate has for use as a potential bioink in adipose tissue engineering. Cell viability assays, namely WST-1 and fluorescein diacetate (FDA)/propidium iodide (PI) live/dead cell staining, revealed that ad-HMSC were viable after 7 days of culture. However, viability of HUVEC encapsulated hydrogels revealed significantly lower cell viability. Live/dead cell staining revealed that the modified printing system was able to print ad-HMSC/HUVEC co-cocultures with a large degree of cell viability after 1 day of culture. However, after 7 days of culture, the majority of cells were revealed to be dead. Furthermore, due to the lack of mechanical integrity possessed by alginate in a liquid-like state, printing sodium alginate hydrogels in air consistently resulted in deformation of printed constructs. The newly developed 3D printing technique termed freeform reversible embedding of suspended hydrogels (FRESH) was therefore investigated as a means for achieving 3D spatial control of printed hydrogels using the modified system. Printing cell-free sodium alginate hydrogels within gelatin sacrificial support baths allowed for fabricating constructs in a spatially defined manner. However, overprinting and swelling of alginate hydrogels negatively affected the overall printing accuracy. The present study aimed to pave the way for further system modifications and refinements, such that the ultimate goal of low-cost bioprinting may be achieved. Further optimisation of printing parameters, hydrogel characteristics and sterilisation techniques may allow for fabricating viable, physiologically relevant tissues using the modified system developed.
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Discontinuous gully erosion as a mechanism of wetland formation: a case study of the Kompanjiesdrif basin, Kromrivier, Eastern Cape, South Africa

- Lagesse, Juliette V

Authors: Lagesse, Juliette V
Date: 2018
Subjects: Arroyos -- South Africa -- Kromme River (Eastern Cape) , Arroyos -- Erosion -- South Africa -- Kromme River (Eastern Cape) , Climatic geomorphology -- South Africa -- Kromme River (Eastern Cape) , Sedimentation and deposition -- South Africa -- Kromme River (Eastern Cape) , Alluvial fans -- South Africa -- Kromme River (Eastern Cape) , Wetland ecology -- South Africa -- Kromme River (Eastern Cape) , Rhizophoraceae , Palmiet (Prionium serratum)
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/60540 , vital:27791
Description: The Kompanjiesdrif basin is an unchannelled valley bottom palmiet wetland located near the headwaters of the Kromrivier in the Eastern Cape of South Africa. The wetland itself is underlain by Bokkeveld shales with the bordering mountain ranges comprising more resistant Table Mountain Group quarzitic sandstones. The valley is relatively planar and broad in form over a width of approximately 200 m. None of the existing controls that are considered to lead to valley widening and longitudinal slope reduction are immediately apparent. The basin lies on the Post Africa II erosion surface; with no evidence of a resistant lithology which might act as a local base level, limiting rates of vertical erosion and inducing lateral planing in upstream reaches via a meandering channel. The possible role of sagging of the basin due to long term deep chemical weathering of bedrock is discounted as the lithologies in the basin are sedimentary in origin and thus not susceptible to chemical weathering. The degree to which climate and sea level changes affected rates of incision and subsequent slope reduction is unclear, although their potential influence should be acknowledged. This study examined the geomorphic dynamics as discerned from the sedimentary record and morphology of the wetland basin, which provide a snapshot into the long-term processes which lowered the longitudinal slope and widened this valley. Coring within the wetland to depths of 1 - 3.3 m revealed that the sedimentary fill generally comprised an upward fining sequence, with sand or fine sand at the base, grading into silt and clay and organic material in the upper sections of cores. Occasional instances of multiple fine sand layers were observed in a few of the cores. An increase in the organic content of material from the north to the south side of the wetland and the occurrence of multiple thin layers of sand in the stratigraphy, highlighted the role of the northern tributary alluvial fans in influencing valley form. Sediment from north bank alluvial fans seem to periodically, partially impound the wetland basin. Surveyed transects across the wetland basin along with subsurface coring to the depth to refusal, illustrated a localised increase in longitudinal slope downstream of the nodes of tributary alluvial fan deposits, which impinge on the trunk stream basin. Coupled with the presence of deep, drowned, trench-like features (up to 8 m deep) beneath floating mats of palmiet, which were predominantly free of sedimentary fill and found opposite tributary alluvial fans; confirmed that the northern tributaries play a major role in the structure and geomorphic dynamics of the basin. The trench-like features appeared to be remnants of deep, narrow, discontinuous gullies. Dating of sediment from the base of these features (460-7040 BP) confirmed that they were formed prior to European settlement in the area. Therefore, it is suggested that the localised increase in longitudinal slope, caused by sediment deposition on the alluvial fans, transgresses a geomorphic threshold slope and that gully erosion is thus initiated. The process of repeated gully erosion leads to planing of bedrock and longitudinal slope reduction. Gully erosion forms an integral component of a cycle of deposition and incision referred to as “cut-and-fill”. During each iteration of the cycle of cutting and filling, gullies form in novel locations leading to gradual valley widening. Over geological time scales, the planing of bedrock and resultant valley widening creates a broad planar valley with a very low longitudinal slope; producing conditions suitable for unchannelled valley bottom wetland formation.
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Donor-acceptor effects on the optical limiting properties of BODIPY dyes

- Hlatshwayo, Zweli Thabiso

Authors: Hlatshwayo, Zweli Thabiso
Date: 2018
Subjects: Dyes and dyeing -- Chemistry , Photosensitizing compounds -- Therapeutic use , Cancer -- Photochemotherapy , Upconversion nanoparticles (UCNPs)
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/63368 , vital:28397
Description: The main objectives of the research described in this thesis were firstly to synthesize and characterize a series of structurally related BODIPY dyes that are potentially suitable for use in applications, secondly to conjugate a carboxylic acid substituted BODIPY dye to amine-functionalized upconversion nanoparticles (UCNPs) through an amide bond to enable singlet oxygen production upon irradiation at 978 nm in the biological window for tissue penetration for biomedical applications, and thirdly to compare the nonlinear optical (NLO) properties of various BODIPY dyes to determine whether push-pull effects enhance their utility for optical limiting (OL) applications. Halogenated BODIPY cores with high singlet oxygen quantum yields were prepared, which absorb in the green portion of the visible region and making it difficult to treat deeper skin tumors in the context of photodynamic therapy (PDT) applications. UCNPs generally absorb in the near-infrared (NIR) region (978 nm), and this is advantageous because, this is where absorption by water, cells and tissues is minimized. NaYF4: Yb/Er/Gd UCNPs were synthesized, amine functionalized and successfully conjugated to a halogenated carboxylic acid functionalized BODIPY. This allowed for favorable Förster resonance energy transfer (FRET) since one of the emission wavelengths of the NaYF4: Yb/Er/Gd UCNPs overlaps with the main absorption band of the BODIPY at 540 nm. The conjugate was irradiated at 978 nm, but instability of the BODIPY dye was observed, which made singlet oxygen quantum yield determination impossible. An enhanced singlet oxygen quantum yield value was observed upon irradiation of the conjugate at 540 nm, suggesting that further studies of this system are warranted. The OL properties of BODIPY cores and dyes, which are π-extended at the 3,5-positions with styryl groups, were studied in a series of different organic solvents at 532 nm by using the z-scan technique on a nanosecond timescale. Many of the dyes were used to compare the effects of introducing electron donor and acceptor groups on the OL properties of the dyes. The dipole moments of these dyes were found to correlate with the OL response. The OL results indicate that BODIPY dyes with push-pull properties, which are π-extended at the 3,5-positions with styryl groups, can be considered as viable candidates for use in OL applications. The studies sought to establish the effect of ESA in the triplet manifold as compared to the singlet manifold in as far as the OL response is concerned. The most promising dyes were embedded in polystyrene thin films, and this was found to significantly enhance their OL properties.
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Effects of CO2-induced ocean acidification on the early development, growth, survival and skeletogenesis of the estuarine-dependant sciaenid Argyrosomus japonicus

- Erasmus, Bernard

Authors: Erasmus, Bernard
Date: 2018
Subjects: Argyrosomus , Argyrosomus -- Growth , Argyrosomus -- Mortality , Argyrosomus -- Ecology , Argyrosomus -- Physiology , Ocean acidification , Marine ecology -- South Africa , Carbon dioxide -- Physiological effect
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/60585 , vital:27799
Description: Although it is increasingly accepted that ocean acidification poses a considerable threat to marine organisms, little is known about the likely response of fishes to this phenomenon. While initial research concluded that adult fishes may be tolerant to changes predicted in the next 300 years, the response of early life stages to end-of-century CO2 levels (~ 1100 µatm according to the IPCC RCP 8.5) remains unclear. To date, literature on the early growth and survival of fishes has yielded conflicting results, suggesting that vulnerability may be species dependant. The paucity of ocean acidification research on fishes is particularly evident when one considers larval skeletogenesis, with no robust studies on its impacts on bone and cartilage development. This study addresses the early life embryogenesis, hatching success, growth, skeletogenesis and survival of an estuarine-dependant species. Dusky kob (Argyrosomus japonicus) were reared in a control (pCO2 = 327.50 ± 80.07 qatm at pH 8.15), intermediate (pCO2 477.40 ± 59.46 qatm at pH 8.03) and high pCO2 treatment (pCO2 910.20 ± 136.45 qatm at pH 7.78) from egg to 29 days post-hatch (dph). Sixty individuals from each treatment were sacrificed at the egg stage and at 2, 6, 13, 18, 21 and 26 dph, measured and stained using an acid-free double- staining solution to prevent the deterioration of calcified matrices in fragile larval skeletons. The proportion of bone and cartilage was quantified at each stage using a novel pixel-counting method. Growth and skeletal development were identical between treatments until the onset of metamorphosis (21 dph). However, from the metamorphosis stage, the growth and skeletal development rate was significantly faster in the intermediate treatment and significantly slower in the high treatment when compared to the control treatment. By 26 dph, A. japonicus reared in high pCO2 were, on average, 47.2% smaller than the control treatment, and the relative proportion of bone in the body was 45.3% lower in the high pCO2 treatment when compared with the control. In addition, none of the fish in the high pCO2 treatment survived after 26 dph. It appears that the combination of the increased energy requirements during metamorphosis and the increased energy cost associated with acid-base regulation may account for reduced growth, skeletogenesis and poor survival in high pCO2. Regardless of the driver, the results of this study suggest that the pCO2 levels predicted for the end of the century may have negative effects on the growth, skeletal development, and survival during metamorphosis.
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Exploration potential for copperbelt - style mineralisation in NW Province, Zambia; soil geochemistry as a targeting tool

- Mwamba, John

Authors: Mwamba, John
Date: 2018
Subjects: Mineralogy -- Zambia -- Copperbelt Province , River sediments -- Zambia -- Copperbelt Province , Soils -- Sampling -- Zambia -- Copperbelt Province , Prospecting -- Geophysical methods , Landsat satellites , Lufilian fold belt
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/62538 , vital:28204
Description: The NW Province of Zambia is fast becoming a major significant mining district challenging to usurp the economic importance of the traditional Copperbelt Province that has been mined for nearly a century. With latest developments at Kansanshi, Lumwana and Kalumbila mines exploration efforts in the search for Copperbelt style mineralisation have doubled up in the province in recent months. Traditional methods of stream sediment and soil sampling, geophysics, aerial photo and Landsat imagery interpretations have been employed in exploration targeting campaigns. This thesis asks the question: Can we use the Copperbelt geochemical footprint as a proxy to finding new copper deposits in NW Province? The challenge faced in such studies is that few geochemical datasets for old mines exist and the little that does is proprietary information. In some mines this dataset is entirely nonexistent - at least not in the public domain. Attempting to run orientation geochemical trials on such mines is not feasible at present due to maturity of mining and the levels of contamination of the natural environment that have occurred over several decades of mining. However, in tackling this question few Copperbelt geochemical datasets from Baluba, Nkana, Mimbula, Nchanga, Bwana Mkubwa, Mufulira West and Lufubu North were used. The findings presented in this report are that for Copperbelt style mineralisation Cu/Co, Cu/Ni, Cu/Ag ratios in soil geochemistry data should be in the ranges of 0.25 to 0.48 provided geochemical studies occurred in residual soils. These ratios hold true for sediment hosted copper-cobalt mineralisation hosted at various stratigraphic levels within the Roan Group or in upper levels elsewhere on the Central African Copperbelt. Geochemical dataset for the study areas presented in this report show that the soil geochemistry footprint in the province is not dissimilar to the soil geochemistry footprint of the traditional Copperbelt Province. This means there is great potential for finding Copperbelt style mineralisation in the province and other styles of mineralisation in which copper is associated with cobalt, lead, zinc, nickel, vanadium and molybdenum. The areas of study also possess requisite geological factors that are conducive to hosting Copperbelt style deposits. These factors include: favourable structural traps with similar trends to existing mines in the province, geophysical characteristics comparable to other deposits in the province, right geological package known to host multi-type deposits in the Katangan stratigraphic sequence, and similar geochemical footprints observed on other deposits within the Lufilian fold belt. For this reason, geochemical dataset must not be looked at in isolation but should be treated in considerations with other factors and geological environment.
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Gaining cyber security insight through an analysis of open source intelligence data: an East African case study

- Chindipha, Stones Dalitso

Authors: Chindipha, Stones Dalitso
Date: 2018
Subjects: Open source intelligence -- Africa, East , Computer security -- Africa, East , Computer networks -- Security measures -- Africa, East , Denial of service attacks -- Africa, East , Sentient Hvper-Optimised Data Access Network (SHODAN) , Internet Background Radiation (IBR)
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/60618 , vital:27805
Description: With each passing year the number of Internet users and connected devices grows, and this is particularly so in Africa. This growth brings with it an increase in the prevalence cyber-attacks. Looking at the current state of affairs, cybersecurity incidents are more likely to increase in African countries mainly due to the increased prevalence and affordability of broadband connectivity which is coupled with lack of online security awareness. The adoption of mobile banking has aggravated the situation making the continent more attractive to hackers who bank on the malpractices of users. Using Open Source Intelligence (OSINT) data sources like Sentient Hvper-Optimised Data Access Network (SHODAN) and Internet Background Radiation (IBR), this research explores the prevalence of vulnerabilities and their accessibility to evber threat actors. The research focuses on the East African Community (EAC) comprising of Tanzania, Kenya, Malawi, and Uganda, An IBR data set collected by a Rhodes University network telescope spanning over 72 months was used in this research, along with two snapshot period of data from the SHODAN project. The findings shows that there is a significant risk to systems within the EAC, particularly using the SHODAN data. The MITRE CVSS threat scoring system was applied to this research using FREAK and Heartbleed as sample vulnerabilities identified in EAC, When looking at IBR, the research has shown that attackers can use either destination ports or IP source addresses to perform an attack which if not attended to may be reused yearly until later on move to the allocated IP address space once it starts making random probes. The moment it finds one vulnerable client on the network it spreads throughout like a worm, DDoS is one the attacks that can be generated from IBR, Since the SHODAN dataset had two collection points, the study has shown the changes that have occurred in Malawi and Tanzania for a period of 14 months by using three variables i.e, device type, operating systems, and ports. The research has also identified vulnerable devices in all the four countries. Apart from that, the study identified operating systems, products, OpenSSL, ports and ISPs as some of the variables that can be used to identify vulnerabilities in systems. In the ease of OpenSSL and products, this research went further by identifying the type of attack that can occur and its associated CVE-ID.
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Generalized linear models, with applications in fisheries research

- Sidumo, Bonelwa

Authors: Sidumo, Bonelwa
Date: 2018
Subjects: Western mosquitofish , Analysis of variance , Fisheries Catch effort South Africa Sundays River (Eastern Cape) , Linear models (Statistics) , Multilevel models (Statistics) , Experimental design
Language: English
Type: text , Thesis , Masters , MSc
Identifier: http://hdl.handle.net/10962/61102 , vital:27975
Description: Gambusia affinis (G. affinis) is an invasive fish species found in the Sundays River Valley of the Eastern Cape, South Africa, The relative abundance and population dynamics of G. affinis were quantified in five interconnected impoundments within the Sundays River Valley, This study utilised a G. affinis data set to demonstrate various, classical ANOVA models. Generalized linear models were used to standardize catch per unit effort (CPUE) estimates and to determine environmental variables which influenced the CPUE, Based on the generalized linear model results dam age, mean temperature, Oreochromis mossambicus abundance and Glossogobius callidus abundance had a significant effect on the G. affinis CPUE. The Albany Angling Association collected data during fishing tag and release events. These data were utilized to demonstrate repeated measures designs. Mixed-effects models provided a powerful and flexible tool for analyzing clustered data such as repeated measures data and nested data, lienee it has become tremendously popular as a framework for the analysis of bio-behavioral experiments. The results show that the mixed-effects methods proposed in this study are more efficient than those based on generalized linear models. These data were better modeled with mixed-effects models due to their flexibility in handling missing data.
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