In 2005, the city of Port Elizabeth, in the Nelson Mandela Bay Municipality (NMBM) of the Eastern Cape Province of South Africa, initiated an urban renewal project of its derelict city centre areas and the southern part of the old Port Elizabeth port. This, after the newly constructed Port of Ngqura, 34-kilometres north of Nelson Mandela Bay, was designed to serve as a state-of-the-art industrial port within a specially established Industrial Development Zone (IDZ). This has freed the existing southern part of the old Port Elizabeth port – strategically centred on the doorstep of the city – up for re-development for nonindustrial purposes, effectively opening it up to retail, residential, office and tourism/leisure/entertainment development; and causing it to become an extension of the inner city. The Urban Renewal Plan and the implementation thereof, address specific local economic growth-related factors, integrated with urban development challenges applicable to the city. Since the process began in 2005, significant progress has been made, embracing a long-term approach incrementally implemented on the basis of a well-researched overall plan. This plan is hinged on the strong foundation of in-depth, extensive market research in the retail, residential, office and tourism/leisure/entertainment sectors and aims at the creation of a strong cluster around these areas of development. The term cluster describes the concept of groups of inter-connected and related firms, suppliers, related industries, and specialized institutions in particular fields, uniting in particular a location to - amongst other reasons - maximise their reach, lower their costs and enhance their business (Porter: 1990: 71). In this study, the cluster concept is broadened to encompass a constellation of urban developments around and complementing retail, residential, office and tourism/leisure/entertainment business. As such, the urban renewal project becomes an important element in the Local Economic Development (LED) planning of Port Elizabeth. The practical experience of traditional, rational and urban planning methodology, often conflicts with the reality of market demand - particularly in the South African case. Therefore, this study explores an alternative method for approaching urban planning, by focussing on the bottom-up approach, which essentially takes into account the needs of the customer – or local community – through a special purpose vehicle: a fresh, alternative approach to urban renewal that still makes a positive contribution to local economic development. The Mandela Bay Development Agency (MBDA) – a separate company formed by the NMBM to manage the redevelopment of the city – strategy embraced an interventionist approach to urban renewal as an alternative framework for encouraging overall development in a particular urban node. The cornerstone of the MBDA’s urban renewal approach is an overarching philosophy of “private sector investment following public sector infrastructure investment” (MBDA: 2010: 2). This research is the result of a long-standing interaction between theory, praxis and reflection. Experiences of practical implementation have been framed by the MBDA project over a five year period and build the case-study presented. viii Urban planning and urban renewal are used in a pro-active, action-orientated manner, to achieve sustainable, competitive LED through the development of a viable multi-purpose, non-industrial retail and leisure cluster in Port Elizabeth. Port Elizabeth is still known as the Friendly City. This epithet originated from an effective tourism marketing campaign in the eighties, but as a true description, has become somewhat diminished by the urban decay of the past twenty years. The Friendly City concept refers to a city that presents a healthy mix of work, housing and leisure – a combination of lifestyle offerings that no longer really exist in Port Elizabeth. However, through interventionary initiatives such as the MBDA’s Urban Renewal Plan, this situation is likely to change as a result of catalytic urban developments. Port Elizabeth was built on an internationally competitive motor manufacturing and industrial cluster, but had few other major industries. As such, the creation of an innovative urban renewal cluster was critical for the diversification of its economy – not only from a local economic perspective, but also from a national and international competitiveness point of view. It is the general feeling amongst city planners, economists and industrialists that the current industrial base of Port Elizabeth is not sufficient and that a more diversified economy would have the potential to improve the domestic and global competitiveness of the city. This interaction between the dual goals of economic and urban development, produces farreaching effects on the discourses of urban management and planning, as the two compete and converge to push development forward. Diversification is, however, not an easy endeavour. Considerations around growth-related objectives on planning demands – a shift from the rational, linear and government-based structure of urban management, to an interactive governance of planning and development – where integrated urban and economic strategies inter-play with planning and implementation, has become important in the creation of a more diversified economy. In Port Elizabeth, this approach is referred to as an “alternative method” of urban planning: An approach that involves a process of guided development through a collaborative bottom-up engagement, involving local government, public participation and the private sector. The alternative method of urban planning is further reinforced by the current economic recession, which is, and will continue to, change property development and its response to the needs of the market for the foreseeable future. The solution to urban renewal does not only lie in well-targeted, well-researched public-sector infrastructure investment (that responds strongly to the market and customer needs), but in a joint participatory process that ensures that the final design of infrastructure projects is the outcome of what the market requires, as a means to ensure sustainability and the biggest possible response in private sector investment. Because of global economic forces, the functional and developmental structure of the neighbourhood – where the epicentre of the growth system is situated – has become of paramount significance. This thesis attempts to demonstrate how urban renewal and the redevelopment of designated, formally idle city buildings and public spaces may serve as a site for the creation of an urban growth node or urban cluster. A key focus of this study is how new economic and social growth based structures can be induced to integrate with the process of urban redevelopment. Further demonstrated is that the agenda for urban management, illuminated in the light of the described practices, conducts a fundamental re-appraisal in its local economic development context. Local economic development has been lauded as the saviour of development at a local level in South Africa. LED, however, has by no means utilized the required level of property development pragmatism and has thus, throughout the duration of its approach, not culminated in specific sustainable, capital-driven projects – which is probably one of the reasons for its overall market failure in South Africa and Port Elizabeth. LED has therefore become an outdated economic approach that leaves in its wake, the necessity and opportunity for a fundamental change. Urban renewal and the city’s economic contribution to LED, requires a completely new conceptualisation of urban renewal in its narrow sense, and urban design and planning in its broader sense. Concepts such as redevelopment and urban renewal are frequently used in planning discourse. Redevelopment is understood to encompass actions of clearing (such as slum clearance), reorganising or reconstruction. Renewal signifies rebirth, breaking new ground or innovatively refashioning; a form of re-growing or bringing new and more prolific life. In this thesis, reference is made to urban renewal as an attempt to influence social and economic forces in a desired direction, integrated with planning and development. It re-conceptualises redevelopment as more than a matter of reconstructing an urban arrangement. These concepts are often used in line with the new governance-based style of urban planning, such as guided development, development planning and efforts for enabling the feasibility thereof. This thesis attempts to clarify under what conditions redevelopment is unified with social and economic regeneration. Its approach intends to scrutinise regional strategies, urban management and urban planning to generate an understanding of the urban environment as it relates to growth issues. Many growth-related discourses are discussed in terms of development and innovation. The grammar of this process, when unified with urban development, is referred to as a Dynamic Place Initiative (DPI). In the DPI, issues of feasibility (enablement) are unified in formal government, planning and implementation, restricted to a specific bounded area. The core focus of interest in this thesis is not primarily concerned with architecture and urban design, but rather with the principles of how the process may be implemented as a leverage tool to encourage a range of factors to interact with government agents in an LED-orientated field of action. This field includes not only the built infrastructure, but also the inherent economic and social targets that come with such infrastructure. This thesis discusses economic and innovation theory, as a method of understanding urban development, yet should be understood as an analysis of urban renewal and urban planning. The MBDA case study is a brownfield (redeveloped/renovated) development within an economic cluster of retail, residential, office and tourism/leisure/entertainment. The MBDA uses greenfield (new) development to complement urban renewal and systems of innovation x that endeavour to meet customer needs. The development case aims to focus on its customer (or local community) needs in an all-encompassing approach. Specifically, this includes guided development - a process using well-defined urban design briefs that ensures urban designs are complementary in their overall impact and culminate in a dynamic place initiative. The situation in Port Elizabeth is not unique. On account of global forces of industrial transformation, many countries have, and continue to, find themselves struggling with the renewal of large and redundant inner urban areas that were formerly used for industry and logistics. A typical challenge in this type of context for renewal is to design development schemes that will encourage economic growth and revitalisation within these areas. Although planning, construction and development are systematically methodical activities, economic and social regeneration are more complex. Due to the on-going transformation of the economy in South Africa, the urban context is under constant pressure to change in tandem with pressurised demand for change. The driving forces in the economy are progressing from a nation-orientated and raw-materialbased production origin, which formed the industrial society, to a global, regional and information-orientated urban growth-based structure. The condition of cities has become one of the qualities – or a prominent part of the overall quality – of this so-called knowledge economy. The urban environment, the territorially bounded areas which comprise it and the conditions of the environment within which it exists, are important factors for competitiveness, at both a city and regional level. Observed in reverse, competitiveness has also become a critical factor in achieving complex urban change from a new perspective of economic growth. Cities are the engines of regional and national growth. The economic success of cities and CBDs in South Africa is vital and will effectively ensure the much-needed upgrading of CBD and township infrastructure, using the revenue streams generated during city-centred economic revival. In South Africa (and likely elsewhere in the world), urban renewal is not only about aesthetics, but also about providing a foundation for urban planning, functional architecture and LED. In situations where cities undertake the urban renewal of redundant areas and buildings, economic competitiveness is foremost on the agenda. In order to understand how the forces of production and growth are linked with urban development, it is important to consider the new growth-orientated context for planning. An awareness of these changes and their trends, expressed as a paradigm shift, is reflected in the current discussions concerning the revision of urban planning in South Africa. This specifically targets integration between the previously disadvantaged communities and the advantaged communities. The Strategic Spatial Implementation Framework (SSIF) (2005), often referred to as the “Master Plan” of the MBDA, is an interventionist plan to ensure that the urban renewal infrastructure programme has well-researched projects with a strong catalytic impact leading xi to private sector investment and that thus secure the highest possible economic multiplier impact. Over the past four years, extensive capital has been deployed in Port Elizabeth’s urban infrastructure to lay the foundation for an enabling environment for private sector investment that will culminate in mobilising people to live, work and play in the city again. Public participation and market research have shown that the demand for residential, office, retail and tourism/leisure/entertainment will be directed largely by the black population; more specifically, the “black diamond” middle class anticipated to dominate the future Port Elizabeth economy (MBDA: 2010). It was the initial infrastructure programme in the CBD – which included projects that codepended or linked up with one another, to form a collective whole – which lifted the inner city to another level. It is these urban projects that culminated in renewed interest in the city, inter-linking this interest with the retail, residential, office and tourism/leisure/entertainment customer needs of the city. In most European countries, as in the case of South Africa, urban planning is in the process of transformation, from being a method for regulation and control into becoming a channel for possibilities and enabling development at local level. It is common cause that society needs to be more involved in a city’s planning processes. Tax payers now increasingly demand the use of government funds for infrastructure and the improvement of public areas and open spaces. In the 1980s, the liberal alternative to meet the shortage of tax money was to rely on private investment for urban development. The society used its organisational and planning capacity to encourage market investment through public-private partnerships (PPPs). This strategy is viable in situations where the level of financial risk is low or where conditions are reasonably predictable. Private actors refrain from investment in complex settings where the returns are projected to be far ahead in the future. In South Africa, this is often perceived as a degree of business fatigue; particularly in respect of public-private partnerships. Urban development through private sector investment requires leadership. This can come in the form of the precreation of an enabling environment, i.e. extensive publicly funded basic urban infrastructure investment. Consequently, the urban context requires development to a level where investment can be motivated by core business economic reasoning. In short, other than making social and political sense, urban planning must adhere to financial and economic sense. The society is an important actor and one that has far-sighted motives. In Port Elizabeth, as in the case of many other municipalities, the revenue pool drawn from rates and taxes is simply insufficient to meet the demands of society. The Dynamic Place Initiative represents an alternative that unifies the advantages of the two previous planning discourses. Through a limited agency – such as the MBDA – positioned to guide urban development, the city is enabled to form advanced, politically-set strategies and at the same time, isolate the financial risk through the response of private sector investment. It should be emphasised that the private sector enters the realm of urban development through property actions guided by the planning system. Planning questions ought to be based around the there and then rather than the here and now. The MBDA has become a conduit for dealing with these systems gaps, ensuring that urban and port planning is not limited in focus but speaks to customer needs and makes financial and economic sense. / Thesis (DPhil)--University of Pretoria, 2013. / gm2013 / Town and Regional Planning / unrestricted

The primary focus of this thesis is to describe the prevailing atmospheric conditions when heavy rainfall occurs over the Gauteng Province in South Africa. This thesis first describes the characteristics of daily heavy rainfall over Gauteng by defining different heavy rainfall classes and considering the seasonal distribution of these events. Late summer (January, February and March) has considerably more heavy rainfall days than early summer. The change of the character of the atmosphere as the summer season progresses is highlighted by the investigation into the monthly average synoptic circulation patterns when heavy rainfall occurs. The weather systems change from extra-tropical in the first few months of the summer rainfall season to tropical in February months. It is also shown how cyclonic vorticity advection occurs in the upper troposphere whenever heavy rainfall occurs, irrespective of the time of the season. A deep layer of horizontal wind convergence is also present when heavy rainfall occurs and this is replaced by horizontal wind divergence above that. A monthly climatology of sounding-derived parameters associated with heavy rainfall is constructed and it is again apparent how the atmosphere changes from one where conditional instability dominates the production of heavy rainfall in early summer to one where convective instability plays a dominant role in late summer. Twelve sounding-derived variables are identified to describe the thermodynamical profile of the atmosphere when heavy rainfall occurs over Gauteng. They include variables not previously used such as the Elevated K-Index and the meridionial wind component near the surface. Self-organizing maps are used to create a climatology of the vertical profile of the atmosphere during heavy rainfall and this methods captures the changes to the atmospheric state during the progression of the summer season. Favourable sounding-derived parameters and circulation criteria are combined in a self-organizing map to predict daily rainfall frequencies. This method produces encouraging results and methods should be explored to create probabilistic daily rainfall forecast for Gauteng in an operational environment. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Geography, Geoinformatics and Meteorology / unrestricted

Malaria is caused by the parasite Plasmodium falciparum and still plagues many parts of the world. To date, efforts to control the spread of the parasites have been largely ineffective. Due to development of resistance by the parasites to current therapeutics there is an urgent need for new classes of therapeutics. The vitamin B6 biosynthetic pathway consists of a PLP synthase which produces pyridoxal 5'-phosphate (PLP) within the parasite. The absence of this pathway in humans makes it attractive for selective targeting using small chemical molecules. The PLP synthase condenses D-ribose 5-phosphate (R5P) and DL-glyceraldehyde 3-phosphate (G3P) with ammonia to form PLP. Two proteins make up this PLP synthase – PfPdx1 and PfPdx2. Computational modelling of Pf Pdx1, and mapping of the R5P-binding site pharmacophore facilitated the identification of several ligands with predicted favourable binding interactions. Confirmatory testing of these on the purified Pf Pdx1 in vitro revealed D-erythrose 4-phosphate (E4P) and an analogue 4-phospho-D-erythronhydrazide (4PEHz) were capable of dose-dependently inhibiting the enzyme. The acyclic tetrose scaffold of E4P, with both aldehyde and phosphate group moieties, was thought to affect R5P imine bond formation in Pf Pdx1, possibly allowing the molecule to enter the R5P-binding site of Pf Pdx1. This hypothesis was supported by molecular docking simulations, and suggested that 4PEHz could similarly enter the R5P-binding site. 4PEHz was detrimental to the proliferation of cultured P. falciparum intraerythrocytic parasites and had an inhibitory concentration (IC50) of 10 µM. The selectivity of 4PEHz in targeting Pf Pdx1 was investigated using transgenic cell lines over-expressing Pf Pdx1 and Pf Pdx2, revealing that complementation of PLP biosynthesis rescued the parasites from the detrimental effects of 4PEHz. Functional transcriptomic and proteomic characterisation of 4PEHz-treated parasites revealed that the expression of Pf Pdx2 increased during 4PEHz treatment, moreover showed that other PLP-related processes were affected. These results supported that Pf Pdx1 is targeted by 4PEHz, and affected PLP biosynthesis de novo. Results from this study allude to alternative regulation of de novo PLP biosynthesis within the parasites by E4P. Moreover, contributions from this work showed that the de novo vitamin B6 pathway of P. falciparum is chemically targetable, and a potential strategy for the development of newer antimalarials. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Biochemistry / Unrestricted

Colombia covers an area of approximately 114 million hectares (ha) of which the potential forestly land has been estimated at 60.7 million ha, about 53% of the total area. Only 54 million ha are considered as natural forest, leaving approximately 29 million ha to be used for livestock and agriculture. In order to provide an alternative source of timber, Colombian groups have planted approximately 327 000 ha to different species of Pinus, Eucalyptus and native species. This clearly represents only a small proportion of the total area that might be used for forestry, which is set to grow in the future. In general, trees established in plantations have been grown as monocultures that allow for substantial productivity per management unit. But this is also a homogeneous genetic resource that is highly susceptible to damage caused by insect pests and diseases. It is therefore, surprising that relatively little work has been conducted on pests and pathogens negatively affecting plantation foresty in Colombia. In this regard, the studies presented in this thesis present the first comprehensive treatment of the topic for the country. It is consequently hoped that these will form a basis for the future management and sustainability of forestry in Colombia. In the first Chapter of this thesis, I provide a historical background and the current pest and disease situation for the forestry sector in Colombia. This includes an overview of the main pest and diseases affecting commercial nonnative trees, especially species of Pinus and Eucalyptus. A wide range of sites occurring in Colombia were considered and the document also includes the impact of different climatic conditions on the incidence and management of the various pests and diseases treated. Some of the most important defoliators in Colombia reside in the order Phasmatodea and one of these, Litosermyle ocanae, was treated in studies presented in chapter two. The overall aim was to contribute basic knowledge of L. ocanae including an understanding of the biology, egg population dynamics, and potential biological control assessments based on early detection of the insect. vi Chapter three includes the discovery of one of the members of the Geometridae that causes serious damage due to defoliation of Pinus and Eucalyptus plantations. This pest, known as Chrysomima semiluteraria, has been known in Colombia for many years and this study included a comprehensive evaluation of its biology and field monitoring contributing to an Integrated Pest Management strategy for it. The insect was studied under field and laboratory conditions and a special emphasis was placed on its biological control using the egg parasitoid Telenomus alsophilae. Pinus plantations in Colombia have been affected by numerous pests, including recently, the adelgid Pineus sp. To establish management strategies to assist commercial forestry operations, the life cycle of this insect and the susceptibility of different Pinus species were determined in Chapter four. In addition, the possible role of a Ceraeochrysa sp. as a biological control agent was investigated. In chapter five, Fusarium circinatum is recorded for the first time on Pinus spp. in Colombia. The discovery of this fungus, known to cause the disease Pitch Canker has had an important impact on forestry, especially with regard to management strategies aimed at reducing its impact. Studies in this chapter included those to evaluate the susceptibility of families and provenances of Pinus spp., which are currently used in forestry planting programs in Colombia. The first emergence of the foliage pathogen Dothistroma septosporum as an important constraint to pine forestry in Colombia is treated in chapter six. This fungus is a serious pathogen of many species of Pinus around the world. It was, however, not recognised as a serious threat to forestry in Colombia until it emerged as a serious source of damage to Pinus tecunumanii. In this chapter, the aim was firstly to confirm the identity of the pathogen based on DNA sequence data. Subsequently, the host range and distribution of the pathogen was established in different Colombian forestry areas. The impact of the disease and the susceptibility of different provenances of P. tecunumanii was also assessed. In chapter seven, the main objective was to described the susceptibility of E. grandis clones to a new species of Ceratocystis and to identify clones resistant to it. The fungus was described as Ceratocystis neglecta and management strategies are suggested for it. This thesis includes two Appendices treating new reports of insect pests and an important Eucalyptus pathogen. In Appendix 1, I report on the importance of three different pest insects. Appendix 2 includes a description of a new disease, as well as the potential risks that this disease poses for the Colombian forestry sector. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Forestry and Agricultural Biotechnology Institute (FABI) / Unrestricted

INTRODUCTION: The menstrual cycle and pregnancy are processes unique to women. Both these processes involve various hormones as well as the coagulation system. Throughout normal pregnancy, platelet activation and increase in blood coagulation factors contributes to the hypercoagulable state observed on a physiological level. METHODS: Fibrin networks and platelets were analysed by electron microscopy and flow cytometry to determine any differences found in different phases of pregnancy compared to healthy control individuals. The fibrin networks from different phases of the menstrual cycle as well as different phases of pregnancy were investigated. RESULTS: It was found that ultrastructural changes in fibrin fiber morphology result from estrogen changes during the menstrual cycle. During pregnancy the minor thin fibers were prominent and thick matted layers of coagulant formation were evident. A large quantity of protein globular clusters similar to those seen in the menstrual cycle was present. Changes observed in platelet ultrastructure during pregnancy showed pregnancy-specific modifications. Platelets were activated and internal organelles showed variation from control participants. Flow cytometric analysis of platelets verified pregnancy-specific modifications. Close interactions between platelets and erythrocytes were evident. CONCLUSION: The female body is equipped to handle alterations in the coagulation system as can be extrapolated from the pregnancy-specific modifications. This study is the first to show alterations in fibrin network and platelet ultrastructure during and after pregnancy when compared to non-pregnant controls. The physiological changes during normal pregnancy can be used as a standard for comparison to abnormal or ailing pregnancy. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Physiology / Unrestricted

In my eleven years of teaching graphic design at Tshwane University of Technology, I have come to realise that education is more than just teaching a student the fundamentals, techniques and new technologies, it is also about their personal development. I conducted this study to ensure that my educational practices challenge my graphic design students to acquire the essential characteristics – or more profoundly, the essential human qualities -­‐ required for a contemporary graphic design career through which the quality of life for all will be enhanced. The study is a participatory action research study involving the second and third year graphic design students at Tshwane University of Technology. It involved five action intervention cycles. In the first cycle I explored the current graphic design education practices in order to determine whether these practices ensure the acquisition of such essential human qualities that a graphic designer should posses. The acquisition of such human qualities has become paramount because of the ethical imperative that graphic designers can change the world (Berman, 2009). I found that my current graphic design education practices as they relate to the commonly most dominant practices are not sufficient to accomplish this purpose. During the research I was exposed to a paradigmatically innovative education practice that focuses on maximizing human potential and it was adopted to improve my existing education practice. Through four additional action intervention cycles I provided evidence that indicated that my improved education practice contributed to my students’ acquisition of an identified four sets of essential human qualities: the artistic quality of creativity; the professional quality of continuous, independent, increasing expertise in creativity within an interdependent, co-­‐operative value based community of graphic design practitioners; the personal quality of maximizing human potential; and the leadership quality of an enlightened change agent. The primary focus on the acquisition of these essential human qualities through the proposed method of graphic design education, also allows for the gaining of the necessary graphic design knowledge and skills (Barnett, 2007:101). / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Humanities Education / Unrestricted

Distribution-free (nonparametric) control charts can be useful to the quality practitioner when the underlying distribution is not known. The term nonparametric is not intended to imply that there are no parameters involved, in fact, quite the contrary. While the term distribution-free seems to be a better description of what we expect from these charts, that is, they remain valid for a large class of distributions, nonparametric is perhaps the term more often used. In the statistics literature there is now a rather vast collection of nonparametric tests and confidence intervals and these methods have been shown to perform well compared to their normal theory counterparts. Remarkably, even when the underlying distribution is normal, the efficiency of some nonparametric tests relative to the corresponding (optimal) normal theory methods can be as high as 0.955 (see e.g. Gibbons and Chakraborti (2010) page 218). For some other heavy-tailed and skewed distributions, the efficiency can be 1.0 or even higher. It may be argued that nonparametric methods will be ‘less efficient’ than their parametric counterparts when one has a complete knowledge of the process distribution for which that parametric method was specifically designed. However, the reality is that such information is seldom, if ever, available in practice. Thus it seems natural to develop and use nonparametric methods in statistical process control (SPC) and the quality practitioners will be well advised to have these techniques in their toolkits. In this thesis we only propose univariate nonparametric control charts designed to track the location of a continuous process since very few charts are available for monitoring the scale and simultaneously monitoring the location and scale of a process. Chapter 1 gives a brief introduction to SPC and provides background information regarding the research conducted in this thesis. This will aid in familiarizing the reader with concepts and terminology that are helpful to the following chapters. Details are given regarding the three main classes of control charts, namely the Shewhart chart, the cumulative sum (CUSUM) chart and the exponentially weighted moving average (EWMA) chart. We begin Chapter 2 with a literature overview of Shewhart-type Phase I control charts followed by the design and implementation of these charts. A nonparametric Shewhart-type Phase I control chart for monitoring the location of a continuous variable is proposed. The chart is based on the pooled median of the available Phase I samples and the charting statistics are the counts (number of observations) in each sample that are less than the pooled median. The derivations recognize that in Phase I the signalling events are dependent and that more than one comparison is © University of Pretoria v made against the same estimated limits simultaneously; this leads to working with the joint distribution of a set of dependant random variables. An exact expression for the false alarm probability is given in terms of the multivariate hypergeometric distribution and this is used to provide tables for the control limits. Some approximations are discussed in terms of the univariate hypergeometric and the normal distributions. In Chapter 3 Phase II control charts are introduced and considered for the case when the underlying parameters of the process distribution are known or specified. This is referred to as the ‘standard(s) known’ case and is denoted Case K. Two nonparametric Phase II control charts are considered in this chapter, with the first one being a nonparametric exponentially weighted moving average (NPEWMA)-type control chart based on the sign (SN) statistic. A Markov chain approach (see e.g. Fu and Lou (2003)) is used to determine the run-length distribution of the chart and some associated performance characteristics (such as the average, standard deviation, median and other percentiles). In order to aid practical implementation, tables are provided for the chart’s design parameters. An extensive simulation study shows that on the basis of minimal required assumptions, robustness of the in-control run-length distribution and out-of-control performance, the proposed NPEWMA-SN chart can be a strong contender in many applications where traditional parametric charts are currently used. Secondly, we consider the NPEWMA chart that was introduced by Amin and Searcy (1991) using the Wilcoxon signed-rank statistic (see e.g. Gibbons and Chakraborti (2010) page 195). This is called the nonparametric exponentially weighted moving average signed-rank (NPEWMA-SR) chart. In their article important questions remained unanswered regarding the practical implementation as well as the performance of this chart. In this thesis we address these issues with a more in-depth study of the NPEWMA-SR chart. A Markov chain approach is used to compute the run-length distribution and the associated performance characteristics. Detailed guidelines and recommendations for selecting the chart’s design parameters for practical implementation are provided along with illustrative examples. An extensive simulation study is done on the performance of the chart including a detailed comparison with a number of existing control charts. Results show that the NPEWMA-SR chart performs just as well as and in some cases better than the competitors. In Chapter 4 Phase II control charts are introduced and considered for the case when the underlying parameters of the process distribution are unknown and need to be estimated. This is referred to as the ‘standard(s) unknown’ case and is denoted Case U. Two nonparametric Phase II control charts are proposed in this chapter. They are a Phase II NPEWMA-type control chart and a nonparametric cumulative sum (NPCUSUM)-type control chart, based on the exceedance statistics, © University of Pretoria vi respectively, for detecting a shift in the location parameter of a continuous distribution. The exceedance statistics can be more efficient than rank-based methods when the underlying distribution is heavy-tailed and / or right-skewed, which may be the case in some applications, particularly with certain lifetime data. Moreover, exceedance statistics can save testing time and resources as they can be applied as soon as a certain order statistic of the reference sample is available. We also investigate the choice of the order statistics (percentile), from the reference (Phase I) sample that defines the exceedance statistic. It is observed that other choices, such as the third quartile, can play an important role in improving the performance of these exceedance charts. It is seen that these exceedance charts perform as well as and, in many cases, better than its competitors and thus can be a useful alternative chart in practice. Chapter 5 wraps up this thesis with a summary of the research carried out and offers concluding remarks concerning unanswered questions and / or future research opportunities. © University / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Statistics / restricted

Cowpeas (Vigna unguiculata L. Walp) are legumes recognised as a good source of proteins in developing countries. Cowpeas are mostly utilised as cooked whole seeds. This is often achieved only after boiling for up to 2 hours, resulting in high energy consumption and a long time for food preparation. Micronisation of pre-conditioned cowpeas (± 41 % moisture at 153 °C) reduces their cooking time. During micronisation, cowpea seeds are exposed to electromagnetic radiation with a wavelength range of 1.8 to 3.4μm. For biological materials, the penetration of infrared rays into the food material causes intermolecular vibration, this result in a rapid increase in temperature and water vapour pressure within the seed. Micronisation changes physico-chemical properties of cowpea seeds that may affect sensory properties of cooked cowpeas. Micronisation may also affect cowpea bioactive components such as phenolic compounds and hence their antioxidant properties and bioactive properties. This study aimed at (1) determining the effects of micronisation of pre-conditioned cowpeas on sensory properties of cooked cowpeas and (2) determining the effects of mironisation of pre-conditioned cowpeas on the phenolic compounds, radical scavenging properties and their protective effects against oxidative damage of biomolecules (i.e. low density lipoproteins (LDL), deoxyribonucleic acid (DNA) and red blood cells (RBC). © University of Pretoria vi Micronisation significantly reduced cowpea cooking time by 28 to 49 %, depending on cowpea type. There were significant (P<0.05) increases in roasted aroma and flavour, mushy texture and splitting in all micronised samples. Bechuana white, a light brown cowpea type, was more mushy and split than others. There were significant decreases in firmness, mealiness and coarseness after micronisation for all cowpea types. Micronised cowpeas were darker (lower L* values) than unmicronised cooked cowpeas. Darkening was more evident in light coloured than dark coloured cowpea types. Although micronisation reduces cowpea cooking time, it also affects sensory properties of cowpeas. This might have an influence on consumer acceptance of micronised cowpeas. Twenty seven phenolic compounds were identified in the cowpea types studied: 6 phenolic acids, 14 flavonols and 7 flavan-3-ols. Protocatechuic acid, p-coumaric acid, 4- hydroxybenzoic acid and ferulic acid were the major phenolic acids in cowpeas. Catechin, catechin-3-O-glucoside, myricetin, rutin, quercetin and its mono and diglycosides were present in all cowpea types analysed. Dr Saunders (701.7−849.2 μg/g) (red in colour) and Glenda (571.9−708.1 μg/g) (dark brown in colour) contained the highest total phenolic contents, followed by Bechuana white (361.5−602.3 μg/g) (light brown in colour) and Blackeye (152.0−224.5 μg/g) (cream in colour). More of the flavonols were identified in red and dark brown compared to light brown and cream cowpea types. The red cowpea type contained all the dimers and oligomeric flavan-3-ol species identified in this study. In all cowpea types, extracts from unmicronised (uncooked) cowpeas inhibited copperinduced LDL oxidation in a dose dependent manner. Extracts from all samples analysed exhibited protective effects against AAPH (2, 2'-azobis (2-amidinopropane) hydrochloride) induced RBC haemolysis and DNA damage. Extracts from more pigmented cowpeas, i.e. Dr Saunders, Glenda and Bechuana white, had significantly (P<0.05) higher levels of total phenolics, total flavonoids and radical scavenging properties than Blackeye (less pigmented). Extracts from more pigmented cowpeas also offered higher protection against AAPH-induced DNA and copper-induced LDL oxidation damage than extracts from less pigmented cowpeas. These results indicate protection of biomolecules e.g. DNA, LDL and RBC) from oxidative damage and have a potential to reduce oxidative stress implicated in the development of chronic diseases. This is because cowpea phenolic compounds possess the ability to reduce oxidative damage associated with development of these diseases. © University of Pretoria vii Pigmented cowpea types may be recommended for health applications as they show more potential as source of antioxidants compared to the less pigmented cowpeas. Extracts from micronised (uncooked and cooked) samples of Dr Saunders and Glenda cowpeas had significantly higher concentrations of ferulic acid and p-coumaric acid compared with unmicronised samples. Para-coumaric acid concentrations were higher in all micronised samples of Blackeye cowpeas than in unmicronised samples. The micronisation process could release cell wall bound ferulic acid and p-coumaric, increasing their concentrations in micronised samples. On the contrary, extracts from all micronised samples of Bechuana white and Glenda cowpeas had lower concentrations of catechin than unmicronised samples. Results indicated that total extractable phenolics were lower in micronised samples of cowpea types than unmicronised samples. Futhermore, extracts from micronised samples of all cowpea types showed less protective effect against LDL oxidation than extracts from unmicronised samples. However, for most cowpea types there was no significant difference in total flavonoid contents (TFC) and Trolox equivalent antioxidant capacity (TEAC) values of cooked samples of both micronised and unmicronised. Micronisation did not affect the protective effects of cowpeas against AAPH-induced RBC haemolysis and oxidative DNA damage. Micronisation, followed by cooking, may have generated heat-induced antioxidants such as Maillard reaction products contributing to radical scavenging properties in micronised (cooked) cowpea samples. Though micronised samples had lower concentrations of some phenolic compounds and total extractable phenolics than unmicronised samples, micronised cowpea samples still exhibited radical scavenging properties and offered protective effects against oxidative damage of LDL, DNA and RBC and therefore may offer potential health benefits to consumers. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Food Science / Unrestricted

The objective of this study was to characterize the mitochondrial genomes of the species within the genus Ceratocystis and investigate the evolutionary process of the ribosomal RNA cistron found within these fungi. Ceratocystis incorporates a number of pathogenic species affecting a variety of hosts, making the study of these fungi economically significant. The fortuitous identification of a Ceratocystis species, C. manginecans, which contained two different internally transcribed spacer sequence types within the ribosomal rRNA cistron, enabled a study of concerted evolution in this fungus. Using this non-model organism we were able to show empirical evidence for unequal crossing over and gene conversion as the ultimate forces acting on this gene region dictating a concerted evolutionary effect. We suggest that this process is true for all eukaryotes. Using the knowledge drawn from previously characterized and annotated mitochondrial genomes of other eukaryotes, the genomes of three Ceratocystis species, namely Ceratocystis fimbriata, Ceratocystis albifundus and Ceratocystis moniliformis were fully assembled and annotated for comparative analysis. This comparative study addressed the genome size, gene content, tRNA presence as well as intron types and their homing endonucleases found among these three mitochondrial genomes. An interspecies characterization was then undertaken using the mitochondrial genomes of six different C. albifundus isolates from different geographical locations in Africa. Genetic variation and similarities among these isolates supports the previous hypothesis that the origin of this fungus is Southern Africa. It is hoped that the research presented in this thesis will contribute to the improved understanding of the mitochondrial genomes in Ceratocystis species. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Genetics / Unrestricted

Cryptosporidium spp. is an oocyst-forming apicomplexan protozoan, which infects humans and a large variety of animals. Several species and genotypes are potentially zoonotic and ruminats are considered as an important source of infection. Pre-weaned calves are major hosts for zoonotic C. parvum, and show higher rates of infection than post-weaned or adult animals. Cryptosporidium infection has been demonstrated in a wide variety of wild animals, which may co tribute to environmental contamination. In sub-Saharan Africa, where the HIV infection prevalence is the highest in the world, high incidence of severe and even fatal Cryptosporidium infection have been reported in humans. This study investigated the epidemiology of Cryptosporidium spp. simultaneously in wildlife, indigenous cattle and young children living at the wildlife, livestock and human interface on the western boundary of the Kruger National Park (KNP) in Mpumalanga Province, South Africa. Initially, a pilot study was carried out to assess the zoonotic or anthroponotic importance of Cryptosporidium in diarrhoeic children in South Africa, representing the human group most likely to be infected. This geographically broad study involved hospitals from four provinces in South Africa. Stool samples from hospitalized diarrhoeic children from 0-1 year of age were analysed by microscopy (modified Ziehl-Neelsen (MZN) acid-fast staining) and molecular techniques: polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequencing. An overall prevalence of Cryptosporidium infection of 12.2% was revealed, mainly involving species of anthroponotic origin, such as C. hominis (76%) and C. parvum of anthroponotic nature (20%). Only one species of uncertain zoonotic importance (C. meleagridis) was detected in this study. These findings were in accordance with reports from sub-Saharan Africa (including South Africa), where anthroponotic species of Cryptosporidium were responsible for most infections in humans. The study then concentrated on the public health importance of cryptosporidiosis at the wildlife/livestock/human interface of the KNP. Cryptosporidium oocysts were detected in elephant, impala and buffalo samples collected in three different study areas of the KNP; two located close to the boundaries of the KNP and a third one in the centre of the KNP. The MZN staining technique and an immunofluorescent antibody (IFA) test were applied to identify oocysts from faecal samples. The prevalence detected with MZN was higher than that detected with IFA, however both tests found a higher prevalence in elephants (25.8% and 4.2%, respectively) compared to the other species. The prevalence of Cryptosporidium in buffalo was 5.5% and 1.4% with MZN and IFA, respectively, and 4.2% and 1.8% respectively in impala. In the two study areas adjacent to the fence of KNP, the combined prevalence was significantly higher compared to the area in the centre of the KNP. The agreement between the MZN staining technique and the IFA test was assessed for each wildlife species; the estimates of kappa suggested moderate agreement in buffalo and impala and fair to poor agreement in elephant. The above results of were analysed further by the use of molecular techniques in order to reveal the species and genotypes of the parasite in wildlife and in addition faecal samples collected from post-weaned calves. A questionnaire was also conducted among farmers to investigate observed contacts between cattle and wildlife species in grazing areas outside and inside the KNP. Four of the 241 wildlife samples were PCR-positive (2.8% each in impala and buffalo and of 0.0% in elephant) and sequencing revealed the presence of C. ubiquitum in two impala and one buffalo and C. bovis in one buffalo. Cryptosporidium ubiquitum has been commonly found in a large number of animals, including humans. Among calf samples, 8% (4/51) were PCR-positive and were identified as C. andersoni (2/4) and C. bovis (2/4). The probability of contact between cattle and wildlife outside the KNP, observed by farmers, was higher for buffalo (Pr=0.6) and impala (Pr=0.46) than for elephant (Pr=0.04). This suggests that the detection of C. bovis in both cattle and buffalo might be due to direct or indirect contact between these two species. The detection of C. ubiquitum in wildlife, with its zoonotic potential, suggests that Cryptosporidium may be of public health concern for people living at the interface. We further investigated the prevalence of Cryptosporidium infection in cattle and humans, this time targeting younger (pre-weaned) calves and children. Children <5 years were sampled at six rural clinics within the same interface and stool samples were screened by the MZN staining technique. All MZN-positive and suspicious samples of children and samples of 36 calves within the age of 0-4 months were analysed by nested PCR. Eight of the 143 children (5.6%) were positive on PCR, and sequencing identified predominantly C. hominis, while one sample was identified as C. meleagridis. Eleven of the 36 calf samples (30.5%) were PCR-positive and were identified as C. bovis and C. ryanae. Due to limited resources, molecular analysis could not be performed on more samples. Variables such as source of drinking water, age and contact with animals for children, were analysed as potential risk factors for humans and cattle; however, none were statistically significant. In conclusion, the prevalence of Cryptosporidium detected in human and wildlife was low compared to that reported in other studies in Africa. The species and genotypes detected in humans were predominantly of anthroponotic nature; however, the isolation of C. Ubiquitum from buffalo and impala shows that at least one species of zoonotic importance is present at the wildlife/livestock/human interface. The prevalence of HIV/AIDS in our study area is one of the highest worldwide; therefore the potential public health importance of this parasite should be investigated further. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Production Animal Studies / unrestricted