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<p>Signal compression is an important problem encountered in many applications. Various techniques have been proposed over the years for adressing the problem. The focus of the dissertation is on signal representation and compression by the use of optimization theory, more shortest path methods.</p><p>Several new signal compression algorithms are presented. They are based on the coding of line segments which are used to spproximate, and thereby represent, the signal. These segments are fit in a way that is optimal given some constraints on the solution. By formulating the compession problem as a graph theory problem, shortest path methods can be applied in order to yeild optimal compresson with respect to the given constraints.</p><p>The approaches focused on in this dissertaion mainly have their origin in ECG comression and is often referred to as time domain compression methods. Coding by time domain methods is based on the idea of extracting a subset of <i>significant </i>signals samples to represent the signal. The key to a successful algoritm is a good rule for determining the most significant samples. Between any two succeeding samples in the extracted smaple set, different functions are applied in reconstruction of the signal. These functions are fitted in a wy that guaratees minimal reconstruction error under the gien constraints. Two main categories of compression schemes are developed:</p><p>1. Interpolating methods, in which it is insisted on equality between the original and reconstructed signal at the points of extraction.</p><p>2. Non-interpolating methods, where the inerpolatian restriction is released.</p><p>Both first and second order polynomials are used in reconstruction of the signal. There is solso developed an approach were multiple error measures are applied within one compression algorithm. </p><p>The approach of extracting the most significant smaples are further developed by measuring the samples in terms of the number of bits needed to encode such samples. This way we develop an approach which is optimal in the ratedistortion sense. </p><p>Although the approaches developed are applicable to any type of signal, the focus of this dissertaion is on the compression of electrodiogram (ECG) signals and image contours, ECG signal compression has traditionally been </p>

Signal compression is an important problem encountered in many applications. Various techniques have been proposed over the years for adressing the problem. The focus of the dissertation is on signal representation and compression by the use of optimization theory, more shortest path methods. Several new signal compression algorithms are presented. They are based on the coding of line segments which are used to spproximate, and thereby represent, the signal. These segments are fit in a way that is optimal given some constraints on the solution. By formulating the compession problem as a graph theory problem, shortest path methods can be applied in order to yeild optimal compresson with respect to the given constraints. The approaches focused on in this dissertaion mainly have their origin in ECG comression and is often referred to as time domain compression methods. Coding by time domain methods is based on the idea of extracting a subset of significant signals samples to represent the signal. The key to a successful algoritm is a good rule for determining the most significant samples. Between any two succeeding samples in the extracted smaple set, different functions are applied in reconstruction of the signal. These functions are fitted in a wy that guaratees minimal reconstruction error under the gien constraints. Two main categories of compression schemes are developed: 1. Interpolating methods, in which it is insisted on equality between the original and reconstructed signal at the points of extraction. 2. Non-interpolating methods, where the inerpolatian restriction is released. Both first and second order polynomials are used in reconstruction of the signal. There is solso developed an approach were multiple error measures are applied within one compression algorithm. The approach of extracting the most significant smaples are further developed by measuring the samples in terms of the number of bits needed to encode such samples. This way we develop an approach which is optimal in the ratedistortion sense. Although the approaches developed are applicable to any type of signal, the focus of this dissertaion is on the compression of electrodiogram (ECG) signals and image contours, ECG signal compression has traditionally been

<p>This thesis contributes to the research on optimization algorithms for nonlinear programming, and to the application of such algorithms to nonlinear model predictive control.</p><p>Regarding the contribution to research on algorithms for nonlinear programming, a novel algorithm is put forward with a complete theory for global and local convergence. This is the main contribution of the thesis. The algorithm, named rFSQP, is a reduced Hessian Feasible Sequential Quadratic Programming method. It remains feasible with respect to nonlinear inequalities at all SQP iterations, but nonlinear equality constraints are treated as in general reduced Hessian SQP methods. The rFSQP algorithm is implemented in MATLAB and tested on a number of small scale problems with encouraging results. However, the algorithm is designed for large scale problems with few degrees of freedom. Some preliminary testing of the algorithm on large scale problems are investigated.</p><p>The thesis also contributes to the understanding of the relation between sequential and simultaneous reduced gradient methods, and to the understanding of the relation between discretization methods for dynamical systems and the choice of optimization algorithms.</p><p>The thesis also contributes to model based control approaches of grate sintering. Grate sintering is a complex metallurgical process, where melting of solids and fast gas dynamics give rise to stiff process models, i.e. the "time constants" of the system differ by many decades in magnitude. Hence, application of real-time optimization methods like nonlinear model predictive control to the grate sintering process is challenging. The thesis gives a framework for implementing nonlinear model based control of grate sintering by giving a control objective, a nonlinear model and choosing an appropriate discretization scheme. The thesis gives a reduced order model which is less computationally demanding. Data from industrial experiments are used to adapt the model and to assess the control objective.</p>

This thesis contributes to the research on optimization algorithms for nonlinear programming, and to the application of such algorithms to nonlinear model predictive control. Regarding the contribution to research on algorithms for nonlinear programming, a novel algorithm is put forward with a complete theory for global and local convergence. This is the main contribution of the thesis. The algorithm, named rFSQP, is a reduced Hessian Feasible Sequential Quadratic Programming method. It remains feasible with respect to nonlinear inequalities at all SQP iterations, but nonlinear equality constraints are treated as in general reduced Hessian SQP methods. The rFSQP algorithm is implemented in MATLAB and tested on a number of small scale problems with encouraging results. However, the algorithm is designed for large scale problems with few degrees of freedom. Some preliminary testing of the algorithm on large scale problems are investigated. The thesis also contributes to the understanding of the relation between sequential and simultaneous reduced gradient methods, and to the understanding of the relation between discretization methods for dynamical systems and the choice of optimization algorithms. The thesis also contributes to model based control approaches of grate sintering. Grate sintering is a complex metallurgical process, where melting of solids and fast gas dynamics give rise to stiff process models, i.e. the "time constants" of the system differ by many decades in magnitude. Hence, application of real-time optimization methods like nonlinear model predictive control to the grate sintering process is challenging. The thesis gives a framework for implementing nonlinear model based control of grate sintering by giving a control objective, a nonlinear model and choosing an appropriate discretization scheme. The thesis gives a reduced order model which is less computationally demanding. Data from industrial experiments are used to adapt the model and to assess the control objective.

The maintenance schedule of generators in power plants needs to match the electricity demand and needs to ensure the reliability of the power plant at a minimum cost of operation. In this study, a comparison is made between the modified generator maintenance scheduling model and the classic generator maintenance scheduling model using the reliability objective functions. Both models are applied to a 21-unit test system, and the results show that the modified generator maintenance scheduling model gives better and more reliable solutions than the regular generator maintenance scheduling model. The better results of the modified generator maintenance scheduling model are due the modified and additional constraints in the modified generator maintenance scheduling model. Due to the reliable results of the modified generator maintenance scheduling model, a robust model is formulated using the economic cost objective function. The model includes modified crew and maintenance window constraints, with some additional constraints such as the relationship constraints among the variables. To illustrate the robustness of the formulated GMS model, the maintenance of the Arnot power plant in South Africa is scheduled with open-loop and closed-loop controllers. Both controllers satisfy all the constraints but the closed-loop results are better than the open-loop results. AFRIKAANS : Die onderhoudskedule vir kragopwekkers (OSK) in kragstasies moet kan voorsien in die vraag na elektrisiteit en moet die betroubaarheid van die kragstasie teen ’n minimum operasiekoste verseker. In hierdie studie word die betroubaarheidsdoelwitfunksie gebruik om ’n gewysigde onderhoudskeduleringsmodel vir kragopwekkers te vergelyk met die konvensionele onderhoudskeduleringsmodel. Beide modelle word toegepas op 'n 21-eenheid-toetsstelsel, en die resultate toon dat die gewysigde model ’n beter en meer betroubare oplossing bied as die konvensionele model. Die beter resultate van die gewysigde model is die gevolg van die gewysigde en bykomende beperkings in die gewysigde model. As gevolg van die betroubare resultate van die gewysigde onderhoudskeduleringsmodel word die koste-ekonomie-doelwitfunksie gebruik om ’n robuuste model te formuleer. Die model sluit gewysigde bemanning- en onderhoudvensterbeperkings in, met ’n paar bykomende beperkings soos die verhoudingsbeperkings tussen die veranderlikes. Om die robuustheid van die geformuleerde OSK-model te illustreer word die instandhouding van die Arnot kragstasie in Suid-Afrika geskeduleer met oop- en geslotelus-beheerders. Beide beheerders voldoen aan al die beperkinge, maar die geslotelusresultate is beter as die ooplusresultate. / Dissertation (MSc)--University of Pretoria, 2011. / Electrical, Electronic and Computer Engineering / Unrestricted

Reverse genetics is an innovative molecular biology tool that enables the manipulation of viral genomes at the cDNA level in order to generate particular mutants or artificial viruses. The reverse genetics system for the influenza virus is arguably one of the best illustrations of the potential power of this technology. This reverse genetics system is the basis for the ability to regularly adapt influenza vaccines strains. Today, reverse genetic systems have been developed for many animal RNA viruses. Selection-free reverse genetics systems have been developed for the members of the Reoviridae family including, African horsesickness virus, bluetongue virus and orthoreovirus. This ground-breaking technology has led to the generation of valuable evidence regarding the replication and pathogenesis of these viruses. Unfortunately, extrapolating either the plasmid-based or transcript-based reverse genetics systems to rotavirus has not yet been successful. The development of a selection-free rotavirus reverse genetics system will enable the systematic investigation of poorly understood aspects of the rotavirus replication cycle and aid the development of more effective vaccines, amongst other research avenues. This study investigated the importance of co-expressed rotavirus proteins in the development of a selection-free rotavirus reverse genetics system. The consensus sequences of the rotavirus strains Wa (RVA/Human-tc/USA/WaCS/1974/G1P[8]) and SA11 (RVA/Simian-tc/ZAF/SA11/1958/G3P[2]) where used to design rotavirus expression plasmids. The consensus nucleotide sequence of a human rotavirus Wa strain was determined by sequence-independent cDNA synthesis and amplification combined with next-generation 454® pyrosequencing. A total of 4 novel nucleotide changes, which also resulted in amino acid changes, were detected in genome segment 7 (NSP3), genome segment 9 (VP7) and genome segment 10 (NSP4). In silico analysis indicated that none of the detected nucleotide changes, and consequent amino acid variations, had any significant effect on viral structure. Evolutionary analysis indicated that the sequenced rotavirus WaCS was closely related to the ParWa and VirWa variants, which were derived from the original 1974 Wa isolate. Despite serial passaging in animals, as well as cell cultures, the Wa genome seems to be stable. Considering that the current reference sequence for the Wa strain is a composite sequence of various Wa variants, the rotavirus WaCS may be a more appropriate reference sequence. The rotavirus Wa and SA11 strains were selected for plasmid-based expression of rotavirus proteins, under control of a T7 promoter sequence, due to the fact that they propagate well in MA104 cells and the availability of their consensus sequences. The T7 RNA polymerase was provided by a recombinant fowlpox virus. After extensive transfection optimisation on a variety of mammalian cell lines, MA104 cells proved to be the best suited for the expression rotavirus proteins from plasmids. The expression of rotavirus Wa and SA11 VP1, VP6, NSP2 and NSP5 could be confirmed with immunostaining in MA104 and HEK 293H cells. Another approach involved the codon-optimised expression of the rotavirus replication complex scaffold in MA104 cells under the control of a CMV promoter sequence. This system was independent from the recombinant fowlpox virus. All three plasmid expression sets were designed to be used in combination with the transcript-based reverse genetics system in order to improve the odds of developing a successful rotavirus reverse genetics system. Rotavirus transcripts were generated using transcriptively active rotavirus SA11 double layered particles (DLPs). MA104 and HEK293H cells proved to be the best suited for the expression of rotavirus transcripts although expression of rotavirus VP6 could be demonstrated in all cell cultures examined (MA104, HEK 293H, BSR and COS-7) using immunostaining. In addition, the expression of transcript derived rotavirus VP1, NSP2 and NSP5 could be confirmed with immunofluorescence in MA104 and HEK 293H cells. This is the first report of rotavirus transcripts being translated in cultured cells. A peculiar cell death pattern was observed within 24 hours in response to transfection of rotavirus transcripts. This observed cell death, however does not seem to be related to normal viral cytopathic effect as no viable rotavirus could be recovered. In an effort to combine the transcript- and plasmid systems, a dual transfection strategy was followed where plasmids encoding rotavirus proteins were transfected first followed, 12 hours later, by the transfection of rotavirus SA11 transcripts. The codon- optimised plasmid system was designed as it was postulated that expression of the DLP-complex (VP1, VP2, VP3 and VP6), the rotavirus replication complex would form and assist with replication and/or packaging. Transfecting codon- optimized plasmids first noticeably delayed the mass cell death observed when transfecting rotavirus transcripts on their own. None of the examined coexpression systems were able to produce a viable rotavirus. Finally, the innate immune responses elicited by rotavirus transcripts and plasmid-derived rotavirus Wa and SA11 proteins were investigated. Quantitative RT-PCR (qRT-PCR) experiments indicated that rotavirus transcripts induced high levels of the expression of the cytokines IFN- α1, IFN-1β, IFN-λ1 and CXCL10. The expression of certain viral proteins from plasmids (VP3, VP7 and NSP5/6) was more likely to stimulate specific interferon responses, while other viral proteins (VP1, VP2, VP4 and NSP1) seem to be able to actively suppress the expression of certain cytokines. In the light of these suppression results, specific rotavirus proteins were expressed from transfected plasmids to investigate their potential in supressing the interferon responses provoked by rotavirus transcripts. qRT-PCR results indicated that cells transfected with the plasmids encoding NSP1, NSP2 or a combination of NSP2 and NSP5 significantly reduced the expression of specific cytokines induced by rotavirus transcripts. These findings point to other possible viral innate suppression mechanisms in addition to the degradation of interferon regulatory factors by NSP1. The suppression of the strong innate immune response elicited by rotavirus transcripts might well prove to be vital in the quest to better understand the replication cycle of this virus and eventually lead to the development of a selection-free reverse genetics system for rotavirus. / PhD (Biochemistry), North-West University, Potchefstroom Campus, 2014

Reverse genetics is an innovative molecular biology tool that enables the manipulation of viral genomes at the cDNA level in order to generate particular mutants or artificial viruses. The reverse genetics system for the influenza virus is arguably one of the best illustrations of the potential power of this technology. This reverse genetics system is the basis for the ability to regularly adapt influenza vaccines strains. Today, reverse genetic systems have been developed for many animal RNA viruses. Selection-free reverse genetics systems have been developed for the members of the Reoviridae family including, African horsesickness virus, bluetongue virus and orthoreovirus. This ground-breaking technology has led to the generation of valuable evidence regarding the replication and pathogenesis of these viruses. Unfortunately, extrapolating either the plasmid-based or transcript-based reverse genetics systems to rotavirus has not yet been successful. The development of a selection-free rotavirus reverse genetics system will enable the systematic investigation of poorly understood aspects of the rotavirus replication cycle and aid the development of more effective vaccines, amongst other research avenues. This study investigated the importance of co-expressed rotavirus proteins in the development of a selection-free rotavirus reverse genetics system. The consensus sequences of the rotavirus strains Wa (RVA/Human-tc/USA/WaCS/1974/G1P[8]) and SA11 (RVA/Simian-tc/ZAF/SA11/1958/G3P[2]) where used to design rotavirus expression plasmids. The consensus nucleotide sequence of a human rotavirus Wa strain was determined by sequence-independent cDNA synthesis and amplification combined with next-generation 454® pyrosequencing. A total of 4 novel nucleotide changes, which also resulted in amino acid changes, were detected in genome segment 7 (NSP3), genome segment 9 (VP7) and genome segment 10 (NSP4). In silico analysis indicated that none of the detected nucleotide changes, and consequent amino acid variations, had any significant effect on viral structure. Evolutionary analysis indicated that the sequenced rotavirus WaCS was closely related to the ParWa and VirWa variants, which were derived from the original 1974 Wa isolate. Despite serial passaging in animals, as well as cell cultures, the Wa genome seems to be stable. Considering that the current reference sequence for the Wa strain is a composite sequence of various Wa variants, the rotavirus WaCS may be a more appropriate reference sequence. The rotavirus Wa and SA11 strains were selected for plasmid-based expression of rotavirus proteins, under control of a T7 promoter sequence, due to the fact that they propagate well in MA104 cells and the availability of their consensus sequences. The T7 RNA polymerase was provided by a recombinant fowlpox virus. After extensive transfection optimisation on a variety of mammalian cell lines, MA104 cells proved to be the best suited for the expression rotavirus proteins from plasmids. The expression of rotavirus Wa and SA11 VP1, VP6, NSP2 and NSP5 could be confirmed with immunostaining in MA104 and HEK 293H cells. Another approach involved the codon-optimised expression of the rotavirus replication complex scaffold in MA104 cells under the control of a CMV promoter sequence. This system was independent from the recombinant fowlpox virus. All three plasmid expression sets were designed to be used in combination with the transcript-based reverse genetics system in order to improve the odds of developing a successful rotavirus reverse genetics system. Rotavirus transcripts were generated using transcriptively active rotavirus SA11 double layered particles (DLPs). MA104 and HEK293H cells proved to be the best suited for the expression of rotavirus transcripts although expression of rotavirus VP6 could be demonstrated in all cell cultures examined (MA104, HEK 293H, BSR and COS-7) using immunostaining. In addition, the expression of transcript derived rotavirus VP1, NSP2 and NSP5 could be confirmed with immunofluorescence in MA104 and HEK 293H cells. This is the first report of rotavirus transcripts being translated in cultured cells. A peculiar cell death pattern was observed within 24 hours in response to transfection of rotavirus transcripts. This observed cell death, however does not seem to be related to normal viral cytopathic effect as no viable rotavirus could be recovered. In an effort to combine the transcript- and plasmid systems, a dual transfection strategy was followed where plasmids encoding rotavirus proteins were transfected first followed, 12 hours later, by the transfection of rotavirus SA11 transcripts. The codon- optimised plasmid system was designed as it was postulated that expression of the DLP-complex (VP1, VP2, VP3 and VP6), the rotavirus replication complex would form and assist with replication and/or packaging. Transfecting codon- optimized plasmids first noticeably delayed the mass cell death observed when transfecting rotavirus transcripts on their own. None of the examined coexpression systems were able to produce a viable rotavirus. Finally, the innate immune responses elicited by rotavirus transcripts and plasmid-derived rotavirus Wa and SA11 proteins were investigated. Quantitative RT-PCR (qRT-PCR) experiments indicated that rotavirus transcripts induced high levels of the expression of the cytokines IFN- α1, IFN-1β, IFN-λ1 and CXCL10. The expression of certain viral proteins from plasmids (VP3, VP7 and NSP5/6) was more likely to stimulate specific interferon responses, while other viral proteins (VP1, VP2, VP4 and NSP1) seem to be able to actively suppress the expression of certain cytokines. In the light of these suppression results, specific rotavirus proteins were expressed from transfected plasmids to investigate their potential in supressing the interferon responses provoked by rotavirus transcripts. qRT-PCR results indicated that cells transfected with the plasmids encoding NSP1, NSP2 or a combination of NSP2 and NSP5 significantly reduced the expression of specific cytokines induced by rotavirus transcripts. These findings point to other possible viral innate suppression mechanisms in addition to the degradation of interferon regulatory factors by NSP1. The suppression of the strong innate immune response elicited by rotavirus transcripts might well prove to be vital in the quest to better understand the replication cycle of this virus and eventually lead to the development of a selection-free reverse genetics system for rotavirus. / PhD (Biochemistry), North-West University, Potchefstroom Campus, 2014