Ph.D. / A lot of chemicals are used in agriculture to increase production per cost. Unfortunately most of these chemicals find their way into the final agricultural product or get washed off into other systems where they may pose health and environmental concerns. As such monitoring of these compounds where they are not needed is necessary to avoid unwarranted pollution and the effects associated with them. This requires the use of analytical techniques and instrumentation. Analytical chemistry, especially in the area of sample preparation and clean-up, has shifted focus mainly on greener methods that produce only minute quantities of waste without sacrificing efficiency. This has led to the conception of a term QuEChERS (acronym for Quick, Easy, Cheap, Effective, Robust and Safe) to reflect this trend in sample preparation. Efforts have been made in this regard to reduce the amount of chemicals used; as a result miniaturised techniques have evolved. One such technique that is easiest and cheapest is solvent micro-extraction especially the single-drop format, wherein only a few micro-litres of an organic solvent are used to sample the aqueous solution with the same volume being transferred into the instrument for analysis. This study reports the advances made in development of a modified single-drop micro-extraction (SDME) technique through the deliberate introduction of an air-bubble to facilitate mass transfer. This is termed bubble-in-drop single-drop micro-extraction (BID-SDME). The method has been reported for the first time in our earlier work. This study started off with the validation of the method using triazine mixture (TP 619) as model herbicides. The method was validated for linearity (0.05 – 5 ng/mL), reproducibility and repeatability (%RSD < 10%), matrix effect, limits of detection (pg/mL range) and quantification as well as accuracy.

Please read the abstract in the section 00front of this document / Dissertation (MSc (Applied Sciences:Chemistry))--University of Pretoria, 2005. / Chemistry / unrestricted

This thesis contributes work to the fields of runtime monitoring and specification mining. It develops a formalism for specifying patterns of behaviour in execution traces and defines techniques for checking these patterns in, and extracting patterns from, traces. These techniques represent an extension in the expressiveness of properties that can be efficiently and effectively monitored and mined. The behaviour of a computer system is considered in terms of the actions it performs, captured in execution traces. Patterns of behaviour, formally defined in trace specifications, denote the traces that the system should (or should not) exhibit. The main task this work considers is that of checking that the system conforms to the specification i.e. is correct. Additionally, trace specifications can be used to document behaviour to aid maintenance and development. However, formal specifications are often missing or incomplete, hence the mining activity. Previous work in the field of runtime monitoring (checking execution traces) has tended to either focus on efficiency or expressiveness, with different approaches making different trade-offs. This work considers both, achieving the expressiveness of the most expressive existing tools whilst remaining competitive with the most efficient. These elements of expressiveness and efficiency depend on the specification formalism used. Therefore, we introduce quantified event automata for describing patterns of behaviour in execution traces and then develop a range of efficient monitoring algorithms. To monitor execution traces we need a formal description of expected behaviour. However, these are often difficult to write - especially as there is often a lack of understanding of actual behaviour. The field of specification mining aims to explain the behaviour present in execution traces by extracting specifications that conform to those traces. Previous work in this area has primarily been limited to simple specifications that do not consider data. By leveraging the quantified event automata formalism, and its efficient trace checking procedures, we introduce a generate-and-check style mining framework capable of accurately extracting complex specifications. This thesis, therefore, makes separate significant contributions to the fields of runtime monitoring and specification mining. This work generalises and extends existing techniques in runtime monitoring, enabling future research to better understand the interaction between expressiveness and efficiency. This work combines and extends previous approaches to specification mining, increasing the expressiveness of specifications that can be mined.

Solid Phase Microextraction (SPME) associated with Microwave Assisted Extraction (MAE)^(1-3) , on-line headspace derivatization ^(4-6) and the selectivity of different SPME coatings ⁽⁷⁾ were studied. Trace amounts of Veltol ®, Veltol Plus® and short chain fatty acids in food samples were analyzed by GC/MS. Since SPME is not directly applicable to solid samples, SPME associated with MAE techniques was studied for solids, primarily food samples. The efficiency of classical solvent extraction and MAE was compared. The parameters which affect SPME, were optimized for the determination of Veltol® and Veltol Plus® in food products such as potato chips and coffee. The technique gave a detection limit of 2 ppb for Veltol Plus ® which is 200 times more sensitive than conventional GC technique. Headspace injection is characterized by simple and easy handling of complicated solid and solution matrices. Headspace injection, however, is not suitable for high molecular weight substances or non-volatile compounds. An on-line derivatization headspace technique was studied for short chain fatty acids. These samples are difficult to do by classical GC. The developed technique simplified the conventional derivatization procedures and combined the sample preparation and GC/MS analysis into one step. The thermostatting temperature, time, solvent and matrix effects were investigated. Low calorie fat and some agricultural samples were analyzed. The detection limit for acetic acid is 8 ppb. SPME is a novel sample introduction technique. The behavior of di(methylsiloxane), polyacrylate and Carbowax coatings on SPME fibers for compounds having different functional groups were investigated. The selectivities of the coating, sample pH and the sample temperature were investigated. / Ph. D.

Recollection is a pattern completion process that enables retrieval of arbitrarily associated information following minimal study. These attributes enable recollection to support retrieval of many kinds of mnemonic representations, from highly associative contextual information to very specific low-level representations. However, recollection is typically studied in the context of declarative memory tasks, in which participants exhibit recollection by explicitly reporting on the recollected information. Is it the case that recollection is limited to declarable representations, or is it a more general process that occurs for any representation? Two experiments and a novel analysis technique are presented to answer this question. The results suggest that recollection is not limited to declarable representations. These results argue against theories of recognition memory that restrict the representational input allowed to mnemonic processes; mnemonic processes in general may act on arbitrary representations.

This thesis describes the development of liquid chromatography tandem mass spectrometry (LC-MS/MS) methods for the trace analysis of active pharmaceutical ingredients (APIs) and their metabolites in aqueous environmental matrices. The research was focused on the development of chiral LC-MS/MS methods for the analysis of fluoxetine and metoprolol, as well as their chiral metabolites in environmental water samples. A method was also developed for the achiral compounds, diazepam and nordiazepam. The LC-MS/MS methods were validated by the use of the isotope-labeled compounds. As these isotope-labeled compounds were not found in the wastewater samples, the validation could be assessed at trace level concentrations in the actual matrices in which the analytes were detected. The analytes were extracted from the water samples using solid phase extraction methods. Different types of solid phase extraction sorbents were evaluated. Fluoxetine and norfluoxetine were extracted through the use of a mixed mode polymeric based extraction sorbent. A hydrophilic and lipophilic balanced sorbent was employed for the simultaneous extraction of metoprolol and its metabolites, the base α-hydroxymetoprolol and the acidic metabolite deaminated metoprolol. Moreover, silica based C18 extraction discs were applied for the sample preparation of diazepam and nordiazepam. The chromatographic separations were conducted in reversed phase LC with MS compatible mobile phases. The enantiomers of fluoxetine and norfluoxetine were simultaneously separated using the chiral stationary phase (CSP), α1-acid glycoprotein (AGP). The Chiral AGP column was also applied for the separation of the enantiomers of deaminated metoprolol. For the simultaneous separation of the metoprolol enantiomers and the four stereoisomers of α-hydroxymetoprolol, the cellobiohydrolase (CBH) protein based CSP was used. An octadecyl silica based LC column was applied for the separation of diazepam and nordiazepam. The analytes were detected by the use of tandem quadrupole mass spectrometry operating in selective reactive monitoring mode. High resolution MS, employing a quadrupole time-of-flight (QqTOF) mass analyzer, was utilized for the identification of an unknown compound in wastewater samples. The APIs and their metabolites, as well as their respective enantiomers, were quantified in raw and treated wastewater from Uppsala, Sweden along with surface water from the River Fyris in Uppsala.

Les techniques d'analyse et de débogage d'applications sont de plus en plus mises à mal dans les systèmes modernes. En particulier dans les systèmes basés sur des composants embarqués multiprocesseurs (ou MPSoc) qui composent aujourd'hui la plupart de nos dispositifs quotidiens. Le recours à des traces d'exécution devient incontournable pour appliquer une analyse fine de tels systèmes et d'en identifier les comportements divergents. Même si la trace représente une source d'information riche mise à disposition du développeur pour travailler, les informations pertinentes à l'analyse se retrouvent noyées dans la masse et sont difficilement utilisables sans une expertise de haut niveau. Des outils dédiés à l'exploitation des traces deviennent nécessaires. Cependant les outils existants prennent rarement en compte les aspects métiers spécifiques à l'application afin d'optimiser le travail d'analyse. Dans cette thèse, nous proposons une approche qui permet au développeur de représenter, manipuler et interroger une trace d'exécution en se basant sur des concepts liés à ses propres connaissances métier. Notre approche consiste en l'utilisation d'une ontologie pour modéliser et interroger les concepts métier dans une trace, et l'utilisation d'un moteur d'inférence pour raisonner sur ces concepts métier. Concrètement, nous proposons VIDECOM l'ontologie du domaine de l'analyse des traces d'exécution des applications embarquées multimédia sur MPSoC. Nous nous intéressons ensuite au passage à l'échelle de l'exploitation de cette ontologie pour l'analyse des traces de grandes tailles. Ainsi, nous faisons une étude comparative des différents systèmes de gestion des ontologies pour déterminer l'architecture la plus adaptée aux traces de très grande taille au sein de notre ontologie VIDECOM. Nous proposons également un moteur d'inférence qui adresse les défis que pose le raisonnement sur les concepts métier, à savoir l'inférence de l'ordre temporel entre les concepts métier dans la trace et la terminaison du processus de génération de nouvelles connaissances métier. Enfin, nous illustrons la mise en pratique de l'utilisation de l'ontologie VIDECOM dans le cadre du projet SoC-Trace pour l'analyse des traces d'exécution réelles sur MPSoC. / Applications analysis and debugging techniques are increasingly challenging task in modern systems. Especially in systems based on embedded multiprocessor components (or MPSoC) that make up the majority of our daily devices today. The use of execution traces is unavoidable to apply a detailed analysis of such systems and identify unexpected behaviors. Even if the trace offers a rich corpus of information to the developer for her work, information relevant to the analysis are hidden in the trace and is unusable without a high level of expertise. Tools dedicated to trace analysis become necessary. However existing tools take little or no account of the specific business aspects to an application or the developer's business knowledge to optimize the analysis task. In this thesis, we propose an approach that allows the developer to represent, manipulate and query an execution trace based on concepts related to her own business knowledge. Our approach is the use of an ontology to model and query business concepts in a trace, and the use of an inference engine to reason about these business concepts. Specifically, we propose VIDECOM, the domain ontology for the analysis of execution traces of multimedia applications embedded on MPSoC. We then focus on scaling the operation of this ontology for the analysis of huge traces. Thus, we make a comparative study of different ontologies management systems (or triplestores) to determine the most appropriate architecture for very large traces in our VIDECOM ontology.We also propose an inference engine that addresses the challenges of reasoning about business concepts, namely the inference of the temporal order between business concepts in the trace and the termination of the process of generating new knowledge from business knowledge. Finally, we illustrate the practical use of VIDECOM in the SoC-Trace project for the analysis of real execution traces on MPSoC.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A ordem Didelphimorphia, de marsupiais americanos, apresenta 19 gêneros e 96 espécies, todos membros da família Didelphidae, que é dividida em duas subfamílias, Caluromyinae e Didelphinae. A subfamília Didelphinae contém (não apenas) as tribos Didelphini e Metachirini. A tribo Didelphini compreende 15 espécies de quatro gêneros: Chironectes (1 espécie), Lutreolina (1), Didelphis (6) e Philander (7) e a tribo Metachirini é monotípica, com apenas uma espécie do gênero Metachirus. Estes cinco gêneros encontram-se distribuídos amplamente pelas Américas, desde o sul do Canadá até a região central da Argentina. O objetivo deste estudo foi buscar identificar e explicar, através de análise pan-biogeográfica, os padrões de distribuição das espécies destes cinco gêneros. Para tal, foi feito um levantamento em banco de dados, coleções científicas e artigos científicos para a obtenção de dados sobre as localidades de registro de cada espécie. Estas foram então marcadas em mapas e a partir destes, as localidades de ocorrência foram conectadas com linhas de menor distância para formação dos traços individuais. Pela sobreposição dos traços individuais chegou-se aos traços generalizados e do encontro destes, aos nós biogeográficos. Os pontos de ocorrência foram também plotados em mapas de biomas para análise. Encontramos três traços generalizados e dois nós biogeográficos, um no centro da Bolívia na província biogeográfica de Puna e outro na Argentina, na província de Misiones. Quatro espécies não participaram de nenhum dos traços generalizados, provavelmente devido à sua distribuição mais restrita (Philander deltae, P. andersoni, P. olrogi e P. mcilhennyi). Chironectes minimus e Metachirus nudicaudatus tiveram seus traços coincidentes com dois traços generalizados, o que está de acordo com suas divisões de subespécies. Identificamos os diferentes padrões existentes para o norte da América do Sul (Venezuela) já apontado por diversos autores, porém apenas quando analisadas as subespécies em separado. Alguns limites para a distribuição das espécies puderam ser identificados, como por exemplo o istmo de Tehuantepec, no México, para Chironectes minimus e Metachirus nudicaudatus e o limite da região neotropical para P. opossum e D. marsupialis. O limite de distribuição sul de Philander opossum e P. frenatus é provavelmente o rio Paraguai, que deve servir de barreira para o contato entre as duas espécies. A descaracterização dos ambientes naturais pelo desmatamento vem alterando os padrões naturais de distribuição das espécies, com o registro de espécies de áreas abertas em biomas de mata. Lutreolina crassicaudata apresenta distribuição disjunta, ocupando duas áreas de vegetação aberta, uma no noroeste e outra no centro e sudeste da América do Sul, padrão provavelmente gerado pelos períodos de retração e expansão de áreas de savana do Mioceno superior ao Holoceno, levando à captura destes enclaves de vegetação aberta, com seu isolamento por áreas de floresta. Os nós e traços generalizados aqui identificados coincidiram com os encontrados por outros autores. Apesar da pan-biogeografia poder ser usada para propor áreas de proteção ambiental, nos locais em que encontramos os nós biogeográficos já existem unidades de conservação, não havendo assim necessidade de propor novas áreas no caso desses marsupiais. Ainda existe uma grande necessidade de um melhor conhecimento da distribuição e taxonomia das espécies estudadas, o que promoveria um melhor entendimento dos padrões biogeográficos existentes / The order Didelphimorphia, family Didelphidae of American marsupials includes 19 genera and 96 species and is divided into two subfamilies, Caluromyinae and Didelphinae. The subfamily Didelphinae contains (not exclusively) the tribes Didelphini and Metachirini. The tribe Didelphini comprises 15 species of four genera: Chironectes (1 species), Lutreolina (1), Didelphis (6) and Philander (7) and Metachirini tribe is monotypic, with only one species of the genus Metachirus. These five genera are widely distributed throughout the Americas, from southern Canada to central Argentina. The aim of this study was to identify and to explain the speciess distribution patterns trough pan-biogeographic analysis. So, a survey was carried on using databases, visiting scientific collections and searching for published records to obtain data on localities were species were registered. Localities, for each separate species were marked on maps and the most close localities were connected with lines (individual tracks). The overlapping of individual tracks are the generalized tracks and the intersection of two or more generalized tracks are called nodes. Localities were also plotted on biomes maps. We found three generalized tracks and two nodes, one in the center of Bolivia in the biogeographic province of Pune and the other in Argentina, in Misiones. Four species do not participated in any generalized tracks, probably due to its restricted distribution (Philander delta, P. andersoni, P. olrogi and P. mcilhennyi). Chironectes minimus and Metachirus nudicaudatus had their tracks overlapped with two generalized tracks, which is in accordance with their known subspecies geographic distribution. In those species which are divided in subspecies, a separate analysis was carried on. Different patterns on the northern South America (Venezuela) were identified, all already pointed out by authors. Some species distribution limits were identified, such as the Tehuantepec Isthmus in Mexico for C. minimus and M. nudicaudatus and the neotropical region north limit to P. opossum and D. marsupialis. The south limit of P. opossum and P. frenatus is the Paraguay river, which seems to be a barrier. The mischaracterization of natural environments by human activities is changing the natural distribution patterns, as we can see by the occurrence of open areas species in forest biomes. Lutreolina crassicaudata presents a disjunct distribution, occupying two open vegetation areas, in northwest and center-southeast South America, probably generated by periods of contraction and expansion of savanna areas during the later Miocene to Holocene, leading to open vegetation enclaves surrounded by forests. The generalized tracks that we identified coincided with those found by other authors. Despite the pan-biogeography methodology can be used to propose protected areas, our nodes are in areas where conservation units already exist. There still is a great need for a better data of the distribution and taxonomy of these species, which would promote a better understanding of their biogeographic patterns

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A ordem Didelphimorphia, de marsupiais americanos, apresenta 19 gêneros e 96 espécies, todos membros da família Didelphidae, que é dividida em duas subfamílias, Caluromyinae e Didelphinae. A subfamília Didelphinae contém (não apenas) as tribos Didelphini e Metachirini. A tribo Didelphini compreende 15 espécies de quatro gêneros: Chironectes (1 espécie), Lutreolina (1), Didelphis (6) e Philander (7) e a tribo Metachirini é monotípica, com apenas uma espécie do gênero Metachirus. Estes cinco gêneros encontram-se distribuídos amplamente pelas Américas, desde o sul do Canadá até a região central da Argentina. O objetivo deste estudo foi buscar identificar e explicar, através de análise pan-biogeográfica, os padrões de distribuição das espécies destes cinco gêneros. Para tal, foi feito um levantamento em banco de dados, coleções científicas e artigos científicos para a obtenção de dados sobre as localidades de registro de cada espécie. Estas foram então marcadas em mapas e a partir destes, as localidades de ocorrência foram conectadas com linhas de menor distância para formação dos traços individuais. Pela sobreposição dos traços individuais chegou-se aos traços generalizados e do encontro destes, aos nós biogeográficos. Os pontos de ocorrência foram também plotados em mapas de biomas para análise. Encontramos três traços generalizados e dois nós biogeográficos, um no centro da Bolívia na província biogeográfica de Puna e outro na Argentina, na província de Misiones. Quatro espécies não participaram de nenhum dos traços generalizados, provavelmente devido à sua distribuição mais restrita (Philander deltae, P. andersoni, P. olrogi e P. mcilhennyi). Chironectes minimus e Metachirus nudicaudatus tiveram seus traços coincidentes com dois traços generalizados, o que está de acordo com suas divisões de subespécies. Identificamos os diferentes padrões existentes para o norte da América do Sul (Venezuela) já apontado por diversos autores, porém apenas quando analisadas as subespécies em separado. Alguns limites para a distribuição das espécies puderam ser identificados, como por exemplo o istmo de Tehuantepec, no México, para Chironectes minimus e Metachirus nudicaudatus e o limite da região neotropical para P. opossum e D. marsupialis. O limite de distribuição sul de Philander opossum e P. frenatus é provavelmente o rio Paraguai, que deve servir de barreira para o contato entre as duas espécies. A descaracterização dos ambientes naturais pelo desmatamento vem alterando os padrões naturais de distribuição das espécies, com o registro de espécies de áreas abertas em biomas de mata. Lutreolina crassicaudata apresenta distribuição disjunta, ocupando duas áreas de vegetação aberta, uma no noroeste e outra no centro e sudeste da América do Sul, padrão provavelmente gerado pelos períodos de retração e expansão de áreas de savana do Mioceno superior ao Holoceno, levando à captura destes enclaves de vegetação aberta, com seu isolamento por áreas de floresta. Os nós e traços generalizados aqui identificados coincidiram com os encontrados por outros autores. Apesar da pan-biogeografia poder ser usada para propor áreas de proteção ambiental, nos locais em que encontramos os nós biogeográficos já existem unidades de conservação, não havendo assim necessidade de propor novas áreas no caso desses marsupiais. Ainda existe uma grande necessidade de um melhor conhecimento da distribuição e taxonomia das espécies estudadas, o que promoveria um melhor entendimento dos padrões biogeográficos existentes / The order Didelphimorphia, family Didelphidae of American marsupials includes 19 genera and 96 species and is divided into two subfamilies, Caluromyinae and Didelphinae. The subfamily Didelphinae contains (not exclusively) the tribes Didelphini and Metachirini. The tribe Didelphini comprises 15 species of four genera: Chironectes (1 species), Lutreolina (1), Didelphis (6) and Philander (7) and Metachirini tribe is monotypic, with only one species of the genus Metachirus. These five genera are widely distributed throughout the Americas, from southern Canada to central Argentina. The aim of this study was to identify and to explain the speciess distribution patterns trough pan-biogeographic analysis. So, a survey was carried on using databases, visiting scientific collections and searching for published records to obtain data on localities were species were registered. Localities, for each separate species were marked on maps and the most close localities were connected with lines (individual tracks). The overlapping of individual tracks are the generalized tracks and the intersection of two or more generalized tracks are called nodes. Localities were also plotted on biomes maps. We found three generalized tracks and two nodes, one in the center of Bolivia in the biogeographic province of Pune and the other in Argentina, in Misiones. Four species do not participated in any generalized tracks, probably due to its restricted distribution (Philander delta, P. andersoni, P. olrogi and P. mcilhennyi). Chironectes minimus and Metachirus nudicaudatus had their tracks overlapped with two generalized tracks, which is in accordance with their known subspecies geographic distribution. In those species which are divided in subspecies, a separate analysis was carried on. Different patterns on the northern South America (Venezuela) were identified, all already pointed out by authors. Some species distribution limits were identified, such as the Tehuantepec Isthmus in Mexico for C. minimus and M. nudicaudatus and the neotropical region north limit to P. opossum and D. marsupialis. The south limit of P. opossum and P. frenatus is the Paraguay river, which seems to be a barrier. The mischaracterization of natural environments by human activities is changing the natural distribution patterns, as we can see by the occurrence of open areas species in forest biomes. Lutreolina crassicaudata presents a disjunct distribution, occupying two open vegetation areas, in northwest and center-southeast South America, probably generated by periods of contraction and expansion of savanna areas during the later Miocene to Holocene, leading to open vegetation enclaves surrounded by forests. The generalized tracks that we identified coincided with those found by other authors. Despite the pan-biogeography methodology can be used to propose protected areas, our nodes are in areas where conservation units already exist. There still is a great need for a better data of the distribution and taxonomy of these species, which would promote a better understanding of their biogeographic patterns

Differential pulse voltammetry is one of the most widely used analytical polarographic techniques especially for trace inorganic analysis. Up to now mercury electrode and different types of carbon electrodes were used for such analysis. The emphasis of the present dissertation is on the design of a new class of electrodes, namely mono crystalline diamond paste based electrodes, to be used in differential pulse voltammetry for trace analysis of inorganic compounds. Monocrystalline diamond and boron doped polycrystalline diamond based electrodes exhibit several superior electrochemical properties that are significantly different from those of other carbon allotropes based electrodes, e.g., glassy carbon electrodes, highly oriented pyrolytic graphite based electrodes, which have been widely used for many years. The advantages are: (a) lower background currents and noise signals, which lead to improve SIB and SIN ratios, and lower detection limits; (b) good electrochemical activity ( pre-treatment is not necessary); (c) wide electrochemical potential window in aqueous media; (d) very low capacitance; ( e) extreme electrochemical stability; and (f) high reproducibility of analytical information. Furthermore, later studies shown the superiority of the mono crystalline diamond as electrode material due to high mobilities measured for electrons and holes. The design selected for the electrodes is simple, fast and reproducible. The diamond powder was mixed with paraffine oil to give the diamond paste used as electroactive material in the electrodes. The results obtained by employing the diamond paste based electrodes proved a high sensitivity, selectivity, accuracy and high reliability. These characteristics made them suitable to be used for the analysis of different cations (e.g., Fe(ll), Fe(Ill), Cr(Ill), Cr(VI), Pb(ll), Ag(I)) as well as of anions (e.g., iodide) in pharmaceutical, food and environmental matricies. / Dissertation (MSc (Chemistry))--University of Pretoria, 2006. / Chemistry / unrestricted