Canonical variate analysis (CVA) is a widely used method for analyzing group structure in multivariate data. It is mathematically equivalent to a one-way multivariate analysis of variance and often goes by the name of canonical discriminant analysis. Change over time is a central feature of many phenomena of interest to researchers. This dissertation extends CVA to longitudinal data. It develops models whose purpose is to determine what is changing and what is not changing in the group structure. Three approaches are taken: a maximum likelihood approach, a least squares approach, and a covariance structure analysis approach. All methods have in common that they hypothesize canonical variates which are stable over time. The maximum likelihood approach models the positions of the group means in the subspace of the canonical variates. It also requires modeling the structure of the within-groups covariance matrix, which is assumed to be constant or proportional over time. In addition to hypothesizing stable variates over time, one can also hypothesize canonical variates that change over time. Hypothesis tests and confidence intervals are developed. The least squares methods are exploratory. They are based on three-mode PCA methods such as the Tucker2 and parallel factor analysis. Graphical methods are developed to display the relationships between the variables over time. Stable variates over time imply a particular structure for the between-groups covariance matrix. This structure is modeled using covariance structure analysis, which is available in the SAS package Proc Calis. Methods related to CVA are also discussed. First, the least squares methods are extended to canonical correlation analysis, redundancy analysis, Procrustes rotation and correspondence analysis with longitudinal data. These least squares methods lend themselves equally well to data from multiple datasets. Lastly, a least squares method for the common principal components model is developed. / Ph. D.

Forest measurements are inherently spatial. Soil productivity varies spatially at fine scales and tree growth responds by changes in growth-age trajectories. Measuring spatial variability is a perquisite to more effective analysis and statistical testing. In this study, current techniques of partial redundancy analysis and constrained cluster analysis are used to explore how spatial variables determine structure in a managed regular spaced plantation. We will test for spatial relationships in the data and then explore how those spatial relationships are manifested into spatially recognizable structures. The objectives of this research are to measure, test, and map spatial variability in simulated forest plots. Partial redundancy analysis was found to be a good method for detecting the presence or absence of spatial relationships (~95% accuracy). We found that the Calinski-Harabasz method consistently performed better at detecting the correct number of clusters when compared to several other methods. While there is still more work that can be done we believe that constrained cluster analysis has promising applications in forestry and that the Calinski-Harabasz criterion will be most useful. / Master of Science

Desert environments are characterised by harsh conditions and possess low biodiversity largely caused by abiotic factors such as; low precipitation, soil organic matter, high temperatures, high levels of evapo-transpiration, pH and salinity. These factors significantly reduce primary production, which influences the availability of food resources for deserts organisms. The diversity and the drivers of diversity for below ground invertebrates including Collembola (springtails) are relatively unknown in the Namib Desert. Previous morphological studies have found only five species on the basis of traditional taxonomy. This study assesses the diversity of Namib Desert Collembola and determines the effect of environmental parameters on this diversity, The diversity of Namib Desert Collembola was assessed using DNA Barcoding. The sequence information of the 178 Collembola specimens, taken from mitochondrial barcoding using the Cytochrome-c oxidase subunit I (COI) gene, was analyzed and Molecular Operational Taxonomic Units (MOTUs) were defined. Collembola community responses to soil physicochemical properties were investigated by using Redundancy Analysis (RDA). MOTUs were successfully indentified to family level (Isotomidae, Neanuridae and Sminthuridae). The researcher found a total of 30 MOTUs, most of which showed limited geographical localisation. The mtDNA COI (barcode) locus revealed high levels of previously unreported genetic diversity of Collembola in the Namib Desert. The RDA indicated that none of the soil physicochemical properties significantly drove variation in Collembola community composition. However, total soil nitrogen was shown to be a strong but not significant driver of variation in community composition (p<0,054). The taxonomic identification of the Collembola specimens was also attempted using traditional morphological analysis. A total of 23 individuals, collected from pitfall traps or extracted from soil samples, were selected for identification. Available European keys were used for identification to genus level where possible. A total eight of specimens were identified to genus level (Folsomides sp), 14 to family level (Entomobryidae) and one to order level (Symphypleona). Both Symphypleona and Entomobryidae were previously unreported from the Namib Desert. The Folsomides genus and the family Entomobryidae were the most abundant groups. This research suggests that soil dwelling Collembola in the Namib Desert have a much higher level of diversity than previously known. However, the study also highlighted the need for a more comprehensive database for Namib Collembola that includes COI sequence data as well as the morphological identification of species. / Dissertation (MSc)--University of Pretoria, 2018. / National Research Foundation (NRF) / Genetics / MSc / Unrestricted

Com a grande demanda por derivados da cana-de-açúcar no Brasil a expansão de área para produção, assim como o aumento da produtividade tem sido foco para áreas agrícolas na região centro-sul. Portanto áreas que anteriormente eram dedicadas a pastagem estão tornando-se cultivo de cana-de-açúcar. Essa mudança está ocorrendo com uma grande rapidez e por esse motivo preocupações com a sustentabilidade do solo estão sendo levantadas. O objetivo deste trabalho foi verificar como a atual mudança de uso da terra de pastagem para cultivo de canade- açúcar impacta atributos microbiológicos quantitativos e funcionais do solo em um transecto edafoclimático na região centro-sul do Brasil tendo a vegetação nativa como referência. Para isso foram feitas análises do carbono e nitrogênio da biomassa microbiana do solo segundo Vance, Brookes e Jenkinson (1987) e análises da atividade enzimática da &beta;-glicosidase, fosfatase ácida e alcalina segundo Tabatabai (1994). Verifica-se a tendência de reduzir a fertilidade na pastagem em relação a mata nativa e posteriormente aumentar com o uso de fertilizantes na cana-de-açúcar. O estoque de C tem um menor valor na pastagem quando não manejada em Lat S 17º, diminui na sequencia de mudança dos sistemas de uso da terra em Lat S 21º, porém uma recuperação na mudança para cultivo de cana-de-açúcar e é maior em Lat S 23º quando a textura do solo é mais argilosa. Existe uma diminuição do estoque de CBM das matas nativas para as pastagens e um aumento nos cultivos de cana-de-açúcar em Lat S 17º e Lat S 21º. Em Lat S 23º a pastagem apresenta maior CBM do que os outros sistemas de uso da terra. Nos locais de estudo a menor relação CBM/C Total foi de 2,54% na mata nativa em Lat S 17º e a maior de 5,74% na pastagem de Lat S 23º. O N é um elemento muito sensível, em todos os atributos analisados a mudança de uso da terra causou uma grande diminuição, e a degradação do solo é o fator que causa o grande impacto nesses atributos. A textura argilosa do solo garante maior atividade enzimática, porém em cultivos de cana-de-açúcar a atividade diminui independente da classe textural. Os mesmos usos da terra em diferentes locais não podem ser analisados como repetições. Sendo assim pode-se concluir que nos casos analisados o impacto da mudança de uso da terra de pastagem para cultivo de cana-de-açúcar se manifestou de forma diferente em cada local, não permitindo uma generalização. / The great demand for derivatives of sugarcane in Brazil is the motive for the area expansion for production as well as the increase of productivity have been the focus of agricultural areas in the center-south region. So areas that were previously pastures have been changing for sugarcane cultivation. This change has occured with great speed and therefore concerns about the sustainability of soil have been raised. The aim of this study was to determine how the current change from pasture to sugarcane cultivation impacts quantitative and functional microbiological attributes of soil in a soil climatic zone in the central-south region of Brazil considering the native vegetation as reference. For it were made analysis of soil microbial biomass carbon and nitrogen according to Vance, Brookes and Jenkinson (1987) and analysis of enzymatic activity of &beta;-glucosidase, acid and alkaline phosphatase according to Tabatabai (1994). There is a tendency to reduce fertility in pasture compared to native vegetation and then increase with the use of fertilizers in sugarcane cultivation. The stock of C has a lower value in the pasture when there is no fertilizers in Lat S 17º, decreases in the land use change in Lat S 21º, but there is a recovery in the switch over to sugarcane cultivation and it is the biggest in Lat S 23º when the soil texture is clayey. There is a decrease in the stock of CBM from native forests to pastures and an increase in sugarcane cultivation in Lat S 17º and Lat S 21º. In Lat S 23º the pasture has higher CBM stock than other land use systems. In the study sites the reason between CBM and C Total was 2.54% in the native vegetation in Lat S 17º and the highest 5.74% in the pasture of Lat S 23º. The N is a very sensitive element, in all attributes analyzed, the land use change caused a large decrease, and soil degradation is the factor that causes serious impact on those attributes. The clayey soil ensures greater enzymatic activity, but in sugarcane cultivation decreases the activity independent of the texture. The same land uses in different locations can\'t be analyzed as repetitions. Therefore in the cases analyzed the impact of the change from pasture to sugarcane cultivation was differently in each place, not allowing a generalization.

Com a grande demanda por derivados da cana-de-açúcar no Brasil a expansão de área para produção, assim como o aumento da produtividade tem sido foco para áreas agrícolas na região centro-sul. Portanto áreas que anteriormente eram dedicadas a pastagem estão tornando-se cultivo de cana-de-açúcar. Essa mudança está ocorrendo com uma grande rapidez e por esse motivo preocupações com a sustentabilidade do solo estão sendo levantadas. O objetivo deste trabalho foi verificar como a atual mudança de uso da terra de pastagem para cultivo de canade- açúcar impacta atributos microbiológicos quantitativos e funcionais do solo em um transecto edafoclimático na região centro-sul do Brasil tendo a vegetação nativa como referência. Para isso foram feitas análises do carbono e nitrogênio da biomassa microbiana do solo segundo Vance, Brookes e Jenkinson (1987) e análises da atividade enzimática da &beta;-glicosidase, fosfatase ácida e alcalina segundo Tabatabai (1994). Verifica-se a tendência de reduzir a fertilidade na pastagem em relação a mata nativa e posteriormente aumentar com o uso de fertilizantes na cana-de-açúcar. O estoque de C tem um menor valor na pastagem quando não manejada em Lat S 17º, diminui na sequencia de mudança dos sistemas de uso da terra em Lat S 21º, porém uma recuperação na mudança para cultivo de cana-de-açúcar e é maior em Lat S 23º quando a textura do solo é mais argilosa. Existe uma diminuição do estoque de CBM das matas nativas para as pastagens e um aumento nos cultivos de cana-de-açúcar em Lat S 17º e Lat S 21º. Em Lat S 23º a pastagem apresenta maior CBM do que os outros sistemas de uso da terra. Nos locais de estudo a menor relação CBM/C Total foi de 2,54% na mata nativa em Lat S 17º e a maior de 5,74% na pastagem de Lat S 23º. O N é um elemento muito sensível, em todos os atributos analisados a mudança de uso da terra causou uma grande diminuição, e a degradação do solo é o fator que causa o grande impacto nesses atributos. A textura argilosa do solo garante maior atividade enzimática, porém em cultivos de cana-de-açúcar a atividade diminui independente da classe textural. Os mesmos usos da terra em diferentes locais não podem ser analisados como repetições. Sendo assim pode-se concluir que nos casos analisados o impacto da mudança de uso da terra de pastagem para cultivo de cana-de-açúcar se manifestou de forma diferente em cada local, não permitindo uma generalização. / The great demand for derivatives of sugarcane in Brazil is the motive for the area expansion for production as well as the increase of productivity have been the focus of agricultural areas in the center-south region. So areas that were previously pastures have been changing for sugarcane cultivation. This change has occured with great speed and therefore concerns about the sustainability of soil have been raised. The aim of this study was to determine how the current change from pasture to sugarcane cultivation impacts quantitative and functional microbiological attributes of soil in a soil climatic zone in the central-south region of Brazil considering the native vegetation as reference. For it were made analysis of soil microbial biomass carbon and nitrogen according to Vance, Brookes and Jenkinson (1987) and analysis of enzymatic activity of &beta;-glucosidase, acid and alkaline phosphatase according to Tabatabai (1994). There is a tendency to reduce fertility in pasture compared to native vegetation and then increase with the use of fertilizers in sugarcane cultivation. The stock of C has a lower value in the pasture when there is no fertilizers in Lat S 17º, decreases in the land use change in Lat S 21º, but there is a recovery in the switch over to sugarcane cultivation and it is the biggest in Lat S 23º when the soil texture is clayey. There is a decrease in the stock of CBM from native forests to pastures and an increase in sugarcane cultivation in Lat S 17º and Lat S 21º. In Lat S 23º the pasture has higher CBM stock than other land use systems. In the study sites the reason between CBM and C Total was 2.54% in the native vegetation in Lat S 17º and the highest 5.74% in the pasture of Lat S 23º. The N is a very sensitive element, in all attributes analyzed, the land use change caused a large decrease, and soil degradation is the factor that causes serious impact on those attributes. The clayey soil ensures greater enzymatic activity, but in sugarcane cultivation decreases the activity independent of the texture. The same land uses in different locations can\'t be analyzed as repetitions. Therefore in the cases analyzed the impact of the change from pasture to sugarcane cultivation was differently in each place, not allowing a generalization.

Tests for detecting faults in analog and mixed-signal circuits have been traditionally derived from the datasheet speci and #64257;cations. Although these speci and #64257;cations describe important aspects of the device, in many cases these application oriented tests are costly to implement and are inefficient in determining product quality. Increasingly, the gap between speci and #64257;cation test requirements and the capabilities of test equipment has been widening. In this work, a systematic method to generate and evaluate alternate tests for detecting parametric faults is proposed. We recognize that certain aspects of analog test generation problem are not amenable to automation. Additionally, functional features of analog circuits are widely varied and cannot be assumed by the test generator. To overcome these problems, an extended device under test (DUT) model is developed that encapsulates the DUT and the DUT speci and #64257;c tasks. The interface of this model provides a well de and #64257;ned and uniform view of a large class of devices. This permits several simpli and #64257;cations in the test generator. The test generator is uses a search-based procedure that requires evaluation of a large number of candidate tests. Test evaluation is expensive because of complex fault models and slow fault simulation techniques. A tester-resident test evaluation technique is developed to address this issue. This method is not limited by simulation complexity nor does it require an explicit fault model. Making use of these two developments, an efficient and automated test generation method is developed. Theoretical development and a number of examples are used to illustrate various concepts that are presented in this thesis.

Rocky desertification (RD) is a process of land degradation that often results in extensive soil erosion, bedrock exposure and considerable decrease of land productivity. The spatio-temporal evolution of RD not only reflects regional ecological environmental changes but also directly impacts regional economic and social development. The study area, Hechi, is a typical karst peak cluster depression area in southwest China. Remote sensing, geographic information systems (GIS) and statistical techniques were employed to examine the evolution, including the identification of driving forces, of karst RD in the Northwestern Guangxi. The results indicate that RD became most apparent between 1990 and 2005 when areas of various types of RD increased. Within the karst RD landscape, slight RD was identified as the matrix of the landscape while potential RD had the largest patch sizes. Extremely strong RD, with the simplest shape, was the most influenced by human activities. Overall the landscape evolved from fragmented to agglomerate within the 15-year timeframe. Land condition changes were categorized as five types; desertified, recovered, unchanged, worsened, and alleviated land. The largest turnover within the RD landscape was between slight and moderate RD. With regards to the driving forces all RD had been increasingly influenced by human activities (i. e., the stronger the RD, the stronger the intensity of human disturbances). Dominant impact factors of the RD landscape had shifted from town influence and bare rock land in 1990 to bare rock and grassland in 2005. Moreover, the impacts of stony soil, mountainous proportion and river density on RD increased over time, while that of others decreased. The significant factors included human activities, land use, soil types, environmental geology, and topography. However, only anthropogenic factors (human activities and land use) were reported as leading factors whereas the others acted simply as constraining factors.

Implementation of the Clean Water Act requires agencies to monitor aquatic sites on a regular basis and evaluate the quality of these sites. Sites are evaluated individually even though there may be numerous sites within a watershed. In some cases, sampling frequency is inadequate and the evaluation of site quality may have low reliability. This dissertation evaluates testing procedures for determination of site quality based on modelbased procedures that allow for other sites to contribute information to the data from the test site. Test procedures are described for situations that involve multiple measurements from sites within a region and single measurements when stressor information is available or when covariates are used to account for individual site differences. Tests based on analysis of variance methods are described for fixed effects and random effects models. The proposed model-based tests compare limits (tolerance limits or prediction limits) for the data with the known standard. When the sample size for the test site is small, using model-based tests improves the detection of impaired sites. The effects of sample size, heterogeneity of variance, and similarity between sites are discussed. Reference-based standards and corresponding evaluation of site quality are also considered. Regression-based tests provide methods for incorporating information from other sites when there is information on stressors or covariates. Extension of some of the methods to multivariate biological observations and stressors is also discussed. Redundancy analysis is used as a graphical method for describing the relationship between biological metrics and stressors. A clustering method for finding stressor-response relationships is presented and illustrated using data from the Mid-Atlantic Highlands. Multivariate elliptical and univariate regions for assessment of site quality are discussed. / Ph. D.

Les avancées en biotechnologie ont permis l’identification d’un grand nombre de mécanismes moléculaires, soulignant également la complexité de la régulation génique. Néanmoins, avoir une vision globale de l’homéostasie cellulaire, nous est pour l’instant inaccessible et nous ne sommes en mesure que d’en avoir qu’une vue fractionnée. Étant donné l’avancement des connaissances des dysfonctionnements moléculaires observés dans les maladies génétiques telles que la fibrose kystique, il est encore difficile de produire des thérapies efficaces. La fibrose kystique est causée par la mutation de gène CFTR (cystic fibrosis transmembrane conductance regulator), qui code pour un canal chlorique transmembranaire. La mutation la plus fréquente (ΔF508) induit un repliement incorrect de la protéine et sa rétention dans le réticulum endoplasmique. L’absence de CFTR fonctionnel à la membrane a un impact sur l’homéostasie ionique et sur l’hydratation de la muqueuse respiratoire. Ceci a pour conséquence un défaut dans la clairance mucocilliaire, induisant infection chronique et inflammation excessive, deux facteurs fondamentaux de la physiopathologie. L’inflammation joue un rôle très important dans l’évolution de la maladie et malgré le nombre important d’études sur le sujet, la régulation du processus inflammatoire est encore très mal comprise et la place qu’y occupe le CFTR n’est pas établie. Toutefois, plusieurs autres facteurs, tels que le stress oxydatif participent à la physiopathologie de la maladie, et considérer leurs impacts est important pour permettre une vision globale des acteurs impliqués. Dans notre étude, nous exploitons la technologie des puces à ADN, pour évaluer l’état transcriptionnel d’une cellule épithéliale pulmonaire humaine fibro-kystique. Dans un premier temps, l’analyse de notre expérience identifie 128 gènes inflammatoires sur-exprimés dans les cellules FK par rapport aux cellules non FK où apparaissent plusieurs familles de gènes inflammatoires comme les cytokines ou les calgranulines. L’analyse de la littérature et des annotations suggèrent que la modulation de ces transcripts dépend de la cascade de NF-κB et/ou des voies de signalisation associées aux interférons (IFN). En outre, leurs modulations pourraient être associées à des modifications épigénétiques de leurs loci chromosomiques. Dans un second temps, nous étudions l’activité transcriptionnelle d’une cellule épithéliale pulmonaire humaine FK en présence de DMNQ, une molécule cytotoxique. Notre but est d’identifier les processus biologiques perturbés par la mutation du gène CFTR en présence du stress oxydatif. Fondé sur une analyse canonique de redondance, nous identifions 60 gènes associés à la mort cellulaire et leur variance, observée dans notre expérience, s’explique par un effet conjoint de la mutation et du stress oxydatif. La mesure de l’activité des caspases 3/7, des effecteurs de l’apoptose (la mort cellulaire programmée), montre que les cellules porteuses de la mutation ΔF508, dans des conditions de stress oxydatif, seraient moins apoptotiques que les cellules saines. Nos données transcriptomiques suggèrent que la sous-activité de la cascade des MAPK et la sur-expression des gènes anti-apoptotiques pourraient être impliquées dans le déséquilibre de la balance apoptotique. / Biotechnical advances have allowed a large number of molecular mechanisms to be identified, and have also underlined the complexity of gene regulation. Nonetheless, we still only have a partial understanding of cellular homeostasis. Even with our current knowledge, molecular dysfunctionality observed in genetic illnesses such as cystic fibrosis remain largely misunderstood, prohibiting us from developing efficient treatments. Cystic fibrosis is caused by a mutation of the CFTR (cystic fibrosis transmembrane conductance regulator) gene which codes for a chloric transmembrane channel. The most frequent mutation (ΔF508) causes the unfolding of the protein and its retention in the endoplasmic reticulum. This absence of a functional CFTR to the membrane has an impact on the ionic homeostasis and the hydration of the respiratory mucus. Consequently, the mucociliary clearance is disrupted, which leads to chronic infection and excessive inflammation - two fundamental factors of CF’s physiopathology. Inflammation plays a key role in the evolution of the illness and despite many studies on this subject, the regulation of the inflammatory process remains a mystery and CFTR’s role is not well established. Additionally, since the physiopathology cannot be explained by mutation alone, several authors suggest the importance of other factors (genetic and/or environmental) which are factors in the clinical picture of the illness. In our study, we use microarray technology to evaluate the transcriptional state of an epithelial lung cell issued from a human with cystic fibrosis. Initially, our analysis identifies 128 inflammatory genes which are over-expressed in the cystic fibrosis cells versus non-cystic fibrosis cells, showing several inflammatory gene families such as cytokines or calgranulins. An analysis of the publications and annotations of these transcripts suggests that their modulations depend upon the cascade of NF-κB and/or signalling pathways associated with interferons (IFN). In other words, their modulations could be associated with epigenetic modifications of their chromosomal loci. Secondly, we study the transcriptional activity of an epithelial lung cell issued from a human with cystic fibrosis in the presence of DMNQ, a cytotoxic molecule. Our goal is to identify the biological processus which are disturbed by the mutation of the CFTR gene in the presence of oxidative stress. Based on a canonical redundancy analysis, we identify 60 genes associated with cell death and their modulation in our study explained by the combined effect of mutation and oxidative stress. By measuring the activity of caspase 3/7, an effector of apoptosis (programmed cell death), we see that the cells containing the mutation ΔF508 could present a problem with apoptosis. Our transcriptomic data suggest that decreased activity of the MAPK cascade and over-expression of anti-apoptotic genes would be a factor in apoptotic imbalance.

Applied statisticians are often faced with the problem of dealing with high dimensional data sets when attempting to describe the variability of a single set of variables, or trying to predict the variation of one set of variables from another. In this study, two data reduction methods are described: Redundancy Analysis and Partial Least Squares. A hybrid approach developed by Bougeard et al., (2007) and called Continuum Redundancy-Partial Least Squares, is described. All three methods are extended to the frequency domain in order to allow the lower dimensional subspace used to describe the variability to change with frequency. To illustrate and compare the three methods, and their frequency dependent generalizations, an idealized coupled atmosphere-ocean model is introduced in state space form. This model provides explicit expressions for the covariance and cross spectral matrices required by the various methods; this allows the strengths and weaknesses of the methods to be identified.