No

Quantitative resistance is controlled by multiple genes and has been shown to be a durable form of resistance to pathogens affecting cultivated crops including soybeans (Glycine max L. Merr). Root rot of soybean caused by Phytophthora sojae ranks among the most damaging soybean diseases. Quantitative resistance has proven durable in soybean against P. sojae, however the molecular mechanisms underlying this form of resistance are still unknown. The objective of this project is to gain insight into molecular basis of quantitative resistance in the soybean-P. sojae pathosystem. The approach was to use global transcriptional profiling based on microarray technology to identify genes that were differentially expressed in four cultivars of soybeans with varying levels of quantitative resistance at different time points during infection by P. sojae. Our results provide a better understanding of the potential regulatory factors that may contribute to quantitative resistance during early hours of P. sojae infection. / Ph. D.

The unequal treatment of racial minorities by police is by no means a new concept. The debate over racial profiling centers on two questions. Does racial profiling actually occur? If so, is racial profiling being used and is profiling a legitimate tool of law enforcement? There are those who debate whether race is or is not a factor in police discretion and there are those who argue that race is a factor that is appropriate for use in profiling. The purpose of this research is to determine whether race is a significant factor in the likelihood of being involved in a traffic stop. In addition to race, other variables, such as gender and age, are explored as possible control variables. This is done by analyzing data collected by the Bureau of Justice Statistics' "Contact between Police and the Public" national survey. By examining several dependent variables that also may be associated with traffic stops, this study determines whether there is or is not a disparity in treatment by race, and whether this is consistent with the alleged purposes of using race in criminal profiles. / Master of Science

No / No Abstract

Yes / Personalized medicine through Pharmacogenomics: choosing the right drug, and the right dose, for the right patients based on patient’s genetic makeup-is gradually being realised in Western countries. Yet, the practice of pharmacogenomics in Asian countries lags behind that of the West, but the medical needs for pharmacogenomics are expected to surge as better patient care is demanded in Asia. As next-generation sequencing technology advances quickly, previous technical challenges for performing pharmacogenomic studies or practices in Asia have been mostly resolved. What is lacking in Asia is an effective model of community-wide pharmacogenomics. On the delivery front, pharmacists, the drug and dosing professionals, can potentially be the main healthcare providers for pharmacogenomic services in Asia. The first large “Genomics for Precision Drug Therapy in the Community Pharmacy” in Canada, which is close to its completion, has successfully identified community pharmacists as key contact professionals for smooth facilitation and implementation of pharmacogenomics for personalized medication. It is anticipated that Asian pharmacists, with appropriate training, can have the capacity to provide expert pharmacogenomic supports for both physicians and patients in Asia. / The School of Biomedical Sciences Start-up Fund, the Chinese University of Hong Kong, the General Research Fund (#17114814; #17121616), the Theme-based Research Scheme (T12-401/13-R), Research Grant Council, Hong Kong, as well as the Hong Kong Cancer Fund, Hong Kong.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The aim of this study was to explore proteomics and microbiome profiling in pigs fed high fibre diets. In the first phase, maize cobs were ensiled using whey, molasses and exogenous enzymes in the laboratory and effects on ensiling characteristics and fibre levels were evaluated. In the second phase South African Windsnyer-type Indigenous pigs (SAWIP) and Large White x Landrace crosses (LW x LR) were fed diets containing ensiled maize cobs and evaluated on; diet preferences, nutrient digestibility and colonic fermentation; growth performance, carcass traits and blood metabolite profiles; the faecal microbiome; and serum and liver proteomic profiles. Ensiling maize cobs with molasses, whey and exogenous enzymes did not improve fermentation characteristics but exogenous enzymes reduced fibre fractions and energy content of maize cob silages. Dets containing two levels of maize cobs ensiled without any additive; a low (LMC) and high (HMC) maize cob inclusion levels and a control diet which did not have any maize cobs (CON) were formulated. The SAWIP preferred the CON diet more than (P < 0.05) diets with maize cobs while the LW x LR had no feed preferences. There was no correlation between preference and diet digestibility in both breeds. The SAWIP digested nutrients better (P < 0.05) than the LW x LR in the high fibre diets. There were no differences in the diversity of the core composition of gut bacterial communities between the breeds and diets. There were differences in the ratios of Bacteroidia to Clostridia between the SAWIP and LW x LR. Verrucomicrobiae was present in SAWIP and LW x LR on HMC diet and not on the CON diet. There was a breed x diet interaction (P < 0.05) for Oscillospira. Analysis of the microbiome revealed breed differences and no dietary differences. There were differences in serum and liver proteins and in serum metabolite levels. Two specific proteins identified were Guanidinoacetate N-methyltransferase-like isoform 1 associated with creatine biosynthetic and Catalase, which is involved in cholesterol metabolic processes. At the grower stage, the SAWIP consumed more feed per metabolic body weight than the LW x LR while at the finisher stage LW x LR consumed more feed per metabolic body weight (P < 0.05) than the SAWIP. The breed of pig influenced most of the growth performance and carcass parameters more than the diet did. The SAWIP demonstrated an adaptation to high fibre diets by consuming more feed than the LW x LR per metabolic body weight at the grower stage. The inclusion of ensiled maize cobs in diets did not negatively affect selected commercial pork cuts. Analysis of faecal microbiomes revealed differences that may explain the enhanced ability of the SAWIP to digest fibrous diets better than the LW x LR breed.Proteomics can identify biomarkers that evaluate the performance of pigs consuming high fibre diets. A proof of principle to assess serum and liver protein profiles of pigs fed a a high fibre diet using a sodium dodecyl sulphate polyacrylamide gel electrophoresis matrix-assisted laser desorption ionization mass spectrometry (SDS-PAGE /MALDI MS) workflow was established. Key words: ensiling, exogenous enzymes, palatability, fermentation, fibre, metageome, biomarkers.

Les machines multicœurs actuelles utilisent une architecture à Accès Mémoire Non-Uniforme (Non-Uniform Memory Access - NUMA). Dans ces machines, les cœurs sont regroupés en nœuds. Chaque nœud possède son propre contrôleur mémoire et est relié aux autres nœuds via des liens d'interconnexion. Utiliser ces architectures à leur pleine capacité est difficile : il faut notamment veiller à éviter les accès distants (i.e., les accès d'un nœud vers un autre nœud) et la congestion sur les bus mémoire et les liens d'interconnexion. L'optimisation de performance sur une machine NUMA peut se faire de deux manières : en implantant des optimisations ad-hoc au sein des applications ou de manière automatique en utilisant des heuristiques. Cependant, les outils existants fournissent trop peu d'informations pour pouvoir implanter efficacement des optimisations et les heuristiques existantes ne permettent pas d'éviter les problèmes de congestion. Cette thèse résout ces deux problèmes. Dans un premier temps nous présentons MemProf, le premier outil d'analyse permettant d'implanter efficacement des optimisations NUMA au sein d'applications. Pour ce faire, MemProf construit des flots d'interactions entre threads et objets. Nous évaluons MemProf sur 3 machines NUMA et montrons que les optimisations trouvées grâce à MemProf permettent d'obtenir des gains de performance significatifs (jusqu'à 2.6x) et sont très simples à implanter (moins de 10 lignes de code). Dans un second temps, nous présentons Carrefour, un algorithme de gestion de la mémoire pour machines NUMA. Contrairement aux heuristiques existantes, Carrefour se concentre sur la réduction de la congestion sur les machines NUMA. Carrefour permet d'obtenir des gains de performance significatifs (jusqu'à 3.3x) et est toujours plus performant que les heuristiques existantes. / Modern multicore systems are based on a Non-Uniform Memory Access (NUMA) design. In a NUMA system, cores are grouped in a set of nodes. Each node has a memory controller and is interconnected with other nodes using high speed interconnect links. Efficiently exploiting such architectures is notoriously complex for programmers. Two key objectives on NUMA multicore machines are to limit as much as possible the number of remote memory accesses (i.e., accesses from a node to another node) and to avoid contention on memory controllers and interconnect links. These objectives can be achieved by implementing application-level optimizations or by implementing application-agnostic heuristics. However, in many cases, existing profilers do not provide enough information to help programmers implement application-level optimizations and existing application-agnostic heuristics fail to address contention issues. The contributions of this thesis are twofold. First we present MemProf, a profiler that allows programmers to choose and implement efficient application-level optimizations for NUMA systems. MemProf builds temporal flows of interactions between threads and objects, which help programmers understand why and which memory objects are accessed remotely. We evaluate MemProf on Linux on three different machines. We show how MemProf helps us choose and implement efficient optimizations, unlike existing profilers. These optimizations provide significant performance gains (up to 2.6x), while requiring very lightweight modifications (10 lines of code or less). Then we present Carrefour, an application-agnostic memory management algorithm. Contrarily to existing heuristics, Carrefour focuses on traffic contention on memory controllers and interconnect links. Carrefour provides significant performance gains (up to 3.3x) and always performs better than existing heuristics.

A maioria dos sistemas embarcados hoje desenvolvidos utilizam complexos sistemas eletrônicos integrados em um único chip, os Systems-on-a-Chip (SoC). A análise do comportamento de uma aplicação em execução, ou seja, o profiling nesses sistemas não é uma tarefa trivial em virtude da complexidade dos SoCs e pela restrição de ferramentas de profiling adequadas. Neste contexto, este trabalho apresenta o P2L, uma ferramenta de profiling que se baseia em métricas de nível de instrução e função para o processador LEON3. O P2L fornece estatísticas detalhadas de uso do processador, memórias e barramento de programas em execução sem uso de instrumentação. A ferramenta é composta por um componente em hardware e drivers e aplicativos em software. Os resultados mostram que o P2L fornece medidas com erro inferior a 1% e overhead desprezível quando comparado ao tempo de execução nativa do programa e ao do profiler GNU gprof. / Most embedded systems developed today use complex electronic systems integrated into a single chip, the Systems-on-a-Chip (SoC). The analysis of the behavior of a running application or profiling in these systems is not a trivial task due to the complexity of the SoC and the restriction of appropriate profiling tools. In this context, this work presents P2L - a profiling tool that is based on instruction and function level metrics for the LEON3 processor. P2L provides detailed usage statistics of the processor, memories, and bus of running programs without the use of instrumentation. The tool consists of a component in hardware, drivers and applications software. The results show that P2L provides measures with an error less than 1% and negligible overhead compared to native runtime program and the GNU profiler gprof.

The goal of this thesis is to summarize and to describe all available know-how and experiences of Adastra employees related to Data Quality Audit in organization. The entire thesis should serve as a guideline for sales and implementation staff within the Adastra Corp. The first part of this thesis (chapter 2 and 3) is generally concerned with Data Quality, i.e. provides various definitions of Data Quality, points out importance/relevance of Data Quality in organization and describes the most important tools and Data Quality Management Solutions. The second part (chapter 4 and 5) uses the theoretical basis of the previous chapters and form the main methodical part of this thesis. Chapter 4 is rather focused on business/sales side, defines the most important terms and used principles, and is considered as a necessary precondition for correct understanding following chapter. Chapter 5 shows detailed procedures of Data Quality Audit. Single activities are written in a standardized form to ensure clear, accurate and brief step description. The result of this thesis is the most detailed description of Data Quality Audit in Adastra Corp. including all identified services/products.

The application of second generation sequencing technology to the characterization of complex microbial communities has profoundly affected our appreciation of microbial diversity. The explosive growth of microbial sequence data has also necessitated advances in bioinformatic methods for profiling microbial communities. Data aggregation strategies should allow the relation of metagenomic sequence data to our understanding of microbial taxonomy, while also facilitating the discovery of novel taxa. For eukaryotes, a method has been established that links DNA sequences to the identification of organisms: DNA Barcoding. A similar approach has been developed for prokaryotes using target genic regions as markers for species identification and to profile communities. A key difference in these efforts is that within DNA barcoding there is a formalized framework for the evaluation of barcoding targets, whereas for prokaryotes the 16S rRNA gene target has become the de facto barcode without formal evaluation. Using the framework developed for evaluating DNA barcodes in eukaryotes, a study was undertaken to formally evaluate 16S rRNA and cpn60 as DNA barcodes for Bacteria. Both 16S rRNA and cpn60 were found to meet the criteria for DNA barcodes, with cpn60 a preferred barcode based on its superior resolution of closely related taxa. The high resolution of cpn60 enabled a method of sequence data aggregation through sequence assembly: microbial profiling using metagenomic assembly (mPUMA). The scoring of metagenomic assemblies in terms of sensitivity and specificity of the operational taxonomic units formed was used to evaluate and optimize the assembly of cpn60 barcodes. Using optimized parameters, mPUMA was demonstrated to faithfully reconstruct a synthetic community in terms of richness and abundance. To facilitate the use of mPUMA, a software package was developed and released under an open source license. The utility of mPUMA was further examined through the characterization of the epiphytic seed microbiomes of Triticum and Brassica species. A microbiome shared across both crop genera including fungi and bacteria was detected: a particularly important observation as it implies that seeds may serve as a vector for microbes that could include both pathogenic and beneficial organisms. The relative abundances of taxa identified by mPUMA were confirmed by qPCR for multiple cases of both fungal and bacterial taxa. By culturing isolates of both bacteria and fungi from the seed surfaces it was demonstrated that mPUMA faithfully assembled consensus sequences for OTUs that were 100% identical to isolated fungi and bacteria. Patterns observed in the relative abundances of the shared microbiome OTUs were used to generate the hypothesis that an Pantoea-like bacterium and an Alternaria-like fungus had an antagonistic relationship, since sequences corresponding to these organisms showed reciprocal abundance patterns on Triticum and Brassica seeds. Studies of the interactions of cultured isolates revealed fungistatic interactions that could account for their reciprocal abundances. These interactions could be directly relevant to plant health, given that Alternaria-like fungi are linked to grain spoilage in wheat, and diseases in canola. Taken together, results of this thesis demonstrate the superiority of the cpn60 universal target as a barcode for Bacteria, forming the basis for an assembly-based strategy for microbial profiling of bacterial and eukaryotic microbial communities that can lead to the discovery of novel taxa and microbial interactions.