Design patterns in software systems are described as a universal reusable solution to a commonly recurring problem in software design. Design patterns were, however, not intended to be reusable in terms of code. A symptom of their non-reusability is the problems experienced with the way the implementation of design patterns negatively affects their traceability, maintainability and contribution to productivity. This thesis shows how design patterns can be elevated to a higher level of reusability. This work presents design patterns as reusable components that developers can use to implement solutions that utilise patterns, without having to implement a major part of a pattern’s structure and behaviour anew each time. A component is a reusable software section, with possible library classes, that is usually in source form. Previous research has shown that a high proportion of patterns (65%) can be “componentized” in Eiffel, which leads to the idea that a language supporting the same set of features would also have the same success in pattern componentization. This thesis has looked at the componentization of twelve design patterns in C#. The C# language has more advanced language features than Eiffel, including functional and dynamic language features and, as such, should lend itself better to pattern componentization than Eiffel does. The language features that are reviewed in this thesis are inheritance, design by contract™, attributes, method references (or delegates), anonymous functions, lambda expressions, mixins (or extension methods), duck typing, dynamic types and meta-programming. Each pattern’s reusable components are discussed in detail, including the success of the reusable component transformation. All the design patterns reviewed in this thesis could be transformed into fully or partially reusable components. Implementing design patterns using reusable library components is thus a step in the right direction in making design pattern implementations more traceable, reusable, maintainable and more productive. Other object-oriented languages implementing the same or similar language features as those reviewed in this thesis should have the same level of success in transforming design patterns into reusable components. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Computer Science / unrestricted

This thesis proposes that there are two kinds of clauses: indexical clauses, which are evaluated with respect to the speech situation; and anaphoric clauses, which are evaluated with respect to a contextually-given (anaphoric) situation. Empirical motivation for this claim comes from the clause-typing system of Plains Cree, an Algonquian language spoken on the Canadian plains, which morpho-syntactically distinguishes between two types of clauses traditionally called INDEPENDENT and CONJUNCT orders. In the current analysis, the INDEPENDENT order instantiates indexical clauses, and the CONJUNCT order instantiates anaphoric clauses. After laying out the proposal (chapter 1) and establishing the morphosyntax of Plains Cree CPs (chapter 2), the remaining chapters discuss the proposal in detail. Chapter 3 focusses on the syntax and semantics of indexical clauses (Plains Cree’s INDEPENDENT order). Syntactically, I show that there is an anti-c-command and an anti-precedence condition on indexical clauses. Semantically, I show that indexical clauses are always and only evaluated with respect to the speech situation, including the speech time (temporal anchoring), speech place (spatial anchoring), and speaker (referential anchoring). Chapter 4 focusses on the syntax and semantics of anaphoric clauses (Plains Cree’s CONJUNCT order). Syntactically, I show that anaphoric clauses must always be either preceded or dominated by some other antecedent clause. Semantically, I show that the value of temporal/spatial/referential dependent elements within an anaphoric clause is determined by an antecedent. Chapter 5 turns to the syntactic subclassification of Plains Cree’s CONJUNCT (i.e., anaphoric) clauses. I propose that there are three classes: chained clauses, adjunct clauses, and mediated argument clauses. I provide two kinds of diagnostics that distinguish these classes, and explore the consequences of this classification for argument clauses and complementation. Finally, Chapter 6 proposes a semantic subclassification of Plains Cree’s CONJUNCT (i.e., anaphoric) clauses. I propose that there is a direct mapping between the morphology and the semantics: one complementizer encodes presupposition of the proposition, the lack of a complementizer encodes a-veridicality of the proposition, and one complementizer is semantically unspecified (the elsewhere case). This means that Plains Cree’s clause-typing is fundamentally concerned with how the truth of the proposition is represented. / Arts, Faculty of / Linguistics, Department of / Graduate

Nous avons étudié le rôle des éléments génétiques mobiles (EGM) dans l’évolution et la virulence de Streptococcus agalactiae, bactérie pathogène opportuniste responsable d'infections chez l’homme. La structure génétique de la population a été analysée par multilocus sequence typing à partir d’un souchier représentatif de la diversité de l’espèce. La distribution de 11 EGM (sept séquences d’insertion, trois transposases, un intron) a été confrontée à la structure de la population. Cette confrontation a permis i) de démontrer que l’acquisition des EGM corrélait avec l’évolution de l’espèce, ii) de proposer une hypothèse de la chronologie d’acquisition des EGM, iii) d’identifier certains EGM comme marqueurs de l’écosystème d’origine des souches, et iv) de conforter l’hypothèse de l’émergence du clone humain invasif CC17 à partir d’un ancêtre bovin. Nous avons également cartographié les copies des EGM présentes sur le génome de S. agalactiae, puis nous avons identifié huit nouveaux sites d’insertion, dont deux sont significativement associés à l’origine écologique de la souche. / We studied the role of mobile genetic elements (MGE) on the evolution and the virulence of Streptococcus agalactiae, an opportunistic bacterium responsible for human infections. The genetic population structure was analyzed by multilocus sequence typing using a collection representative of the species diversity. The distribution of 11 MGE (seven insertion sequences, three transposases, one intron) was compared to the population structure. We demonstrated that the MGE prevalence strongly correlates with the genetic lineages. We proposed an evolutionary scheme for the acquisition of the MGE. Several MGE appeared to be markers of the origin of the strains. MGE analysis brought evidence for a bovine origin of the human virulent clone CC17. We also identified the position of the MGE copies on the S. agalactiae genome and we identified eight new MGE insertion sites, from which two were significantly associated with the ecological origin of the isolates.

There are situations in which it is very important to quickly and positively identify an individual. Examples include suspects detained in the neighborhood of a bombing or terrorist incident, individuals detained attempting to enter or leave the country, and victims of mass disasters. Systems utilized for these purposes must be fast, portable, and easy to maintain. The goal of this project was to develop an ultra fast, direct PCR method for forensic genotyping of oral swabs. The procedure developed eliminates the need for cellular digestion and extraction of the sample by performing those steps in the PCR tube itself. Then, special high-speed polymerases are added which are capable of amplifying a newly developed 7 loci multiplex in under 16 minutes. Following the amplification, a postage stamp sized microfluidic device equipped with specially designed entangled polymer separation matrix, yields a complete genotype in 80 seconds. The entire process is rapid and reliable, reducing the time from sample to genotype from 1-2 days to under 20 minutes. Operation requires minimal equipment and can be easily performed with a small high-speed thermal-cycler, reagents, and a microfluidic device with a laptop. The system was optimized and validated using a number of test parameters and a small test population. The overall precision was better than 0.17 bp and provided a power of discrimination greater than 1 in 106. The small footprint, and ease of use will permit this system to be an effective tool to quickly screen and identify individuals detained at ports of entry, police stations and remote locations. The system is robust, portable and demonstrates to the forensic community a simple solution to the problem of rapid determination of genetic identity.

The expressive nature of typing has been mostly neglected in research. The possibilities of our full expressive selves are not included in typing experiences.The aim of this thesis is to explore the expressive qualities and experiences of typing and open up new opportunities and possibilities for interaction designers. To fulfil this aim, the qualities of typing itself as a medium are investigated, as well as how handwriting can be used as inspiration and guidance to investigate the potential expressive qualities of typing.The result of this investigation showed how typing possesses personal, behavioral and emotional expressions. Additionally, the investigation lead to the discovery of how typing possesses impressionable experiences. These impressions changed the feeling while typing, could make the user write in a particular way and be used as an expressive tool to another person.

In the United States, symptoms caused by pathogenic strains of Escherichia coli are on the rise. A major source of these pathogenic strains is the E. coli in the digestive tract of cattle. The purpose of this project was to determine if E. coli are transferred between individuals of the same species and if interspecies transmission is possible. Proximity of cattle was also studied as a contributing factor to the transfer of E. coli. To accomplish this goal, E. coli isolates from cattle and cohabitating ground squirrels were compared through a new method of bacterial strain typing called pyroprinting. Bulls from the Cal Poly Bull Test were sampled every summer from May to September when around 200 bulls from ranches across California are housed together to be tested and eventually auctioned off. The impact of cattle origin (ranch, city) and habitation (pen) on E.coli isolate strain type were evaluated via pyroprinting . The cattle were studied to see if transfer was related to proximity of cohabitation. Since the complete population of intestinal E. coli could not be sampled, transfer could not be directly seen. The probability of sharing E. coli in each time point was used to infer transfer. There was an increase in the probability of sharing E. coli from the May sample date to the September date, indicating that some form of transfer was occurring. There was an even greater increase in the probability of sharing E. coli when the bulls were housed in close proximity. Lastly, ground squirrels cohabitating in the area were found to house some of the same strains as the cattle. This makes transfer between squirrels and cattle a possibility. Overall, this paper shows that the intestinal E. coli composition of bulls may be readily altered by the introduction of new bulls into a population.

This master thesis deals with typing of Klebsiella pneumoniae isolates. The first part of the thesis introduces molecular typing methods. Then bacterial genomes and Klebsiella pneumoniae are characterized. Following part describes data validation, assembly of genomes and proposed algorithm for finding genes with high variability. In last part obtained results are presented and validated on other genomes of Klebsiella pneumoniae.

Molecular typing of strains among the highly diverse population of Helicobacter pylori (H. pylori) is an important approach for both basic and clinical studies. Genomic DNAs prepared from 18 gastric biopsy specimens, 21 H. pylori clinical isolates obtained from gastric biopsy specimens, and five isolates collected from a single patient at weekly intervals, were subjected to a combined single- and double-stranded conformational polymorphism (SDSCP) assay. The results showed that 19 of 21 isolates tested were discriminated by SDSCP analysis. SDSCP analysis of five H. pylori isolates collected from the same patient at different times resulted in five identical profiles, suggesting the reproducibility of the method. When DNA preparations from 18 gastric biopsy specimens were subjected to SDSCP analysis, 18 unique profiles were generated that matched those of their corresponding cultured H. pylori isolates from each patient. For comparison, polymerase chain reaction (PCR)-based restriction fragment length polymorphism analysis yielded only nine profiles for 20 strains. The data suggest that SDSCP analysis may be an effective and reliable method for differentiation of H. pylori strains directly from gastric biopsy specimens without requiring isolation of the organisms by culture.

Les noyaux de systèmes d'exploitation manipulent des données fournies par les programmes utilisateur via les appels système. Si elles sont manipulées sans prendre une attention particulière, une faille de sécurité connue sous le nom de Confused Deputy Problem peut amener à des fuites de données confidentielles ou l'élévation de privilèges d'un attaquant. Le but de cette thèse est d'utiliser des techniques de typage statique afin de détecter les manipulations dangereuses de pointeurs contrôlés par l'espace utilisateur. La plupart des systèmes d'exploitation sont écrits dans le langage C. On commence par en isoler un sous-langage sûr nommé Safespeak. Sa sémantique opérationnelle et un premier système de types sont décrits, et les propriétés classiques de sûreté du typage sont établies. La manipulation des états mémoire est formalisée sous la forme de lentilles bidirectionnelles, qui permettent d'encoder les mises à jour partielles des états et variables. Un première analyse sur ce langage est décrite, permettant de distinguer les entiers utilisés comme bitmasks, qui sont une source de bugs dans les programmes C. / Operating system kernels need to manipulate data that comes from user programs through system calls. If it is done in an incautious manner, a security vulnerability known as the Confused Deputy Problem can lead to information disclosure or privilege escalation. The goal of this thesis is to use static typing to detect the dangerous uses of pointers that are controlled by userspace. Most operating systems are written in the C language. We start by isolating Safespeak, a safe subset of it. Its operational semantics as well as a type system are described, and the classic properties of type safety are established. Memory states are manipulated using bidirectional lenses, which can encode partial updates to states and variables. A first analysis is described, that identifies integers used as bitmasks, which are a common source of bugs in C programs. Then, we add to Safespeak the notion of pointers coming from userspace. This breaks type safety, but it is possible to get it back by assigning a different type to the pointers that are controlled by userspace. This distinction forces their dereferencing to be done in a controlled fashion. This technique makes it possible to detect two bugs in the Linux kernel: the first one is in a video driver for an AMD video card, and the second one in the ptrace system call for the Blackfin architecture.

Abstract  There is increasing use of technology in the education system, such as computers, and different programs learners can use to study vocabulary. In this study, the goal was to find out if pupils in secondary education learn new vocabulary more efficiently when handwriting or typing on a computer. To study the matter, firstly, a recall and recognition test was conducted followed by a word acquisition test. Finally, two group interviews were performed to find out if there was an agreement between pupils’ understanding of how they learn most efficiently, by typing or by handwriting, and the results of this study.  The study departs from the theory that learners acquire new vocabulary more efficiently when writing by hand since the motor process of handwriting increases activity in the brain, which possibly makes learners remember better what they have written. In addition, we have considered the theory that young people who have lived their whole life with technology are more proficient in typing, rather than writing by hand and if that is the case, will it affect their motor memory? Finally, the theory that computer-assisted language learning makes vocabulary acquisition more efficient will be discussed through pupils’ own opinions from the interviews.  The result from this study shows that pupils in secondary education in Sweden, learn vocabulary in a foreign language more efficiently when typing on a computer rather than writing by hand. This is not in agreement with pupils’ thoughts, nevertheless, it is in accordance with their preferences.