No / To investigate whether there are differences between members of the Burkholderia cepacia complex in their ability to invade human respiratory epithelial cells, 11 strains belonging to genomovars I-V were studied in an antibiotic protection assay using the A549 cell line. Strains belonging to genomovars II and III were more invasive than those of genomovars I, IV and V. There was also intra-genomovar variation in invasiveness. No correlation between invasiveness and other putative virulence factors of importance in B. cepacia infection in individuals with cystic fibrosis, cable pilus and B. cepacia epidemic strain marker was identified.

Gaze-typing opens up a new input channel, but its keyboard designs are not ready for everyday use. To investigate the gaze-typing keyboards for such use that are easy to learn, fast to type, and robust to use differences, I analyzed the usability of three widely used gaze-typing keyboards by a user study with typing performance measurements, synthesized the design space of everyday used gaze-typing keyboards under the topics of typing schemes and keyboard letter layouts, feedback, ease of text editing, and system design. In particular, I found gaze-typing keyboards need “tolerant” designs that allow implicit gaze control and balance between input ambiguity and typing efficiency. Therefore, I prototyped a gaze-typing keyboard using a shape-writing scheme meant for everyday typing by gaze gestures, with the adaption on segmenting the gaze locus when writing a word from continuous gaze data stream. The system affords real-time shape-writing in the speed of 11.70 WPM and the error rate of 0.14 evaluated with an experienced user and supports to type 20000+ words from the lexicon. / Blick-skrivande möjliggör en ny inmatningskanal, men dess tangentborddesign är inte än redo för dagligt bruk. För att utforska blick-skriftstangentbord för sådant bruk, som är enkla att lära sig använda, snabba att skriva med, och robusta för olika användning, analyserade jag användbarheten hos tre brett använda blick-skriftstangentbord genom en användarstudie med skrivprestationsmätningar, och syntetiserade ett designutrymme för blick-skriftstangentbord för dagsbruk baserat på teman av typningsscheman och tangentbordslayout, feed-back, användarvänlighet för text redigering, och system design. I synnerhet identifierade jag att blick-skriftstangentbord behöver ha "toleranta" designer som tillåter implicit blickkontroll och balans mellan Inmatningsambiguitet och typningseffektivitet. Därför prototypade jag ett blick-skriftstangentbord som använder ett formskriftsschema som är avsett för vardagligt skrivande med blickgester, och anpassat till att segmentera blickpunkten när du skriver ord från en kontinuerlig ström av blickdata. Systemet erbjuder realtidsformskrivning i hastigheten 11.70 WPM och felfrekvensen 0.14 utvärderat med en erfaren användare, och har stöd för att skriva fler än 20000 ord från lexikonet.

This thesis describes the analysis of over 1300 spelling and typing errors. It introduces and describes many empirical rules which these errors obey and shows that a vast majority of errors are variations on some 3000 basic forms. It also describes and tests an intelligent, knowledge based spelling error correction algorithm based on the above work. Using the Shorter Oxford English dictionary it correctly identifies over 90% of typical spelling errors and over 80% of all spelling errors, where the correct word is in the dictionary. The methodology used is as follows: An error form is compared with each word in that small portion of the dictionary likely to contain the intended word, but examination of improbable words is rapidly abandoned using heuristic rules. Any differences between the dictionary word and the error form are compared with the basic forms. Any dictionary word which differs from the error form only by one or two basic forms is transferred to a separate list. The program then acts as an expert system where each of the basic forms is a production or rule with a subjective Bayesian probability. A choice is made from the list by calculating the Bayesian probability for each word in the separate list. An interactive spelling error corrector using the concepts and methods developed here is operating on the Bradford University Cyber 170/720 Computer, and was used to correct this thesis. The corrector also runs on VAX and Prime computers.

The genus Mycobacterium contains many pathogenic bacteria that are known to cause serious diseases in humans. One of the most well-known of these bacteria is Mycobacterium tuberculosis, or Mtb, which is the causative agent of tuberculosis. It infects nearly one-third of the world’s population and kills 1.4 million people annually. Another important mycobacterial pathogen is Mycobacterium abscessus, or Mabs, which causes respiratory infections in cystic fibrosis patients. One of the biggest difficulties in combating these pathogens is the lack of effective diagnostics, as current strategies hold many pitfalls and can be unreliable. One common method used is sputum smear microscopy which involves acid fast staining of the bacteria present in a patient’s sputum. This method of detection fails to detect more than 50% of infections and is unable to differentiate between species of mycobacterium. This project introduces a novel method of mycobacterial diagnostics using binary deoxyribozymes (DNAzymes). Binary DNAzymes recognize bacteria-specific nucleic acid sequences and bind to them, forming a catalytic core which cleaves a substrate molecule. This cleavage separates a quencher molecule from a fluorophore, which results in a fluorescent output. This flexible assay platform has great potential for the detection of Mtb or Mabs. Our data shows the specificity of the DNAzymes allowing for a differential diagnosis of various species of Mycobacteria. It also shows the limit of detection of this technology and its additional utility in molecular typing of Mtb clinical isolates as well as drug resistance characterization. This multipurpose tool can contribute to disease management in multiple ways.

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[pt] As características dinâmicas de linguagens de scripting introduzem um gargalo significativo no tempo de execução quando comparadas a linguagens de sistemas. A arquitetura scripting pode ser usada para melhorar o desempenho ruim de linguagens de scripting. O programador deve usar a linguagem de sistemas para tarefas que consomem muitos recursos, e a de scripting para flexibilidade. Entretanto, essa arquitetura tem duas falhas significativas quando usada para melhorar o desempenho de linguagens de scripting. Primeiro, existe uma lacuna conceitual entre as duas linguagens, logo migrar da linguagem de scripting para linguagem de sistemas pode exigir enorme esforço. Segundo, existe um gargalo escondido ao manipular as estruturas de dados da linguagem de scripting a partir da linguagem de sistemas. Pallene é uma linguagem de sistemas projetada particularmente para Lua que almeja resolver essas duas falhas. Pallene é um subconjunto estaticamente tipado de Lua, o que facilita o processo de migração. Além disso, Pallene manipula diretamente as estruturas de dados de Lua sem introduzir gargalo. Neste trabalho, nós propomos dois tipos de registros para Pallene, e nós apresentamos a implementação do compilador de Pallene. Nós avaliamos o desempenho do nosso compilador para compará-la com Lua padrão, LuaJIT, e programas C que utilizam a API C de Lua. Nossos experimentos mostram que Pallene é competitiva com as soluções existentes para melhorar o desempenho de Lua. / [en] The dynamic features of scripting languages introduce significant overhead in execution time when compared to system languages. The scripting architecture can be used to improve the poor performance of scripting languages. The programmer should use a system language for resourceintensive tasks, and a scripting one for flexibility. However, this architecture has two significant flaws when used to improve the performance of scripting languages. First, there is a conceptual gap between both languages; so migrating from the scripting language to the system language may require enormous effort. Second, there is a hidden overhead when manipulating the scripting-language data structures from the system language. Pallene is a system language designed particularly for Lua that aims to solve these two issues. Pallene is a statically-typed subset of Lua, which facilitates the migration process. Moreover, Pallene manipulates Lua s data structures directly without introducing overhead. In this work, we propose two types of records for Pallene, and we present the implementation of the Pallene compiler. We benchmarked our compiler to compare it to standard Lua, LuaJIT, and C programs using the Lua-C API. Our experiments show that Pallene is competitive with the existing solutions to improve Lua s performance.

Omnia HR är en HR-plattform utvecklat för Microsofts SharePoint. I denna artikel beskrivs hur en liten del av plattformen är skapad – onboardingen. När en ny person anställs på ett företag bör det göras förberedelser inför den nyanställdes första dag, det är vad onboardingen handlar om. I detta projekt skapades förutsättningar för att administrera och hantera dessa förberedelser.   Projektet skrevs i Microsoft-utvecklade programmeringsspråket TypeScript, en påbyggnad på JavaScript. TypeScript transpileras ned till JavaScript och har stöd för de senaste funktionerna. I rapporten diskuteras fördelarna samt nackdelarna med att använda TypeScript för ett projekt, hur vida det faktiskt underlättar arbetet eller om det går lika bra att använda vanlig JavaScript. / Omnia HR is a HR-platform developed for Microsoft SharePoint. In this article, the creation of a smaller part for the platform – the onboarding – is described. When a new employee is hired, the company need to do some tasks before the new employees first day, that’s what the onboarding is all about. In this project conditions to administrate and handle these tasks were made.   The project was written in the programing language TypeScript, developed by Microsoft. TypeScript is superset of JavaScript and is transpiled down to pure JavaScript with support for the latest functions. In this rapport pros and cons by using TypeScript for a project is discussed, and if it actually makes the process easier or if it’s just as good to use regular JavaScript.

Les méthanogènes sont des Archaea anaérobies stricts, connus pour être les seuls êtres vivants capables de produire du méthane comme sous-produit de leur métabolisme. Notre revue de littérature a montré qu’outre les espèces environnementales, l’ordre des Methanomassiliicoccales ne comptait à ce jour qu’une seule espèce Methanomassiliicoccus luminyensis isolée et cultivée dans notre laboratoire. Aucours de notre thèse, nous avons développé une nouvelle méthode permettant la culture et l’isolement des méthanogènes en absence de source externe de dihydrogène (H2) d’une part et d’autre part une méthode de génotypage Multispacer Sequence Typing (MST) basée sur le séquençage d’espaces intergéniques pour typer Methanobrevibacter smithii et M. oralis. Par la suite, nous avons mis en évidence la présence de méthanogènes en situation pathologique chez l’homme. Nous avons détecté et isolé pour la première fois au sein de flores anaérobies, M. oralis à partir d’échantillons d’abcès cérébraux, et de sinusite d’une part, et d’autre part M. smithii à partir d’un échantillon de patient souffrant d’abcès para-vertébral. Enfin, dans la cinquième partie de notre thèse, nous avons testé in vitro la sensibilité de cinq méthanogènes associés aux flores humaines à la lovastatine qui est une pro-drogue utilisée pour abaisser la concentration de cholestérol chez l’homme dans le cadre de certaines pathologies. Les cinq méthanogènes se sont avérées sensibles à une concentration minimale inhibitrice de 1µg/mL, après activation par hydrolyse de la lovastatine par des bactéries anaérobies du microbiote digestif, via une l’inhibition de la croissance et de la production du méthane. / Methanogens are strict anaerobic Archaea, known to the only being able to producing methane gas as a byproduct. Methanogens which are not detected in clinical microbiology laboratories were present in oral, digestive, vaginal and cutaneous microbiota of human. Only five species on the thirteen known in human have been cultivated before the beginning of our thesis. In our thesis, we initially reviewed the state of knowledge about methanogens in human microbiota, particularly the new order Methanomassiliicoccales of methylotrophic methanogens, the as member of human microbiota. In the second part of this work, we performing new method for methanogens culture and isolation without any dihydrogen atmosphere, by co-cultured in tubes methanogens with Bacteroides thetaiotaomicron, which produces hydrogen. We also developed Multispacer Sequence Typing (MST), a genotyping method based on intergenic spacers sequencing, to genotype M. oralis and Methanobrevibacter. Smithii. We demonstrated that methanogens could be part of polymicrobial infection in the case of brain and sinusal abscesses, and also in skeletal muscle abscess, by isolating for the first time M. oralis and M. smithii in these pathologies, using culture-based and molecular-based approaches, and suggested that methanogens could be considered as human opportunistic or emerging pathogens. Finally, we tested the in vitro susceptibility of lovastatin which is a prodrug used as a powerful serum cholesterol-lowering drug in some human diseases and showed that it’s inhibits growth and methane production in human-associated methanogens without affecting intestinal bacteria.