This dissertation considers a class of closely related NP-hard otpimization problems on graphs that arise in many important applications, including network-based data mining, analysis of the stock market, social networks, coding theory, fault diagnosis, molecular biology, biochemistry and genomics. In particular, the problems of interest include the classical maximum independent set problem (MISP) and maximum clique problem (MCP), their vertex-weighted vesrions, as well as novel optimization models that can be viewed as practical relaxations of their classical counterparts. The concept of clique has been a popular instrument in analysis of networks, and is, essentially, an idealized model of a “closely connected group”, or a cluster. But, at the same time, the restrictive nature of the definition of clique makes the clique model impractical in many applications. This motivated the development of clique relaxation models that relax different properties of a clique. On the one hand, while still possessing some clique-like properties, clique relaxations are not as “perfect” as cliques; and on the other hand, they do not exhibit the disadvantages associated with a clique. Using clique relaxations allows one to compromise between perfectness and flexibility, between ideality and reality, which is a usual issue that an engineer deals with when applying theoretical knowledge to solve practical problems in industry. The clique relaxation models studied in this dissertation were first proposed in the literature on social network analysis, however they have not been well investigated from a mathematical programming perspective. This dissertation considers new techniques for solving the MWISP and clique relaxation problems and investigates their effectiveness from theoretical and computational perspectives. The main results obtained in this work include (i) developing a scale-reduction approach for MWISP based on the concept of critical set and comparing it theoretically with other approaches; (ii) obtaining theoretical complexity results for clique relaxation problems; (iii) developing algorithms for solving the clique relaxation problems exactly; (iv) carrying out computational experiments to demonstrate the performance of the proposed approaches, and, finally, (v) applying the obtained theoretical results to several real-life problems.

Nous avons pour but de développer un système microfluidique en gouttes, capable, à l’échelle de la cellule/bactérie unique, de détecter et de co-localiser plusieurs marqueurs génétiques, en utilisant une version digitale et multiplexée de la réaction de polymérisation en chaîne (PCR). Les systèmes de PCR digitale actuellement commercialisés ne le permettent toujours pas. Un tel prototype garantira la présence de multiples marqueurs à l’intérieur d’un même génome, ce qui permettra l’identification du pathogène avec précision et un taux de faux-positifs proche de zéro. Comme première application, nous démontrerons la possibilité de co-localiser quatre gènes de virulence de la souche O157:H7 d’Escherichia coli, un pathogène majeur, qui est détecté dans des échantillons alimentaires ou provenant de fèces cliniques pouvant aussi contenir des E. coli non pathogènes porteuses d’une partie des gènes de virulence. Avant de procéder à des tests TaqMan multicolores en point final, E. coli sera d’abord encapsulée dans des gouttes micrométriques et lysée par la chaleur in situ. Notre objectif est de démontrer que ce test peut être appliqué avec succès à un petit ensemble d’échantillons cliniques ou alimentaires / We aim to develop a prototype of droplet-based microfluidic system capable of detecting and colocalizing multiple genetic markers at the single cell/bacteria level, using the Polymerase Chain Reaction (PCR) in a digital multiplexed version. This cannot be achieved using current commercial digital PCR systems, and should increase the sensitivity and reliability of the detection of pathogens. Importantly, the system will guarantee the presence of multiple markers within the same genome and enable accurate identification, and bring the false positive rate close to zero. As a first application, we will demonstrate the possibility to co-localize 3 virulence genes in the E.coli strain O157:H7, a major foodborne pathogen, which has to be detected in clinical feces samples or food samples, which may also contain non pathogenic E. coli carrying only a subset of these virulence genes. E. Coli will be encapsulated in micrometric droplets, lysed by heating in situ prior performing a multicolour end-point Taqman assay. Our objective is to demonstrate that this test can be successfully applied to real clinical or food samples

Amastigotes are forms of Leishmania, naturally occurring in vertebrate hosts within phagocytic cells - especially the macrophages. The aim of this project was to compare three types of amastigotes of Leishmania that can be used for experiments under laboratory conditions - namely the axenic amastigotes, cultured extracellularly (without vertebrate phagocytic cells), amastigotes isolated from macrophages infected ex vivo, and "true" amatigotes isolated from lesions of the infected BALB/c mice. Amastigotes were compared with respect to the development in the natural vector and at the proteome level. L. mexicana, the causative agent of cutaneous leishmaniasis in the New World, was chosen for this comparison. In experiments comparing the development of Leishmania in the natural vector Lu. longipalpis we found significantly weaker infections in the sand flies infected with axenic amastigotes compared to other types of amastigotes. In addition to the intensity of infection, we compared the localization of promastigotes in the digestive tract of the phlebotomine sand flies. The following localizations were observed: the abdomen, the thorax, the cardia and the stomodeal valve, which is crucial for infectivity of the sand fly. There was no significant difference in localization in any of the groups of...

There is a general consensus that play can bring a more enjoyable user experience and can make users realize new things by providing them with a different look and approach. It is often found in games, social media applications aimed at young audiences and similar playful scenarios. However, claims have been made that it actually exists in most everyday situations, and that designers can leverage it to have a positive impact on users. In this work, we have carried out a complete design iteration to ideate and design for playfulness in a non-playful context: a concrete design case on career guidance for the French region of Grand Est. The ideation has been driven by the PLEX framework and PLEX Cards, along with their techniques. As a result, we produced an interactive prototype and evaluated users’ perception of playfulness, as well as some specific PLEX experiences. We found that the PLEX framework and PLEX Cards allow designing for playfulness in non-playful contexts, and that such play is perceived positively. The results also show that we can design to elicit specific playful experiences to some extent. / Det är allmänt känt att lek i datorinteraktion kan ge användare roligare upplevelser och lärdomar genom att erbjuda nya synvinklar och tillvägagångssätt. Det förekommer ofta i spel, sociala medier och applikationer som riktar sig till en ung publik och liknande lekfulla scenarier. Det har dock hävdats att lek faktiskt finns i de flesta vardagssituationerna och att designers kan utnyttja den för en positiv inverkan på användarna. I det här arbetet har vi genomfört ett designarbete innehållande konceptgenerering och design för implementation av lekfullhet i en icke lekfull kontext: ett konkret design case om karriärvägledning för den franska regionen Grand Est. Idéutvecklingen har drivits av PLEX-ramverket och PLEX Cards, tillsammans med tillhörande tekniker. Som ett resultat producerade vi en interaktiv prototyp och utvärderade användarnas uppfattning om lekfullhet samt några specifika upplevelser. Vi fann att PLEX-ramverket och PLEX Cards gör det möjligt att erbjuda lekfullhet i ett icke lekfullt sammanhang, och att sådan lek uppfattas positivt. Resultaten visar också att vi i viss utsträckning kan designa för att framkalla specifika lekfulla upplevelser

The purpose of this paper is to explore the technical implementation of common game design theory in successful PC games today. The study uses a quantitative study to analyze 23 modern successful PC games to identify common success factors which are connected to Arrasvuors et al. (2009) theory of the Playful Experiences Framework, Sutton-Smiths (2001) seven rhetorics of play and Max-Neefs (1991) human needs matrix. The results is a practical checklist of 63 success factors for use in game development. These success factors are present in the successful games and described for implementation in game design for the PC platform. These success factors are then divided into the 7 categories: freedom, immersion, challenge, multiplayer, personal, preference and human needs to provide a better overview of the success factor checklist and connect them to proven game design theory.

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Foodborne illnesses are a significant public health challenge in the United States, with an estimated 9.4 million illnesses annually attributed to the consumption of contaminated food, of which 59% are estimated to be caused by viruses, 39% by bacteria and 2% by parasites. Timely detection and identification of the pathogens causing foodborne outbreaks is vital for the implementation of outbreak control strategies, allowing public health officials to prevent additional illnesses and maintain confidence in the food supply. Public health laboratories employ a variety of traditional and molecular testing techniques to identify foodborne outbreak etiologic agents. One technology is the Luminex XMap® microsphere system, which is also marketed as the Bio-Plex™ 200. This platform has a multiplexing capability with the potential to simultaneously detect up to 100 targets in one reaction. The studies described here show that the combination of two Bio-Plex assays with real-time virus assays and one extraction method provides a flexible foodborne outbreak screening algorithm that potentially identifies an outbreak-associated pathogen on the first day of specimen submission and aids in focusing confirmatory laboratory testing. In these studies, two microsphere-based assays were designed for use on the Bio-Plex 200 system as screening assays for the detection of four enteric protozoa (Giardia intestinalis, Cyclospora cayetanensis, Cryptosporidium parvum, Entamoeba histolytica) and six virulence determinants of shiga toxin-producing Escherichia coli (STEC), enterotoxigenic Escherichia coli (ETEC), enteroinvasive Escherichia coli (EIEC) and Shigella spp. Precision and limits of detections were established for both assays. The sensitivity and specificity of the protozoan assay as compared to reference methods ranged from 81.25% to 100% for most targets, while sensitivity for the E. histolytica target was 42.86%. Sensitivity and specificity for the bacterial assay was 100% as compared to reference methods. However, cross-reactivity of the protozoan assay E. histolytica target with E. dispar and of the bacterial assay uidA target with enteropathogenic E. coli strains was noted. Additionally, real-time detection of norovirus and rotavirus nucleic acids extracted with the QIAamp DNA Stool Mini Kit was statistically comparable to detection when extracted with the Ambion® MagMAX™-96 Viral RNA Isolation Kit combined with the KingFisher® Magnetic Particle Processor.

The general public is at risk of ionising-radiation exposure. The development of high-throughput methods to triage exposures is warranted. Current biodosimetry techniques are low-throughput and encumbered by time and technical expertise. Although there has been an emergence of gene-profiling tools for the purpose of photon biodosimetry, similar capacities do not exist for alpha-particle radiation. Herein is the first genomic study useful for alpha-particle radiation biodosimetric triage. This work has identified robust alpha-particle induced gene-based biomarkers in isolated, ex-vivo irradiated leukocytes from multiple donors. It was found that alpha-particle and photon radiation elicited similar transcriptional responses, which could potentially be distinguished by aggregate-signature analysis. Although no distinct genes were sole indicators of exposure type, clustering algorithms and principal component analysis were able to demarcate radiation type with some success. By comparing the biological effects elicited by photon and alpha-particle radiation, significant contributions have been made to the field of radiation biodosimetry.

The general public is at risk of ionising-radiation exposure. The development of high-throughput methods to triage exposures is warranted. Current biodosimetry techniques are low-throughput and encumbered by time and technical expertise. Although there has been an emergence of gene-profiling tools for the purpose of photon biodosimetry, similar capacities do not exist for alpha-particle radiation. Herein is the first genomic study useful for alpha-particle radiation biodosimetric triage. This work has identified robust alpha-particle induced gene-based biomarkers in isolated, ex-vivo irradiated leukocytes from multiple donors. It was found that alpha-particle and photon radiation elicited similar transcriptional responses, which could potentially be distinguished by aggregate-signature analysis. Although no distinct genes were sole indicators of exposure type, clustering algorithms and principal component analysis were able to demarcate radiation type with some success. By comparing the biological effects elicited by photon and alpha-particle radiation, significant contributions have been made to the field of radiation biodosimetry.

<p>The Ericsson AXE-based systems are programmed using an internally developed language called Plex-C. Plex-C is normally compiled to execute on an Ericsson internal processor architecture. A transition to standard processors is currently in progress. This makes it interesting to examine if Plex-C can be compiled to execute on the JVM, which would make it processor independent. </p><p>The purpose of the thesis is to examine if parts of the run-time environment of Plex-C can be translated to Java and if this can be done so that sufficient performance is obtained. It includes how language constructions in Plex-C can be translated to Java. </p><p>The thesis describes how a limited part of the Plex-C run-time environment is implemented in Java. Optimizations are an important part of the implementation. </p><p>It is also described how the JVM system was tested with a benchmark test. </p><p>The test results indicate that the implemented system is a few times faster than the Ericsson internal processor architecture. But this performance is still not sufficient for the JVM system to be an interesting replacement for the currently used processor architecture. It might still be useful as a processor independent test platform.</p>