Yes / Rapid point of care tests for bacterial infection diagnosis are of great importance to reduce the misuse of antibiotics and burden of antimicrobial resistance. Here, we have successfully combined a new class of non-biological binder molecules with electrochemical impedance spectroscopy (EIS)-based sensor detection for direct, label-free detection of Gram-positive bacteria making use of the specific coil-to-globule conformation change of the vancomycin-modified highly branched polymers immobilized on the surface of gold screen-printed electrodes upon binding to Gram-positive bacteria. Staphylococcus carnosus was detected after just 20 min incubation of the sample solution with the polymer-functionalized electrodes. The polymer conformation change was quantified with two simple 1 min EIS tests before and after incubation with the sample. Tests revealed a concentration dependent signal change within an OD600 range of Staphylococcus carnosus from 0.002 to 0.1 and a clear discrimination between Gram-positive Staphylococcus carnosus and Gram-negative Escherichia coli bacteria. This exhibits a clear advancement in terms of simplified test complexity compared to existing bacteria detection tests. In addition, the polymer-functionalized electrodes showed good storage and operational stability.

Until now, tracing the genealogical lines of EEC/EU Antibiotic Resistance policy has been a gap in social science research that has focused on the policies of individual countries. This Working Paper raises the question how Antimicrobial Resistance (AMR) has developed as an epistemic object in terms of biopolitical and spatial regulatory design of EEC/EU. It also asks what cultural ideas and imaginations have been associated with antibiotics since their introduction. To this end, a historical discourse analysis was conducted combining the perspectives of human geography and historical sociology. First cases of resistance occurred at short intervals with the introduction of new antibiotics in both human and veterinary medicine, and the discovery of the mechanism of horizontal gene transfer attracted global attention in the 1960s. Nevertheless, the belief in the need for an expansionary mode of production outweighed scientific doubt and the longer-term health of the population, so that regulatory interventions were more appearance than substance. Only in the wake of the geopolitical rise of the EU and BRICS countries and new ‘pandemic risks’, a general turn to security dispositif and neoliberal-individualist governmentality rearranged the coordinates of AMR policy to some extent. The interpretation of our present as a “multi-crisis”, which has become increasingly established in the “West” in the wake of climate crisis and Covid19, is apparently contributing to an increasing assessment of AMR as an unintended side-effect of an expansionary economy and lifestyle, with no regulatory responses to date that address systemic causes rather than suggesting a fiction of control.

DNA damage occurs to all living things; its subsequent repair is a crucial component of life. The most dangerous, and potentially most useful form of DNA damage is the double strand break (DSB). A DSB is defined by breaks occurring to both sugar phosphate backbones in close enough proximity that they lead to the separation of the two pieces of the DNA. This type of damage will kill the cell if left unrepaired. It is the most lethal type of DNA damage. Most living organisms have also developed ways to take advantage of DSBs through their repair systems, primarily as a means of introducing genetic variation. There are two primary DSB repair pathways across life: homologous recombination (HR) and non-homologous end-joining (NHEJ). The focus of this work is NHEJ. NHEJ is known as “error-prone” because it does not use a homologous template and can introduce small addition or deletion mutations during the repair process. This pathway has been extensively studied in eukaryotes and is known as the primary form of DSB repair in mammalian cells, however the prokaryotic NHEJ system was more recently identified and as a result, a void of information surrounds it. NHEJ is comprised of 3 core steps: DSB recognition and binding, DNA end processing, and ligation. In the eukaryotic version of NHEJ these 3 steps involve a plethora of factors; conversely, in the prokaryotic version, the same functionality is accomplished by just 2 proteins, bacterial Ku and LigD. The focus of this research is Ku: the DNA end-binding protein responsible for identifying the DSB, binding and protecting the DNA end, as well as recruiting LigD to the break. Ku is composed of 2 domains, the first of which is predicted to be highly homologous to eukaryotic Ku’s equivalent domain; this is the core domain which forms a ring-like structure that DNA threads through. The second is completely unique to bacterial Ku, it is the C-terminal domain, which can further be split into 2 sub-domains, the minimal C-terminus, and the extended C-terminus. The sub-domains are defined by their level of conservation across bacterial species, with the minimal C-terminus being highly conserved, while the extended C-terminus is highly variable. Using DNA-binding assays and several mutant constructs which affect the C-terminal domain, I show that this C-terminus is unexpectedly responsible for destabilizing the Ku-DNA interaction. This observation leads me to hypothesize that maintaining a weak interaction with DNA is important for Ku because of the other proteins which need access to the DNA (e.g. replicative helicase). While Ku is bound, it could be capable of blocking regions of DNA, in turn blocking other vital cellular processes like replication. Ku maintaining a lower affinity for DNA should facilitate Ku displacement by other proteins. A tighter binding would restrict Ku’s freedom to move on DNA making it more likely to inhibit other critical pathways. To better understand Ku, I attempted to solve the Ku structure using X-ray crystallography, and was able to achieve crystals of Ku, however diffraction was too limited for a structure. Another way to investigate the validity of my proposed model is to use a biophysical approach with atomic force microscopy (AFM) to visualize protein-DNA complexes. The initial work has established key controls for future Ku-DNA AFM work by imaging and analyzing Ku on its own. Interest in bacterial NHEJ is two-fold from the antimicrobial perspective: NHEJ is a highly mutagenic pathway, so it serves as a proverbial well for differentiation and thus the development of antimicrobial resistance (AMR); NHEJ is very important in bacteria that enter a stationary phase due to their lack of a homologous piece of DNA for HR. Thus, NHEJ inhibition could be useful for slowing bacterial evolution and potentially as a treatment for infections such a Mycobacterium tuberculosis, which is known to lie dormant in host macrophages for long periods of time. To investigate the viability of NHEJ inhibition, I had begun the process of creating ∆ku strains of Pseudomonas aeruginosa to simulate Ku inhibition under various conditions. This Ku project is the focus of the first two chapters, however, during my Master’s degree I participated in 2 other major projects. The third chapter details a bacterial DNA damage tolerance pathway, which similarly is highly mutagenic and poorly characterized: the ImuABC translesion synthesis polymerase complex. The fourth and final chapter details the work for a Journal of Visualized Experiments article meant to highlight the benefits of AFM as a means of studying protein-DNA interactions. / Thesis / Master of Science (MSc)

Les travaux de thèse présentés dans ce mémoire s’inscrivent dans le cadre du projet ANR BARPPRO. Ce programme de recherche vise à étudier l’influence d’une barrière de protection face à une explosion en régime de détonation. L’objectif est d’établir des méthodes de calcul rapides de classement des zones d’effets pour aider les industriels au dimensionnement des barrières de protection. L’une à partir d’abaques, valable pour des configurations en géométrie 2D, sur des plages spécifiées de paramètres importants retenus, avec une précision de +/- 5%. L’autre à partir d’une méthode d’estimation rapide basée notamment sur les chemins déployés, valable en géométrie 2D et en géométrie 3D, mais dont la précision estimée est de +/- 30%. Afin d’y parvenir, l’étude s’appuie sur trois volets : expérimental, simulation numérique et analytique. La partie expérimentale étudie plusieurs géométries de barrière de protection à petites échelles pour la détonation d’une charge gazeuse (propane-oxygène à la stoechiométrie). Les configurations expérimentées servent à la validation de l’outil de simulation numérique constitué du solveur HERA et de la plateforme de calcul TERA 100. Des abaques d’aide au dimensionnement ont pu être réalisés à partir de résultats fournis par l’outil de simulation (3125 configurations de barrière de protection, TNT). L’étude des différents phénomènes physiques présents a également permis de mettre en place une méthode d’estimation rapide basée sur des relations géométriques, analytiques et empiriques. L’analyse de ces résultats a permis d’établir quelques recommandations dans le dimensionnement d’une barrière de protection. Les abaques et le programme d’estimation rapide permettent à un ingénieur de dimensionner rapidement une barrière de protection en fonction de la configuration du terrain et de la position de la zone à protéger en aval du merlon. / This thesis is a part of the ANR BARPPRO project. This research program studies this influence of the protection barrier during an explosion detonation. The goal of this project is to establish fast-computation methods of area classification effects to help the industrial to design the protection barrier on the SEVESO sites. One from abacus, for configurations in 2D geometry on specified parameters used, with an accuracy of +/- 5%. The other from a fast-running method based on broken lines for configurations in 2D and 3D geometries, but the accuracy is +/- 30%. This study includes three approaches: experimental, numerical simulation and analytical approaches. The experimental part studies several geometries of the protection barrier for a gaseous explosion (stoichiometric propane-oxygen mixture) at small scales. The experimental configurations used to validate the numerical simulation tool constituted of the HERA software and the TERA 100 supercomputer. The overpressure charts were able to generate from the numerical results (3125 configurations of the barrier for a TNT charge). The analysis of these results allows to establish different recommendations in the design of the protection barrier. The study of the different physical phenomena present has also helped to set up a fast-running method based on the geometrical, empirical and analytical relations. All these tools will enable an engineer to analyze and estimate the evolution of overpressure around the barrier as a function of the site’s dimensions.

Globally, the incidence of infection caused by Neisseria gonorrhoeae is the second highest among the bacterial sexually transmitted infections. In Canada, declining rates during the 1990s suggested progress toward curbing gonorrhea; however, those have been increasing since 1999, with rates in Saskatchewan among the highest in the country. Infection can cause serious complications in men and women, and reported resistance to third-generation cephalosporins could lead to potentially untreatable infections. Increased understanding of gonorrhea transmission dynamics, sexual networks, and predictors of antimicrobial resistance development is needed to inform the development of improved approaches to prevention and treatment. The research presented herein draws upon data from Shanghai, China, and Saskatchewan, Canada, to compare and contrast varying epidemiologic approaches to enhancing understanding of gonorrhea in the two settings. Using traditional statistical approaches, multi-level statistical modeling, social network analysis, and dynamic simulation modeling, questions related to sexual behavior, partner presentation, and antimicrobial resistance development are explored. Each technique is evaluated for its potential contribution to overall understanding of the issues related to the ongoing gonorrhea epidemic, globally, and in Saskatchewan. The relative strengths and limitations of the application of the analytical approaches in the different settings are described. Socio-demographic characteristics provided useful indicators of antimicrobial resistant infection among patients with gonorrhea from Shanghai. Further, socio-demographic characteristics were also useful for predicting presentation of a partner for testing and treatment and the use of condoms during intercourse, among this study population. In Saskatchewan, socio-demographic characteristics were useful in predicting coinfection with gonorrhea and chlamydia at the time of diagnosis as well as repeat infection with gonorrhea. Social network analysis of the Saskatchewan dataset provided little additional understanding of the gonorrhea epidemic in the province. This result was largely related to how STI data are collected and stored in the province. The utility of dynamic simulation modeling to investigate the potential impact of antimicrobial resistance in Saskatchewan was also limited due to the same data constraints. However, the insight gained from the model building process and findings from the working model did offer a starting point for conversations around the best ways to postpone the development of antimicrobial resistance in N. gonorrhoeae in Saskatchewan, as well as contribute additional information about how the ways in which STI data are collected and stored in the province considerably restrict the applicability of otherwise powerful epidemiologic tools. With persistently high rates of disease transmission, and the threat of untreatable infections due to antimicrobial resistance, N. gonorrhoeae remains a substantial public health threat locally and globally. The research presented herein describes various approaches to understanding and controlling this disease, applied in contrasting settings. There are a wide variety of elements that should be considered when choosing the appropriate tool(s) to address gonorrhea in a given population; there is no “one size fits all” solution. The local epidemiology of disease, cultural and behavioural norms, the characteristics of the notifiable disease reporting and information systems, and the availability of suitable data all affect the relative strengths and weaknesses of the available analytic methods and disease control approaches.

Ce mémoire propose un algorithme de compression sans perte des indices binaires d'un quantificateur algébrique encastré utilisé par le codec AMR-WB+ pour encoder certaines des trames d'un signal audio. Une étude détaillée des statistiques a été menée dans le but de développer un algorithme efficace de compression et réduire par conséquent la longueur moyenne du code binaire utilisé par le codec AMR-WB+. En se basant sur cette étude des statistiques, deux techniques ont été combinées : l'encodage par plage et l'encodage par contexte qui se sont montrés très efficaces pour estimer les probabilités des différents indices. En utilisant l'encodage arithmétique en version entière pour générer le code binaire, l'algorithme proposé permet de réduire sans perte jusqu'à 10% de la longueur du code utilisé par le AMR-WB+ tout en respectant la contrainte d'une application temps réel destinée à des terminaux GSM.

Dans le cadre de la fusion par confinement inertiel en attaque directe, l'utilisation de mousses en tant qu'ablateur permet de réduire les instabilités hydrodynamiques créées sur la cible par l'irradiation directe des faisceaux laser. Des études antérieures ont été réalisées en considérant cette mousse comme homogène. Or, étant composée de fibres de CH baignant dans du DT, elle présente un aspect hétérogène. Le but de cette thèse est d'étudier l'effet de cette hétérogénéité sur la vitesse du choc lors de l'irradiation laser de la cible. Une étude expérimentale sur tube à choc et des études numériques avec le code HERA nous ont permis de trouver que le choc se propage plus rapidement dans le milieu hétérogène que dans le milieu homogène de densité moyenne équivalente. Cette écart de vitesse dépend du taux de présence des fibres de CH, du rapport de densité entre les deux matériaux constituant la mousse, de leur coefficient adiabatique et de la géométrie de la mousse. Nous avons modélisé la mousse de diverses manières, en partant du plus simple au plus compliqué, afin de se rapprocher d'une configuration réaliste. La modification de la vitesse du choc étant dûe à la baroclinicité qui, lors de l'interaction du choc avec l'interface entre le CH et le DT, crée un dépôt de vorticité, responsable de l'accélération du choc. Par conséquent, une interface plane et perpendiculaire au front de choc maximise ce dépôt de vorticité et augmente les écarts de vitesse entre milieux hétérogènes et homogènes. Une corrélation entre l'énergie cinétique derrière le choc et la différence relative des vitesses de choc a été trouvée. Nous avons comparé nos résultats à deux modèles analytiques, mais le système n'étant pas fermé, nous ne pouvons pas, pour le moment, élaborer de modèle prédictif.

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ACKNOWLEDGEMENTS I would like to take this moment to extend my utmost appreciation for all the support provided by my supervisor, Dr. Russell de Souza. He assisted me along the way and ensured that I was always on the right path to achieve all my goals and checkpoints in every circumstance. I would also like to thank my committee for providing me with fantastic support: Ms. Laura Banfield for always being there to help solve any problem in this process, and Dr. Zain Chagla for providing a plethora of knowledge from the technical perspective of infectious disease and being so patient. Special thanks to Dr. Alexandra Mayhew for her support in our prevalence meta-analysis. Finally, I would like to thank my family, my wife, Dr. Sanjida Rowshan Anannya, for whom I am here today, and my parents, siblings, and in-laws; you are always there for me in every walk of life. You are why I have gotten to where I am today and are my daily inspiration. / Background: Bacteria is a major cause of many infectious diseases, and the treatment for these diseases is antibiotics designed to kill or subdue the growth of the bacteria. However, bacteria evolve, and if an antibiotic prescription is not the right antibiotic for the right patient at the right time with the correct dose and the right route, Antimicrobial Resistance (AMR) may result. During this pandemic, the use of antibiotics to treat hospitalized COVID-19 patients without any bacterial coinfection threatens the effectiveness of antibiotic treatment for current and future bacterial infections. Methods: A systematic search was conducted of the Embase, Medline, Web of Science, and Cochrane Library databases by generating search terms using the concepts of “COVID-19,” “Bacterial Coinfection,” “Secondary bacterial infection,” and “Antimicrobial resistance” to identify studies that reported the prevalence of antibiotic prescription for the treatment of COVID-19 in hospitalized patients with and without bacterial coinfection. The pooled estimate of the percentage of the total and confirmed appropriate antibiotic prescriptions provided to hospitalized COVID-19 patients was generated using a random effect meta-analysis with inverse variance weighting. Result: Of 157,623 participants from 29 studies included in our review, 67% (CI 64% to 71%, P<0.00001) were prescribed antibiotics, among which 80% (CI 76% to 83%, P<0.00001) prescriptions were given for the COVID-19 patients without any bacterial coinfections. The use of antibiotics varied during the pre-immunosuppressive period (before 16 June 2020) and post-immunosuppressive period of the pandemic and between the High-Income Countries and Upper and Lower Middle-Income Countries. Conclusion: This Systematic Review and Meta-analysis finds greater than expected use of antibiotics to treat hospitalized COVID-19 patients without bacterial coinfections, which can worsen AMR globally. Clear and concrete guidelines for the use of antibiotic prescriptions to treat COVID-19 patients, strict monitoring, and compliance with Antimicrobial Stewardship are needed to prevent over-prescription. / Thesis / Master in Advanced Studies (MAS) / Bacteria is a major cause of many infectious diseases. Before the discovery of Antibiotics in 1928, hundreds of thousands of people used to die due to infectious diseases caused by bacteria. While Antibiotics are essential to treat bacterial infectious diseases, overuse or misuse can accelerate Antibiotic Resistance, a phenomenon when bacteria change and/or develop the ability to escape the drugs designed to kill them. Self-medication, availability of antibiotics without a prescription, and inappropriate dosing of antibiotics can worsen the situation. During the COVID-19 pandemic, antibiotics were commonly prescribed as part of the treatment regime for COVID-19, even when a clear bacterial infection was not identified. In our Systematic Review and Meta-analysis, we aimed to see the frequency of antibiotic prescriptions to treat hospitalized COVID-19 patients without any bacterial coinfections.

Driven by recent technical advances, vehicle-based transportation systems in intralogistics are currently shifting from automated guided vehicles (AGVs) to autonomous mobile robots (AMRs). Unlike AGVs, AMRs are not bound to a physical or virtual track and autonomously determine their movements. While the increase in freedom for routing leads to improvements in terms of system flexibility and scalability, it also poses new challenges in terms of coordination and thus the high-performance routing behavior of an entire fleet. Accepted and widely used algorithms in the AGV field are often barely applicable to large fleets of free-ranging AMRs, while typical algorithms from the field of mobile robotics usually focus on different objectives. This thesis presents a novel concept for determining global routes, the so-called lanemap, that enables the synchronized movements of multiple free-ranging vehicles in arbitrary layouts without increasing calculation effort during online operations. The basic idea consists in creating a lanemap offline that provides the AMRs with a set of suggested global lanes from various starting positions to different destinations. On the one hand, the application of a lanemap lowers each AMRs’ individual degree of freedom. However, coordinating lanes sensibly beforehand enables short travel distances as well as a low probability of routing conflicts, which improves the performance of the entire AMR fleet on the other hand. Since the lanemap only provides an offline calculated global route as suggestion, the concept can be combined with any established online approach, such as a local conflict avoidance/resolution approach, or with in-depth coordination of all vehicle movements. This thesis presents a theoretical mathematical model and a practically applicable heuristic approach for the creation of a lanemap. As proof of concept, simulation experiments show that the heuristic is generally capable of creating lanemaps for all different kinds of layouts. Furthermore, the concept allows for the determination of customized routes for a specific fleet size and an anticipated transportation demand. Therefore, once system requirements are known, a beneficial set of lanemaps for typical constellations can be calculated in advance and integrated into routing as needed.