Francisella tularensis is a highly virulent zoonotic pathogen that is the causative agent of tularemia in humans. Two subspecies of F. tularensis are the most virulent in humans: tularensis (type A) and holarctica (type B), with less than 10 organisms via aerosol of a type A strain having the ability to cause fatal infection. Over the last decade much research has been done on the pathogenesis of this unique intracellular bacterium and many different virulence factors have been identified. The goal of this dissertation has been to identify and characterize the capsule-like complex (CLC) surface antigen of F. tularensis, and to determine its role in virulence and immunoprotection in a mouse model. In addition, I have investigated the role of CLC in biofilm formation. The CLC appears as a negatively staining material surrounding F. tularensis cells during transmission electron microscopy (TEM). I found that the CLC in the type B live vaccine strain (LVS) could be significantly diminished by deleting two glycosyl transferase genes (LVSΔ1423-22) in the putative polysaccharide locus, FTL_1432-FTL_1421. In addition, I determined that the CLC was not a typical polysaccharide capsule, but was in fact composed of over 50 proteins and glycoproteins including known virulence determinants, such as GroEL, DnaK, and ClpB. Upon further evaluation of the CLC, I determined that it was composed of an increase in production of outer membrane vesicles and tubules (OMV/T). These OMV/T appeared to be self-aggregating into what I visualized through TEM as the CLC. LVSΔ1423-22 was attenuated in the mouse model, and BALB/c mice immunized with CLC and adjuvant were protected against challenge with LVS. In addition to virulence, the CLC appears to play a role in biofilm formation and development. F. tularensis type B strains lacking the surface antigens CLC or CLC and O-antigen, develop a 2-7-fold more robust biofilm than the parent strains. The biofilm matrix contains a glucan-like EPS, proteins, and extracellular DNA, and further characterization may lead to determining if the biofilm acts as an environmental survival mechanism for F. tularensis. In summary, the CLC appears to be a novel surface antigen composed of upregulated OMV/T that is present in type A and B F. tularensis. Deficiency in CLC contributes to increased biofilm formation that could contribute to the survival of F. tularensis in a wide range of environmental niches. Furthermore, the CLC contributes to virulence of type B strains and elicits a protective immune response to type B challenge. A CLC-deficient type A strain could be a candidate for a new live vaccine strain, and therefore further investigation of such a mutant is warranted. / Ph. D.

by Chan Yawen. / Thesis submitted in: September 12, 2005. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 57-64). / Abstracts in English and Chinese. / Acknowledgement --- p.ii / Abstract --- p.iv / 摘要 --- p.vii / Table of Contents --- p.ix / List of Figures --- p.xii / List of Tables --- p.xiv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Diseases of the Gastrointestinal (GI) Tract --- p.1 / Chapter 1.2 --- Wireless Capsule Endoscopy --- p.2 / Chapter 1.3 --- Goals of My Research Project --- p.9 / Chapter Part I - --- Experimental Study to Determine the Frequency of Wireless Transmission --- p.11 / Chapter Chapter 2 --- Background --- p.11 / Chapter 2.1 --- Analog and Digital Wireless Video Transmission --- p.11 / Chapter 2.2 --- "Industrial, Scientific and Medical (ISM) Bands" --- p.11 / Chapter 2.3 --- Adsorption of RP Energy by Biological Tissue --- p.13 / Chapter 2.4 --- Frequency used by Implanted/Ingested Devices --- p.13 / Chapter 2.5 --- Incentives of using Higher Frequencies --- p.14 / Chapter 2.6 --- Radiation Efficiency from an Implanted/Ingested Source --- p.15 / Chapter Chapter 3 --- Material and Method --- p.18 / Chapter 3.1 --- Human Body Trunk Experimental Model --- p.18 / Chapter 3.2 --- Radiating and Receiving Antennas --- p.19 / Chapter 3.3 --- Experimental Procedures --- p.21 / Chapter Chapter 4 --- Results and Discussions --- p.23 / Chapter Chapter 5 --- Conclusions --- p.30 / Chapter Part II - --- Prototype Design and Implementation --- p.31 / Chapter Chapter 6 --- Background --- p.31 / Chapter 6.1 --- Prototype Overview --- p.31 / Chapter 6.2 --- Digital and Analog Cameras --- p.32 / Chapter 6.3 --- Digital and Analog Transmitters --- p.34 / Chapter Chapter 7 --- Possible Solutions --- p.38 / Chapter 7.1 --- Analog Camera + Analog Video Transmission --- p.38 / Chapter 7.2 --- Digital Camera + Analog Video Transmission --- p.38 / Chapter 7.3 --- Digital Camera + Digital Video Transmission using WLAN Technology --- p.40 / Chapter 7.4 --- Digital Camera + Digital Video Transmission with Video Compression --- p.42 / Chapter Chapter 8 --- Implementation of the Analog Camera + Analog Transmission Solution --- p.44 / Chapter 8.1 --- Circuit Implementation --- p.44 / Chapter 8.2 --- System Verification --- p.49 / Chapter 8.3 --- Conclusions --- p.51 / Chapter Chapter 9 --- Conclusions and Future Work --- p.53 / Chapter 9.1 --- General Conclusions --- p.53 / Chapter 9.2 --- Future Work --- p.55 / List of Abbreviations --- p.65

Among all thermal energy storage (TES) systems, latent heat thermal energy storage (LHTES) attracts high interest due to its high energy density and high exergetic efficiency. Due to the high enthalpy of fusion and low cost, inorganic salts are becoming popular as phase change materials and are used as the storage media in LHTES systems. The main drawbacks for the inorganic salts are their low thermal conductivity and high reactivity above 500°C. Therefore, designing a cost-effective containment at these conditions with longevity is a challenge. Macro-encapsulation of the PCM is one way to solve both the PCM containment issue as well as the low thermal conductivity problem. However, finding a practically viable encapsulation technique is a challenge especially for temperatures above 500°C. In the present study, encapsulation techniques were investigated for two temperature ranges; 500°C – 600°C and 600°C above. Metallic encapsulation was adopted for the 500°C – 600°C temperature. Commercially available, low-cost carbon-steel tubes were used, and the encapsulation shape was cylindrical. A 200µm coating of Ni was applied to strengthen the corrosion resistance. For temperatures above 600°C, a novel approach involving the use of ceramic materials was investigated for encapsulating chloride based PCMs. Low-cost ceramics with excellent thermal and chemical stability under molten-salt conditions were identified as the encapsulants. The influence of sintering temperature on the reactivity of feldspar, ball clay, kaolin and the mixture thereof with molten sodium chloride was investigated. The results were used to develop an optimum ceramic capsule fabrication procedure, using a green ceramic body followed by sintering at 1190°C. An innovative sealing process of in-situ layered eutectic formation was introduced. Sealing was performed at a temperature above the eutectic melting point of the salt mixture but below the individual melting points of each salt. The fabricated capsule survived more than 500 thermal cycles without showing degradation in its thermo-physical properties. Alumina (99%) based capsule containing NaCl-KCl was tested successfully for 1000 thermal cycles with a PCM weight loss of less than 5%. A lab-scale setup was designed and constructed to test an industry scalable LHTES system suitable for supplementing heat to a steam-powered cycle. Metallic cylindrical capsules were used with a eutectic of sodium sulfate (Na2SO4) and potassium chloride (KCl), which melts at 515°C, as the PCM for energy storage. This system was modeled and validated with experimental measurements. The calculated ratio of exergy to energy efficiency was around 89% (for 380-535°C). Flow irregularities were found due to a bend in the flow channel. Therefore, flow conditioners were investigated. A modified system with the flow conditioners and radiation shields showed 98% exergy to energy efficiency ratio (for 495-535°C). The overall efficiency of the system, however, was found to be low due to the heat losses from the storage tank. Finally, a novel design of a TES system using spherical capsules is proposed with additional enhancement gained from the experimental work on the lab-scale LHTES system. The innovation of this design lies in the manufacturing process to forms multiple spherical capsules using sheet metals. The adoptability of this technique for higher or lower temperature LHTES applications depends on the properties of the selected sheet metal. Any formable sheet metal can be used depending on the compatibility with PCM and HTF.

Les exopolysaccharides (EPS) produits par les bactéries lactiques ont longtemps été considérés comme des composés indésirables dans le vin. En effet, le β-glucane produit par certaines souches bactériennes est responsable d’une altération qui rend le vin impropre à la consommation. Cependant, les polysaccharides produits par Oenococcus oeni, principale espèce de la fermentation malolactique (FML) qui est une étape essentielle participant à la stabilisation et la qualité du vin, n’ont jamais été associés à un quelconque défaut. Notre premier objectif était d'identifier le matériel génétique impliqué dans la production de polysaccharides, en termes d'évolution phylogénétique et de diversité, parmi une collection de 50 souches d’O. oeni. L'analyse bioinformatique des 50 séquences génomiques a révélé la présence de deux loci organisés en opéron et potentiellement impliqués dans la production d'hétéropolysaccharides, mais aussi la présence de gènes isolés de glycosyltransférases et glycosides hydrolases impliqués dans la synthèse d’homopolysaccharides. L’ensemble des souches analysées présentent au moins une des voies de biosynthèse des EPS, suggérant un rôle essentiel chez O. oeni. Par la suite, une approche biochimique des polysaccharides produits a été mise en place et a permis de confirmer les données génomiques. Une glycosyltransférase membranaire, jouant un rôle clé dans la production d'EPS, a été caractérisée afin de mieux comprendre le mécanisme de la synthèse EPS. Par ailleurs, l’étude physiologique des polysaccharides produits a révélé l’existence de deux phénotypes (forme libérée et capsulaire), chacun jouant un rôle dans la survie et l’adaptation de la bactérie au vin et au procédé de lyophilisation industriel, forme sous laquelle les souches commerciales sont proposées pour induire la FML. / Exopolysaccharides (EPS) of lactic acid bacteria have long ago been undesirable in wine. Indeed, β-glucan produced by certain strains of bacteria provokes wine spoilage and makes the wine commercially defective. However, the polysaccharides produced by Oenococcus oeni which is the main species to drive malolactic fermentation (MLF), an essential step for wine stabilization and quality improvement, are not to be blamed for any spoilage effect. Our first aim was to identify the genetic material implicated in polysaccharides production, in terms of phylogenetic evolution and diversity among the strains of our collection. The bioinformatic analysis of 50 O. oeni genomic sequences revealed the presence of two organized loci potentially implicated in the production of heteropolysaccharides and also the presence of isolated genes of glycosyltransferases and glycoside-hydrolases implicated in the production of homopolysaccharides. The presence of at least one biosynthetic pathways in all the strains tested shows the importance of the polysaccharides genes for Oenococcus oeni. Thereafter, we reached-up a biochemical approach of the produced polysaccharides, confirming the results of the bioinformatics research. Initially we characterized a membrane glycosyltranferase, playing a key role in the EPS production. The results allow us to better understand the mechanism of the EPS synthesis. Furthermore the physiology of the produced polysaccharides showed two possible phenotypes (liberated and capsular form) each one playing his role for the bacterial survival at his natural environment (wine) as well as at industrial level (production of malolactic starters).

Escherichia coli is an incredibly diverse group of bacteria that consist of both commensal and pathogenic strains that cause disease in a wide variety of tissues in many different animals. The current dogma, based on years of extensive molecular and genetic studies, is that individual strains have adapted to specific environments through acquisition of specific genes or come from lineages that are particularly suited to a unique tissue or host. However, mastitis-associated E. coli (MAEC) have thus far resisted such descriptions. The fitness and virulence factors of MAEC are poorly understood and molecular tools are rarely applied. This dissertation reports new approaches to assess virulence of MAEC strains, enabling comparative genomic studies across multiple strains as well as genome-wide analysis of specific successful MAEC isolates. I outline the identification of the first virulence factor of MAEC, a ferric dicitrate receptor that is essential for colonization of a lactating mammary gland in a murine model. Genes previously studied in the contexts of other extraintestinal E. coli infections were also implicated in mastitis. These include a type III capsule found in the MAEC strain M12, which is crucial for dissemination from the mammary gland to the spleen. A mutant unable to produce capsule had diminished lethality in Galleria mellonella and decreased kidney colonization in a mouse urinary tract infection. I also report a link between zinc uptake, bile salts, and capsule production. I have utilized a transposon mutant library paired with deep sequencing of transposon junctions to elucidate the fitness factors needed to grow in milk and colonization of both murine and insect models. This analysis implicates a broad set of genes and metabolic pathways pertinent to these conditions. In addition to Tn-seq, I sequenced 94 MAEC genomes and identified genes associated with disease severity, growth in milk, and colonization of mammary glands in cow and mouse models. Employing bioinformatic tools to interrogate the pan-genome, I identified genes that are involved in biofilm formation and adhesion that were specifically associated with either mild or severe disease. In summary, I have employed several powerful genetic, genomic, computational, and molecular approaches to the characterization of mastitis associated E. coli. This work provides the groundwork for future experiments to better understand the host-pathogen interface and a model for mastitis-associated E. coli.

<div>Machine learning models are rising every day. Most of the Computer Vision oriented</div><div>machine learning models arise from Convolutional Neural Network’s(CNN) basic structure.</div><div>Machine learning developers use CNNs extensively in Image classification, Object Recognition,</div><div>and Image segmentation. Although CNN produces highly compatible models with</div><div>superior accuracy, they have their disadvantages. Estimating pose and transformation for</div><div>computer vision applications is a difficult task for CNN. The CNN’s functions are capable of</div><div>learning only shift-invariant features of an image. These limitations give machine learning</div><div>developers motivation towards generating more complex algorithms.</div><div>Search for new machine learning models led to Capsule Networks. This Capsule Network</div><div>was able to estimate objects’ pose in an image and recognize transformations to these</div><div>objects. Handwritten digit classification is the task for which capsule networks are to solve</div><div>at the initial stages. Capsule Networks outperforms all models for the MNIST dataset for</div><div>handwritten digits, but to use Capsule networks for image classification is not a straightforward</div><div>multiplication of parameters. By replacing the Capsule Network’s initial layer, a</div><div>simple Convolutional Layer, with complex architectures in CNNs, authors of Residual Capsule</div><div>Network achieved a tremendous change in capsule network applications without a high</div><div>number of parameters.</div><div>This thesis focuses on improving this recent Residual Capsule Network (RCN) to an</div><div>extent where accuracy and model size is optimal for the Image classification task with a</div><div>benchmark of the CIFAR-10 dataset. Our search for an exemplary capsule network led to</div><div>the invention of RCN2: Residual Capsule Network 2 and RCNX: Residual Capsule NeXt.</div><div>RCNX, as the next generation of RCN. They outperform existing architectures in the domain</div><div>of Capsule networks, focusing on image classification such as 3-level RCN, DCNet, DC</div><div>Net++, Capsule Network, and even outperforms compact CNNs like MobileNet V3.</div><div>RCN2 achieved an accuracy of 85.12% with 1.95 Million parameters, and RCNX achieved</div><div>89.31% accuracy with 1.58 Million parameters on the CIFAR-10 benchmark.</div>

This observational study was conducted to evaluate the anatomic relationship between the proximocaudal femoral joint capsule insertion and the femoral caudolateral curvilinear osteophyte (CCO), across ancient and modern domestic and non-domestic canids. Museum specimens of proximal femora were screened for presence of remnant enthesophytes of the caudal joint capsule insertion (first inclusion criterion) and then for the CCO (second inclusion criterion). The initially screened population included 267 dry bone specimens: Six Canis species, hybrid coyote × domestic dog, and five vulpines (three Vulpes species, one Urocyon, and one Nyctereutes). Proximocaudal joint capsule insertion remnant enthesophytes were limiting at n = 19 specimens: Seven ancient domestic dogs, four modern coyotes, two ancient coyotes, two modern hybrid coyote × dog, two modern red foxes, and two modern raccoon dogs. The joint capsule enthesophytes are associated with inflammation, but are observed far less frequently than the CCO. The CCO is seen radiographically but is visible more frequently by direct inspection. The primary inclusion criterion necessarily was a visible caudal joint capsule insertion; spatial relationships of the CCO can be assigned with confidence only when a capsule insertion line can be recognized clearly. We demonstrate that the anatomic CCO associates with the joint capsule insertion being nonspecific and species-independent. A joint capsule insertion-CCO spatial relationship across species is an important new observation, strongly indicating that both are pathological features. Our data indicate need for new research to characterize the canid coxofemoral joint and its overt and incipient pathology in a phylogenetic context. Anat Rec, 302:2164–2170, 2019.

Doctor of Philosophy / Department of Biology / Lynn E. Hancock / Enterococci are gram-positive bacteria typically found as commensals in the gastro-intestinal tracts of most mammals. Enterococci, most notably Enterococcus faecalis and Enterococcus faecium, have become problematic causative agents of several nosocomially acquired infections including urinary tract infections, bacteremia, surgical sight infections, and endocarditis. These bacteria must first overcome the innate immune response in order to establish infection. Many bacteria produce capsular polysaccharides that contribute to pathogenesis by helping the microbe evade the host innate immune response. The capsular polysaccharide produced by E. faecalis has been shown to play a role in pathogenesis; however the mechanisms of innate immune avoidance were unknown. Moreover, the number of capsule serotypes produced by E. faecalis and the genetic differences that contribute to capsule serospecificity were in doubt. In the current study it is made clear that only two capsule serotypes are produced by E. faecalis and that both capsule serotypes contribute to evasion of the host innate immune system. This work shows two mechanisms by which the capsule of E. faecalis contributes to immune evasion. First, the presence of capsule inhibited complement mediated phagocytosis through limiting the detection of opsonic complement protein C3 on the surface of the bacteria. Secondly, the presence of capsule altered cytokine signaling of macrophages by shielding bacterial components from detection. Many pathogenic strains of E. faecalis also produce an extracellular protease known as gelatinase (GelE). This work also shows a novel mechanism involving GelE in innate immune evasion through the degradation of the anaphylatoxin C5a. Degradation of C5a by GelE resulted in decreased neutrophil recruitment in vitro. A rabbit model of endocarditis was employed to assess the effect of GelE production on disease development and progression. Rabbits infected with GelE producing strains had increased bacterial burdens in the heart compared to rabbits infected with strains that were GelE negative. Reduced phagocyte infiltration at primary and secondary infection sites was also observed in rabbits infected with GelE producing strains compared to GelE negative strains. The work presented here demonstrates that both the capsular polysaccharide and GelE play roles in E. faecalis evasion of innate immune responses. Moreover, these pathogenic determinants would be suitable targets for developing alternative therapeutics used to treat E. faecalis infections.

The fascinating field of molecular capsules has recently begun to see the creation of structures that, medicated by the encapsulation of guest molecules within their central cavity, are able to change the properties or reactivity of the substrate. The current capsule designs are however, prone to exchange of either part or whole ligands. This exchange or the capsule's subsequent disassembly can lead to loss of the cavity or modification of their external properties, and is a barrier to their more widespread application, a problem this work seeks to address by creating more a robust capsule structure. This thesis presents the design, synthesis and properties displayed by three novel capsules. All the species presented share a similar supramolecular tetrahedral structure, but their properties deviate significantly, showing either switchable behaviour, spin-crossover or a novel synthetic route to a kinetically inert structure. Improvements in the design have led to a final capsule that is water-soluble, robust, non-toxic and has been shown to encapsulate a range of guests. Chapter 1 includes an overview of the types of capsule constructed in literature and their possible application. The fundamental properties of these capsules are identified, with emphasis given to a discussion of mechanisms underlying their encapsulation phenomena. Chapter 2 describes efforts to construct a tetrahedral capsule based on iron(II) and an oxime ligand. While the use of an oxime motif achieved the aim of preventing exchange of the external groups, the capsule also displayed the surprising property of possessing a solvent responsive assembly-disassembly process. This potentially provides a basis for 'on-demand' encapsulation by being able to choose when to have hydrophobic cavity available for guests. Chapter 3 details the synthesis of a tetrahedral capsule containing iron (II) coordinated by a pyridyl-triazole bonding motif. the spin-crossover properties of the complex were initially demonstrated in the solid state, however, when in solution the capsule displayed the unusual ability of spin-crossover mediated structural rearrangement. Chapter 4 demonstrates the synthesis of a robust capsule. The synthetic route shown alleviates the problems surrounding the construction of inert species in a self-assembly process. Based around a cobalt (III) cation, the stability of the capsule to carious conditions is examined and its host-guest chemistry is explored, revealing some insights into the encapsulation behaviour of this structure.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.