Open Theses and Dissertations
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Item Open Access Proactive Traffic Sampling with Dynamic Flow Rates in Software-Defined Networks(2024-12-12) Esmaeilian, Soroosh; Ghaderi, Majid; Abou-Zeid, Hatem; Safavi-Naini, ReihanehAs modern networks continue to grow in scale and speed, traffic sampling has become an indispensable tool in network management. While there exists a plethora of sampling systems, they generally assume flow rates are stable and predictable over a sampling period. Consequently, when deployed in networks with dynamic flow rates, some flows may be missed or under-sampled, while others are over-sampled. This thesis presents the design and evaluation of dSamp, a network-wide sampling system capable of handling dynamic flow rates in Software-Defined Networks (SDNs). The key idea in dSamp is to consider flow rate fluctuations when deciding on which network switches and at what rate to sample each flow. We formulate the network-wide sampling with dynamic flow rates as a robust optimization problem. Our proactive approach leverages statistical information about flow rates to cope with fluctuations in flow rates. Since our initial formulation is an Integer Second Order Cone Program (ISOCP), which is infeasible for both small-scale and large-scale network instances, we shift our focus to developing an efficient approximate Integer Linear Program (ILP) called APX, which can compute sampling allocations even for large-scale networks. To show the efficacy of dSamp for network monitoring, we have implemented APX and several existing solutions in ns-3 and conducted extensive experiments using both model-driven and trace-driven simulations. Our model-driven results indicate that APX outperforms the approaches in [50] and [21] by up to 10%. Similarly, our trace-driven results show that APX surpasses these works by up to 6.37%. Unlike [50] and [21], which require fine-tuning in model-driven simulations for use in trace-driven simulations, APX works across all simulations without such a requirement.Item Open Access Investigating the impact of bio-oil components in esterification upgrading(2024-12-13) Bonatti, Erika; Hill, Josephine; Hu, Jinguang; De La Hoz Siegler, HectorBio-oil, an organic liquid derived from biomass pyrolysis, shows promise as a sustainable fuel but faces limitations due to its low energy density, corrosiveness, and low stability. Upgrading technologies to improve bio-oil properties exist, but the impact of its constituents during these processes is not well understood. Hence, this study evaluates the impact of phenol and furfural on the performance of solid acid catalysts during acetic acid and methanol esterification. The acid conversion over three different catalysts was examined. Phenol effect on esterification over Amberlyst-15 was evaluated in detail, including kinetic studies and catalyst structural modifications. The presence of phenol led to a decrease in catalyst performance due to their adsorption on the same sites as acetic acid over the Amberlyst-15 structure. The work emphasized how phenol and other bio-oil components could inhibit solid acid catalysts during bio-oil upgrading, offering valuable insights for the upgrading processes.Item Open Access Atlas of Normal Articular Cartilage: Structural and Functional Comparison Across Species(2024-12-16) Oduba, Oyindamola Oladunni; Manske, Sarah Lynn; Krawetz, Roman; Edwards, Brent William; Sparks, Holly DanielleOsteoarthritis (OA) is a joint disease and the most common form of arthritis in older populations. Articular cartilage (AC) is one of the predominant tissues affected in OA. This tissue is crucial in joint function and essential for the maintenance of joint mobility and stability. The development of novel treatments for OA typically begins with pre-clinical studies involving any one of a number of species; therefore, it is important to select species with similar cartilage structure-function properties to humans. Most studies that have characterized AC properties typically include few species or use different test techniques to obtain the properties. In this study, a universal test method was utilized across eight different species to characterize AC properties, thereby potentially eliminating variability in results. Testing involved biomechanical testing to evaluate functional characteristics of cartilage and histology to assess structure across species. The results show that AC properties vary independently across species; however, several patterns observed across the species suggest inter-species similarities. Histological analysis further confirmed the similarities and differences in AC morphology and structure across the species. Characterizing these structure-function relationships in AC across species is critical to understanding how different pre-clinical species compare to human cartilage. Ultimately, this study provides an atlas of reference data for researchers to use when determining which pre-clinical species is most appropriate for their studies.Item Open Access Investigating the Polymicrobial Nature of Bovine Digital Dermatitis in Natural Infections and Animal Models(2024-12-12) Petersen Dias, Angelica; De Buck, Jeroen; Orsel, Karin; Cobo, Eduardo; Morck, Douglas Walter; Sycuro, Laura K.; Plummer, Paul J.Digital Dermatitis (DD) is a multifactorial, polymicrobial skin disease on cattle’s feet and is the leading cause of lameness in Canadian dairy cattle, with an etiology that remains unclear. This thesis aimed to investigate the polymicrobial nature of DD by identifying potential bacterial reservoirs and investigating the roles of specific bacteria in lesion initiation in natural infections. Additionally, efforts were made to optimize a bovine infection model. Four studies were conducted, three field studies in commercial dairy farms and an experimental infection study. We relied on quantitative molecular techniques, real-time qPCR, targeting three DD-associated Treponema spp. and four other anaerobes. First, we validated swabs as an alternative to invasive skin biopsies in detecting and quantifying DD bacteria. We then mapped and quantified DD bacteria in potential reservoirs in dairy cows from herds with or without DD. Next, we assessed the temporal changes in bacterial counts preceding lesions and determined whether bacterial presence in reservoirs was persistent or transient in a longitudinal study. Finally, we explored a novel tattoo-based inoculation method to optimize DD bovine models. DD-Treponema spp. were detected only in DD-affected herds, while non-treponemal anaerobes were widespread in both affected and DD-negative herds. Although all target bacterial species were occasionally detected on healthy skin and in saliva, only Porphyromonas levii and Fusobacterium necrophorum seem to persist in these sites. Despite their detection in environmental samples, we did not detect any of the target species in feces. All target species increased in numbers before lesion onset, with sequential colonization starting with non-treponemes two weeks before DD occurred, followed by DD-Treponema spp. Lastly, the tattooing method showed potential for future use in experimental induction of DD by depositing Treponema spp. at the epidermis-dermis junction; however, we were unable to induce lesions in dairy calves likely due to factors missing in our model. While DD etiology remains undetermined, this thesis supports the key role of Treponema spp. in the disease, offers a change in perspective on the involvement of non-treponemes in lesion initiation, discusses the challenges in reproducing this disease experimentally, and proposes a hypothetical scheme of pathogenesis for this complex disease.Item Open Access Evaluation of Best Practice Guidelines Implementation in an Undergraduate Nursing Curriculum(2024-11-28) Zohra, Hasnani-Samnani; Koh, Kim; Lock, Jennifer; Spring, ErinThis mixed methods study sought to understand the implementation of Registered Nurses Association of Ontario’s (RNAO) Best Practice Guidelines (BPGs) in the undergraduate nursing program in the State of Qatar. The RNAO has disseminated over 50 BPGs on clinical topics and on healthy work environment topics (Melnyk, 2015). All BPGs whether clinical or related to a healthy work environment, are developed to improve patient care and provide easy access to evidence-based research to students, instructors, and practicing nurses (Edwards et al., 2005). For this research, Yrjö Engeström’s (1987) Cultural Historic Activity Theory (CHAT) was selected due to its explanation of the interactions among various participants and factors within the activity system (or environment) towards the achievement of a common goal (Greig et al., 2012). The implementation and evaluation of the RNAO BPGs in the undergraduate nursing program in Qatar required an understanding of interactions and relationships among the various participants. CHAT enabled the researcher to examine these complex relationships. The participants’ experiences with the teaching and learning of RNAO BPGs were explored using a mixed methods approach. Quantitative methods included questionnaires, while qualitative methods consisted of interviews and document analyses. Both methods enabled the triangulation of the findings to gain an in-depth understanding of the RNAO BPGs implementation process. The findings showed that the integration of RNAO BPGs into the undergraduate nursing program successfully strengthened the curriculum through the intentional incorporation of evidence-based guidelines, though there were areas for improvement. Students and instructors were aware of the BPGs but needed more education to incorporate them efficiently and effectively. Moreover, the use of BPGs in courses as evidence-based tools was evident but lacked depth. The guidelines were perceived as lengthy, somewhat outdated, and not inclusive of all topics. However, there was also a lack of awareness among students and instructors regarding the status of updates to the guidelines. There was a perception of bias, with a focus on RNAO guidelines over other evidence-based guidelines and resources. Additionally, there were reports of actual and perceived cultural barriers due to the Western-based examples in some of the guidelines. On the other hand, the review of the guidelines revealed that it was explicitly mentioned to “use the guidelines if culturally appropriate”. The statements by students and some of the experiences shared by the instructors about cultural appropriateness could be interpreted as a sense of being “othered” and the need for the guidelines to be “read” as culturally appropriate. Due to time constraints, an evaluation of the impact of the BPGs on students’ application of guidelines in clinical practice could not be conducted. It is proposed to include an evidence- based practice (EBP) course and a scaffolded approach to integrate EBP teaching, learning, and assessment strategies. This approach is recommended to improve the integration, monitoring, and application of EBP in clinical practice courses using outcome indicators. While the findings are limited to students who participated in the research study, the recommendations will help the participating academic institution refine its strategies as it continues to monitor the implementation process. The findings may also benefit other academic institutions aiming to incorporate RNAO BPGs into their nursing curricula.Item Open Access Molecular characterization of clinically important phenotypes of Staphylococcus aureus in a large cohort of bloodstream infections(2024-12-15) Mapar, Maryam; Lewis, Ian A.; Earl, Ashlee M.; Surewaard, Bas G. J.; Turner, Raymond J.Staphylococcus aureus is known for its ability to thrive in diverse host niches through various adaptive strategies. A key feature of this species is its ability to exhibit various phenotypes, such as the small colony variants (SCVs) and the inoculum effect, both of which are associated with persistent and difficult-to-treat infections. However, our current understanding of these phenotypes mostly comes from studies on relatively small cohorts, with findings that, while valuable, may not fully represent the complexity seen in real-world infections. To address this gap, I leveraged a collection of 7,604 S. aureus samples from a larger study cohort of over 38,000 bloodstream infections (BSIs) collected in the Calgary health zone from 2006 to 2020. Whole-genome sequencing on these isolates was completed at the Broad Institute of MIT and Harvard. Metabolomics and proteomics data were generated using ultra-high-performance liquid chromatography mass-spectrometry (UHPLC-MS) and tandem mass tag (TMT)-labeling LC-MS based analyses, respectively, at the Calgary Metabolomics Research Facility. This uniquely large cohort of isolates, integrated with multi-omics data and administrative health records, provided a great opportunity to reevaluate existing knowledge and deeply investigate the molecular underpinnings of these two clinically important phenotypes. Additionally, from my experience with working in the field of microbial metabolomics I learned that one of the key challenges in studying metabolism in the complex systems is the variability in metabolomic phenotypes across different batches of culture media. To address this, along the way of understanding the molecular underpinnings of SCVs and the cefazolin inoculum effect (CzIE) in S. aureus BSIs, I developed a chemically defined medium—Biomarker Enrichment Medium (BEM)—that not only supports the growth of BSI pathogens (including S. aureus), but also enables antibiotic susceptibility testing and restores key metabolic biomarkers used to differentiate six common BSI pathogens. My thesis has two main biological findings. First, my research on SCVs differs from previous reports regarding phenotypic instability and more severe infections while confirming prior findings related to SCV-linked protein expression patterns. Furthermore, this research has shown a greater molecular diversity underlying the SCV phenotype than previously appreciated, as my genomic analysis identified >300 candidate mutations associated with SCVs. These findings suggest that characterization of SCVs as a single phenotype is a simplification of what they are in real-world infections. Second, my research on the β-lactamase-producing methicillin-susceptible Staphylococcus aureus (MSSA) isolates from the Calgary BSI cohort collected in 2012-2014 and 2019 study did not find a significant association between CzIE and higher mortality rates. However, specific molecular characteristics for the majority of CzIE isolates were identified: clonal complex 30, accessory gene regulatory group III, and type A β-lactamase. Additionally, a novel single nucleotide polymorphism in the bla operon was identified in MSSA isolates exhibiting the non-CzIE phenotype, which led to a disruption in the inducibility of the bla operon in these isolates. Collectively, these studies have provided a deeper understanding of epidemiologic, phenotypic, and molecular characteristics of the SCV phenotype and CzIE in S. aureus BSIs.Item Open Access The role of vector-derived microbiota and co-localization in the dissemination of vector transmitted pathogens(2024-12-16) Melo, Léon; Peters, Nathan; Geuking, Markus; Khan, Nargis; McKay, Derek; Yipp, BryanVisceral Leishmaniasis poses significant challenges to prophylactic vaccination and treatment strategies due to the ability of Leishmania spp. parasites to disseminate from the initial site of infection in the skin to the internal organs following transmission by the bite of an infected sand fly vector. This study investigated the role of inoculation method and the vector, sand fly gut-derived microbiota in modulating the host immune response and facilitating parasite dissemination. Utilizing a novel skin prick model that closely mimics natural sand fly transmission, we explored the influence of sand fly gut-derived (SFGD) bacteria on neutrophil recruitment, IL-1β production, and parasite dissemination in both wild-type and IL-1β-deficient mice. Our findings reveal an enhanced influx of neutrophils IL-1β+ in the early stages of infection, underscoring the importance of vector-derived microbiota in shaping the initial immune response. However, the absence of a significant impact of SFGD bacteria on dissemination or parasite burden challenges the hypothesis and previously published observations that SFGD bacteria facilitate dissemination. While we observed that IL-1β deficiency did not significantly alter parasite dissemination overall, a specific increase in liver burden was observed in IL-1β-/- mice exposed to SFGD bacteria, suggesting a potential liver-specific role of IL-1β in the control of disseminated parasite burden. This study highlights the complex interplay between host, pathogen, and vector-derived factors in Leishmania pathogenesis and opens avenues for further investigation into the molecular mechanisms driving these interactions. Future research should focus on the quantification of the inoculated bacterial load during transmission, the broader impacts of SFGD bacteria on other immune cell populations, the role of the host skin microbiota, and the potential therapeutic targeting of IL-1β to mitigate visceral leishmaniasis.Item Open Access The PROMISE of CRYPTO PROTOTYPE: PLATFORM POWER & CENTRALIZED CRYPTO EXCHANGE PLATFORMS(2024-12-11) McLean, Jenny; Shepherd, Tamara; Karimi, Ali; Hogan, Mél; Elliott, CharleneCentralized crypto exchange (CEX) platforms offer to eliminate the technical barriers to crypto adoption. But how has an industry ostensibly committed to decentralization come to rely on such centralized entities? The literature analyzing CEX platforms through a political economy lens is sparse, and as crypto grows and becomes more interconnected with the traditional finance system, deeper understanding is required. This study explores how centralized CEX platforms (Binance, FTX, and Coinbase) mediate the promises of crypto through the financialization and regulatory logics of platform power, in the context of the entangled technology and venture capital industries. I construct a theoretical framework of platform power framework that captures a set of analytical perspectives on platforms, and I employ a modified stack economization model as a tool to enable a platform power political economic analysis. My findings demonstrate that CEX platforms extract and transform the original visions for crypto to produce the current promise of crypto prototype. They eclipse the neoclassical conception of the market and instead constitute stacked opportunities for financialization, where CEX platform power manifests in power asymmetries premised upon recentralization and extraction. In so doing, CEXs leverage neoliberal discursive strategies in their policy advocacy. Based on these findings, I argue that CEX platforms deploy the promise of crypto prototype to accumulate, benefit from, and perpetuate platform power.Item Open Access “You’ve Got a Friend in Me”- Social Skills and Friendship Building in Adolescents with Attention-Deficit/Hyperactivity Disorder(2024-12-05) Neprily, Kirsten; Climie, Emma; McCrimmon, Adam; Makarenko, EricaAttention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder causing impairment in multiple areas of functioning, including behavioural, emotional, and social abilities. Social skill challenges and poor interpersonal relationships are often found in adolescents with ADHD. Specifically, adolescents with ADHD may struggle with social skills resulting in less friendships, lower friendship quality, and engaging in more inappropriate social behaviours compared to their neurotypical peers. Researchers have promoted the need for long term interventions that not only address social skill development but directly address dyadic friendship making for adolescents with ADHD. One such intervention, the Program for the Education and Enrichment of Relational Skills (PEERS) has the potential to address these challenges. The current study expanded on previous research by examining the effectiveness of PEERS on social skill development and friendship making in adolescents with ADHD in a Canadian context. After inclusionary criteria were applied and data quality were examined, the final sample included 46 participants (23 adolescents and 23 caregivers/parents), with adolescents ranging in age from 13.0-18.1 years of age. The research design involves repeated time points and analyses were conducted using linear mixed models. Participation in PEERS was associated with significant gains in social skills knowledge, formation of a new friendship, increased get togethers, and improved quality of existing friendships at post intervention; these were maintained at follow-up. The results suggest that PEERS may be an effective tool to build adolescents with ADHD’s social skills and improve friendship making, reducing the potential negative outcomes in this population.Item Open Access Cellulose Filaments, A novel Nanocellulose for Advanced Colloidal Applications(2024-12-11) Varamesh, Amir; Hu, Jinguang; Bryant, Steven L.; Roberts, Edward; Lu, QingyeWith growing global awareness of sustainability, environmental protection, and the harmful effects of fossil fuel-derived materials, biorenewable sources, such as nanocellulose, have gained considerable attention over the past decades. This thesis explores the potential applications of a less studied yet more economically viable and scalable form of nanocellulose, cellulose filaments (CFs). Specifically, the thesis investigates CFs' role in different colloidal systems including emulsion stabilization and the development of aerogels for water treatment and fire-retardant thermal insulation. The application of CFs in oil in water Pickering emulsion stabilization was explored and compared with conventional nanocellulose including cellulose nanofibrils (CNFs) and TEMPO-oxidized CNFs (TEMPO-CNFs), and nanocrystals (CNCs). Emulsion stability analysis revealed that CFs outperform CNCs and TEMPO-CNFs in forming stable emulsions. Investigations into the stabilization mechanism suggest that the superior performance of CFs is likely due to the high viscosity of the aqueous phase and the formation of an entangled network of fibrils within the continuous phase. Furthermore, CFs exhibit strong adsorption at the oil-water interface, providing enhanced emulsion stability under environmental stresses such as varying pH (2–10) and ionic strength (0–500 mM NaCl). These findings indicate that CFs are a promising nanocellulose for the sustainable and cost-effective formulation of stable Pickering emulsions, with potential applications across a wide range of industries. The application of CFs in creating fully biobased aerogels (FBAs) for water treatment and fire-retardant thermal insulation was also explored. CFs, combined with chitosan (CS) and citric acid (CA), were used to develop mechanically robust composite aerogels. The resultant aerogels were tested for their ability to remove three major water pollutants: dyes, heavy metals, and oil/organic solvents. Due to the unique structure and the abundance of active sites provided by the biobased composite system, the aerogels exhibited exceptionally high adsorption capacities for methylene blue (619 mg/g) and copper (206 mg/g). Surface modification through silanization rendered the FBAs highly efficient for oil-water separation, achieving over 96% separation efficiency. Additionally, the FBAs demonstrated excellent reusability, recyclability, and antibacterial properties, making them an ideal adsorbent for water treatment applications. Finally, the application of the developed FBAs was extended to fire-resistant thermal insulation via layer-by-layer (LBL) assembly using oppositely charged biomaterials, namely phytic acid and chitosan. Aerogels with six bilayer depositions (LBL6) exhibited an outstanding peak heat release rate (pHRR) of 6.0 kW·m−2 and a total heat release (THR) of 0.4 MJ·m−2, significantly lower than previously developed cellulose-based aerogels and foams. LBL6 also demonstrated immediate self-extinguishing behaviour with an impressive limiting oxygen index (LOI) of 63%, the highest reported for a biobased aerogel. Furthermore, the aerogels showed a superior Young’s modulus of up to 4.5 MPa, outperforming other flame-retardant aerogels, and exhibited excellent thermal insulation properties, with a thermal conductivity of less than 38.2 mW·m−1·K−1, on par with or even better than commercial thermal insulators. Given the simplicity of the fabrication process and the inherent benefits of a fully biobased system, these aerogels represent a sustainable and environmentally friendly alternative to current petroleum-based thermal insulators.Item Open Access Stress in the Aftermath of Psychological Contract Disruption: An Integration of Cognitive Activation Theory and Psychological Contract Theory Dynamics(2024-12-11) Jones, Samantha K.; O'Neill, Thomas A.; Hansen, Samantha D.; Turner, Nicholas; Zweig, David; Willness, Chelsea R.; Cronin, Matthew A.The psychological contract (PC) represents the mental schema an employee has about what they are obligated to provide to their organization (e.g., performing in-role duties) and what their organization is obligated to provide in return (e.g., fair pay). When employees perceive that their organization has not provided what is obligated to them and has impeded their personal goals, they experience a negative PC disruption. Negative PC disruptions are known to cause stress and negative affect and are associated with poor mental and physical health over time. However, previous theorizing and empirical investigations have under-represented the role of system dynamics in understanding how these relationships evolve over time. This dissertation describes two stand-alone papers that extend previous PC and stress theorizing through a system dynamics lens. Chapter 2 presents a theoretical integration of PC and stress dynamics and proposes a System Dynamics Model of Negative Affect and Stress, supported by 17 testable propositions. The model highlights key factors that influence the inflow (i.e., history of PC disruption, stimulus expectancies) and outflow (i.e., individual and organizational actions, outcome expectancies) of stress and negative affect and how these factors influence the experience of PC disruption over time. This model sheds light on how the PC evolves in response to changes in stress and negative affect and provides a framework for better understanding how individuals and organizations can support healthy employment relationships. Chapter 3 then presents an experimental vignette study (N = 356) that empirically tests a subset of propositions from Chapter 2. More positive outcome expectancies (compared to negative outcome expectancies) were associated with lower reports of anticipated stress and negative affect. Participants’ self- reported rumination did not appear to alter anticipated stress and negative affect across experimental blocks. Findings demonstrate the importance of employees’ beliefs about what can be done to repair the PC and encourage further exploration of factors like rumination that can alter stress and negative affect recovery. Theoretical and practical implications, as well as future research directions and challenges, are discussed.Item Open Access Strongly Linearizable LL/SC from CAS(2024-12-06) Naderi Semiromi, Fatemeh; Woelfel, Philipp; Eberly, Wayne; Censor-Hillel, KerenLinearizability is the standard correctness condition for shared memory algorithms and is generally considered to be the practical equivalent of atomicity for deterministic algorithms. However, Golab, Higham, and Woelfel [16] showed that if we replace atomic objects used in a randomized algorithm with their linearizable implementations, then some of the properties of the algorithm may be lost. They introduced a stronger correctness condition, called strong linearizability, and proved that strongly linearizable objects can be used in both deterministic and randomizes algorithms as if they were atomic. In this thesis, we present an efficient strongly linearizable implementation of the load-linked/ store-conditional (LL/SC) primitive from compare-and-swap (CAS) objects. Our algorithm has constant step complexity, and uses a bounded number of CAS objects and registers that can each store O(log n) bits, where n is the number of processes. To the best of our knowledge, we are the first ones introducing a constant-time strongly linearizable LL/SC implementation, which uses bounded memory and bounded word-size.Item Open Access Theaetetus and the Making of a Philosopher: Character and the Nature of Philosophical Discussion in Plato's Theaetetus(2024-12-07) Kerklaan, Nicholas; Migotti, Mark; Inwood, Brad; Burch, Robert; Hume, James; Fantl, JeremyTraditional approaches to Plato’s Theaetetus have it that it is only, or at least primarily, about knowledge. Yet large sections of the dialogue, including the so-called “Digression” of 172c-177c, do not appear to be concerned with knowledge at all, but with the nature of the philosopher and the activity the philosopher engages in, i.e. philosophical discussion. I offer a reading of the Theaetetus that proceeds from the assumption that the inclusion of such material suggests that the dialogue is also about philosophy and the philosopher, and I find such concerns in fact present throughout both explicitly and implicitly. On my view, the dialogue is both dramatically and philosophically a portrayal of the philosophical progress of Theaetetus, whose first encounter with philosophical discussion, when Socrates asks him if he can help find what knowledge is, not only demonstrates that he has, but draws out and develops in him, an essentially philosophical character – where to be “philosophical” is much more than to just be adept with arguments or quick to come up answers to philosophical questions, but to be willing to try out answers to such questions without attachment to them, to learn from the shortcomings of previous attempts, and ultimately to have a certain kind of orientation toward the world.Item Open Access Towards Precision Measurements of the Hyperfine Splitting of Antihydrogen(2024-12-04) Suh, Jay Hyung; Friesen, Timothy; Barzanjeh, Shabir; Oblak, Daniel; Orlandi, JavierThe observed asymmetry between matter and antimatter in our universe remains to be one of the foremost mysteries that contradicts our current theories of physics. The search for possible causes of the asymmetry lies at the leading edge of experimental particle physics, with experiments around the world dedicated to the study of antimatter. The study of the antihydrogen atom, the antimatter analogue to the hydrogen atom, is the primary motivation of the ALPHA Collaboration based at CERN. Through detailed observations and measurements of the antihydrogen atom structure, we can draw comparisons with the well-known structure of the hydrogen atom and search for possible asymmetries between matter and antimatter. The hyperfine structure of antihydrogen is both sensitive to fundamental interactions and has been measured to a high precision in hydrogen, making it a prime candidate for study. Any observed discrepancy between the hyperfine structure of hydrogen and antihydrogen would be a pivotal discovery and advancement in our understanding of the universe. This thesis will describe the measurement of the hyperfine splitting of antihydrogen performed by ALPHA, with the aim of providing an improved result and precision to previously published values [1]. It will briefly include a historical review of antimatter, then will discuss the theory behind the hyperfine structure, the various apparatuses used by the ALPHA Collaboration to produce, confine and manipulate antimatter particles, and the experimental procedure used to perform this measurement. I also demonstrate the usage of electron cyclotron resonance (ECR) to provide precise measurements of the magnetic field used to trap the antihydrogen atoms. I will summarize my work done on the hyperfine splitting and ECR measurements performed over the last two years, and present details regarding my work quantifying some of the prominent systematics of the experiment.Item Open Access Exploring Barriers to, and Facilitators of, Diabetes Self-Management Among Patients with Kidney Failure Receiving Dialysis(2024-12-05) Younis, Kokab; McCaffrey, Graham; Quinn, Rob; King-Shier, Kathryn; Raffin Bouchal, ShelleyDiabetes mellitus is the leading cause of kidney failure in Canada and around the globe. The treatment of kidney failure may require dialysis - a life-sustaining therapy. Dialysis therapy places significant demands on patients, adding an extra health burden for those navigating the transition to living with chronic diseases. It is well reported in literature that dialysis patients with diabetes compared to those without diabetes have poorer quality of life, longer lengths of hospital stay, a higher burden of morbidity and mortality, and significantly higher economic costs. However, literature on barriers to, and facilitators of, optimal self-management of diabetes are scant in patients with kidney failure. The aim of this thesis work was to understand, describe and interpret the perspectives of patients on barriers to, and facilitators of, diabetes self-management. A narrative review and interpretive descriptive qualitative study were undertaken to address the study aim. Semi-structured interviews with fourteen patients were conducted. A total of 134 articles were identified whereas eight articles met our inclusion criteria. A review of the articles and qualitative study revealed barriers to and facilitators of diabetes self-management. Emerging themes from the included studies and semi-structured interviews were identified using inductive thematic analysis. Barriers reported by participants were financial and physical limitations, limited access to healthcare services, siloed and fragmented care, increased medical complexity, and the higher burden of health. Facilitators of diabetes self-management were self-management support and education, coordinated care between healthcare providers, and supportive environments. Findings from this thesis work contribute to a broader scientific literature, facilitate further research in this domain to address barriers, and guide resource allocation concerning the improvement of diabetes care and self-management practices among patients with kidney failure on dialysis therapies.Item Open Access MOLECULAR INTERACTIONS OF NK CELL CYTOTOXIC GRANULE TRAFFICKING DURING ANTIFUNGAL ACTIVITY(2024-12-04) Mok, Adley Ching Ho; Mody, Christoher H.; Peters, Nathan; Ganguly, AnutoshCryptococcus neoformans is a fungal pathogen that causes life-threatening meningitis and pneumonia, particularly in immunocompromised hosts. Natural Killer (NK) cells are critical in the host defence against this pathogen acting by contacting fungal cells and triggering cell death by releasing cytotoxic effector molecules. Movement and positioning of the granules to the membrane during this process involves mechanical steps wherein granules laden with the effector proteins traverse the microtubule tracks using motor proteins (kinesins and dyneins). However, granule trafficking in response to fungal cells differs from the movement of granules during NK cell killing of tumour cells. During the final stages of fungal killing, immediately before degranulation, the microtubule organizing centre is positioned some distance from the synapse with the fungal cell, and granules are positioned between the Microtubule Organising Center and synapse. I explored the possibility that a kinesin transports the granules to the plasma membrane before release. I found that kinesin-1 is expressed in NK cells and kinesin-1 is required for granules to polarize and maintain its polarized position for degranulation against C. neoformans. This unique granule trafficking mechanism in response to fungal cells suggests a specialized adaptation for antifungal immunity. The positioning of granules between the Microtubule Organizing Center and the synapse may allow for more precise targeting and efficient release of antifungal agents. The identification of kinesin-1 as a key player in this process provides valuable insight into the molecular machinery underlying NK cell-mediated fungal killing.Item Open Access The role of phenotypic plasticity in threespine stickleback (Gasterosteus aculeatus) adaptation to thermally variable habitats(2024-12-06) Stanford, Brenna Callista Moreau; Rogers, Sean; Jamniczky, Heather; Morris, MatthewPhenotypic plasticity, the ability of a genotype to give rise to multiple phenotypes dependent on environmental cues, is a well-established phenomenon that allows organisms to rapidly modify their phenotype in response to environmental change. It has been recommended that phenotypic plasticity be included in predicting population and species’ response to climate change. However, there remains substantial debate regarding its role in population persistence, adaptation, and evolutionary theory. While phenotypic plasticity occurs at all biological levels, it is largely driven by changes in gene regulation, and it has been suggested that resolving these molecular mechanisms will facilitate its integration into studies of adaptation and evolution. In this thesis, I use threespine stickleback (Gasterosteus aculeatus) to investigate how evolution has shaped reversible (i.e., phenotypic flexibility) and irreversible (i.e., developmental plasticity) plastic responses to temperature, a key abiotic environmental variable. To do so, I first tested if local adaptation to freshwater habitats has altered plasticity within key biological pathways by comparing gene expression of freshwater and marine ecotypes acclimated to cold or warm temperatures. Using Weighted Gene Co-expression Network Analysis, I found evolutionary conserved and divergent responses between the ecotypes, with freshwater stickleback having evolved increased thermal plasticity in several gene modules. I then determined that marine stickleback exhibit substantial developmental plasticity induced by egg temperature that persists into adulthood, over a year after the thermal stressor was removed. The effect of developmental temperature was found in both liver and muscle tissue, however, each tissue type exhibited distinct patterns of gene expression and thermal plasticity. At the whole organism level, egg developmental temperature was found to significantly alter the lower critical thermal limit in all families in the direction cued (i.e., eggs developed at cool temperatures had decreased lower critical thermal limit). The upper critical thermal limit showed inconsistent patterns of plasticity across families but was found to already be higher than temperatures predicted under climate change scenarios. Collectively, these data illustrate that organisms exhibit thermal plasticity from the molecular to whole organism level and that these responses have been shaped by evolution to generate the current patterns of plasticity that will underlie species’ response to future conditions.Item Open Access Development of Novel Automated Methods for Quantitative Analysis of Bone with High-Resolution Peripheral Computed Tomography and Application to Investigate Bone Changes Following ACL Injury(2024-12-02) Neeteson, Nathan John; Boyd, Steven Kyle; Edwards, William Brent; Walker, Richard Edward Allan; Forkert, Nils Daniel; Kazakia, Galateia J.Knee osteoarthritis (OA) is a prolific and devastating disease. The processes leading to the development of OA are poorly understood, but periarticular bone adaptations are theorized to play an important role. High-resolution peripheral quantitative computed tomography (HR-pQCT) can resolve human bone microarchitecture in vivo, and is uniquely suited to investigate these hypotheses. This thesis develops automated methods for quantifying bone microarchitecture at the knee with HR-pQCT. First, a deep learning workflow is developed for segmenting bone compartments in HR-pQCT images of the distal radius and tibia using data from a large normative cohort, achieving excellent accuracy and equal or better precision than the established semi-automated workflow. Building on this, a deep learning algorithm for segmenting subchondral and trabecular bone in HR-pQCT images of the knee is developed using similar methods and an atlas-based segmentation workflow is developed for automatic contact surface identification, again achieving excellent accuracy and improved precision compared to the established workflow. Separately, a large dataset is leveraged to analyze the statistical and geometric interdependence of four parameters that quantify trabecular microarchitecture, and evidence is found that these four parameters represent only two true degrees of freedom, with important implications for inferential testing and study design. Next, an alternative, model-based method for measuring cortical thickness and subchondral bone plate thickness on HR-pQCT is developed by reformulating Cortical Bone Mapping as a global optimization with spatial regularization of fitted parameters. Finally, methods developed herein are applied to study the one-year changes in periarticular bone microarchitecture in the knee following both ACL injury and surgery. The main effects for the injured side are consistent with theory, but the contrasts for OA risk factors are not significant while contrasts for baseline microarchitectural factors are. This evidence suggests that the effects of OA risk factors on OA pathogenesis may be mediated through the state of the microarchitecture at the onset of OA development, rather than directly impacting tissue changes that lead to OA from a common baseline state.Item Open Access Remote Sensing of Monitoring Forest Fire Dynamics in Near/Ultra Real Time(2024-12-04) Bhuian, Md Hanif; Hassan, Quazi Khalid; Hassan, Quazi Khalid; Billah, Muntasir; Ahmed, Mohammad RazuForest fires cause extensive environmental damage, significant carbon emissions, and economic losses, posing major challenges for disaster management and emergency response. Accurate and timely delineation of fire perimeters is essential for minimizing these impacts. The overall aim of this study was to develop an early forest fire monitoring model that enables automatic clustering of active fire points and precise delineation of fire perimeters using satellite-based active fire data from VIIRS and MODIS datasets. Various algorithms—buffer, concave, convex, and combination methods—are assessed for their efficiency in near real-time (NRT), real-time (RT), and ultra-real-time (URT) fire perimeter delineation. Additionally, this study also introduced the automated Timely Active Fire Progression (TAFP) model for clustering and calculating active fire perimeter consistently. The results indicate that increasing the concave α (alpha) values (e.g., 0.1 to 0.5) enhances the matching percentage with ground fire areas but also leads to higher commission errors, signifying a risk of overestimation. Combination methods achieved the highest matching percentages but were also associated with increased commission errors. However, the TAFP model demonstrated an 85.13% matching rate for fire perimeters across various size classes, with a 95.95% clustering accuracy for fires larger than 100 hectares. This research was the first to scientifically evaluate multiple algorithms, both individually and synergistically, using NRT/RT/URT active fire data. The insights gained underscore the trade-offs between enhancing perimeter accuracy and avoiding overestimation, providing a critical foundation for optimizing sensor data alignment techniques. By improving the timeliness and accuracy of forest fire monitoring, the proposed models can significantly bolster operational responses by fire management agencies, aiding in resource allocation, evacuation planning, and mitigation strategies. This study lays the groundwork for future advancements in automated forest fire perimeter assessment, essential for effective disaster management and rapid response efforts.Item Open Access Exploring the Experiences of Black Muslim Women in Alberta Emergency Departments: An Interpretive Description Study(2024-12-04) Ali, Asmaa; dela Cruz, Aniela; Jackson, Jennifer; Venturato, LorraineBackground: Black Muslim women have a unique set of religious and cultural beliefs that impact how they receive healthcare. A growing body of literature on health equity suggests that gaps in healthcare providers’ systemic, social, and cultural awareness of the unique needs of diverse patient populations can add to poor patient health outcomes. Aim: This research project aims to explore how race, faith, and gender impact Black Muslim women’s experiences receiving care in emergency departments (EDs) in Alberta. Methods: Six Albertan Black Muslim women who self-reported a personal ED visit within the last five years were interviewed, and data were analyzed using qualitative interpretive description methodology. Findings: Participants described patient-provider relations as strained due to communication challenges rooted in past experiences of racism and distrust in the healthcare system. Further, participants’ race, faith, and cultural needs in a healthcare setting fundamentally impacted their ED care experience. Lastly, participants highlighted that healthcare system challenges such as lack of access to family physicians across the province, long wait times, and rural barriers to care were exceedingly difficult to navigate when compounded with past experiences of discrimination. Discussion: This study provides insight for healthcare professionals on the experiences of Black Muslim women who present to the ED. Using the Population Health Promotion Model (Hamilton & Bhatti, 1996) as a framework, I located and analyzed the findings of this study in the context of the social systems and determinants of health that impact Black Muslim women. Discussing the findings from a health promotion perspective highlights the barriers and challenges Black Muslim women face. Further, it supports knowledge translation to practically inform clinical best practices and health promotion initiatives for this population.