Restricted Theses and Dissertations
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Item Embargo Electrolysis using Solid Oxide Cells: From CO2 Splitting to CO2/H2O Co-Electrolysis(2025-06-09) Pidburtnyi, Mykhailo; Birss, Viola Ingrid; MacCallum, Justin; Dolgos, Michelle; Trudel, Simon; Lu, Qingye; O'Hayre, RyanThe electrochemical performance, structural stability, and catalytic behavior of La0.3Ca0.7Fe0.7Cr0.3O3-δ (LCFCr), a mixed ionic-electronic conducting perovskite oxide, were systematically investigated for solid oxide electrolysis cell (SOEC) applications. Particular focus was placed on the CO2 reduction (CO2RR), H2O reduction (HER), and oxygen evolution (OER), as well as the viability of LCFCr as a single-phase, symmetrical electrode catalyst for co-electrolysis. Electrochemical characterization of LCFCr in a three-electrode configuration under 90:10 CO2:CO and air at 700–800 °C revealed distinct reaction pathways and rate-limiting steps for both the CO2RR and OER, occurring at the double-phase boundary. A notably long conditioning period also suggested a gradual structural or redox change of the material. Structural studies of LCFCr under CO2:CO mixtures revealed a gradual phase transformation to an oxygen-deficient, ordered brownmillerite phase (BM-LCFCr). This transition, driven by oxygen loss and changes in the Cr and Fe oxidation state, was found to be largely irreversible but resulted in a structurally stable phase with excellent long-term catalytic activity. This newly identified BM-LCFCr phase was likely active in prior studies but remained undetected due to its subtle structural differences from the parent perovskite. Further testing demonstrated that LCFCr exhibits nearly identical electrochemical activity for both the CO2RR and HER, achieving consistent syngas production in the co-electrolysis mode, with the output product composition directly reflecting the feed gas ratio, confirming the suitability of the LCFCr for tunable syngas generation. Computational modeling also revealed similar adsorption steps for CO2 and H2O, potentially explaining the comparable catalytic behavior. Finally, the role of Au current collectors was examined, showing that even "inert" materials can induce irreversible interfacial changes to the contacted metal oxides under reducing bias. This highlights the need for careful consideration of current collector–catalyst interactions in SOEC design. Overall, this work provides a comprehensive understanding of the structural evolution, electrochemical behavior, and suitability of LCFCr for high-temperature CO2 and H2O electrolysis. By linking reaction mechanisms to catalyst structure and operating conditions, this thesis offers valuable insights for the rational design of stable and efficient perovskite-based electrodes for next-generation SOEC systems.Item Embargo From Association to Causation: Deep Learning Approaches for Imaging Genetics(2025-06-06) Dagasso, Gabrielle Christina; Forkert, Nils; MacEachern, Sarah; de Koning, JasonPersonalized medicine is becoming increasingly viable due to the explosion in acquisition and availability of data in health care. For example, in the last twenty years, science has moved from sequencing the first human genome to sequencing full genomes for large number of patients at a much cheaper cost. Technological advancements are not limited to genomics, and big datasets are also emerging in areas like radiomics (anatomical and functional imaging), among other big "omics" datasets. Genomics data in tandem with these radiomics, have the potential to enable better phenotype predictions (traits such as disease status) and more precise genotype-phenotype association analyses. However, it is challenging to combine both data modalities because of their size and complexity. Thus, it remains an open question how such complex imaging and genetic/genomic data can be effectively used and combined in traditional setups, like genome-wide association studies, as well as novel deep learning models. Therefore, the overarching goal of this work is to develop advanced dimensionality reduction techniques for imaging data and explore how best to handle genomic data in deep learning setups as well as to investigate novel classification and a causal deep learning method for combining imaging and genetic/genomic data. More precisely, a novel localized principal component analysis approach was developed to enable full-brain magnetic resonance imaging integration into a genome-wide association study, revealing new genotype-phenotype associations. Moreover, it was found that uncorrected genetic data may lead to biased deep learning models due to related ancestry. Aiming to combine the two data modalities into deep learning models, an intermediate fusion model for Parkinson’s disease was shown to achieve improved classification results, especially when considering specific genetic subtypes. Finally, a causal deep learning framework was developed and was shown to enable counterfactual simulations, known as `digital twins', of effects of allele alteration on downstream observed endophenotypes. Overall, this research has the potential to advance personalized medicine through advanced genotype-phenotype fusion and analysis.Item Embargo Tailoring Particle-Polymer Interfaces for High-Performance Solid Electrolytes: A Multi-Scale Investigation of Structure and Ionic Transport(2025-06-04) Bobrov, Gleb; Trifkovic, Milana; Hu, Jinguang; Karan, Kunal; Ponnurangam, Sathish; Birss, Viola; Adams, StefanComposite solid polymer electrolytes (CSPEs) offer a promising pathway toward safe, high-energy-density lithium-ion batteries by replacing flammable liquid electrolytes and supporting the use of lithium metal anodes. However, understanding how nanoscale structure affects ionic transport, and long-term stability remains an outstanding challenge. This thesis presents a multi-scale investigation of CSPEs, uncovering how polymer–salt interactions, nanoparticle–polymer, and particle–particle interactions collectively influence mesoscale morphology, bulk structure, ionic transport, and electrochemical performance. The impact of nanofillers on polymer crystallization is investigated using TEMPO-oxidized cellulose nanofibrils (t-CNF) in poly(ethylene oxide) (PEO) matrices of varying molecular weight. In low-molecular-weight PEO, t-CNF is incorporated between lamellae within spherulites, while in high-molecular-weight PEO, the strong nanofiber network arrests the spherulitic growth into non-equilibrium cubic shapes. Electrochemical strain microscopy (ESM) and solid-state NMR confirm that t-CNF does not directly contribute to Li⁺ transport; however, its effect on morphology and crystallinity significantly impacts dendrite resistance, mechanical stability, and long-term cycling. The role of lithium salt chemistry on local conduction pathways is also examined using current-sensing atomic force microscopy (CS-AFM). In the presence of LiClO₄, PEO undergoes rapid crystallization and spherulitic growth, which causes salt to be expelled from the crystalline regions. This results in strong spatial heterogeneity in local salt distribution and ionic conductivity, creating regions with poor transport that contribute to interfacial instability and reduced long-term battery performance. In contrast, LiTFSI, a strong plasticizer, suppresses crystallinity, yielding a more amorphous and uniform microstructure with homogeneous ion transport and improved stability. To enhance ionic conductivity, directional structuring is employed as a strategy to reduce transport tortuosity. Uniaxial stretching of PEO-based systems reveals that long-range alignment of crystalline domains and polymer chains is only achievable in systems with sufficient baseline crystallinity, such as those containing LiClO₄. In contrast, highly plasticized LiTFSI-based systems exhibit predominantly amorphous morphology that prevents effective alignment. At 20 wt% loading, t-CNF forms a percolated nanofiber network that kinetically traps the stretched, far-from-equilibrium morphology, even after thermal cycling. Confocal microscopy confirms that alignment becomes fully developed beyond 450% strain, correlating with a threefold improvement in through-plane conductivity and stable lithium cycling with reduced overpotentials. Informed by these insights, a scalable, single-step CSPE fabrication approach is developed using PEO, LiTFSI, lithium aluminum titanium phosphate (LATP), t-CNF, and asphaltene-derived carbon dots (ACDs). ACDs act as dual-function additives: forming a protective interface around LATP particles to prevent their degradation during cycling and enhancing LATP dispersion within the polymer matrix. Together with t-CNF, ACDs help maintain a percolated LATP network, reduce polymer–ceramic interfacial resistance, and improve mechanical robustness. The resulting CSPE achieves a room-temperature ionic conductivity of 2 × 10⁻⁴ S cm⁻¹, a lithium transference number of 0.75, and 99.8% Coulombic efficiency over 500 cycles at 0.2 C in a LiCoO₂|CSPE|Li full cell. These performance metrics are achieved without sintering, liquid additives, or interfacial modification layers.Item Embargo Navigating the Third Space: Exploring Stories of Intercultural Competence Development and Use Among Canadian International Teachers in China(2025-06-04) Kersey, Jacalyn Elizabeth; Dressler, Roswita; McDermott, Mairi; Roy, SylvieThis study focuses on the development and use of intercultural competencies among Canadian international teachers who have worked in complex intercultural settings in China. Using a narrative inquiry approach, the research examines the lived experiences of four participants, highlighting their navigation of cultural differences. Guided by the question—What do the narratives of Canadian international teachers’ experiences navigating complex intercultural situations in China reveal about the development and use of intercultural competencies? —this study examines the stories of teachers who remained in China beyond their initial two-year employment contracts. Third space serves as the conceptual framework to describe and analyze the intercultural complexities within international classrooms. Participant narratives highlight three key themes: frames of reference shift, symbolic competence, and critical cultural awareness. These competencies do not emerge in a linear progression but interact recursively, shaping how educators mediate cultural differences. The findings emphasize the role of critical reflection, reflexivity, and lived experience in intercultural competency development, revealing a dynamic and reciprocal relationship between these competencies and Third Spaces. This study concludes by discussing broader implications for teacher preparation, international school retention strategies, and avenues for further research.Item Embargo Unconditional Verification of Unit Groups of Number Fields(2025-06-03) Yee, Randy Keit-Meng; Jacobson, Michael, Jr.; Tran, Ha T. N.; Bauer, Mark L.; Nguyen, Dang Khoa; Scheidler, Renate; Hamieh, AliaOne of the main computational problems in algebraic number theory is that of determining a set of fundamental units, which is an explicit sets of generators for the unit group of a number field. Data of this nature is often valuable in helping to develop, refine or prove conjectures, with large-scale projects, such as the L-Functions and Modular Forms Database, dedicated to advancing related computations and ensuring accessibility of information. Current state-of-the-art methods for computing sets of fundamental units rely on the Generalized Riemann Hypothesis (GRH) for their correctness. Although widely believed to be true, there are certain applications in which the data must be unconditionally correct, and cannot rely on any unproved assumptions. This thesis considers the task of unconditionally verifying unit groups of arbitrary degree number fields by removing GRH-type assumptions. Our contributions include a detailed comparison of the known methods for unconditional unit verification, with novel analyses of precision requirements and asymptotic complexity. Furthermore, we introduce a new algorithm referred to as \textsf{Hybrid}, which is asymptotically faster than previous unconditional methods. All relevant algorithms were implemented fully in Pari/GP, and empirically tested to compare their performance in number fields of varying signature and discriminant size. Our experiments demonstrate that the \textsf{Hybrid} algorithm is effective in practice, and outperforms existing methods in a number of low rank signatures.Item Embargo Investigating tumor intrinsic mechanisms of resistance to targeted immunotherapies in multiple myeloma(2025-06-02) Lee, Holly Yeo Jin; Bahlis, Nizar Jacques; Santamaria, Pere; Mahoney, DouglasT cell based immunotherapies, including chimeric antigen receptor (CAR) T cells and bispecific T cell engagers (TCEs) targeting B cell maturation antigen (BCMA) or G protein–coupled receptor, class C, group 5, member D (GPRC5D), have demonstrated high response rates in patients with relapsed refractory multiple myeloma (MM). However, these responses are not universal, and relapse remains inevitable for most patients, highlighting an urgent need to understand and overcome mechanisms of resistance. This thesis identifies antigen escape as the dominant tumor-intrinsic mechanism of acquired resistance to TCEs, present in >50% of relapses following anti-BCMA or anti-GPRC5D TCE therapies. Longitudinal multi-omic profiling of primary tumor samples reveals both epitope-selective mutations and complete loss of target antigen expression, often through convergent evolution. This raises the possibility that immune evasion in MM may arise through functionally convergent but genetically divergent subclones, shaped by both local microenvironmental factors and therapy-induced selective pressure. To functionally map key resistance determinants, I performed a comprehensive alanine-scanning mutagenesis screen of the BCMA extracellular domain, identifying critical residues required for TCE binding and surface stability. Single amino acid substitutions on BCMA differentially impair TCE cytolytic activity, depending on epitope specificity and valency. These findings establish a mechanistic rationale for sequential or combinatorial use of BCMA-targeted agents based on epitope coverage. In contrast, primary resistance to TCEs is driven by a distinct immune context, including low effector (T cell) to target (tumor cell) ratio and elevated soluble BCMA, which collectively create a state of immunologic insufficiency that limits initial T cell cytotoxicity. These findings suggest that early resistance reflects quantitative failure of immune engagement, whereas acquired resistance reflects qualitative evolution of immune escape clones. Together, this work provides biological underpinnings of TCE resistance in MM, highlighting immune context and antigen evolution as distinct but interdependent determinants of therapeutic failure. It generates a new conceptual framework in which multi-clonal antigen escape is not merely a late event but a potentially predictable evolutionary outcome under strong immunologic selection. These insights inform the rational sequencing of targeted therapies, support the development of multi-epitope strategies, and underscore the need for patient-specific approaches to immunotherapy.Item Embargo Trajectories of Maternal Pain and Mental Health: Associations with Child Brain Microstructure at 2-years(2025-06-02) Jessa, Jenna; Miller, Jillian Vinall; Lebel, Catherine; Kopala-Sibley, DanielChronic pain and mental health conditions are a growing epidemic. Normal pregnancy may give rise to recurrent, or constant pain, which may persist into the postpartum. Pregnant individuals with worse pain symptoms are more likely to report symptoms of anxiety and depression during the perinatal period, which may have implications on their labour and delivery. Maternal chronic pain persisting into the postpartum may also have profound impacts on maternal and child wellbeing. However, in the context of pregnancy and the postpartum, much is unknown about pain experience, the link between anxiety and depression, and pain experience, or the association between maternal pain incidence and child neurodevelopment. This thesis leveraged data from two longitudinal cohorts, the first of which was collected prior to the COVID-19 pandemic, and the second of which was initiated at the onset of the pandemic. Latent class mixed modelling was utilized to identify trajectories of maternal pain and mental health symptomology during pregnancy and into the postpartum, adaptive lasso and imputation were used to identify significant predictors of trajectory membership, and diffusion tensor imaging was used to assess white matter differences associated with maternal pain in children aged 2-years. In the pre-pandemic cohort, a single trajectory of pain intensity, 2 trajectories of pain catastrophizing, 2 trajectories of anxiety, 2 trajectories of depression and 3 trajectories of pain interference were identified. Individual associations with worse pain symptomology and mental health trajectory membership included baseline symptoms of anxiety, depression, insomnia, and pain symptomology. In the cohort recruited amidst the COVID-19 pandemic, 3 trajectories of pain intensity were observed, with anxiety and depression identified as significant risk factors for chronic pain incidence. Differences in child white matter microstructure were associated with maternal chronic pain incidence at 2-years postpartum. This work highlights heterogenous maternal pain and mental health experiences throughout pregnancy and the postpartum, with possible impacts on child neurodevelopment. Identifying mothers at risk for experiencing prenatal and postpartum pain and mental health symptomology could aid in improving pain assessment in this population and developing targeted treatment strategies to prevent mothers and their children from deleterious impacts of chronic pain.Item Embargo Posthumanism and After: The Human and the Non-human in Fiction from Bengal(2025-06-02) Som, Tathagata; Vanek, Morgan Erin; Srivastava, Aruna; Forlini, Stefania; Xie, Shaobo; O'Brien, Susie; Dolata, PetraThis dissertation examines the representations of the relationship between the human and the non-human in contemporary fiction from Bengal. Over the last three decades, academic enquiries into humans’ relations to their physical environment, at least in the humanities and the social sciences, have been increasingly informed by posthumanism, a theoretical paradigm associated with Bruno Latour, Rosi Braidotti, and Jane Bennett. Posthumanism challenges the privileged position of the human in Enlightenment discourses and argues for the dissolution of the boundary between the categories of the human and the non-human. But posthumanism has also received criticism from postcolonial, decolonial, Indigenous, and Marxist scholars for the perpetuation of Eurocentrism and the depoliticization of the environmental movement. Posthumanism and After joins these critiques of posthumanist thinking by intervening in discourses about the relations between the human and the non-human from the disciplinary position of literary studies. Questioning the universality with which posthumanist thinkers insist on the human as a privileged category, this dissertation contends that the categories of the human and the non-human remain relevant tools to investigate socio-economic power relations – even as science shows us that the boundary between the two categories is porous. Beginning with the Anglophone novels of Amitav Ghosh in the first chapter, I move on to Bengali-language novels and short fiction by Sunil Gangopadhyay, Sadhan Chattopadhyay, Anita Agnihotri, and Mahasweta Devi in the following three chapters. Through my examinations of these texts, I argue that writers from Bengal use the relationship between humans and non-humans as a means to critique colonial and capitalist systems that thrive on the exploitation of humans and the destruction of the environment. Thus, this dissertation insists that to better address the intertwined social and environmental justice issues the world faces in the twenty-first century, we need a more nuanced understanding of the social, material, and natural forces that shape the relationship between the human and the non-human.Item Embargo Assessing Surface Water Dynamics of Young Boreal Wetlands with Satellite Based Remote Sensing(2025-05-21) Biederstadt, Erik; Samavati, Faramarz; Runions, Adam; Bonnell, TylerWetland landscapes are important ecological environments that provide many valuable ecological and socio-economic functions including water management and filtration, habitat provision for many plants and ani-mals, sources for tourism and recreation, and sources for peat and timber for industrial applications. Wet-lands are also under threat from factors such as climate change, industrial activity and development, and urban development. Many wetland restoration projects are underway to reclaim and restore damaged land-scapes to their previous state, but methods to evaluate the success of these reclamation activities need to be developed. Additionally, there is the need to compare and contrast these reclaimed landscapes with natural wetlands. In this thesis we present a comprehensive framework for evaluating and measuring water and vegetation dynamics in young wetlands using satellite based remote sensing. We use a combination of optical and radar imagery, and we approximate imagery obscured by clouds or shadows where appro-priate to build a complete picture of the landscape. We developed software tools to perform classification, visualize the results, and approximate missing data. We focused our measurement on open water areas, semi-aquatic emergent vegetation, and upland vegetation in areas surrounding the wetlands. We create easy to understand summary statistical images that can be used to measure the rate of occurrence of different phenomena or the variability of the phenomena. We also compare and contrast our approach with existing, established techniques for monitoring and measurement of Boreal wetlands. We show how our approach is able to improve on the results generated from these existing techniques. In some cases we are able to detect and measure wetlands that other techniques miss, while in other cases we are able to provide additional temporal context that other techniques might be missing.Item Embargo Uncovering the Role of Primary Cilia in Astrocyte Reactivity Following Adolescent Repetitive Mild Traumatic Brain Injury(2025-05-23) Malhotra, Mehr; Guo, Jiami; Lohman, Alexander; Ousman, Shalina; Kuipers, Hedwich; Yong, V. WeeMild traumatic brain injury (mTBI) is typically caused by forces to the head or body that result in movement of the brain. Symptoms of mTBI vary greatly, ranging from mild, transient disturbances in brain activity to debilitating, long-term cognitive, physical, and emotional deficits. Repetitive mild TBIs (RmTBIs) are of particular concern, as subsequent injuries can interrupt the healing process and induce cumulative damage. Adolescents are especially prone to repetitive injuries due to their frequent involvement in contact sports and high-risk behaviours. The brain initiates injury responses to RmTBI, a process in which astrocytes, a major type of glial cells, are key players. Upon RmTBI, astrocytes respond to injury-induced cues and become reactive to control inflammation and promote healing. However, prolonged or dysregulated reactive astrocyte responses can induce further damage. Currently, the mechanisms behind activation and regulation of astrocyte reactivity are poorly understood. I propose that primary cilia, signalling antennae protruding from the astrocytic soma, play an important role in detecting injury-induced cues to modulate astrocyte reactions in response to RmTBI. To test my hypothesis, I utilized a mouse model with cilia dysfunction inducible specifically in astrocytes during adolescence. Following repetitive mTBIs, I examined changes in mouse behaviour, astrocyte reactivity, and microglial responses. My results suggest that mice with dysfunctional astrocytic cilia show enhanced functional recovery from injury, decreased astrocyte reactivity, and altered microglial reactions post-injury, in a sex-dependent manner. The results of this study indicate for the first time that primary cilia signalling plays a role in the modulation of astrocyte reactivity after mild traumatic brain injury.Item Embargo Anxiety and Depression Symptoms in the Mother-Child Dyad and Incident Migraine in Adolescence: An "All Our Families" Prospective Cohort Study(2025-05-20) Sjonnesen, Kirsten Mary; Orr, Serena Laura; Pringsheim, Tamara Milka; Noel, Melanie; Patten, Scott BurtonBACKGROUND: Migraine is a well-known cause of neurological disability. Given increasing migraine incidence in youth globally, the prevention of migraine and its related disability is a rising priority. A child’s likelihood of developing migraine may be predicted to a degree by genetic factors. However, mental health symptoms and early experiences have been recognized as potentially modifiable migraine risk factors. Characterizing the contributions of anxiety and depressive symptoms, referred to collectively as internalizing symptoms, towards the development of migraine may be highly impactful. By analysing the prospectively collected “All Our Families” (AOF) cohort data, insights into the modifiable mental health contributors to incident migraine were expected. Applying this knowledge may prevent or delay the development of new migraine cases (“incident migraine”), substantially reducing migraine prevalence and its related disability burden. OBJECTIVES: To use prospectively collected, longitudinal data to better understand the association between mental health symptoms experienced by a community-recruited sample of urban Canadian youth and their mothers, and youth incident migraine. Are elevated child and/or maternal internalizing symptoms across childhood (ages 4-12) associated with an increased odds of incident migraine in early adolescence? METHODS: The study sample consisted of Calgary, Alberta mother-child dyads followed through the AOF prospective cohort study from 2008-2023, which collected longitudinal data concerning maternal and child health determinants and outcomes. Data collection occurred through written and online questionnaires, which were exclusively distributed to mothers initially, and then simultaneously to mothers and consenting youth participants aged 9 and older. The cohort sampling frame consisted of women accessing pregnancy-related community healthcare services in Calgary from 2008-2009, who were recruited voluntarily through multiple strategies. Measures used in the analysis originated from AOF questionnaire data. Data were assessed in stages using descriptive and analytical methods. AOF attrition weights were applied to reduce vulnerability to bias due to attrition, and multiple imputation with chained equations was used for missing covariate data. The outcome, migraine, was ascertained through an analysis of youth responses to the questionnaire’s migraine diagnosis items, administered between youth ages 11-14. The exposures of interest, youth and maternal internalizing symptoms, were incorporated from each timepoint when these symptoms were measured from ages 4-12. Covariates included: age, sex, gender, ethnicity, history of parental migraine, and annual household income. Multivariable logistic regression modelling estimated adjusted odds ratios for migraine diagnosis comparing youth exposed to clinically significant internalizing symptoms to unexposed youth. Estimates were examined for effect modification of youth internalizing symptoms by sex, and then confounding. Mediation of the impact of maternal internalizing exposures through youth internalizing exposures was explored. RESULTS: In our sample of 1062 participants, 47.7% were female (n=507/1062), 47.0% had a parent with diagnosed or suspected migraine (n=499/1,062), and 19.4% met criteria for definite or probable migraine (n=206/1,062) on the outcome survey. With attrition weighting, at least one youth anxiety exposure or youth depression exposure occurred in 35.06% (32.04-38.2%) and 30.60% (27.73-33.63%) of youth, respectively, prior to incident migraine ascertainment. Exposure to at least one maternal anxiety exposure or maternal depression exposure affected 39.14% (36.01-42.37%) and 43.55% (40.35-46.79%) of weighted youth, respectively. Exposure counts of earlier childhood youth anxiety (Wilcoxon rank-sum p<0.001), youth depression (p<0.001), and exposure to maternal anxiety (p<0.001), differed significantly between children with and without migraine. Exposure to significant maternal anxiety symptoms across childhood (ages 4-12) was consistently associated with elevated adjusted odds of youth incident migraine at a mean age of 12.86 years (SD 0.82) in a dose-dependent manner (aOR 1.290 per exposure, 95% CI 1.017-1.637, p=0.0363), as was exposure to significant youth depression symptoms across childhood (aOR 1.286 per exposure, 95% CI 1.031-1.606, p= 0.0263). Sex did not modify the association between youth anxiety or youth depression symptom exposure and incident migraine. No significant mediation by youth anxiety or depression symptoms was found to influence the relationship between maternal anxiety and youth incident migraine. SIGNIFICANCE: Maternal anxiety and youth depression symptoms appear to have an antecedent role in youth migraine risk. Internalizing symptoms and/or disorders are treatable across the lifespan, through both pharmacological and psychological methods. Regardless of one’s genetic risk profile, a reduction in one’s exposure to internalizing symptoms is achievable, through evidence-based mental health treatment. To further our incomplete current understanding of genetic contributions to each of internalizing symptoms and pediatric migraine, a randomized prevention trial, offering monitoring and treatment of subthreshold internalizing symptoms in children at elevated risk of migraine and their mothers, may be the next step towards preventive care in migraine.Item Embargo Interactions between Shiga toxin-producing Escherichia coli -infecting bacteriophages and murine macrophages(2025-05-12) Faizal, Akeel; Niu, Dongyan; Canton, Johnathan; De Buck, JeroenShiga toxin-producing Escherichia coli (STEC) are responsible for major foodborne illness worldwide. Cattle are a major reservoir and asymptomatic carrier of STEC, widely spreading pathogens to the environment and food supply chains. Human infections, particularly for children < 5 years old, can be life-threatening. Antibiotics are effective against many bacterial infections but are not recommended for treating STEC infection in humans due to concerns of aggravated clinical manifestations. Bacteriophages (phages), viruses that specifically infect bacteria, could be developed as novel antimicrobials to effectively control STEC shedding in cattle and potentially treat the bacterial infection in humans. In addition to its bacterial killing activity, phages can cross mucosal barriers and encounter immune cells. One immune cell population encountered by the phages is professional antigen presenting cells (APCs), including dendritic cells (DCs), macrophages and B cells. Interactions of bacteriophages and APCs culminate in APCs uptaking phages rather than an infection. This interaction has many implications, due to mounting innate and adaptive immune responses against phages, although the information is scarce for phage-APC interactions and their consequences. This MSc research aimed to study phage-murine macrophage interactions, with a focus on: 1) investigating if STEC phages induce innate host responses, particularly nitric oxide (NO) and other pro-inflammatory mediators in murine macrophages and the underlying mechanisms; 2) determining if STEC phages alter the phagocytic ability of macrophages; and 3) evaluating if uptake of STEC phages causes cell death in murine macrophages. For this work, a murine macrophage cell line (J774A.1) and two phages, representing Tequintavirus (T5, AKFV33) and Tequatrovirus (T4, wV7) that can efficiently lyse common types of bovine and human STEC strains, were selected. Both wV7 and AKFV33 phages were capable of stimulating nitric oxide (NO) production via toll like receptor (TLR) 4 signaling. Moreover, wV7 phage mounted a qualitatively and quantitatively better innate response, characterized by upregulation of proinflammatory mediators and type 1 interferon (IFN) response in a TLR4 and TLR9 dependent manner in murine macrophages when compared to AKFV33 phage. In addition, both phages reduced phagocytosis function in murine macrophages at a multiplicity of infection (MOI) of 50 (5×107 plaque forming units (PFU)/mL for 1× 106 cells). At the AKFV33 and wV7 phage MOI of 50, 100 and 200 (phage titer ranging from 5×107 to 2×108 PFU/mL for 1×106 cells), viability of murine macrophages was not adversely affected. In conclusion, STEC-infecting Tequintavirus and Tequatrovirus primed innate immunity by inducing NO and cytokine production and regulating phagocytic function of macrophages. These phage-mediated immunological function may help in the rational design of effective STEC control strategies in animals and humans.Item Embargo Molecular characterization of mycobacteriophage Mcgavigan through targeted gene mutations and deletions(2025-05-12) Shafer, Natali; De Buck, Jeroen; Niu, Dongyan; Savchenko, AlexeiMycobacteriophage Mcgavigan was previously shown to be a promising candidate for use as a Johne’s disease preventative agent. Bioinformatic analysis of its genome revealed the presence of certain genes which made it less ideal for widespread agricultural use. Therefore, using recombineering techniques with CRISPR counter selection, we deleted two genes: integrase and an acquired repressor, which facilitate lysogeny and heterotypic superinfection immunity, respectively. Several parameters such as burst size, latency period, and killing efficiency were measured for each knockout mutant and lysogeny was tested using AttP/AttB site primers. The integrase deletion mutant had complete lysogeny abolishment and performed similarly to wild-type phage on all measured parameters. The acquired repressor deletion mutant was completely resensitized to heterotypic superinfection. Additionally, we efficiently generated knockout mutants using CRISPR only, with no required recombineering, by leveraging the phage’s ability to escape CRISPR attack through mutagenesis resulting presumably from non-homologous end-joining mechanisms. We observed that when CRISPR was targeting an essential gene, fewer phages survived CRISPR attack, due to their intolerance of mutations at that site, so we designed an experiment to survey gene essentiality. By targeting eight genes of unknown function using CRISPR, we determined that one gene was essential for phage lytic growth. In M. smegmatis that is deficient in non-homologous end joining, the phage did not show widespread large deletions or phage titer reduction after CRISPR attack was increased. Overall, we created an efficient lytic-only mycobacteriophage and heterotypic superinfection immunity was eliminated. Lastly, we harnessed the phage’s ability to survive CRISPR attack through mutagenic DNA repair to create efficient knockouts and evaluate gene essentiality.Item Embargo Carbohydrate supplementation: Effects of exercise intensity domain, dose, and menstrual cycle phases on endurance performance, metabolic responses, and perceived and performance fatigability(2025-05-20) Fleitas Paniagua, Pablo Rafael; Murias, Juan Manuel; Aboodarda, Saied Jalal; Alvarez, Thiago; Zagatto, Alessandro; Sigal, Ronald Jeremy; Pellicer-Chenoll, Maria TeresaOne of the main goals of carbohydrate (CHO) supplementation during long-duration exercise is to enhance endurance performance by increasing exogenous CHO oxidation. However, current literature exploring the benefits of different doses of CHO supplementation for endurance performance and its connexions with different phases of the menstrual cycle, perceived and performance fatigability is minimal and/or remains inconclusive. Interestingly, no previous study has compared the effect of CHO supplementation on endurance performance, perceived and performance fatigability, subsequent to continuous exercise performed within precisely defined portions of the moderate- (MOD) and heavy-intensity (HVY) domains. Additionally, no study has compared the effect of CHO supplementation on endurance performance, perceived and performance fatigability in different phases of the menstrual cycle, when exercise prescription was based on the exercise intensity domains model. Therefore, the main objectives of this thesis were: (i) to determine the effect of CHO supplementation on endurance performance, perceived and performance fatigability following a bout of constant-PO exercise performed within different exercise intensity domains (in males); and (ii) to evaluate the effects of CHO supplementation on endurance performance, perceived and performance fatigability following a bout of HVY constant-PO exercise, during different phases of the menstrual cycle. The main findings were that i) the recommended dose of CHO supplementation improved endurance performance following exercise in the lower portion of the HVY, but not in the MOD or upper region of the HVY; ii) the ergogenic effect of CHO supplementation was no longer beneficial when a high CHO dose was consumed; iii) recommended or high doses of CHO supplementation do not enhance performance or perceived fatigability following cycling within the MOD, lower or upper portion of the HVY when continuous PO is performed for less than 2 h. iv) CHO supplementation affects endurance performance and performance fatigability similarly across the menstrual cycle phases during and after continuous exercise performed in the lower portion of HVY. Collectively, these findings provide a novel framework for understanding the benefit of CHO supplementation to enhance endurance performance and its connection with different exercise intensity domains, phases of the menstrual cycle, perceived, and performance fatigability.Item Embargo Microbial Modification of the Vaginal Glycome: A Risk Factor for Chlamydia Infection?(2025-05-12) Heger, Katherine Chantelle; Sycuro, Laura; Surewaard, Bas; Brennand, Erin; Willis, LisaChlamydia is the most common bacterial sexually transmitted infection (STI) and disproportionately affects young females. Mechanistic understanding of this discrepancy remains limited, but dysbiotic Gardnerella and Prevotella spp. – coined “Gateway Bacteria” – may produce sialidase enzymes capable of cleaving protective terminal sialic acids from Type II LacNAc glycans. Chlamydia can hijack the human galectin-1 (Gal-1) to bind desialylated Type II LacNAc and invade. Yet, links between vaginal microbes, glycomes, Gal-1, and other biomolecules essential to health, remains understudied – despite its potential for novel therapeutics. We performed 16S rRNA Gene Amplicon Sequencing, high-throughput Lectin Microarray Technology (Mahal Laboratory), and biochemical assays to quantify changes in the vaginal niche of forty low-risk Kenyan participants assigned female at birth who contracted chlamydia during a five-year longitudinal study. Preceding Chlamydia infection, protective Lactobacillus crispatus decreased and Prevotella spp. increased. Lactic acid, a product of Lactobacilli essential for a low vaginal pH, decreased. A concurrent, but independent, decrease in IgG1 and higher serum testosterone, a potential immune suppressant understudied in females, was associated with a decrease in vaginal IgM and IgA. Consistent with this loss of protection phenotype, sialic acid decreased approximately 50% preceding infection in both the soluble and cellular glycomes. When Lactobacillus species are depleted, sialic acid decreased in the glycomes and, complimentarily, Type II LacNAc increased in cellular. Finally, Gal-1 increased at incident Chlamydia and was negatively correlated with LacNAc – potentially indicating that Gal-1 may bind up LacNAc. Surprisingly, presence of Lactobacillus iners also marked an increase in Gal-1 supporting epidemiological evidence associating L. iners with decreased protection. Finally, Gal-1 negatively correlated with lactic acid and serum estradiol, suggesting novel protective roles for both in the vaginal niche. Connecting the diverse facets of the vaginal niche allowed us to denote shifts in the microbiome and glycome preceding infection, while unexpectedly illuminating novel associations between Gal-1, estradiol, lactic acid, and expanding our mechanistic understanding of L. iners’ transitional phenotype. Most notably, our data connected increasing Gateway Bacteria, decreasing sialic acid, and increasing Gal-1, suggesting a treatable mechanism for this disproportionate infection – hopefully aiding in alleviating the intense burden of Chlamydia infection.Item Embargo AI-Augmented Intelligent Radio Frequency Integrated Circuits for Transmitter Predistortion for 5G and 6G Wireless and Space Communication Applications(2025-05-13) Lalenoor, Morvarid; Helaoui, Mohamed; Abou-Zeid, Hatem; Ghannouchi, Fadhel; Souza, RobertoThe increasing demands of 5G, 6G, and space communication systems necessitate highly efficient and linear power amplification as the power amplifier (PA) plays a crucial role in transmitting signals efficiently over long distances while maintaining signal integrity. An analog predistorter (APD) is a circuit designed to pre-compensate for the nonlinearities of a PA in RF systems, improving signal linearity and efficiency. APDs help reduce adjacent channel interference, spectral regrowth, and power consumption. However, they face several challenges, including variability in analog components, limited adaptability to changing PA characteristics, and susceptibility to temperature and aging effects. Additionally, their design requires precise tuning of nonlinear elements, making optimization complex, and they struggle with wideband signals. Due to these limitations, this study presents an AI-augmented approach to optimize analog predistortion for PAs for greater flexibility and adaptability. The proposed approach uses machine learning to predict gain and phase transformations. A dataset derived from the APD circuit measurement was used to train predictive models to enable data-driven optimization of control voltages in predistortion circuits. Predictive analysis was performed using the dataset from APD samples, where gain and phase variations were studied under different control voltage configurations, and extensive data extraction was performed across diverse voltage combinations. Principal Component Analysis (PCA) was employed for dimensionality reduction and feature extraction. A comparative evaluation of machine learning models identified Random Forest as the most effective. Grid search optimization further refined the PCA-component selection and classification algorithms. To validate the proposed AI-driven predistortion technique, continuous wave (CW) and modulated signal characterization tests were performed, evaluating the PD-PA cascade using Adjacent Channel Power Ratio (ACPR) measurements. The results demonstrated a 10 dB improvement in ACPR at 36 dBm output power, confirming a significant reduction in nonlinear distortions. Overall, this work shows how machine learning can improve RF frontend systems which leads to smarter transmitters for future wireless networks.Item Embargo Advanced Passive Microwave Sensing Tags for Label-free Biosensing Applications(2025-05-12) Yazdanicherati, Amirhossein; Abbasi, Zahra; Murari, Kartikeya; Curiel, LauraRecent developments in microwave biosensing technologies have provided opportunities for substantial advancements in noninvasive, label-free detection and monitoring, which are especially useful in biomedical diagnostics and environmental sensing applications. Despite these advancements, existing microwave sensing platforms continue to face critical challenges, including limited sensitivity, reduced operational range, and reliability issues in harsh, lossy, or complex environments. This thesis presents innovative methods designed to significantly enhance sensitivity, resolution, and detection distance in microwave sensing systems through the development of novel multisurface passive tag structures and targeted electromagnetic field manipulation. In the first phase, a flexible, chipless microwave sensor leveraging coupled resonators was developed, improving the sensing range while preserving high sensitivity and reliability. Practical implementations of this novel sensor include real-time detection and monitoring of hydrocarbon contaminants in environmental settings, accurate tracking of lubricant depletion on medical implant surfaces, and reliable sensing of ammonium chloride contamination. Building upon this initial concept, the thesis introduces an advanced electromagnetic-engineered multisurface passive sensor system interconnected via vertical vias. This refined architecture notably enhances electromagnetic field confinement, enabling precise and reliable sensor performance even in highly absorptive and challenging media. Applications demonstrated include the characterization of complex liquid environments and the detection of minute dielectric variations crucial for biomedical diagnostics. Furthermore, the thesis focuses on specialized microwave sensing platforms specifically tailored for characterizing lubricant-infused surfaces (LIS) on biomedical implants. These sensor platforms effectively measure lubricant evaporation dynamics, monitor lubricant depletion and gas bubble forming, and evaluate self-healing behaviors, contributing significantly to the durability, reliability, and overall functionality of medical implants. In conclusion, the research described in this thesis substantially advances the state-of-the- art in microwave sensing technology. By introducing flexible, scalable, and highly sensitive solutions capable of functioning effectively across diverse biomedical and environmental scenarios, the outcomes of this work hold significant potential for broad practical adoption and further technological innovation.Item Embargo Comprehensive Simulation Studies on Hydrogen-Oriented Underground Coal Gasification Across Different Scales(2025-05-07) Wei, Zixiang; Chen, Zhangxing; Hu, Jinguang; Nourozieh, Hossein; Lu, Qingye; Chen, ZhimingThe hydrogen-oriented underground coal gasification (HUCG) technology is emerging as a highly promising approach to address energy demand and environmental concerns while producing clean hydrogen from abundant but inaccessible coal resources. Due to the complexity and high costs of field tests and the challenges of simulating underground conditions in the laboratory, numerical simulation is an effective method for studying the HUCG process. Therefore, this dissertation investigates the mechanisms and feasibility of hydrogen production and storage in UCG systems through multi-scale modeling and simulation approaches. The research includes large-scale numerical simulations and molecular dynamics (MD) simulations to address key challenges in UCG-driven hydrogen production and in-situ hydrogen storage. In the first study, a three-dimensional UCG model with water injection was developed to investigate the evolution of a pore structure and permeability in a coal seam during cavity formation. The results demonstrate that water injection affects both the growth trajectory of a cavity and coal pore characteristics, revealing the complex interactions between hydrological and thermochemical processes. The second study focuses on optimizing hydrogen production through water-assisted strategies in large-scale UCG. Different injection locations and perforations were compared, and the mechanism of hydrogen production and a better strategy of the water injection can be figured out. In addition, a novel water injection technique, which can lead to a fivefold increase in daily hydrogen output and improved cavity stability, was proposed to effectively increase hydrogen production. Finally, molecular dynamics simulations were employed to examine the adsorption and diffusion behaviors of hydrogen and other syngas components (CH₄, CO₂) in low-rank coal. The results showed that H₂ has weak adsorption but high mobility in coal, whereas CO₂ exhibits strong interactions. These findings provide microscopic insights into hydrogen behavior, discussing the feasibility of UCG cavities for in-situ hydrogen storage.Item Embargo Patient Perspectives on Health Behaviour Support Programs after Hypertensive Disorders of Pregnancy: A Mixed-Methods Study(2025-05-12) Macphail, Meghan; Nerenberg, Kara; Chaput, Kathleen; Butalia, Sonia; Metcalfe, AmyBACKGROUND: Those who experience a hypertensive disorder of pregnancy (HDP) have a 2- 4 times increased risk of premature cardiovascular disease (CVD) compared to those without HDP, largely due to accumulation of CV risk factors (e.g., diabetes, hypertension, dyslipidemia) within the first ten years after delivery. Many of these chronic diseases may be prevented through early health behaviour modifications. At present, postpartum health behaviour support programs are limited by a lack of 1) participant completion; 2) tailoring specifically for women post-HDP; 3) support for gender-related responsibilities in the postpartum period; and 4) mental health support. Understanding participant perspectives on post-HDP health behaviour support is a needed next step in developing tailored, sustainable CVD prevention programs for these high- risk women. PURPOSE: To explore participant-perspectives on health behaviour support programs following pregnancies with HDP and factors impacting participation, in order to inform equitable access to CVD preventive care for post-HDP women. METHODS: This thesis utilized a mixed-methods approach to investigate participant experiences and preferences for postpartum health behaviour programs. It employed the constructivist and pragmatic paradigms while contextualizing results within the Social Ecological Model for behaviour change. It also included a systematic review focused on nutrition modifications post-HDP. RESULTS: Nineteen women completed a questionnaire and eleven completed an interview. Eight had participated in a postpartum health behaviour support program for varying amounts of time, while 11 had declined to participate in the program. Common reasons for participation included an interest in focusing on their own health, the accountability of check-ins with a health coach, and encouragement from healthcare providers. Common reasons for non-participation included postpartum effects on mood and lack of energy or sleep. Non-participation was attributed to postpartum effects on mood, feeling overwhelmed, and lack of energy or sleep. Participants emphasized their maternal burden, the importance of their support network, and difficulty navigating the healthcare system. CONCLUSION: Insights gained from this study on participant preferences will inform the design and implementation of evidence-based CVD prevention programs for women after HDP.Item Embargo Domain-Specific Generative AI in Energy Engineering: A Case Study in Geothermal Energy(2025-05-07) Haddadian, Kamran; Chen, Shengnan; Shor, Roman; Sumon, Kazi; Brennan, BobThe integration of large language models (LLMs) in domain-specific applications has been limited due to high computational costs, and the need for expensive and challenging training datasets. This thesis explores Retrieval-Augmented Generation (RAG) and Graph-RAG pipelines to enhance question-answering precision in geothermal energy, addressing these challenges while optimizing computational efficiency. In this thesis, a domain-specific RAG pipeline for geothermal energy is firstly developed by fine-tuning an open-source classifier and embedding model to improve information retrieval. The RAG pipeline uses an open-source LLM to address concerns over proprietary models. The classifier effectively filters relevant geothermal data, increasing domain focus, while the optimized embedding model enhances retrieval accuracy. The results demonstrate that applying RAG improves question-answering accuracy from 55.5% using an untrained embedding model to 72.5% with a fine-tuned embedding model. Additionally, the fine-tuned classifier achieved over 99% precision in classifying text based on context. Meanwhile, the study highlights the environmental impact of increased computational demands, emphasizing the trade-offs between retrieval accuracy and CO2 emissions. A Graph-RAG approach, which enhances RAG by integrating structured relationships between entities, is then employed to improv contextual understanding. Unlike traditional RAG, which relies solely on similarity-based retrieval, Graph-RAG incorporates concept relationships to refine responses. The study evaluates Graph-RAG’s performance in geothermal energy question-answering tasks and demonstrates a 13% improvement in precision compared to RAG, particularly when retrieving fewer nodes and relationships. Moreover, Graph-RAG reduces computational costs by achieving similar accuracy to RAG while using 35% fewer input tokens. This ii improvement comes from Graph-RAG’s ability to leverage nodes and their relationships to better understand the concept. The study further reveals that Graph-RAG is more resilient against misleading statements by cross-referencing nodes and relationships between concepts. This research contributes to the advancement of AI-driven information retrieval in energy engineering by demonstrating the effectiveness of RAG and Graph-RAG pipelines. The findings highlight the benefits of structured entity relationships in improving precision, reducing computational costs, and optimizing knowledge retrieval. The thesis concludes that Graph-RAG offers a more efficient and reliable approach for domain-specific question answering, paving the way for future applications in geothermal energy and beyond.