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Faculty of Graduate and Postdoctoral Studies collections containing Graduate Theses and Practica. The content will include textual material with images of data when available.
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Recent Submissions

Access status: Open Access ,
Non-halogenated and halogenated heterocyclic aromatic compounds in the Canadian environment
(2026-08-25) Vitharana, Nipuni N; Tittlemier, Sheryl (Chemistry); Stetefeld, Jorg (Chemistry); Fry, Mark (Biological Sciences); Peng, Hui (University of Toronto); Tomy, Gregg
Polycyclic aromatic compounds (PACs) are a broad class of pollutants with two or more fused aromatic rings, originating from petrogenic, pyrogenic, and biogenic sources. Hetero-polycyclic aromatic compounds (HPACs), a subclass of PACs that contains nitrogen, sulfur, and/or oxygen in their aromatic structure, are understudied despite growing evidence of their persistence, bioaccumulation, and toxicity. This is largely because the United States Environmental Protection Agency and Canada's Environmental Protection Act, 1999, recognize only 16 polycyclic aromatic hydrocarbons (PAHs) as priority pollutants, leaving other subclasses of PACs underrepresented in environmental monitoring. Consequently, my research was geared toward addressing the paucity of scientific data on HPACs. In doing so, I generated new knowledge on HPACs across several fronts. First, I developed and validated both targeted and non-targeted analytical methods for accurately measuring HPACs in environmental matrices. These methods were then applied to generate baseline concentration data for a broad suite of PACs, including 50 HPACs in Lake Erie biota, and Lake Ontario sediments, many of which had not previously been reported in these systems. Second, using advanced chemometric techniques, such as multivariate and cluster analysis, I demonstrated that HPACs have greater diagnostic power in deriving the sources, fate, and behaviour of PACs relative to their homocyclic counterparts. Notably, comparison of HPAC profiles in Lake Ontario sediments against coal-tar- and non-coal-tar-based reference materials revealed that Hamilton Harbour sediments are primarily contaminated by coal-tar-derived PAC sources, illustrating the real-world diagnostic value of HPACs. Third, I showed that HPAC distribution patterns clearly differentiated fish communities by habitat and physiological traits, such as biotransformation capacity and body size, whereas homocyclic PAC profiles were comparatively uniform, indicating weaker habitat-specific influences. Fourth, I developed a multi-tiered data-filtering framework to help the scientific community streamline the interpretation of high-resolution mass spectra to elucidate PACs in complex environmental matrices. Taken together, my research demonstrates the importance of this overlooked class of contaminants and highlights the need for the inclusion of HPACs into long-term monitoring and risk assessment frameworks, which will ultimately improve our understanding of the environmental behaviour and impacts of PACs across Canadian environmental systems.
Access status: Open Access ,
The autonomisation of decision-making: autonomous warfare, legal coding, and the limits of international humanitarian law
(2026-08-21) Tarachandani, Paarth; Anderson, Kjell (Law); MacNeil, Gillian (Law); Shariff, Mary
With the advent of autonomous weapon systems, International Humanitarian Law (IHL) has been presented with a significant challenge. Autonomous technologies used in decision-making processes during times of conflict expose loopholes in the current principles of IHL that regulate the use of force, such as the principles of distinction and proportionality. Contemporary conflicts, particularly the Russia–Ukraine War and the 2025 India–Pakistan escalation, readily demonstrate how autonomous and semi-autonomous systems are increasingly involved in surveillance, targeting, and even striking decisions. This thesis examines whether existing international legal frameworks adequately regulate autonomous warfare and addresses the legal gaps created by AI-enabled decision-making. This thesis adopts a mixed-methods approach grounded in doctrinal legal analysis, supplemented by policy analysis, assessment of legal institutions and regulatory systems, and interdisciplinary theoretical perspectives. This approach corresponds most closely with Martha Minow’s categories of doctrinal restatement, policy analysis, and the study and assessment of legal institutions, systems, and institutional actors. The research integrates Katharina Pistor’s theory of legal coding and modest insights from Science and Technology Studies (STS), which provide additional critical perspectives on regulatory complexity and how law structures power and responsibility. The thesis concludes with recommendations for reform to preserve meaningful human oversight and ensure that humanitarian protections remain effective in an era of algorithmic warfare.
Access status: Open Access ,
Optimizing quasi-metagenomic sequencing for strain-level detection and genomic surveillance of foodborne pathogens in complex food matrices
(2026-08-24) Ryz, Jillian; Graham, Morag (Medical Microbiology and Infectious Diseases); Lix, Lisa (College of Community and Global Health); McClarty, Grant (Medical Microbiology and Infectious Diseases); Langille, Morgan (Dalhousie University); Knox, Natalie; Nadon, Celine
Foodborne disease surveillance relies heavily on whole-genome sequencing (WGS) of bacterial isolates to support outbreak detection and source attribution. However, culture-based workflows introduce delays that can limit timely public health response, particularly for perishable foods and complex matrices. This thesis evaluates quasi-metagenomics, defined as sequencing enriched food matrices without secondary isolate recovery, as a culture-independent approach for strain-level pathogen detection and characterization. The objective was to determine whether quasi-metagenomic sequencing can provide strain-resolved genomic information suitable for foodborne outbreak detection. This thesis therefore investigates the laboratory and analytical requirements needed to achieve outbreak-level genomic resolution directly from enriched food samples. Chapter 3 establishes the bioinformatic foundation by benchmarking taxonomic classifiers, reference databases, and analytical parameters. Results demonstrated that a curated foodborne pathogen (FBP)-specific reference database used with KrakenUniq provided the most accurate and consistent taxonomic classification while reducing computational burden. Chapter 4 applies this optimized workflow to short-read quasi-metagenomic datasets generated from enriched food matrices artificially contaminated with Listeria monocytogenes, verotoxigenic Escherichia coli (VTEC), and Shigella spp. Selective enrichment had a greater influence on pathogen recovery than eukaryotic DNA depletion. When sufficient pathogen DNA was recovered, quasi-metagenomic sequencing enabled accurate pathogen detection, serotype prediction, genome assembly, and whole-genome multilocus sequence typing (wgMLST)-based outbreak characterization with genomic distance ranges comparable to isolate-derived WGS. To support standardized interpretation of quasi-metagenomics, a pathogen-presence likelihood metric was developed that integrates sequencing depth-normalized unique k-mer counts (unique KPMR; k-mers per million reads) with robust z-scores to distinguish true pathogen signal from background noise. Chapter 5 extends this workflow to Oxford Nanopore Technologies (ONT) long-read sequencing. Despite higher raw read error rates, long-read quasi-metagenomic sequencing supported accurate taxonomic classification, genome assembly, and outbreak characterization. Single nucleotide polymorphism (SNP)- and wgMLST-based analyses produced genomic distance ranges comparable to those obtained using short-read quasi-metagenomics and isolate-derived WGS. Overall, this research establishes an end-to-end quasi-metagenomic workflow for strain-level pathogen detection and outbreak characterization directly from enriched food samples. These findings provide a strong methodological foundation for the continued development of culture-independent genomic approaches to support foodborne disease surveillance and outbreak response.
Access status: Open Access ,
Reconnecting with nature: digital detox retreat for well-being
(2026-06-12) Jacques, Shelby; Abdullaev, Umid (Interior Design); Campbell, Michael (Environment & Geography); Karpan, Cynthia
The consumption of digital media has significantly increased in the 21st century, resulting in negative effects to mental well-being, which include heightened levels of stress, anxiety, and self-criticism (Karim et al, 2020). Research indicates that reducing time on digital devices and reconnecting with nature through forest bathing can provide a remedy to these effects. Digital detox involves reducing digital media use (including social media) and has been shown to improve psychological well-being (Vasile, 2024, 1). Forest bathing, the act of immersing oneself in nature allows participants to be more aware of their physical, mental, and emotional well-being, resulting in positive effects on their mental well-being (Farkic, Isailovic, and Taylor, 2021). The benefits of forest bathing have been investigated and integrated into the design of the retreat. Biophilic design influenced design decisions, focusing on attributes of direct experiences of nature (e.g., water, plants, natural landscapes) and indirect experiences of nature (e.g., natural materials and colours, organic shapes and forms, and evoking nature) (Kellert, 2018, 10). The practicum proposes the design of a wellness retreat aimed at helping adults unplug from digital media and reconnect with nature to reduce stress, anxiety, and self-criticism. The Manitoba-based retreat features nature-immersed spaces (shared wellness areas and private cabins for recovery) that mimic the exterior landscape through local materiality for an enhanced forest bathing experience. Also included in the experience are thermotherapeutic spaces, such as saunas, meditation spaces, and other wellness amenities. The goal of this practicum is to create a wellness retreat that encourages users to reconnect with nature through an immersive design that is informed by theories related to forest bathing, biophilia, and digital disconnection.
Access status: Open Access ,
The role of an evolved mammalian genomic signature and a DNA methylation regulator in transcriptome integrity and diversity
(2026-08-24) Ogunsola, Samuel; Mai, Sabine (Physiology and Pathophysiology); Mishra, Suresh (Internal Medicine); Mckenna, Sean (Chemistry); Alfonzo, Juan ( Brown University); Xie, Jiuyong
The mammalian transcriptome is shaped by interconnected layers of co- and post-transcriptional regulation, yet the mechanisms that maintain its integrity remain incompletely understood. This thesis investigates two dimensions of transcriptome integrity regulation: the genome-wide role of an evolutionarily conserved mammalian genomic signature in regulating alternative splicing, and the capacity of a DNA methyltransferase inhibitor to restore transcript length in cancer cells. Guanosine-tract closely upstream of an AG dinucleotide (G-tract-AG signatures) emerged in mammals and they have been found in over 2000 annotated human 3′SS as a repressor of 3′AG usage through hnRNP H1/F binding. However, their distribution and function across the broader non-coding genome were unknown. Here, we demonstrate that G-tract-AG signatures are widely distributed across mammalian non-coding regions, occurring over six million times in the human genome. Approximately 9,000 G-tracts in G-tract-AG signatures within human genes are disrupted by single nucleotide variants (SNVs) of the cis-splicing quantitative trait loci in the Genotype-Tissue Expression project. Mechanistically, G-tract elements repress splicing in vitro primarily by stalling the second transesterification step. Moreover, we also showed that it stabilized a repressive stem-loop structure between the branchpoint and the adjacent AG. Interestingly, G-tract-disrupting SNVs destabilize this stem-loop, relieve AG repression, and activate cryptic splicing, generating novel transcript isoforms. These G-tract-disrupting SNVs include thousands of rare alleles implicated in Mendelian disease, providing a mechanistic framework for functional annotation of non-coding variants. At the polyadenylation level, treatment of GH3 pituitary tumor and MOLM-13 leukemia cells with the DNA methyltransferase inhibitor 5-aza-cytidine promotes a transcriptome-wide shift from proximal polyadenylation sites toward genomic terminal exons with more optimal poly(A) signal motifs. This shift is accompanied by upregulation of anti-termination factors, SCAF4 and SCAF8, downregulation of the early termination enhancer, E2F2. These findings reveal a previously unrecognized role for 5-aza-cytidine in driving a switch from shortened to full-length mRNA transcripts in tumor cells. Taken together, this thesis establishes that transcriptome integrity and diversity emerge from the interplay of multiple mechanisms, and that perturbation of any of these has broad consequences in health and disease.
Access status: Open Access ,
Indigenous traditional foods and culturally appropriate care: exploring community experiences and developing a tool to assess healthcare provider knowledge
(2026-08-25) Sarviha, Sina; Myrie, Semone (Food and Human Nutritional Sciences); Edgerton, Jason ( Sociology and Criminology); Redmond, Leslie
The prevalence of gestational diabetes mellitus (GDM) is three times higher among Indigenous women than non-Indigenous women in Canada. While culturally appropriate programs exist to promote healthy pregnancies, they are often designed for rural contexts where traditional foods and activities are more readily accessible. Considering the steady migration of Indigenous populations to urban centers, it is vital to assess the availability and clinical support regarding traditional foods within urban healthcare systems. This necessitates an evaluation of the care provided by healthcare professionals to ensure it meets the unique needs of urban Indigenous women. To explore the experiences of urban Indigenous women with prenatal programs and healthcare, a multi-method and Community-Based Participatory Research (CBPR) approach was utilized. The research team conducted focus groups and in-depth interviews and analyzed the data using Classical Grounded Theory, revealing six themes from the focus groups and two additional themes from the interviews. These themes highlighted the vital importance of traditional foods during pregnancy, the challenges of accessing them in urban settings, and a significant inability among healthcare providers to offer culturally appropriate care or recommendations. This finding pointed to a critical lack of foundational knowledge on the topic, which led to the initiation of a second study to develop a valid and reliable Indigenous Traditional Foods Knowledge Questionnaire. Guided by an advisory board of Indigenous knowledge keepers from across Canada, a modified eight-step psychometric approach was used to develop the survey instrument. The advisory board established the definitions for traditional foods and related knowledge, and the research team developed questionnaire items using academic and grey literature, including Indigenous traditional food guides, Indigenous organizations websites, and organizational reports and books. Five registered dietitians evaluated the first draft for content validity, and ten healthcare practitioners assessed its face validity. While the psychometric evaluation of the questionnaire remains to be completed, this solution-focused project will provide a reliable instrument to identify specific knowledge gaps and improve healthcare professionals’ knowledge of traditional foods.
Access status: Open Access ,
Economic evaluation of therapies for the treatment of motor fluctuations in advanced stage Parkinson's disease
(2026-08-25) Tang, Quoc An; Falk, Jamie (Pharmacy); Nguyen, Dung (Internal Medicine); Mital, Shweta
Background: Up to half of all patients with Parkinson’s Disease (PD) will progress to its advanced stage, when quality of life is severely hampered and treatment costs escalate. Advanced, device-assisted therapies are usually considered in these patients. Existing surgical interventions, including deep brain stimulation (DBS) and levodopa-carbidopa intestinal gel (LCIG), are invasive and difficult to access in the United States. Subcutaneous infusion therapies, namely continuous subcutaneous apomorphine infusion (CSAI) and continuous subcutaneous foslevodopa-foscarbidopa infusion (LDp/CDp) are the latest advanced therapies approved by the US Food and Drug Administration in October 2024 and February 2025, respectively. They promise to be minimally invasive alternatives to existing surgical interventions and alleviate access issues plaguing the advanced PD treatment landscape in the US. However, there is no direct efficacy comparison between subcutaneous infusions and surgical interventions. These new therapies are also costly, raising questions about their cost-effectiveness. My thesis provides the first evidence to address these questions. Methods: First, we conducted a systematic review and Bayesian network meta-analysis of randomized clinical trials studying advanced therapies to estimate the comparative efficacy and safety of these treatments. We further evaluated whether the differences between the treatments, if there are any, are clinically meaningful. Next, we performed a cost-effective analysis to assess whether the new subcutaneous infusions offer good value for money and whether they are more economically efficient than surgical interventions. Results: In the systematic review and network meta-analysis, we identified and analyzed 13 randomized controlled trials with a combined 2,069 participants. We found that the newly approved therapies generally fall behind existing treatments, most notably DBS. Foslevodopa-foscarbidopa is less effective than DBS at improving OFF time [mean difference (MD) vs. DBS, +1.13 hours (95% CrI: −0.01 to +2.29)] and clinical motor functions [UPDRS-III, MD vs. DBS, +2.36 points (95% CrI: −0.10 to +4.89)]. Similarly, CSAI is less effective than DBS at improving quality of life [PDQ-39, MD vs. DBS, +5.09 points (95% CrI: −0.37 to +10.67)]. However, the differences between therapies at improving OFF time and motor functions are not clinically important. In terms of safety, the risk of serious adverse effects is elevated with DBS. In the cost-effective analysis, we found that the newly approved subcutaneous infusions are not cost-effective compared with existing surgical therapies. DBS is the optimal therapy from a cost-effectiveness perspective, costing less but providing more quality-adjusted life years (QALYs) compared to all other treatments. Infusion therapies are not cost-effective versus best medical therapy (BMT) at a willingness-to-pay threshold of $100,000/QALY. LDp/CDp and CSAI have incremental cost-effectiveness ratios of $1.69 million and $1.98 million per QALY compared to BMT, respectively. Their prices would have to be reduced by 82-83% for them to be cost-effective versus BMT. However, in cases where infusion therapies are used as intermediate treatment before DBS, the novel therapies only need price reductions of 4-20% to be the best infusion option. Conclusion: The findings of my thesis provide the first evidence on the economic value of LDp/CDp. It, also provides evidence on the value of subcutaneous infusions vs existing treatments for advanced PD in the United States. The systematic review and network meta-analysis highlighted the lower efficacy of subcutaneous infusions but also the small comparative differences between therapies. Furthermore, the cost-effectiveness analysis indicated that using DBS is cost-saving, while LDp/CDp and CSAI are not cost-effective, mainly due to high drug acquisition prices. At the same time, a modest price reduction can make subcutaneous infusions valuable options amidst limited DBS access. Altogether, the findings provided insights into the worth of eliminating barriers to accessing DBS, the economic value of novel infusion therapies as bridging treatments, and the need to negotiate price discounts for these therapies.
Access status: Open Access ,
Performance of UHPC in shear key connections
(2026-08-26) Asmamaw, Chalachew; Fiorillo, Graziano (Civil Engineering); Semendary, Ali (Civil Engineering); Shehata, Emile (Civil Engineering); Svecova, Dagmar
Ultra-high-performance concrete (UHPC) is a promising material for shear-key connections in adjacent box beam girder bridges because of its high strength, bond capacity, and durability. However, the long-term performance of UHPC cast against hardened high-strength concrete (HSC), and the effects of surface condition and transverse reinforcement on shear-key behaviour, require further investigation. This thesis addressed these issues through two independent experimental studies. This thesis used specimens cast by Tan (2021) and Erfani (2023). The strengths found in these studies were compared with the strength values obtained in this experimental program. One study Tan (2021) provided a durability-related assessment of material and interface specimens that were exposed to outdoors environment for approximately 7 years. Temperatures in Winnipeg, MB ranged from −40°C to +37°C. Compression, indirect tension, pull-off, slant-shear, and bi-shear tests were conducted to evaluate retained mechanical and bond-related performance. The HSC specimens had average compressive and indirect tensile strengths of 101.6 and 6.25 MPa, respectively. Pull-off specimens developed an average resistance of 3.96 MPa and failed within the HSC substrate. Slant-shear specimens also failed within the HSC rather than through complete interface separation, while bi-shear specimens developed an average shear strength of 9.42 MPa. All average strength results exceeded the average strength values obtained 7 years ago. These results demonstrate that the materials and UHPC–HSC systems retained measurable mechanical and interface resistance after long-term outdoor exposure. The second study investigated shear-key specimens representative of shear keys in adjacent box beam girders. The specimens that were tested in shear were cast by Erfani (2023) and the test parameters investigated included interface surface preparation and presence/absence of transverse reinforcement. Surface roughness increased the peak load by 38.7%, while the presence of reinforcement in addition to the roughness increased peak load by 61.5%. Load–displacement measurements, Digital Image Correlation, and strain instrumentation showed that the smooth, unrestrained specimen experienced localized damage and an abrupt post-peak reduction in resistance. In contrast, the rough, reinforced specimens exhibited delayed crack initiation, greater deformation capacity, and higher residual load-carrying capacity. These observations indicate that surface roughness and transverse reinforcement improved shear resistance, ductility, crack control, and residual strength of the shear key specimens. Overall, the results emphasize the importance of interface preparation, and reinforcement detailing in UHPC–HSC shear-key performance.
Access status: Open Access ,
Foodservice emergency preparedness in Canadian long-term care
(2026-08-20) Santos Pezzi Dullius, Juliana Maria; Riediger, Natalie (Food and Human Nutritional Sciences); Thompson, Genevieve (College of Nursing); Lengyel, Christina
Introduction: Food provision is vital for meeting the daily nutritional needs of long-term care (LTC) home residents and ensuring nutrition continuity during emergencies, such as natural disasters and infectious disease outbreaks. These events can disrupt foodservice operations in distinct ways, increasing vulnerability and potentially compromising the overall resilience of the home. Therefore, assessing Canadian LTC foodservice preparedness is essential to safeguard residents’ nutritional health and mitigate operational burdens during emergencies. Objectives: This exploratory and descriptive study assessed self-reported emergency preparedness procedures and operational practices among a multi-provincial sample of Canadian LTC foodservice professionals during natural disasters and outbreaks. Methods: A cross-sectional online survey was conducted among LTC foodservice professionals across Canada. The 55-question survey explored respondent demographics, facility characteristics, previous emergency experiences, and components of preparedness. Data were analyzed using descriptive statistics and Fisher's exact test. Results: A total of 84 participants were included. Most respondents reported having emergency measures in place, such as contingency menus and staff guidelines. Staffing shortages and the need for menu modifications were common challenges in both scenarios, while natural disasters introduced unique barriers like food supply shortages and utility disruptions. Outbreak training for staff was provided by 62% of respondents, compared to 52% for natural disasters, and 71% rated their operations as prepared for outbreaks versus 63% for natural disasters. Having a plan for outbreaks was associated with providing emergency training to staff (p = 0.003) and perceived preparedness (p = 0.043). Conclusion: While participating LTC foodservice professionals indicated basic readiness for outbreaks, their reports suggested that notable gaps remain regarding natural disaster preparedness. Developing comprehensive emergency plans and implementing targeted staff training are important steps to help address these gaps, maintain nutrition continuity, and safeguard resident safety during future emergencies.
Access status: Open Access ,
Identification of the functional mechanisms of alcohol–Wnt signaling pathway interactions in taste sensory organ development: Insight from the mexican tetra (Astyanax mexicanus)
(2026-06-02) Goel, Gandhrav; Chelikani, Prashen (Oral Biology); Pauls, Samantha (Pharmacy); Atukorallaya, Devi
Animal models provide critical insight into conserved mechanisms underlying development and disease. The Mexican tetra (Astyanax mexicanus), which exists as both surface and cave morphs, offers a powerful system to study craniofacial and sensory development. Canonical Wingless/Integrated beta-catenin (Wnt/β-catenin) signaling is an important cell signaling pathway in early embryonic development and its disruption is implicated in various birth defects. Prenatal alcohol exposure (PAE) has been consistently associated with characteristic birth defects, categorized as Fetal Alcohol Spectrum Disorders (FASD). Alcohol exposure during embryogenesis suppresses both canonical and non-canonical Wnt signaling, associated with craniofacial abnormalities, while folic acid has been shown to minimise the early developmental defects. This study examined how alcohol exposure affects taste bud formation and gustatory associated chemoattractive behaviour, and whether modulation of Wnt signaling or folic acid supplementation alters these outcomes in surface fish (SF) and cavefish (CF) morphs. Embryos were exposed to ethanol (EtOH), Lithium chloride (LiCl) (Wnt activator), Wnt-C59 (WC-59) (Wnt inhibitor), or folic acid 10 hours post-fertilization (hpf). Taste bud patterning and distribution was assessed across larval stages at 8, 15 and 30 days post-fertilization (dpf) using live whole mount Ponceau S stain. The chemosensory attractive behaviour was assessed using the various taste stimulants in DanioVision observation system. CF consistently exhibited increased taste bud size and broader spatial distribution compared to SF, with divergence becoming more pronounced over development. Regional analysis revealed iii sequential emergence of taste bud subtypes, with T1, T3, and T4 appearing earlier, while T2 emerged later and was observed exclusively in CF within the stages examined. These findings suggest that differences in developmental timing and spatial organization underlie morph-specific sensory architectures. Across both surface and cave morphs of Mexican tetra, chemical perturbation of canonical Wnt signaling resulted in only limited and inconsistent effects on gustatory morphology. Although minor stage-specific differences were detected, these changes were not maintained across developmental stages or anatomical regions. Behavioral responses were similarly resilient to treatment, as chemoattractive behavior showed no consistent alterations in time spent near feed, distance to feed, or locomotor activity. Together, these findings suggest that modulation of canonical Wnt signaling has a minimal impact on taste bud development and feeding-related behavior in either morph under the conditions tested. Instead, behavioral outcomes were strongly morph-dependent: SF exhibited more variable and exploratory movement patterns, whereas CF demonstrated more consistent feed engagement and elevated locomotor activity. Overall, intrinsic differences between morphs were the dominant factor shaping both gustatory morphology and chemoattractive behaviour, indicating that these traits are robust to short-term developmental perturbation. These results suggest that sensory system organization in Astyanax mexicanus is primarily governed by developmental programming and evolutionary adaptation rather than acute modulation of signaling pathways under the conditions tested.