VictorJuiz/thesis huggingface dataset:
Cross-Modal Data Fusion for 3D Instance Segmentation of Indoor Scenes

Tremendous strides have been made in image-based scene understanding over the past decade, thanks to larger datasets and enhanced model capacity. However, 3D-based understanding still struggles, in part because 3D data are so costly to annotate. Top 3D instance segmentation models, trained exclusively on 3D data, outperform models using both 2D and 3D data, suggesting untapped potential in merging 2D data to enrich 3D pipelines. Interestingly, while instance segmentation has not yet benefited from 2D-3D data fusion, the sequential fusion of outputs from 2D and 3D models that are trained separately does improve object detection. This thesis applies sequential fusion to instance segmentation and investigates what and where to fuse. We demonstrate that current 2D models do not perform well enough compared to 3D models to enhance instance segmentation results, but that future, higher-performing 2D models should show performance gains using the sequential fusion method.

Keywords: Artificial Intelligence
Computer Vision
Fusion
Robotics
Segmentation
Advisor: Kelly, Jonathan
The Health System of the First Nation of Na-Cho Nyäk Dun and its Ability to Meet the Community’s Needs

Ambiguous federal, provincial, and territorial policies in Canada have led to a jurisdictional dispute over the responsibility of Indigenous health, resulting in a fragmented system that has hindered Indigenous peoples access to high-quality, culturally appropriate care. The Government of Canada has begun to acknowledge the inadequacy of the contemporary health legislation for Indigenous peoples and has committed to developing distinct legislation for First Nations, Inuit, and Métis Peoples. Collaborative engagement is underway, and as the health policy climate continues to encourage increased collaboration, it is imperative that the voices of all Indigenous communities are adequately heard and reflected in future legislation. Among the 14 First Nations in Yukon, the First Nation of Na-Cho Nyäk Dun (FNNND) faces significant challenges within their health system. This exploratory community-partnered study drew on the WHO Health System Framework and used qualitative interviews and document review to gain deeper insights into the FNNND's health system and its alignment with the community's health needs. By identifying strengths and weaknesses, the research intends to inform future healthcare policy and legislation to better meet community needs.The study unveiled numerous issues concerning the role of the Government of Canada and the Government of Yukon, such as the failure to transfer meaningful health programs and services to the community, and those that have been transferred and assumed by the FNNND are often not in line with the priorities of the community. This research sheds light on the territorial context in the delivery of health services to Indigenous communities, and the findings may be beneficial to other Yukon First Nations with similar structures within their health systems.

Advisor: Mashford-Pringle, Angela
Allin, Sara
A Quantitative and Qualitative Analysis of Household Organic Waste Diversion in Toronto, Canada

Improving waste diversion is identified as one of the important strategies for municipalities to reduce carbon emissions. Toronto has developed a set of climate goals and one goal aims to reach higher residential diversion rates. However, it has not yet reached the target in the single-family homes and multi-residential buildings sectors. However, the current organic waste diversion situation indicates that there is potential to reach those targets. Considering that there will be a growing population and the low diversion rate in this sector, an analysis that focuses on improving household organic waste diversion in both sectors was conducted. Using quantitative and qualitative methods, the research evaluated the carbon emissions of Toronto's household organic waste, identified effective strategies to increase household organics diversion, explored their applicability in Toronto, and recommended six strategies to help Toronto reach its climate targets, increase organic waste diversion, and facilitate low-carbon transition.

Keywords: Carbon Emissions
Household Organic Waste
Sustainability Transition
Waste Diversion
Waste Management
Advisor: Robinson, John JR
Maternal Antibody Transfer and Atopic Sensitization in Offspring

Maternal antibody transfer in pregnancy and breastmilk is implicated in the development of allergen-specific responses in children. Human studies investigating the effect of maternal allergen-specific IgG (sIgG) on allergic diseases in offspring are limited. Maternal sIgG in breastmilk and serum was measured in a subset of the CHILD birth cohort using an allergen macroarray and compared against sIgE of the child at 12-months (n=266). Hierarchical clustering of breastmilk sIgG was used to analyze the impact on atopic outcomes via multivariable logistic regression models. Breastmilk sIgG did not directly correlate with 12-month outcomes regardless of maternal atopic status. Higher breastmilk sIgG was a significant risk factor for skin prick test positivity at 12-months to food (OR 1.90 [1.07-3.41], p=0.030). Mean breastmilk/serum sIgG were significantly lower among IgE-sensitized children for cashew and Ara h 2, and higher for almond and ovalbumin. Relative abundance of breastmilk/serum sIgG may affect IgE-sensitization in offspring.

Keywords: antibodies
atopic sensitization
birth cohort
breastmilk
IgE
oral tolerance
Advisor: Moraes, Theo J.
Eiwegger, Thomas
The Effects of Antipsychotics on Central Lipid-Mediated Regulation of Glucose Metabolism

Antipsychotics are associated with adverse metabolic side effects. Central fatty acids strongly regulate whole-body glucose homeostasis. We examined the effects of the antipsychotics olanzapine and haloperidol on central sensing of the fatty acid oleic acid and subsequent regulation of peripheral glucose metabolism. Pancreatic euglycemic clamps were used to assess changes in glucose kinetics. Male rats were co-treated with a continuous central infusion of oleic acid or vehicle into the third ventricle and a subcutaneous injection of olanzapine, haloperidol, or vehicle. Intracerebroventricular (ICV) oleic acid infusion caused an increase in peripheral glucose infusion rate compared to ICV vehicle which was prevented by co-treatment with olanzapine or haloperidol. ICV oleic acid suppressed hepatic glucose production and increased glucose utilization. Both effects were abolished by co-treatment with olanzapine or haloperidol. Olanzapine and haloperidol disrupt the ability of central oleic acid to regulate peripheral glucose kinetics, resulting in impaired whole-body glucose metabolism.

Keywords: Antipsychotics
Glucose homeostasis
Hypothalamus
Nutrient sensing
Schizophrenia
Advisor: Hahn, Margaret K
Object-centric Approaches for the Abstraction and Reasoning Corpus

This thesis explores two object-centric approaches to solving the Abstraction and Reasoning Corpus (ARC), a benchmark dataset for Artificial General Intelligence. The first approach employs a search-based technique, introducing a novel framework, Abstract Reasoning with Graph Abstractions (ARGA), which represents images as graphs and performs a constraint-guided search in a Domain Specific Language based on the abstracted graph space. Our experiments show the promise of ARGA in tackling some of the complicated object-centric tasks of the ARC rather efficiently, producing programs that are correct and easy to understand. The second approach uses Large Language Models (LLMs), and explores their direct application to the ARC as well as their augmentation with ARGA as an external tool. We find that LLMs reason much better when provided with object-based representations. These contributions advance our understanding of the capabilities and limitations of current AI models in abstract reasoning tasks, provide valuable insights into the design of future models and benchmarks for general artificial intelligence, and align our methods with fundamental aspects of human cognition, potentially bringing us closer to the goal of achieving Artificial General Intelligence.

Keywords: Abstraction and Reasoning Corpus
Few-shot Learning
Graph Representation
Heuristic Search
Large Language Models
Prompt Engineering
Advisor: Khalil, Elias
Sanner, Scott
Cognitive and Emotional Well-being of Preschool Children Before and During the COVID-19 Pandemic: Evidence from a Canadian Birth Cohort

The current study examines the association between pandemic exposure and child neurocognitive and socioemotional development at 24 months (N =718) and 54 months (N =703). Participants were recruited as part of the Ontario Birth Study (OBS), a prospective pregnancy cohort in Canada. Neurodevelopment was measured using the ASQ-3 and MCHAT-R at 24 months. The NIH Toolbox was used to assess neurocognitive and socioemotional function at 54 months. Analyses included logistic or linear regression with covariate adjustment. At 24 months, pandemic-exposed children had higher problem-solving and fine motor skills, but lower personal-social skills, compared to non-exposed children. At 54 months, pandemic-exposed children had significantly higher receptive vocabulary, visual memory, and overall cognitive performance compared to non-exposed children, with no differences found for socioemotional development. In this relatively advantaged and somewhat homogenous Canadian sample, evidence for both positive and negative associations between pandemic exposure and preschool children’s cognitive and emotional well-being were observed.

Advisor: Wade, Mark
It’s time to go: Ecological and Social Drivers of Nest Emergence in Turtles

At the hatchling life stage, turtles are hypothesized to coordinate digging activity to synchronize nest emergence and adapt to unpredictable environmental conditions. However, as the social life history of non-avian reptiles remains relatively incomplete, understanding the social and ecological mechanisms behind this behavior is crucial. In this study, we investigated whether acoustic communication facilitates nest emergence in hatchling snapping turtles (Chelydra serpentina). Through in-situ field experiments spanning two summers, we monitored subterranean nest behavior using acoustic recorders and emergence behavior with wildlife cameras. We found that snapping turtles showed some evidence of within-nest emergence synchrony but did not show evidence of among-nest emergence synchrony. Structural Equation Modeling revealed that hatchling vocalizations, temperature, and time of day primarily influenced movement within the nest. These findings offer evidence that hatchling turtles synchronize their behaviors with above-ground conditions, with vocalizations potentially playing a role in cueing synchronized nest emergence.

Keywords: Behaviour
Bioacoustics
Deep Learning
Evolutionary Ecology
Field Ecology
Non-avian reptile
Advisor: Rollinson, Njal
Davy, Christina M
Pedestrian-Oriented Communities: Regenerating Critical Neighborhoods using GIS, Multi-Objective Optimization Design, and Simulation Tools to increase Social and Environmental Sustainability Performance

With cities generating 70% of global greenhouse gas (GHG) emissions and struggling to effectively manage population growth, housing affordability, social equity, and environmental justice, this thesis seeks to assess the capacity data-driven and climate-responsive urban renovations have to address climate change challenges and inequity present in Toronto neighborhoods when implementing green infrastructure and setting transit and pedestrian mobility targets. With the use of multi-objective optimization design algorithms and subsequent digital simulation tools, the intent of this thesis is to virtually simulate the effects of site redevelopment and to discuss the ways in which the domains of civil engineering, urban planning, and architecture are limited in addressing inequity while reflecting on the roles of monetary systems, upfront carbon, social structures, policy, and governance. The outcome is the generation of a decision-making process designed to support GHG emission reduction targets for a neighborhood while promoting its sustainable development.

Keywords: GHGs
GIS
Multi-Objective Optimization
Parametric Design
Simulation
Sustainability
Advisor: Jakubiec, Alstan
Streptococcus Salivarius Secretes Novel Lantibiotics with Dual Antibiofilm and Immunomodulation Bioactivities

Commensal bacteria that rarely cause any infections in humans are a rich source of beneficial peptides. Streptococcus salivarius, a predominant commensal colonizing the oral cavity, produces a diverse group of peptides called salivaricins, most of which belong to the lantibiotics family. Lantibiotics are ribosomally synthesized and posttranslationally modified peptides (RiPPs) capable of impairing pathogens’ colonization and promoting healthy microbiomes. This study identified a novel salivaricin produced by S. salivarius strain SALI-10 isolated from a healthy human adult that exhibits selective antimicrobial activities against known periodontitis-associated and other multi-drug resistant (MDR) pathogens while sparing the commensals. Further structural characterization revealed that the antimicrobial compound consists of three related lantibiotics, collectively referred to as salivaricin 10. A saliva-derived multispecies biofilm model developed in this study showed salivaricin 10’s selective antibacterial properties. Moreover, confocal microscopy imaging revealed that salivaricin 10 can reduce biofilm thickness and destroy biofilm architecture. Strikingly, salivaricin 10 was found to suppress pro-inflammatory and promote anti-inflammatory macrophages polarization. This study sets the stage for future development of salivaricin 10 as an oral antimicrobial therapeutic agent with multiple distinct bioactivities.

Advisor: Glogauer, Michael MG
An Automated Impedance Matching Network for Wireless Power Transfer

Wireless power transfer (WPT) is an emerging technology that enables the transmission of electrical energy without the need for physical connections. The extensive applications and growing popularity of WPT make it a promising technology for convenient and efficient charging in various industries, such as consumer electronics, biomedical devices, and electric vehicles. However, the efficiency of WPT systems can vary due to changes in device types and distances, leading to impedance mismatches and energy losses. To address these challenges, this thesis introduces an innovative transmitter-side automated impedance matching network (IMN) that intelligently detects and adapts the transmitter's impedance to optimize power transfer, thereby enhancing the overall efficiency of the WPT system. Experimental validation confirms the effectiveness of the IMN design, showcasing efficiency gains of up to 12.4% across the operating range for a WPT system delivering up to 16 W at 250 kHz.

Keywords: Impedance Matching Network
Power Electronics
Wireless Power Transfer
Advisor: Ng, Wai Tung
Social (Media) Justice Education: The Neoliberal Limitations of a Popular Feminist Instagram Account

This study looks at the changes of popular social justice-oriented Instagram account @feminist between January 2020 and May 2022, with regard to the ways the murder of George Floyd on May 25, 2020, and the Atlanta Spa shooting on March 15, 2021, may have influenced these changes. Informed by critical race feminisms and anticolonialism (among other frameworks), this critical discourse analysis examines the content, language, frameworks and posting patterns of @feminist to discern whether the apparent changes in public discourse since the summer of 2020 have led to meaningful shifts towards more critical and radical social justice frameworks. Findings from this study demonstrate shifts in the subject matter and the format of @feminist’s content. Originally reposting more memes and artwork, @feminist began gradually including more informative slideshows and infographics on anti-racism in their content following the civil unrest of Spring 2020 and eventually shifted to include intersectional feminisms and broader social justice topics by the start of 2021, following an administrative change. However, despite these shifts in subject matter, analysis shows a continued neoliberal framework in @feminist’s content across the two years examined that point towards a reliance on individualism and social media activism that does not advocate for community and that does not incite more radical action for systemic change. This study brings into perspective a critique of the current state of social media activism and the limitations of social justice advocacy on Instagram.

Keywords: black feminism
Black Lives Matter
critical race feminism
Instagram
social media activism
Stop AAPI Hate
Advisor: hampton, rosalind
Delisted Routine Eye Exams and the Increased Use of Family Physicians and Ophthalmologists for Glaucoma Diagnosis

Purpose: To investigate if delisting routine eye exams in 2004 for Ontarians aged 20-64 was associated with increased use of family physicians (FPs) and ophthalmologists for new glaucoma diagnoses.Methods: The utilization of FPs and ophthalmologists for new glaucoma diagnoses from 1997-2019 was analyzed using administrative data and interrupted time series analysis. Results: In policy-affected groups, FP utilization for glaucoma diagnoses significantly increased post- versus pre-delisting: 14.6% (95% confidence interval [CI] 11.0%~18.3%) for the 20-39 group and 9.9% (95% CI 8.2%~11.5%) for the 40-64 group. Ophthalmologist utilization for glaucoma diagnoses increased substantially: 41.5% (95% CI 37.8%~45.3%) for those 20-39 and 40.3% (95% CI 35.7%~45.0%) for those 40-64. In the policy-unaffected 65+ group, minimal increases were observed: 1.9% (95% CI 0.6%~3.2%) for FPs and 4.4% (95% CI 0.4%~8.4%) for ophthalmologists. Conclusions: Delisting routine eye exams for individuals aged 20-64 was associated with increased use of FPs and ophthalmologists for glaucoma diagnoses.

Keywords: Delisting
Glaucoma
Health Policy
Routine Eye Examinations
Utilization of family physicians
Utilization of ophthalmologists
Advisor: Jin, Ya-Ping
Impact of Traumatic Spinal Cord Injury on Income and Employment Status in a National Canadian Cohort

Background: Spinal Cord Injury (SCI) causes drastic changes to an individual’s health that can affect returning to work. Objective: To use national administrative health and tax databases to estimate the impact of SCI on income and employment. Study Design: A retrospective cohort study of adults who were hospitalized with SCI in Canada between January 2005 and December 2017. Main outcomes: The first outcome was the change in individual annual earnings up to 5 years postinjury. The second outcome was the changes in employment status up to 5 years postinjury. Results: The mean annual decline in earnings in the 5 years postinjury was -$21,435 (95% CI, −$26,028 to −$16,841). Five years postinjury 50% of injured individuals were employed, a decrease of -18 (95% CI, -22, to -17) percentage points. Conclusions: SCI had a significant association with a decrease in employment and earnings postinjury for adults aged 18 to 64 in Canada.

Keywords: econometrics
health economics
Spinal Cord Injury
Advisor: Witiw, Christopher
The Association Between Maternal Preconception BMI and Early Childhood Nutrition

Background: It is unknown if maternal preconception BMI is associated with nutritional risk factors in early childhood and whether total breastfeeding duration plays a mediating role. Methods: Children ages 18 months to 5 years were recruited from TARGet Kids!, a primary care practice-based research network in Canada. Linear mixed effects models were fitted to analyze associations between maternal preconception BMI and child nutritional risk (measured through the NutriSTEP®), and mediation analyses were completed to investigate if total breastfeeding duration played a mediating role. Results: This study included 4733 children with 8611 observations. Each 1 unit increase in maternal preconception BMI was associated with a 0.09 increase in nutritional risk (95% CI 0.05, 0.12, p= <0.001), where 13.2% (95% CI: 7.1, 21.2) of the association was mediated through total breastfeeding duration. Conclusion: Higher maternal preconception BMI was associated with higher child nutritional risk, which was partially mediated by total breastfeeding duration.

Keywords: Body Mass Index
Breastfeeding
Child Eating Behaviours
Child Nutritional Risk
Preconception Health
Prospective Cohort
Advisor: Birken, Catherine S
Acceptability of Sexual Orientation Disclosure Interventions in Primary Care Survey

Background: Coming out is a barrier for gay, bisexual, and other men who have sex with men (gbMSM) accessing primary care. The objective was to quantify and explore correlates of the acceptability of interventions that could support sexual orientation disclosure to providers among gbMSM.Methods: I conducted a cross-sectional survey among Ontario gbMSM to ascertain the acceptability of ten potential interventions using a 4-point Likert-scale. I used logistic regression to identify characteristics associated with acceptance of the two least acceptable interventions. Results: Most participants (n=404, Mean age=39, SD=12.2) were cis-male (91.3%), gay (81.6%), and White (60.8%). A performance-based incentive program and an inclusive intake process intervention were the two least acceptable. Acceptability was associated with being non-Canadian born, PrEP eligible, generally “out", and reporting household-income ≤$90,000, high discriminatory experiences, and LGBT community connectedness. Conclusions: The least acceptable interventions may be deprioritized but could still support gbMSM experiencing minority stressors.

Keywords: gbMSM
HIV
minority stress theory
primary care
sexual and gender minorities
sexual orientation disclosure
Advisor: Tan, Darrell DT
Outcomes of Oral Epithelial Dysplasia Managed by Observation versus Excision

Background: The purpose of this study was to determine if surgical excision of oral epithelial dysplasia (OED) impacts malignant transformation or improves survival outcomes in lesions that progress to cancer. Design: All patients diagnosed with OED between 2009 and 2016 at SBHSC were included and clinicopathological findings were monitored until January 2022. Chi-squared test, Fisher’s exact test, and logistic regression models were used to assess associations between OED management and clinical outcomes. Kaplan-Meier survival curves and Cox proportional hazard models were used for survival analyses. Results: 155 cases of OED met the inclusion criteria. The overall malignant transformation rate was 27%, with an annual rate of 6.4%. Surgical excision did not decrease malignant transformation rate but was associated with lower oncologic staging at the time of diagnosis and improved survival. Conclusions: Surgical excision of OED did not reduce the rate of transformation to oral cancer but resulted in lower oncologic staging at diagnosis. Our data supports that appropriate sampling, independent of margin status is critical for early diagnosis of cancer and should be considered the standard of care in patients with OED.

Keywords: Epithelial Dysplasia
Erythroplakia
Leukoplakia
Oral Cancer
Oral potentially malignant disorders
Oral Precancer
Advisor: Magalhaes, Marco
Blanas, Nick