VictorJuiz/thesis huggingface dataset:
Reduce, Reuse, Refill: Understanding the Refill-based Sector in Ontario

As a reuse-based system, refills offer a starting point in reducing packaging waste and shifting our capitalist, linear economies towards more circular approaches. The concept of ‘refilling’ has been present since the advent of milk delivery services (Vaughan et al., 2007), however the study of what a refill is, and how it works in practice, is insufficiently understood. The purpose of my research is to fill this gap in understanding by investigating the motivations and challenges faced by retailers who offer refills of household and personal care products in a case study of Ontario. This qualitative study involved one-on-one, semi-structured interviews (n=23) with refill-based retailers across Ontario. Key findings include challenges such as customer education and recruitment, COVID-19 and having to ‘do it all alone’, and motivations, including environmental motivations. The implications of this study reveal that further research is needed on the accessibility of refills, and their economic and environmental viability.

Keywords: Circular economy
Refill
Reuse
Waste
Advisor: Maclaren, Virginia
Bone Health in Young Adults with Type 1 Diabetes and Progressive eGFR Decline

Introduction: Type 1 Diabetes (T1D) is associated with increased risk of fractures, worsened by microvascular complications.Objectives: To determine if progressive eGFR decline in youth with T1D is associated with worsened bone health and to assess the impact of demographic and diabetes variables on bone health. Methods: eGFR slopes were determined using four CKiDU25 measurements. Bone health was assessed in adulthood by HRpQCT and bone biomarkers. Linear regression analysis with adjustment for covariates was performed. Results: 44% of 99 participants had progressive eGFR decline. eGFR decliners had higher cortical porosity diameter than non-decliners. Longer diabetes duration was associated with higher trabecular separation and lower trabecular number. Higher 25 hydroxy-vitamin D was associated with decreased trabecular separation. Higher A1C and BMI were associated with lower bone formation. Conclusion: There was subtle micro-architectural changes in T1D associated with progressive eGFR decline. Low 25 hydroxy-vitamin D, long diabetes duration, poor glycemic control and higher BMI are associated with worsened bone health.

Keywords: bone biomarkers
Bone Health
eGFR
HRpQCT
Type 1 Diabetes
Advisor: Mahmud, Farid
Assessing Chronotype and Mood in an Integrated Day Treatment Program in Patients with a Major Depressive Episode (MDE)

Major Depressive Disorder (MDD) is the leading cause of disability worldwide. Most patients with a Major Depressive Episode (MDE) have sleep complaint(s). Chronotype is one’s preferred time of day to be active and awake. Having an evening chronotype has been associated with greater depression severity, and a higher likelihood of non-remission. Prior work in MDE patients attending Integrated Day Treatment (IDT) revealed that receiving treatment at a time opposite to one’s chronotype was associated with reduced depression severity. The present work aims to extend this work using objective measures of actigraphy and momentary mood assessment. Individual case analysis was conducted to assess changes in sleep, activity and mood from early-to-late treatment. Sleep and activity changes across treatment, and their relationship to treatment response, varied by patient. Participants treated during the COVID-19 pandemic had shorter sleep duration and higher sleep fragmentation. These preliminary findings will require further elaboration in larger samples.

Advisor: Levitan, Robert
Relation of Honey and its Constituent Rare Sugars on Cardiometabolic Health – An Epidemiological Analysis

The effect of honey and its constituent rare sugars on cardiometabolic outcomes is unclear. I conducted a systematic review and meta-analysis (SRMA) of controlled trials assessing the effect of honey on cardiometabolic outcomes. Independent reviewers extracted data and assessed risk of bias. Data was pooled using random-effects model. Heterogeneity was assessed (Cochrane’s Q) and quantified (I2). Certainty of evidence was assessed using GRADE. Pooled analysis of 33 trial comparisons (n=1105) showed that honey improved glycemic control and lipid levels. Rare sugars make up roughly 14% of sugars present in honey and may be contributing to the benefits observed. I conducted a second SRMA of clinical trials assessing the effect of rare sugars on cardiometabolic outcomes. Pooled analysis of 16 trial comparisons (n=1014) showed that allulose, isomaltulose, and tagatose may improve adiposity and glycemic control. In conclusion, both honey and its individual rare sugars may benefit cardiometabolic outcomes.

Keywords: honey
rare sugars
sugar
Advisor: Sievenpiper, John L
Pragmatic Development and a Learner’s Life on Study Abroad: A Case Study of a Japanese Learner of English

The present study examines L2 pragmatic development in requesting in study abroad, focusing on how an individual’s experiences impact development. The study reports on a longitudinal case study of a Japanese learner of English in her first two months studying in Toronto, Canada. The data consists of naturalistic recordings and memos the participant made herself throughout the two months and role plays conducted at the beginning and end of the study, for a total of 106 requests. Additional data includes the participant’s reflections made on her requests, and weekly semi-structured interviews, diaries, and L2 engagement logs. The analysis focuses on the evolution of the participant’s use of politeness strategies and her knowledge of rules and structures, considering the role of noticing, language socialization, and personal (e.g., motivation) and social (e.g., networks) matters. Findings reveal a complex relationship between the person, her experiences, and her use and development of requesting.

Keywords: Pragmatic Development
Requests
Study Abroad
Advisor: Kerekes, Julie
The Task- and Sex-specific Function of FTO During Memory in Female and Male Mice

Work investigating N-6 methyladenosine (m6A) established RNA modifications as novel regulators of memory in the male brain. Our lab showed that m6A demethylase fat-mass and obesity associated (FTO) protein is depleted, while m6A is accumulated during fear memory. Moreover, hippocampal FTO depletion improves fear memory in male mice, but the role of FTO and m6A has yet to be characterized in the female brain. I observed (1) if FTO and m6A are regulated similarly between sexes during fear memory and (2) the effect of hippocampal FTO depletion between sexes on fear and spatial memory tasks. I found that FTO and m6A expression is sex-specific during fear memory and FTO depletion has no effect on fear or spatial memory performance in females. However, FTO depletion impairs spatial and fear memory performance on harder but not easier learning tasks in males, suggesting that FTO has a sex- and task-specific function during memory.

Keywords: FTO
m6A
Memory Formation
RNA Modifications
Sex Differences
Advisor: Walters, Brandon J
Zovkic, Iva B
An Exploration of TRAP Exposure and Patterns of Environmental Inequality at a High Spatial Resolution in Etobicoke-York, Ontario

This thesis addresses two objectives. The first objective explores the use of high spatial density urban sampling and regression kriging to improve land use regression (LUR) modelling performance for predicting ambient nitrogen dioxide (NO2) at a high spatial resolution across Etobicoke-York, Ontario. The second objective explores marginalization as a potential mechanism for disparate NO2 exposure in Etobicoke-York. This objective was met by using ordinary least squares (OLS) regression and simultaneous autoregressive (SAR) modelling techniques to identify spatial associations between NO2 exposure and fine-scale metrics of marginalization and by computing odds ratios (ORs) to capture the effect of marginalization on the odds of high versus low NO2 exposure levels. This thesis highlights improvements in exposure modelling performance for the incorporation of high spatial density monitoring data and regression kriging, as well as identifies significant patterns of disparate NO2 exposure in Etobicoke-York related to ethnic concentration, material deprivation, and residential instability.

Keywords: Environmental Health
Environmental Inequality
Exposure Modelling
Geographic Information Science
Spatial Statistics
Transportation-Related Air Pollution
Advisor: Adams, Matthew
Drug-Induced Stabilization of G-Quadruplex-Duplex Hybrid Structures

A combination of spectroscopic techniques were used to investigate the stabilizing influence of the minor groove binders (MGBs) netropsin and Hoechst 33258 on a family of G-quadruplex-duplex hybrids (QDHs). Binding affinities were measured to monitor the extent of drug binding to QDH structures studied. Thermal stability measurements were conducted to evaluate the degree of stabilization afforded to each QDH structure by drug binding. Our results revealed a significant increase in the global stability of all DNA structures examined following binding of netropsin or Hoechst 33258. The hierarchal order of the increases in thermal stability suggests that the stabilization arises from drug binding to both the stem-loop and the GQ domains of the QDH structure, if the former contains an AT-rich binding site. Our results point to a novel, allosteric mechanism for the selective stabilization of four-stranded DNA structures at predetermined genomic loci, with implications for the control of genomic events.

Advisor: Chalikian, Tigran
Communication Subsystem Design and Assembly, Integration, Testing of the GHGSat Remote Sensing Microsatellite Constellation

The efforts of industrial operators to measure and quantify their environmental impact have been increasing exponentially in the past years. This interest lies particularly on greenhouse gas (GHG) and air quality gas (AQG) emissions. The GHGSat constellation aims to detect and quantify GHG emissions from orbit with pin-point accuracy. The GHGSat satellites were designed based on the NEMO bus developed by the Space Flight Laboratory. This thesis describes the design process of the communication subsystem for the newest iteration of the NEMO bus which is being developed to support the GHGSat constellation. Emphasis is given on miniaturized antenna design, development and testing process, link budget analysis and Assembly, Integration and Testing effort to build these satellites. The first cluster of GHGSat satellites was launched in May 2022 and is healthy in-orbit. This thesis also outlines the testing standards and procedures which ensure the success of the satellite missions following SFL’s design philosophy.

Keywords: antenna
communications
microsatellite
RF
satellite
Advisor: Zee, Robert E
Genetic Iinteractions between dNSF2 and l(2)gl, nwk, puc in Wing Development of the Drosophila melanogaster

In the development of the wings of the Drosophila melanogaster, dNSF2 is an important protein that functions to recycle SNARE proteins to allow vesicular trafficking to transport molecules necessary for development. Previous pilot studies observed three new genes l(2)gl, nwk and puc that have never been implicated in wing development. I have extended these studies by determining a genetic interaction between the three genes and dNSF2. I observed that l(2)gl is expressed in the wing disc where Wingless is expressed and that l(2)gl has effects of its own on wing development. Furthermore, puc is also expressed in the same region that Wingless and Decapentaplegic is expressed. Various mutations of nwk exhibit the same results on wing development as they did in the development of the Drosophila NMJ. Overall, these results suggest that these three genes are involved in wing development through multiple signaling pathways.

Keywords: Developmental Biology
Drosophila
NSF
Wing Development
Wingless
Advisor: Stewart, Bryan
Of Commoners' Ears and Eyes: Epistemic Status of Common People in Mozi and Xunzi

In the political discourse of early China, social-political stability and moral ethics could not be discussed separately from epistemology. To pursue the ideal dao, which is the way to flourish humanity, theorists strive to explain its nature epistemically. This thesis seeks to fill a gap in the existing discussion by going beyond the social elites in early China and inquiring into the epistemic status of the common people in two classics from two prominent schools, Mozi and Xunzi. I argue that the commoners’ apparent lower epistemic status in Xunzi than in Mozi is the result of competing conceptions of dao; specifically, that to Xunzi, dao is esoteric, while the Mohist dao is easily perceivable. These two opposing conceptions of dao lead to different outlooks on the common people’s understanding of dao, as the complexity of knowing the Xunzian dao is radically harder than understanding the Mohist one.

Keywords: Epistemology
Mohism
Mozi
Pre-Qin
Ruism
Xunzi
Advisor: Fraser, Chris
On the Explanation and Localization Ability of the Class Activation Map

Deep models such as Convolutional Neural Networks (CNN) are widely used in image classification. To explain the decisions made by these models, Class Activation Map (CAM) produces heatmap-style visualization that highlights discriminative image regions for the prediction by weighting over the feature map activation from the model. A critical problem when applying CAM-based methods to CNN explanation is that they are inconsistent over spatial transformations. In this thesis, we are interested in whether minimizing such inconsistency would benefit the overall explanation quality. We propose a loss function that regularizes the distance between CAM-based explanation maps of the original image and the transformed image during training. Our extensive evaluation demonstrates that this method improves the localization ability of CAM-based explanation maps while preserving classification accuracy. However, our results show no improvement in explanation faithfulness. Besides the CNN explanation, CAM is widely adopted to generate the pixel-level pseudo labels for the weakly supervised semantic segmentation (WSSS) task, thanks to its class-specific object localization ability. However, due to the local receptive field of CNNs, CAM applied to CNNs suffers from partial activation -- highlighting the most discriminative part instead of the entire object area, limiting the quality of the pseudo labels. To address this problem, we leverage the existing Conformer architecture, which contains a vision transformer branch with a global receptive field. We further propose a novel method that explicitly leverages the attention weights from the transformer branch of the Conformer to refine the CAM generated from the CNN branch. It is motivated by our observation that attention weights from shallow transformer blocks can capture low-level spatial feature similarities while attention weights from deep transformer blocks capture high-level semantic context. Our empirical result shows substantial improvement in CAM for WSSS. In summary, this thesis addresses the practical challenges of applying CAM to CNN explanation and pseudo label generation for the WSSS task.

Advisor: Sanner, Scott
Developing a Compound Computational Pathology Workflow for Automated and Integrated Analyses of Morphologic and Molecular Histopathological Features

Despite recent innovations in deep learning, attempts to automate the integration of histomorphologic and molecular information found on respective H&E- and IHC-stained tissue sections are scarce. Here, I aim to address this issue by incorporating computer vision tools, including deep learning and scale-invariant feature transform (SIFT), to align H&E-stained sections with accompanying IHC studies for automated subclassification of gliomas. I first trained a VGG19 convolutional neural network (CNN) to recognize histological patterns of 16 common tissue and lesion classes. Afterwards, I optimized several deep learning classifiers to recognize various IHC markers relevant for molecular subclassification of gliomas. For downstream integrated analyses, I employed SIFT to align lesional regions of H&E and IHC slides. The quantitative analysis of IHC WSIs significantly improved by using SIFT in conjunction with the classifiers. Collectively, these tools can provide a pathologist-inspired workflow to help automate advanced histopathology-based diagnostic tasks, such as subclassification of gliomas.

Keywords: Computer vision
Deep learning
Digital pathology
Histopathology
Image registration
Immunohistochemistry
Advisor: Diamandis, Phedias
The Role of Branched Chain Fatty Acids in Cardiometabolic Disorders Underlying Type 2 Diabetes in the PROMISE Cohort

Various fatty acids are linked with risk of type 2 diabetes (T2DM), although the branched chain fatty acids (BCFA) are under-investigated. This thesis aimed to (1) systematically review the available literature on the association of BCFAs with cardiometabolic disorders; and (2) investigate the relationship of BCFAs across 4 serum fractions with dietary intake and analyze the longitudinal association between BCFAs and pathophysiological disorders underlying T2DM. Three of the 4 studies identified in our review reported significant inverse associations between circulating BCFAs/monomethyl BCFAs and insulin sensitivity. Correlations between total dairy and BCFAs showcased pool specific results. Our longitudinal analysis documented heterogenous results that were largely modest in magnitude and significance. Most notably, iso15:0 and anteiso15:0 (NEFA) were positively associated with measures of insulin sensitivity while iso14:0 and anteiso14:0 (NEFA) were inversely associated with the same measures. Our findings highlight the need for additional research on BCFAs and their role in cardiometabolic outcomes.

Keywords: Branched chain fatty acid
Cardiometabolic
Diabetes
Advisor: Hanley, Anthony J
Bazinet, Richard P
The Effects of USMB Combined with Fractionated Radiation Therapy on Tumour Vasculature and the ASMase-Ceramide Pathway

Radiation therapy induces damage to tumor cells directly or indirectly via DNA damage, leading to tumor response. Previous studies have indicated that radiation therapy can be enhanced when combined with the vascular targeting effects of ultrasound-stimulated microbubbles (USMB). This USMB radioenhancement occurs via the activation of acid sphingomyelinase (ASMase). Clinical studies are currently looking into implementing USMB alongside radiation therapy to treat cancer patients. The work presented in this thesis determined the effects of fractionated radiation therapy combined with USMB on the tumor vasculature. Mice were divided into 3 categories, ASMase wild type, ASMase double knockout and ASMase wild type treated with sphingosine-1-phosphate. The results demonstrated the enhancement of cell death and reduced vasculature in combination treatments. Power Doppler ultrasound was used to observe vascular changes non-invasively. In conclusion, USMB can induce vascular disruption in an ASMase dependent manner, while enhanced tumor cell death potentially occur independent of ASMase activity.

Keywords: ASMase
Cancer
Ceramide
Microbubbles
Radiation
Ultrasound
Advisor: Czarnota, Gregory GJ
Hardening the Soft Information in Earnings Calls

Analyzing textual corpora in the finance domain flourished when Tetlock first introduced “soft” information analysis that can help predict market reactions. Most approaches quantify soft information using static dictionaries and do not take advantage of the recent state-of-the-art language processing techniques. This thesis proposes a new text mining methodology that analyzes the sentiment of public companies’ earnings calls to forecast market reactions. We expand on past literature by applying one of the most contemporary natural language processing techniques (i.e., FinBERT) to the transcripts of earnings calls. The resulting sentiment scores are compared against those produced by existing dictionary-based mechanisms: (a) the static dictionary of Loughran and McDonald and (b) dynamic dictionaries constructed based on multinomial inverse regression. Our experiments demonstrate that FinBERT outperforms static dictionaries and is on par with dynamic dictionaries. Finally, we observe that the Q&A portion of earnings calls explains the company returns better than other segments.

Advisor: Veneris, Andreas
A Mathematical Model of Promoter Methylation in the Circadian Clock

Recent experiments suggest that DNA methylation plays a role in altering the period of the circadian clock. We add a mechanistic perspective to these findings by showing that DNA methylation contributes to period regulation in a simple mathematical model of the circadian clock. Perturbative analysis reveals that methylation only compresses the period in a certain limit, similar to the experiments that motivated this work. Analysis of a reduced model suggests that methylation regulates the period through a two-step mechanism involving Hopf bifurcations. Our reduced model is similar in structure to a model studied by Kim and Forger. We show how both models can be obtained as approximations of a more detailed model. Finally, we show that methylation may allow the clock to operate with effectively altered parameters for the non-methylated promoter states. Our entire analysis supports the argument that DNA methylation plays an important regulatory role in the circadian clock.

Keywords: Asymptotic analysis
Bifurcation theory
Circadian biology
Epigenetics
Mathematical biology
Nonlinear dynamics
Advisor: Stinchcombe, Adam R
“Next Stop, Sayville”: COVID-19, Precarious Labour, and Queer Memory Work on Fire Island

Grounded within the experience of seasonal workers on Fire Island, New York during the Summer 2020 vacation season, this thesis exists at the intersection of COVID-19, precarious labour, and queer memory work. Examining the impulse toward forgetting held by many community members on the island, the author parses out the concept of “safe havens,” exploring both their value and their limitations – most acutely in relation to 2020’s Black Lives Matter protests. Turning inward, Evans explores the difficulty of embodied research creation amid overwhelming grief and personal loss. Finally, he uses oral history interviews conducted with Fire Island colleagues to position the concepts of recreation, refusal, and reciprocity as integral to an understanding of Fire Island during COVID-19. Through the modalities of oral history and autoethnography, Evans engages in a historiographical project that centres subjects often left out of Fire Island’s storied past and present.

Keywords: COVID-19
Fire Island
leisure
mental health
precarious labor
safe haven
Advisor: Keilty, Patrick
Effects of Mild Corrosion on the Tensile Strength of Reinforced Concrete Specimens with Transverse Cracks

The effect of mild corrosion on the tensile response of reinforced concrete was studied. Ten 700 mm-long specimens were fabricated with varying reinforcement ratios. Transverse cracks were generated on all specimens by uniaxial tension to 0.3% strain. At this stage, lower reinforcement ratios led to higher tension stiffening. Half of the specimens were then placed in a corrosion chamber for eight weeks for accelerated chloride-induced corrosion under a continuous 5 wt.% NaCl solution spray. Subsequent tensile tests on corroded and uncorroded specimens suggested that mild corrosion slightly improved the tension stiffening behaviour, increased the structural capacity by 4.7% to 9.4%, and only slightly reduced stiffness by 2.8% on average. These results imply that timely maintenance at early-stage corrosion can be effective in preventing loss of capacity that further corrosion will undoubtedly cause. Future research will examine the effects of severe corrosion, longitudinal cracks, and simultaneous corrosion and loading.

Keywords: Accelerated Corrosion
Corrosion of Steel Reinforcement
Reinforced Concrete
Tension Stiffening
Advisor: Azhari, Fae