VictorJuiz/thesis huggingface dataset:
Cell Permeant Peptides to Address SARS-CoV-2 Infectivity in vitro

Long COVID comprises a constellation of debilitating symptoms that persist following acute SARS-CoV-2 infection. Its causes are poorly understood, and there are no specific treatments. We hypothesized that SARS-CoV-2 infectivity is governed by discrete spike protein/human angiotensin-converting enzyme 2 (hACE2) interactions. Such interactions within the CNS may promote long COVID’s neurological manifestations. We aimed to identify peptides that inhibit these interactions in vitro for development as HIV-1 Tat-conjugated, cell and blood-brain barrier permeant, long COVID therapeutics. 5 SPOT array- or literature-derived peptides were evaluated in direct and competition enzyme-linked immunosorbent and fluorescence polarization assays. All peptides bound their target protein but failed to outcompete spike receptor binding domain (RBD)/hACE2, or their own, binding. The latter suggests non-specific binding. This was confirmed for one peptide, Spike_7-8, using a scrambled version. The published peptide, hACE2 P3, may therefore lack therapeutic potential, despite binding reproducibly. Additional strategies should be explored for future work.

Advisor: Tymianski, Michael
Exploring the Self-Diagnosis Experiences of Self-Diagnosed Autistic Women

BACKGROUND: Many Autistic women are misdiagnosed, diagnosed as Autistic later in life, or not identified or diagnosed at all. Some women choose to self-diagnose as Autistic, yet their experiences have not been explored in depth in Autism literature. This qualitative study explored the self-diagnosis experiences of Autistic women. METHODS: Seven people living in Ontario were asked about their self-diagnosis experiences through either a virtual interview or an open-ended questionnaire. Drawing on reflexive thematic analysis procedures, data was analyzed using critical Autism studies as a theoretical lens. RESULTS: Self-diagnosis aims were described as a way to find answers through professionals, the internet, and people in their lives. Self-diagnosis processes were described as increasing one’s self-acceptance, allowing one to sense-make life experiences, and make connections to Autistic communities. IMPLICATIONS: This research highlights the need for neurodiversity-affirming training for health professionals and the importance of Autistic communities for the wellbeing of Autistic people.

Keywords: Autism
Self-Diagnosis
Advisor: Hamdani, Yani
The Use of Variable Lymphocyte Receptor Tetramers to Characterize Circulating Plasmablasts in Antibody Deficiency

Early diagnosis of Common Variable Immunodeficiency and antibody deficiency (CVID/AbD), often due to impaired B cell development, can be challenging. A novel sea lamprey-based Variable Lymphocyte Receptor B antibody (V-CD38) that recognizes multimeric CD38 expressed on CD3-CD19+CD27hi plasmablasts, B cells that secrete antibodies, might better characterize peripheral blood B cell subsets, and help identify patients with CVID/AbD. Significantly reduced (p=0.002) plasmablasts were identified by V-CD38 in 11 patients with CVID/AbD (0.09%±0.13%) compared to 36 healthy controls (0.52%±0.57%), akin to the differences observed with a commercial anti-CD38 antibody (C-CD38). Furthermore, a strong correlation (p<0.00001) between V-CD38 and C-CD38 was observed. However, significantly (p=0.029) higher plasmablasts percentages were identified by a clinical lab using C-CD38, likely attributed to the increased specificity of V-CD38. Additionally, 54.1% of transitional B cells were recognized by V-CD38 antibodies. In conclusion, V-CD38 antibodies enable more accurate characterization of B cells and identification of patients with CVID/AbD.

Advisor: Grunebaum, Eyal
Microcosm Characterization of Microbial Sulfur and Carbon Interactions within the First Pilot Oil Sands Pit Lake, Base Mine Lake

This experimental study examined sulfur reduction, methanogenesis, anaerobic oxidation of methane and their relative responses to labile organic carbon amendment (lactate and microal-gae) in simulated oil sands pit lake (PL; Base Mine Lake; BML) fluid fine tailings- water inter-face (FWI) microcosms. Respective sulfate reduction and methanogenesis rates of 1.7 and 1.1 μmol/L/day both increased up to 240 μmol/L/day with labile organic carbon supplementa-tion. Further, sulfur reduction inhibited methanogenesis under labile carbon limiting conditions, but increased methanogenesis under high labile carbon loads. Increasing the rates of both pro-cesses pose a risk to BML water cap oxygen dynamics associated with the generation of oxygen consuming constituents, sulfide, and methane. Results identify that managing the balance be-tween oxygen producing primary production and subsequent oxygen consumption through aer-obic and anaerobic algal biomass decomposition will be critical to prevent increasing episodic anoxia currently observed in BML, informing future PL design as a fluid fine tailings (FFT) closure reclamation strategy.

Advisor: Warren, Lesley
Examining the Influence of Sex on the Risk of Future Musculoskeletal Injury Following Sports-Related Concussion

Background: Several studies have demonstrated that athletes are at a significantly increased risk of lower-extremity musculoskeletal injury following return to sport from a concussion. However, the risk of musculoskeletal injury and potential sex differences have not been adequately examined within the interuniversity athlete population. Objective: To determine if interuniversity athletes are at an increased risk of musculoskeletal injury following concussion and if there are any sex differences regarding this risk. Methods: A retrospective cohort study was completed involving 392 cases of 346 interuniversity athletes at the University of Toronto between 2015-16 to 2019-20. Athletes who suffered a concussion during this period (CONC group, n = 98) were matched, with replacement, to an athlete who suffered an index musculoskeletal injury (MSI group, n = 98) and to two healthy control athletes (CTL group, n = 196). Participant athletes’ musculoskeletal injury history for one year after returning to play were extracted from patient medical records. Generalized linear models using a Bernoulli distribution were developed to determine the difference in risk of future musculoskeletal injury between the three groups. Sex-stratified analyses were then performed using similar models to examine the presence of a potential sex difference. Results: The CONC group had an 82% (89% compatibility interval [CI] = 76 – 88%) likelihood of suffering a musculoskeletal injury within one year following return to sport compared to 73% (89% CI = 66 – 80%) for the MSI group and 56% (89% CI = 50 – 61%) for the CTL group. This translates to a 9 percentage point difference (89% CI = -0.01 – 0.18, 93.4% probability mass [PM] > 0) between the CONC and MSI groups, a 27 percentage point difference (89% CI = 0.18 – 0.35, 100% PM > 0) between the CONC and CTL groups, and a 18 percentage point difference (89% CI = 0.09 – 0.27, 100% PM > 0) between the MSI and CTL groups. Sex-stratified analyses demonstrated that males in the CONC group had an 86% (CI = 78 – 93%) probability of future injury compared to 75% (CI = 66 – 83%) among the female athletes in the CONC group. Conclusions: These results suggest that concussions pose the greatest risk of future injury, musculoskeletal injuries also pose a significant risk of injury following a return to sport. Furthermore, male athletes appear at greater risk for future injury following concussion than female athletes.

Advisor: Hutchison, Michael
Exploring the Context of Youth and Young Adult Immigrants in Stepfamilies in Canada

This phenomenological qualitative study explores the psychological adjustmentexperiences of youth and young adult immigrants in the context of stepfamily dynamics in Canada. Semi-structured interviews were conducted with five participants identified as immigrants who have lived in stepfamilies in Canada and grounded in Bronfenbrenner's Bioecological Model. The findings reveal the nuanced psychological adjustment experiences of youth and young adult immigrants in stepfamily settings in Canada, emphasizing the significant influence of individuals and communities on their adjustment. Close relationships particularly within families emerge as sources of both conflict and support. Results highlight the importance of social workers in identifying and addressing the diverse experiences of youth and young adult immigrants in stepfamilies and/or blended families in order to provide better services to support their needs. These findings aim to inform and improve social work practice, resulting in better outcomes for youth and adult immigrants in stepfamily and/or blended family contexts.

Keywords: Blended Families
Psychology
Stepfamilies
Young Adults
Youth
Advisor: Begun, Stephanie SB
In-Ear EEG Device for Auditory Brain-Computer Interface Communication

Scalp-based electroencephalography (EEG) is often deployed in non-invasive brain-computer interfaces with electrodes that are uncomfortable, not conducive to long-term wear and conspicuous. In-ear EEG devices have potential to address these limitations by measuring brain activity from within the ear canal. We designed, constructed, and tested a portable in-ear EEG device using commercially available components. Fifteen typically developing adolescents participated in a single session where simultaneous scalp and in-ear EEG were recorded during deliberate creation of artefacts. Data from 5 were analyzed. We confirmed that the new in-ear device was capable of alpha wave detection. In-ear measurements were most susceptible to contamination by head and biting motions, likely due to displacement of wires and related muscle activations. In the presence of artefacts, in-ear EEG signals appear to exhibit an inherent robustness to extreme values (strictly platykurtic amplitude distributions) and may afford a low-pass filtering benefit (narrower bandwidths than over scalp signals).

Keywords: Augmentative and Alternative Communication
Brain-Computer Interface
Electroencephalography
In-Ear EEG
Advisor: Chau, Tom
Public Health Financing in British Columbia: A Case Study Investigating Factors Influencing Decision-Making

To address the gap in research on public health financing in Canada, this study aimed to 1) describe public health budget-setting processes in British Columbia (BC), including roles of stakeholders involved, and 2) identify and analyse the factors influencing decision-making for public health resource allocation. My case study of the BC public health system consisted of a jurisdictional review of academic and grey literature on BC financing processes and trends spanning two decades, and semi-structured interviews with 14 key informants influential in budget-setting for public health. Taking an inductive analytical approach, I constructed a conceptual model of the political, structural, and external factors influencing public health financing decisions based on results from the case study. I conclude by identifying policy directions with potential for promoting stable public health funding, such as including public health experts in financial decision-making, and strengthening partnerships with external public health organizations. Pour répondre au manque de recherche sur le financement de la santé publique au Canada, cette étude a visé à 1) décrire les processus budgétaires de santé publique en Colombie Britannique (CB) en incluant les rôles des parties prenantes, et 2) identifier et analyser les facteurs influant la prise de décisions pour l’allocation de ressources à la santé publique. Mon étude de cas du système de santé publique de la CB a consisté en une revue juridictionnelle des littératures académique et grise sur les processus et tendances de financement en CB au cours des deux dernières décennies, et de 14 entrevues semi-structurées avec des participants clés influant l’élaboration du budget de santé publique. En prenant une approche analytique inductive, j’ai construit un modèle conceptuel des facteurs politiques, structurels, et externes influant les décisions de financement de la santé publique basé sur mes résultats de l’étude de cas. Je conclus en identifiant des options politiques avec le potentiel de promouvoir un financement de santé publique stable, telle qu’inclure les experts en santé publique dans la prise de décisions, et de renforcer les partenariats avec les organisations de santé publique externes.

Keywords: British Columbia
Budgeting
Financing
Funding
Health Policy
Public Health
Advisor: Pinto, Andrew D.
Allin, Sara
Comparing Sampling Methods for Measuring Atmospheric Microplastics in Rural and Urban Sites, using Laser Direct Infrared Spectroscopy (LDIR)

In recent years, there have been growing concerns regarding atmospheric-related microplastics and anthropogenically sourced particles. Atmospheric transport disperses these particles quickly and worldwide, deposition being an important source to terrestrial and ocean surfaces. Traditional air sampling methods were deployed and compared during this study, to investigate atmospheric-related microplastics and anthropogenically sourced particles using; active-air, bulk deposition, and wet deposition. Samples were deployed in a densely populated urban centre and at a rural site, between February 2022 and February 2023. Number of particles and diversity of polymer type and morphology were higher at the urban site. There was no statistical difference between the sampling methods used at either site. This implies the simple bulk deposition samplers can be confidently used to determine abundance and the diversity in polymer types and morphology in ambient air. The dominant polymer types at both sites were polyester, polypropylene, and anthropogenic cellulose (e.g., denim, cellulose acetate, etc.).

Keywords: Anthropogenic Fibre
Atmospheric Deposition
Atmospheric Pollution
Method Comparison
Microplastic
Advisor: Diamond, Miriam L
Jantunen, Liisa M
MRI-based Neurodevelopmental Outcome in Very Preterm Neonates

Preterm birth is the leading cause of lifelong disability globally and in Canada. Gaining insight to the different factors and variables that affect preterm neonatal neurodevelopmental trajectory can aid clinicians in introducing beneficial interventions. The work in this thesis focuses on using early in life brain imaging to predict the neurodevelopmental outcome as measured by the Bayley Score of Infant and toddler Development (BSID) at 18 months of age. The proposed method combines the usage of a convolutional neural network to segment the brain into coarse regions. The segmentation information, along with other patient metadata are used in a random forest model to predict the aforementioned outcome. Precision medication can be facilitated by utilizing the SHapley Additive exPlanations (SHAP) to highlight which factors are most in need of clinical intervention.

Advisor: Taati, Babak
Brudno, Michael
The Effect of Full-Fat Dairy Consumption on Body Weight, Body Composition, Energy Metabolism, and Blood Lipids

The hypothesis was that the addition of full-fat dairy combined with dietary advice based on Canada’s Food Guide would result in greater loss of weight and improved health markers in overweight and obese adults compared to an energy restricted diet. Three daily servings of full-fat dairy of milk, cheese, and yogurt were added to an energy restricted or ab libitum diet without energy restriction and compared to a low-dairy energy restricted diet in 65 healthy males and females. The design was a 12-week, randomized, parallel, multi-site study. Dietary treatments had no effect on body weight, body composition, waist or hip circumference, resting metabolic rate, or blood lipid concentrations, including LDL cholesterol and triglycerides. The results encourage further examination of the effects of full-fat dairy in the context of Canada’s Food Guide.

Keywords: Blood Lipids
Body Composition
Dairy
Energy Metabolism
Advisor: Anderson, Harvey
Waterborne 2-Component Polyurethane Coatings Based on Acrylic Polyols with Secondary Alcohols

While two-component waterborne polyurethane (2K-WB-PUR) coatings offer an environmentally friendly alternative to their solventborne counterparts, their performance is subpar in comparison to solventborne coatings. Characteristics of the components affect the miscibility and the formation of the film in ways which are not well understood. In this thesis, I investigated the film formation of a two-component waterborne polyurethane system comprised of an acrylic polyol with secondary hydroxyl groups (Mn ≈ 5100, 10300 or 12900 g/mol, Ð ≈ 3, Tg ≈ 20 °C) and a hydrophilically modified polyisocyanate (Basonat HW1000). I followed the film formation using spectroscopic techniques and found that higher molecular weight polyols limited the extent of molecular mixing in the film and lead to a higher relative ratio of polyurea to polyurethane in the film.

Keywords: Polyurethane
Two component polyurethane
waterborne coating
Advisor: Winnik, Mitchell A
Generation of Backward-Looking Complex Reflections for a Motivational Interviewing-Based Smoking Cessation Chatbot using GPT-4

Motivational Interviewing (MI) is a validated therapy for behavioural change that has shown success in helping smokers reduce or quit their smoking. The development of conversational agents that can guide a client through an MI therapeutic conversation may help increase the accessibility of MI across a wider populations of smokers. In the MIbot project a chatbot, named MIBot, aims to guide clients towards the decision to quit smoking, by MI-style reflections generated with a Transformer-based neural net architecture. Current iterations of MIBot have focused on the generation of both simple and complex reflections in a 5-question conversation, but these reflections are limited to the context of the immediate prior utterance of the client, and do not incorporate a client’s utterances from earlier in the conversation by themselves. In this work, we introduce the concept of the backward looking complex reflection (BLCR) which does incorporate earlier utterances as a relevant basis for a reflection. We present a method to automatically generate BLCRs using the prompting capabilities of Large Language Models (LLMs) such as GPT-4. To assess the effectiveness of this method, we generate 150 BLCRs over real MIBot-Client conversational interactions, and use a 4-point BLCR Rating Scale that measures the quality of a BLCR as assessed by three independent human raters. The results of this experiment indicate that an average of 88% BLCRs generated by this method were deemed acceptable, and all three raters agreed on these scores at least 80% of the time. We present examples of the generated BLCRs, make comparisons to earlier versions of MIBot reflections to display qualitative improvement.

Keywords: artificial intelligence
chatbot
motivational interviewing
natural language processing
smoking
Advisor: Rose, Jonathan
Investigating the Effect of Bedding Planes and In-situ Stress on Hydraulic Fracturing of Finely Laminated Rock Formations

Unconventional hydrocarbon development has witnessed increased activities in recent years. Unconventional target formations are composed of marine layered silts, shales, and carbonates and are characterized by ultra-low permeability. All these “shale” plays have also strongly layered anisotropic heterogeneity due to their depositional environment in anoxic, low energy, marine settings. Hydraulic fracturing is the process used to create and enhance permeability in such formations. Rock fabric and other directional-dependent (anisotropy) properties of shale rocks affect their failure modes and hydraulic fracturing (HF) propagation. In this work, the effect of anisotropy on the failure mechanism and strength of Montney siltstone was investigated by performing non-destructive wave velocity and uniaxial compressive strength (UCS) experiments on samples with different bedding plane orientations. The experimental results suggested the significance of bedding orientation on the strength, dynamic and static elastic moduli, failure mode, and wave velocity of the Montney siltstone. Also, the effect of differential in-situ stress on the HF propagation of two types of Montney siltstone rocks, namely "Middle" and "Lower" Montney, was evaluated by performing Finite Discrete Element Method (FDEM) simulations in the Irazu software. The numerical results showed that the direction, complexity, and failure mode of the fluid-induced fractures are highly dependent on the direction of the maximum principal stresses, as well as the differential in-situ stresses. Higher differential stress proved to induce offset shear-dominated fractures, while single tensile-dominated fractures were associated to lower differential stress conditions.

Advisor: grasselli, giovanni GG
The Transdermal Delivery of 1α,25-Dihydroxyvitamin D3 to Treat Secondary Hyperparathyroidism in Chronic Kidney Disease

Impaired renal formation of 1α,25-Dihydroxyvitamin D3 (1,25D) due to chronic kidney disease (CKD) is the primary cause of secondary hyperparathyroidism (SHPT) in CKD. Current 1,25D formulations are indicated only in advanced CKD due to risk of hypercalcemia. By delivering 1,25D via a transdermal patch, we aim to reduce hypercalcemia risk while effectively treatingSHPT. Methods: Utilizing 1,25D transdermal patches in a mouse model of CKD, single and repeated dose studies were conducted with 0.0048%w/w and single dose with 0.001%w/w strength patches. Results: 0.0048%w/w patches reduced parathyroid hormone (PTH); however, hypercalcemia arose. 0.001%w/w patches increased PTH via rebound once the concentration gradient from the patch to systemic circulation depleted. Conclusion: Hypercalcemia was not prevented by the patch. However, transdermal 1,25D delivery may be a viable option to treat SHPT in CKD by selecting a more representative CKD animal model and optimization of strength, dosing regimen and stability of the current formulation.

Keywords: calcitriol
chronic kidney disease
secondary hyperparathyroidism
transdermal
transdermal patch
Advisor: Macgregor, Robert
Determining the Mechanism of Rasputin (RIN) in Stimulating the Expression of mRNA in Drosophila melanogaster

Post-transcriptional regulation (PTR) in the cytoplasm controls mRNA stability, translation, and subcellular localization, and is mediated by RNA-binding proteins (RBPs). PTR plays an important role in conditions of stress where translational initiation is inhibited and stress granules (SGs) form. An essential component in SGs is the RBP family, G3BPs, which are conserved across eukaryotes. G3BPs have been extensively studied for their roles in SGs; their function in unstressed conditions remains relatively unknown. This thesis examines the Drosophila G3BP homolog, Rasputin (RIN), in unstressed cells. In the early fly embryo, I show that RIN is polysome-associated. I show specific residues within RIN’s conserved Nuclear Transport-like 2 (NTF2) domain are important for RIN-mediated stimulation. An IP-MS approach identified 19 proteins that interact with the wild type and not a defective mutant NTF2 domain. I show that 6 of them, MSP300, FMR1, ART1, ATX2, LIG, and TRAL, have a role in RIN function.

Advisor: Smibert, Craig