VictorJuiz/thesis huggingface dataset:
Exploring Seasonal Variation of Liver and Muscle Mercury in a Freshwater Sport Fish, Lake Trout (Salvelinus namaycush)

Mercury (Hg) is a contaminant that reaches elevated concentrations in fish, posing a threat to human health. Hg in fish varies widely among populations and species; however, the influence of seasonal dynamics in temperate fish feeding ecology, behaviour, and physiology on their Hg concentrations is unexplored. We investigated whether liver and muscle Hg varied seasonally in a freshwater sportfish, lake trout (Salvelinus namaycush), in two lakes and two consecutive years. We foundthat Hg varied seasonally in muscle, but liver Hg was variable and did not display consistent seasonal patterns. Fork length, liver C: N and, in some models, δ15N (trophic position), were predictors of liver Hg, but not sex or δ13C (habitat use). 44% of fish captured had muscle Hg that exceeded Health Canada commercial consumption guidelines. Our findings shed light on temporal dynamics of fish Hg and suggest that consumption advisories should consider seasonal variability of Hg concentrations in temperate freshwater fishes.

Keywords: consumption advisory
ecotoxicology
fish ecology
mercury
seasonal variation
spawning
Advisor: McMeans, Bailey C
Identifying BBK32 Sequences Mediating the Borrelia burgdorferi Catch Bond Adhesion Mechanism

Lyme disease, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne disease in North America. The bacterium's dissemination within the host is facilitated by its adhesion to endothelial cells (ECs), a process mediated by the bacterial protein BBK32. This study aimed to identify the specific BBK32 sequences essential for B. burgdorferi adhesion to ECs under physiological shear stress conditions. We generated a library of BBK32 internal deletion and truncation variants and examined their ability to mediate dragging interactions on human umbilical vein endothelial cells (HUVEC) under shear stress. Our results revealed that BBK32 amino acids 158-182, which are located within the core fibronectin (Fn)-binding domain and have previously been implicated in the formation of polymerized superfibronectin (sFn), were crucial for pFn-dependent catch bond interactions with ECs. Deletion of these residues resulted in a significant reduction in dragging interactions. Furthermore, we found that multiple non-Fn-binding sequences throughout BBK32 were not essential for but contributed to dragging on ECs under shear stress, suggesting that these sequences may play supportive or modulatory roles in Fn-interacting and catch bond activation functions. Our findings provide new insights into the molecular mechanisms of B. burgdorferi adhesion to ECs, highlighting the potential of BBK32 as a target for therapeutic strategies to prevent Lyme disease dissemination. Future research should focus on validating these findings in vivo and exploring the development of therapeutics targeting the Fn-binding region of BBK32.

Keywords: Borrelia burgdorferi
catch bond
Lyme disease
Shear stress
Advisor: Moriarty, Tara J
HIV-Related Stigmas, Health Care Empowerment, and Self- Rated Health Among People Living with HIV in Ontario

HIV-related stigma negatively impacts the health of people living with HIV; however, uncertainty remains around the mechanisms through which this occurs. Health care empowerment, which is defined as being engaged and committed to one’s care, and resilient to setbacks in health, may be a significant factor. As such, this study examined if health care empowerment mediated the relationship between HIV-related stigmas and self-rated health and how demographics may play a role, using the 2018 Ontario People Living with HIV Stigma Index Study. Results using ANOVA/Students t-tests and multiple linear regression/mediation showed that internalized, enacted, and anticipated stigma were all significantly elevated and related to self-rated health. Additionally, health care empowerment mediated internalized stigma and self-rated health’s association and was significantly lower for those who were younger, living with HIV for 10 or less years, heterosexual, and had less than high school education. Findings suggest the potential benefits of focused interventions.

Keywords: Health care empowerment
HIV
Ontario
Self-rated health
Stigma
Advisor: Rourke, Sean B
Automated Diagnosis of Liver Allograft Fibrosis using Machine Learning Approaches

Purpose: To determine if machine learning can be leveraged to develop non-invasive diagnostic tools for liver graft fibrosis.Methods: Using 1,804 ultrasound (US) studies from 1,131 patients with a nested 10-fold cross-validation approach, we trained artificial neural network (ANN) and support vector machine models on demographic, clinical, and serum data to predict significant fibrosis. US images was used to train a residual network 18 (ResNet18) model to non-invasively diagnose advanced fibrosis. Results: The ANN model’s performance was superior with the best models’ validation AUCs ranging from 0.74-0.77 and test set AUC range of 0.77-0.81. The ResNet18 model was unable to diagnose advanced graft fibrosis using US images, leading to the training AUCs range from 0.89-0.97, while the validation and testing AUCs were between 0.43-0.63. Conclusion: This study determined machine learning may be leveraged to non-invasively diagnose graft fibrosis using demographic, clinical, and serum data but not with US imaging.

Advisor: Bhat, Mamatha
Mitigating Aviation’s Climate Change Impact: An Analysis of Post-Pandemic State Action Plans

The international aviation industry is a contributor to climate change because of its large and growing release of greenhouse gas emissions. The International Civil Aviation Organization (ICAO) encourages its member states to develop strategies aimed at tackling climate change impacts from the industry, which are known as State Action Plans (SAPs). As the industry returns to growth following the Covid-19 pandemic, many are thinking of ways to decarbonize. Through the analysis of 61 SAPs, this research aims to identify the mitigation measures undertaken by states to limit emissions from the aviation industry, and importantly also looks for any evidence of policy transfer or lesson drawing between states, and between states and ICAO. Findings demonstrate that the actions undertaken by most countries are minimal and will not lead to sufficient decarbonization for the industry. Additionally, policy transfer and lesson drawing are found to be evident amongst the SAPs but not extensive.

Keywords: aviation industry
climate change
policy
sustainability
Advisor: Besco, Laurel
Interactive Storytelling System Design for Children’s Picture Books

Reading picture books is a promising learning method for early-age children to develop their language and literacy skills. With technology advances, children are exposed heavily to interactive media and read less traditional books. Therefore, a potential for incorporating interactive technology into children’s picture books emerges. Considering picture books are categorized by their unique features, i.e., the synergy between text and images in delivering information, the co-reading between caregivers and children, and the language and literacy development effect, this master thesis proposed seven design guidelines for an automated interactive storytelling system based on a comprehensive understanding of prior literature around the relevant fields and results from an empirical study observing online user-generated videos featuring sessions of caregivers-children joint picture book reading activities.

Keywords: Interactive System Design
Advisor: Kuzminykh, Anastasia
Applications of Clinical Engineering and Interaction Design to the Neurovascular Clinic

Novel computational tools often face difficulty in clinical adoption due to lack of clinical user involvement in the design process. While there is extensive research in Computational Fluid Dynamic (CFD) modeling of the vascular system, there remain challenges in translating this knowledge into the clinical domain for data-driven treatment decisions. To facilitate the clinical adoption of CFD technology, a co-design-centered approach was used to involve practitioners in the design of user interfaces for several clinical challenges: a custom interface was prototyped for medical image segmentation; interactive flow visualization interfaces were tested by clinical practitioners and fluid researchers; and a methodology was developed for recording, visualizing, and categorizing pulsatile tinnitus sounds. Based on work conducted in this thesis, recommendations are provided for implementing multi-sensory design theories (audio, visual and tactile) in design and engineering education and their implications for improving the design of clinical diagnostic tools.

Keywords: Clinical Engineering
Computational Fluid Dynamics
Human Computer Interactions
Human Factors
Neurovascular
User Interface Design
Advisor: Steinman, David A
Coppin, Peter
Methodology and Equipment Improvements to Radiation Test Campaigns and Electrical Developments for Microsatellites

Satellites operating near earth are subject to less radiation than deep space. This has allowed the use of commercial off the shelf electronic components for small satellites operating in low-earth orbit. Even though radiation levels in low-earth orbit are far lower than deep space, there is significantly more radiation than on the surface of the planet. Commercial off the shelf electronic components must therefore be screened and tested to ensure proper operation on orbit. This thesis begins by giving an overview of the Modular Power System, which controls and regulates power aboard Space Flight Laboratory satellites. It then delves into the process, the findings, and the improvements made to the radiation test methodology at the Space Flight Laboratory. The knowledge gained during a radiation test campaign allowed for better test equipment and procedures to be envisioned. This lead to the design of two pieces of test equipment which could more accurately quantify radiation effects. Finally, the redesign of a switch-mode power supply to fit into a satellite is summarized. These works are presented in part as a chronological overview of the works performed during the 2021-2023 Master’s Program.

Keywords: Proton Beam
Radiation
Radiation Effects
Advisor: Zee, Robert E
Reflecting Attention to Auditory and Vsual Working Memory in Older Cochlear Implant Users

The association between hearing loss and cognitive decline has been explored extensively in prior research, particularly in the domain of attention to memory. However, cognitive functioning after hearing restoration with a cochlear implant (CI) requires further exploration. The current study assessed the ability to orient attention to an item held in visual or auditory working memory (i.e., reflective attention) in CI users. Participants completed a delayed match- to-sample task in which a visual gradient and a piano tone were presented simultaneously. A cue (i.e., retro-cue) retrospectively oriented their attention to an item held in visual or auditory working memory. The cue was followed by a probe of which participants were asked to indicate whether the probe matched the cued item in working memory. The behavioral results indicated that CI users and age-matched normal hearing (NH) adults exhibit comparable performance in reflective attention towards a visual and auditory item in memory. Although CI users have had a history of severe deafness and experience coarse sound information, they are able to reflect attention to both visual and auditory working memory at the normal level. This reflective attention ability in CI users remains stable after one year of CI use.

Advisor: Alain, Claude
Dimitrijevic, Andrew
Dental Specialty Graduate Students’ Experience with Clinical and Online Education during the COVID-19 Pandemic: A Qualitative Study

The COVID-19 pandemic forced dental students to transition towards online distance education (ODE) and led to reduced clinical experience. The objectives of this study were to identify the opportunities and challenges in didactic and clinical education. This study recruited a purposeful sample of dental specialty graduate students (DSGS) at the Faculty of Dentistry, University of Toronto to participate in individual semi-structured interviews analyzed via thematic analysis. Three themes were identified: impact on clinical experience, transition to ODE, and overall well-being. Decreased clinical experience led to sentiments of dissatisfaction; however, most students minimized the impact on their educational development. Participants valued the flexibility of ODE and there was a willingness amongst DSGS to continue some courses via ODE after the pandemic, however it was not considered conducive to all courses. Overall, participants adapted well given the circumstances and ODE should be considered as an alternative format of education for DSGS.

Advisor: Dempster, Laura
Mendes, Vanessa
Behavioural Isolation between Populations that Evolved in Different Larval and Mating Environments

Behavioural isolation (BI) is often the beginning of speciation. BI is the result of evolved differences in response to the mating environment (ME). MEs may mediate if BI evolves for two reasons. Ecological speciation occurs because of different traits being favoured in alternative environments. Alternatively, MEs vary in the selective constraint they impose such that populations evolving in a ‘constraining’ ME would be less likely to evolve BI. In this case, the ME is not the direct cause of BI but permits its evolution via other drivers. We test these ideas with 28 populations, evolved under one of two MEs and one of two larval environments. BI is not maximal between populations evolved in different MEs. Rather, BI is stronger among populations from one ME. This ME promotes BI, but it does not drive it; BI occurs if they evolved in different larval environments, indicating a role for ecological speciation.

Keywords: Behavioural isolation
Drosophila
Ecological speciation
Experimental evolution
Mating environment
Speciation
Advisor: Agrawal, Aneil F
Hormonal and Inflammatory Features of Heart Failure with Preserved Ejection Fraction

Heart failure with preserved ejection fraction (HFpEF) is a common form of heart failure with few therapies and grievous outcomes. The importance of sex hormones and specific inflammatory drivers are yet to be understood within the condition. This thesis presents results addressing these gaps. Under one study, the influence of menopause, a feature common amongst HFpEF patients, was examined using a mouse model leveraging chemically accelerated ovarian failure (AOF). Despite the loss of cardio-protective ovarian function, AOF did not worsen HFpEF phenotype severity. The presence of infiltrating immune cells within the heart was however elevated due to AOF. A separate investigation applied systems biology to public cardiac gene expression data derived from HFpEF patients. This uncovered evidence for inflammation driven by interferon regulatory factor 3 (IRF3) as consequence of obesity. These two lines of work provide direction for further studies examining both the presentation and molecular underpinnings of HFpEF.

Keywords: Heart failure
Inflammation
Menopause
Advisor: Cheng, Hai-Ling Margaret
Single-Nucleus Profiling Identifies Accelerated Oligodendrocyte Precursor Cell Senescence in a Mouse Model of Down Syndrome

Down Syndrome (DS) is the most common genetic cause of intellectual disability (ID) worldwide and is associated with lifelong cognitive deficits. However, the precise mechanisms driving neurologic impairment and neuroinflammation in DS are poorly understood. Using the Ts65Dn mouse model of DS, I performed an integrated single-nucleus ATAC-seq and RNA-seq analysis of the mature adult cortex. I identified cell type-specific mRNA and chromatin-associated changes in the Ts65Dn cortex, including regulators of transcription, translation, myelination, and inflammation. I discovered enrichment of a senescence-associated transcriptional signature in trisomic oligodendrocyte precursor cells (OPCs), epigenetic changes consistent with a loss of heterochromatin, and a senescence phenotype characterized by the upregulation of senescence-associated-β-galactosidase (SA-β-gal) activity, loss of LaminB1 (LMNB1), and reduced proliferation. Treatment of Ts65Dn mice with the senescence-reducing flavonoid, fisetin, rescued cortical OPC senescence activity and restored the number of OPCs. Together, these findings suggest that cortical OPC senescence may be an important driver of accelerated aging and neuroinflammation in DS.

Keywords: Down syndrome
Genetics
Molecular biology
Neurosciences
Oligodendrocyte precursor cells
Single-cell genomics
Advisor: Kalish, Brian T
Uncovering General and Specific Relationships Between Psychopathology and Neurocognition: A Hierarchical, Dimensional Approach Using Latent Variable Models

Discriminable relationships between psychiatric disorders and neurocognition have not been strongly established despite evidence of associations between the two. This may be due to prevailing psychiatric classification systems that define psychiatric disorders as discrete entities, contrasting with alternative empirically based approaches of hierarchical dimensional structures which may better elucidate broader and narrower relationships between psychopathology and neurocognition. In this remote study, 1000 adults with mental health concerns completed a dimensional and hierarchical measure of psychopathology and a comprehensive neurocognitive battery. A six-factor bifactor model of psychopathology and a three-factor bifactor model of neurocognition were supported by both theory and standard fit indices. Hierarchical regressions based on estimated factor scores suggested significant negative association of general psychopathology with general neurocognition, and detachment with general neurocognition and social cognition. A positive association was found between anxiety and social cognition. These preliminary findings suggest associations between psychopathology and neurocognition are largely non-specific.

Keywords: cognition
dimensional psychopathology
hierarchical taxonomy of psychopathology
neuropsychology
transdiagnostic
Advisor: Ruocco, Anthony C
Exploring the Conversations of a Motivational Interviewing Chatbot: A Topic Modeling Approach

The advent of large language models, such as BERT, GPT-3, and ChatGPT has galvanized research in chatbots, particularly in the context of addiction therapy. One such chatbot is MIBOT, developed through active collaboration between researchers at the University of Toronto and MI clinicians at the Centre for Addiction and Mental Health (CAMH). The goal of the MIBOT project is to develop a chatbot to emulate the principles of Motivational Interviewing in the context of smoking cessation therapy. While chatbots provide benefits in reaching underserved populations, there is a challenge in reviewing conversation transcripts due to the large number of conversations they may have. To address this challenge, topic modeling methods are analyzed in their ability to review transcripts. We find that topic modeling approaches help researchers (1) explore and summarize the MIBOT transcripts; (2) plan appropriate responses in an M-Iinspired conversation; and (3) stimulate further research and question generation.

Keywords: Chatbot
Motivational Interviewing
Natural Language Processing
Topic Modeling
Transformers
Advisor: Ratto, Matt
Rose, Jonathan
All that SustainsUs: A Study of the Values, iIvestments and Returns of Flemo Farm

Urban agriculture (UA) initiatives have proliferated in the Global North over the last couple of decades in response to the many social, economic, and environmental problems caused by the dominant industrial agri-food system. Despite the ‘good intentions’ of these spaces, their meaning and impact are contested; scholars and activists of UA are caught between emphasizing its radical, transformative potential on the one hand, and highlighting its status as co-opted by an all-consuming capitalist system on the other. My research contributes to this conversation through an in-depth study of the values, investments and returns of one of these urban agriculture projects: a small, half-acre urban farm in Northwest Toronto called Flemo Farm. I use the Community Economies Return on Investment (CEROI) framework to guide the investigation, and McClintock’s three-dimensional theory of metabolic rift to analyse the results. Ultimately, I find that blending McClintock’s theory of metabolic rift with the CEROI approach unlocks an understanding of the meaning and impact of the activities of Flemo Farm that would otherwise be missed.

Advisor: Vieta, Marcelo
Meta-Learning-Based Fronthaul Compression for Cloud Radio Access Networks

This thesis investigates the fronthaul compression problem in a cloud radio access network, where a transform-compress-forward scheme consisting of well-designed transformation matrices and uniform quantizers is proposed to satisfy the fronthaul capacity constraint. To reduce the communication overhead for designing the transformation matrices, this thesis further proposes a deep learning framework to first learn a suboptimal transformation matrix at each remote radio head (RRH) based on the local channel state information (CSI), and then to refine it iteratively. To facilitate the refinement process, we propose an efficient signaling scheme that only requires the transmission of low-dimensional effective CSI and its gradient between the central processor and RRH, and further, a meta-learning based gated recurrent unit network to reduce the signaling transmission rounds. Simulation results under three applications show that the proposed two-stage neural network can perform close to the fully cooperative global CSI based benchmark with significantly reduced communication overhead.

Keywords: cloud radio access networks
deep learning
fronthaul compression
meta-learning
transform coding
Advisor: Yu, Wei
Athletes’ Experiences of Addressing Maltreatment Through a Reporting Process: A Critical Narrative Analysis as Guided by Trauma-Informed Practice

A critical narrative approach guided by trauma-informed practice explores athletes’ experiences of addressing maltreatment through a formal reporting process. Safe Sport initiatives often marginalize the knowledge and needs of athletes, particularity those from equity-denied groups. This study aims to amplify the voices and experiences of athletes who have been harmed within what I interpreted as oppressive institutions and structures. An overview of maltreatment in sport within a Canadian context and an autoethnography on the importance and challenges of implementing a research project as a (developing) trauma-informed practice are offered. The results are presented as idiographic narratives on four athletes’ experiences of the reporting process, which illuminate the harm and re-traumatization perpetuated within reporting processes. The trauma-informed practice within this study offers an alternative modality of engaging with athletes who have experienced harm; one that prioritizes the on-going consent, autonomy, and well-being of the athletes with a commitment to harm reduction.

Keywords: Abuse
Healing
Justice
Maltreatment
Sport
Trauma
Advisor: Kerr, Gretchen