VictorJuiz/thesis huggingface dataset:
Assessing a n Novel Synthetic FZD4 Agonist to Rescue Blood Brain Barrier Ddysfunction

The Blood Brain Barrier (BBB) is a selective structure controlling the passage of molecules between the blood and the brain. It is characterized by the formation of tight junctions between endothelial cells (ECs). The Wnt/β-catenin signalling pathway controls angiogenesis and barrier integrity, both crucial for vascular development and homeostasis of the BBB. FZD4 is required for angiogenesis and barrier functions in brain vasculature, forming a receptor complex with WNT7/GPR124/RECK/LRP5/6 to evoke Wnt-mediated signalling in brain vasculature. Our lab has engineered novel synthetic antibody-based Frizzled/LRP Agonists mimicking Wnt ligands. This thesis investigated activation of the FZD4 receptor complexes using F4L6 and its efficiency to promote CNS barrier function and promote recovery in stroke animal models. A GPR124 siRNA knockdown in ECs was established showing F4L6 acts independently of GPR124. Weassessed F4L6 in an endothelin-1 induced ischemic stroke model and showed decreased leakageat day 10 post-stroke and significant behavioural rescue.

Keywords: Blood Brain Barrier
Frizzled
GPR124
Wnt
Advisor: Angers, Stephane
Lake Ice and Snow in the Canadian High Arctic: In Situ Monitoring Using Ground-Based Techniques

Arctic warming is leading to a rapid loss of lake ice and snow cover in recent years. Cryosphere monitoring includes ground-based cameras which provide the ability to monitor study sites that generally have poor accessibility. This study maximized the usage of field imagery for ice and snow studies within the context of the changing Arctic climate. Camera imagery (2016-2022) was collected from five study lakes near Resolute and Nanuit Itillinga, Nunavut in the Canadian High Arctic. An image classification technique was developed to quantify ice and snow from the in situ digital imagery. Recent variability in phenology was examined, and these results were compared to the existing long-term records from Resolute Lake to see how the recent years compare to past records. Thus, a new, accessible methodology to assess Arctic climate change was presented, which will support better projections for future responses to climate change.

Keywords: Arctic
Camera imagery
Cryosphere
Ground-based monitoring
Lake ice
Snow
Advisor: Brown, Laura C
Climate Data Practices in Toronto's Municipal Government

Since the declaration of a climate emergency in 2019, the City of Toronto has placed an increased focus on climate change mitigation and adaptation strategies. In the effort to combat climate change, municipal policymakers utilize various forms of data ranging from greenhouse inventories to resident testimonies in order to define targets, monitor progress and communicate results. This project draws on research in environmental justice, data justice and human-computer interactions to explore uses of climate data within the City from a practice-theory perspective and to describe five climate data practices. Reflexive thematic analysis of data collected through interviews with policymakers as well as a document analysis of City reports are used to illustrate four aporias created in the pursuit of data driven climate governance that span these practices. To help overcome these contradictions we propose three alternative strategies for future design and research.

Keywords: climate
data
data justice
environmental justice
municipal government
Toronto
Advisor: Soden, Robert
Characterizing Molecular Alternations in Glioma Growth and Progression

High grade gliomas (HGG) are incurable, aggressive brain malignances that occur in patients of all ages. These cancers carry universally poor prognoses. Significant scientific advances made over the last decade have uncovered many of the features of these diseases, culminating in the latest World Health Organization (WHO) classification of Central Nervous System (CNS) tumors integrating histopathologic and molecular information for diagnosis. However, it is unclear how genetic and epigenetic features change as the CNS tumor grows. To elucidate mutations and transcriptional changes driving glioma growth and progression, we used a Nestin-Cre mouse model in combination with an extrinsic chemical mutagen (N-ethyl-N¬-nitrosurea, ENU), to sample discrete lesions during premalignant, early stage tumor, and end stage tumor phases. We show that the somatic mutations, copy number changes, and transcriptional profiles of tumors vary depending on the stage of growth. Importantly, we show that the Raf/Ras pathway is key for tumor growth with a recurring Braf mutation occurring in early stage lesions. Additionally, gene set enrichment analysis (GSEA) shows that end stage tumors have increased immunogenic/inflammatory activity, and increased signaling through Raf/Ras. Overall, this work sheds light on important differences between early and late stage tumors.

Keywords: BRAF
copy number alteration
Cre-Lox
glioma
mutagenesis
whole exome sequence
Advisor: Dirks, Peter
The Effect of Ovariectomy on the Repeated Bout Effect

The repeated bout effect (RBE) occurs when a bout of lengthening contractions (LCs) is used to confer protection to the skeletal muscle (SKM) from a subsequent, bout of LCs. LCs stimulate an increase in heat shock protein content, and ovarian hormones mediate HSP content following LCs, thus ovariectomy (OVX) may impact the RBE. To investigate these relationships, Tibialis anterior muscles (TAs) from ovary intact (OVI) and OVX rats were subjected to no preconditioning or preconditioning with 15 LCs, and both were subjected to 60 LCs 24 hrs later. Preconditioning improved peak torque; however, OVI maintained peak torque beyond OVX. HSP25 and HSP72 increased in OVI and OVX TAs in a trend reflective of an RBE. Preconditioning reduced discernable morphological damage in OVI and OVX TAs. In conclusion, preconditioning induced a stress response in SKM from OVI and OVX animals; however, OVI animals demonstrated an improved response compared to OVX animals.

Keywords: Heat Shock Proteins
Lengthening Contraction
Muscle Damage
Ovariectomy
Preconditioning
Repeated Bout Effect
Advisor: Locke, Marius
Vascularized Human Lung Organoids as a Model to Study Multiciliate Epithelial Tissue and Disease of the Airways

Ex vivo models for lungs are not yet able to recapitulate the full complexity of cell types and organization found in adult lung tissue. There is a need for a model which can be used to accurately study the intricacy of adult human lung tissue for use in personalized and regenerative medicine, research on diseases, and development. Here I describe an ameliorated 3D lung organoid model grown from human embryonic stem cells with incorporated vasculature and compare it to unvascularized organoids and organoids grown by the current standard method. The resulting lung organoids were characterized by immunofluorescence microscopy and analyzed by cell detection programs. Overall this work showed the improved maturation of these ameliorated organoids over alternatives. They displayed more highly organized epithelial structure and cell population proportions of goblet, multiciliated, and basal cells closer to those of adult human lungs than currently available lung organoids.

Advisor: Pelletier, Laurence
Exploration of Epistemic Diversity in Computer Science Education

This thesis examines the meaning of epistemic diversity in computer science education and how to embed it in an algorithm ethics course. Previous research has shown that epistemic traditions can act as gatekeepers, making it difficult to think of other futures, epistemologies, and ontologies. This thesis uses a design-based methodology to analyze the first iteration of an algorithm ethics course at a large North American university. Three surveys were collected, the first focused on student identity, the second focused on pedagogy, and the third on improvements to the course. The surveys helped inform and design the next iteration of the algorithm ethics course. The thematic analysis of survey results and narrative analysis of ethical frameworks provided an avenue to investigate how to embed epistemic diversity into the course topics and discover the meaning of epistemic diversity in computer science education.

Keywords: Computer Science Education
CS Ethics
CS Pedagogy
Curriculum
Design-based methodology
Epistemic diversity
Advisor: Slotta, Jim
Developing a Custom Handheld Diagnostic Device for Noninvasive Detection of Oropharyngeal Dysphagia using High Resolution Cervical Auscultation Recordings

Dysphagia (impaired swallowing) is a debilitating disease, causing malnutrition, pneumonia, and death. In recent years, many studies have shown the effectiveness of high-resolution cervical auscultation (HRCA) signals obtained during swallowing for diagnosis of dysphagia via machine learning algorithms. The aim of this study was to develop a custom handheld device for obtaining and processing HRCA signals, based on an existing benchtop system at the University of Pittsburgh. A custom printed circuit board was designed to acquire, process, and relay the sensor data to a computer via Python. Patient data was collected simultaneously through both the existing and newly developed systems. HRCA features were extracted from the data collected and statistically compared. It was found that 27 out of 36 HRCA features were not significantly different between the 2 systems, concluding that with some design iteration, the developed system could replace the existing system in dysphagia diagnosis research trials.

Keywords: cervical auscultation
diagnostics
dysphagia
hardware design
signal processing
Advisor: Sejdic, Ervin
Exploring Narratives of Solidarity Between Palestinian and Indigenous Activists on Turtle Island

Palestinian and Indigenous anti-colonial movements have long understood that their struggles are inextricably linked. At the same time as Indigenous peoples are re-writing and re-righting history, there has been an increased interest in scholarly contributions that have made a compelling case for anti-colonial and anti-capitalist Indigenous resurgence and liberation rooted in transnational solidarity. Expanding upon this work in the fields of Indigenous and Palestine/ian Studies, this study engages grey literature materials to consider how Palestinian and Indigenous activists on Turtle Island (North America) define, build, and enact solidarity with one another. This analysis maps narratives of relationship building to contribute to a claiming back of our shared histories, and further our understanding of how Palestinian and Indigenous activists can deepen relations and imagine collective liberatory futures.

Keywords: Collective liberatory futures
Indigenous Studies
Palestine/ian Studies
Relationship building
Social Movements
Transnational solidarity
Advisor: Tuck, Eve
Wemigwans, Jennifer
The Development of a Diffraction Based Sensor for the Detection of Bacterial Growth on LB/Agar Surfaces

The main bottleneck in infection treatments remains in the process of Antibiotic susceptibility testing (AST). AST is the process of determining a proper antibiotic treatment regimen for a person diagnosed with an infectious disease, bacterial in origin. Standard clinical AST techniques require a minimum of 48-72 hrs, due to the large sample of bacteria needed, thus raising concerns regarding their effectiveness. During the 48-72 hrs, the patient is provided with a multitude of antibiotics to prevent further progress of the illness, yet the excessive antibiotic use allows bacterial resistance to occur, and the immune system is further compromised. While a few emerging techniques are effective, they are costly and require trained personnel, making them inaccessible in developing countries. In this work, a diffraction-based sensor is developed as a means of determining antibiotic susceptibility in a smaller timeframe. Growth experiments were carried out using two different types of bacteria: Escherichia coli (E. coli) (DH5α) and Bacillus subtilis (B. subtilis). Results from growth experiments were compared against the control, it was observed that diffraction intensity decreased as the bacteria grew on the surface, while the results from the control (a gel without the bacteria) remained relatively flat. E. coli was further tested on a gel containing the antimicrobial ampicillin, and very small changes were observed in the diffraction intensity, implying that the agent has successfully inhibited bacterial growth, making the experiment a success.

Advisor: Goh, Cynthia
Racialized Diasporas in Taylor-Massey, Toronto: Sustainability-Programming Impacts on Neighbourhood Improvement Areas

Taylor-Massey is a largely racialized immigrant neighbourhood that is designated as a Neighbourhood Improvement Area (NIA) by the City of Toronto. This indicates there are social inequities present in Taylor-Massey. This research asks how diasporic communities in Taylor-Massey are accessing, understanding, and taking up sustainability-related programming through community organizations such as Access Alliance Multicultural Health and Community Services. Interviews and participant observations guided by a qualitative approach were utilized to explore this research question. This thesis contributes insights into how culture, mediated through diasporic networks, plays a role in understandings of sustainable living. Findings further examine prominent internal and external barriers for Taylor-Massey residents that prevent them from achieving the sustainable practices they aspire to integrate into their everyday lives. Ultimately, these findings advance interdisciplinary understandings of the cultural dimensions and social dynamics of sustainability and contribute to the fields of sustainability and diaspora studies. Moreover, this study’s analysis is relevant for contextualizing systemic inequities in similar NIAs in the Greater Toronto Area.

Keywords: cultural studies
diaspora and transnationalism
environment and community
race/ethnicity
social networks
social sustainability
Advisor: Morris, Hanna
Towards Efficient Data Analysis using Computational Notebooks

Using computational notebooks (e.g., Jupyter Notebooks) to conduct Exploratory Data Analysis (EDA) presents certain challenges. When dealing with large and unfamiliar datasets, analysts need to identify the most important aspects of the data, apply appropriate EDA operations, and derive key insights. Additionally, as the analysis progresses and the notebook becomes long, it becomes difficult for analysts to keep track of their work by repetitively scrolling up and down the notebook. To address these challenges, this work focuses on leveraging existing data analysis works (i.e., notebooks on Kaggle) to improve analysts’ efficiency in analyzing unfamiliar large datasets and deriving insights. We proposed a framework of data analysis workflow, the \textit{Subset-Method-Insight} (SMI) framework, which formally models the EDA process in notebooks, especially on how the authors of these notebooks navigate through complex datasets and uncover valuable insights. Building upon the SMI framework, we present Tangerine, a JupyterLab extension that offers two main features: (1) tracking: visualizing the notebook into a tree-like structure to give the user a quick overview of their existing EDA process; (2) guiding: providing the user with recommendations about the subsequent data field(s) in the dataset to explore to guide the user through the EDA process. We evaluated Tangerine with real users, and results show that overall participants acknowledged the helpfulness of Tangerine in improving the efficiency of their EDA.

Keywords: Computational notebooks
Data analysis
Exploratory data analysis
Advisor: Zhou, Shurui
A Novel Association Between a Cytotoxic Helper T Cell Subtype and Peri-implantitis

Objectives: To assess the potential association between the cytotoxic CD4+CD28null helper T cell and peri-implantitis (locally and systemically). To characterize the unique microbiome of peri-implantitis. Materials and methods: This study assesses the tissue infiltration and peripheral blood concentrations of CD4+CD28null helper T cells (surface expression of CD markers; flow cytometry) in patients with peri-implantitis. The microbiome profile of peri-implantitis will be characterized (rRNA sequencing). Results: Significantly higher levels of CD4+/CD28null T cells (tissue and peripheral blood) and expression of cytolytic molecules perforin and granzyme were found in patients with peri-implantitis compared to healthy patients. The peri-implantitis biofilm exhibited a unique microbial composition, with a notable prevalence of the Prevotella species compared to the periodontitis biofilm. Conclusions: Peri-implant disease may be associated with senescent CD4+CD28null helper T cells locally and systemically. The prevalence of Prevotella appears to be increased within the biofilm of patients with peri-implantitis.

Keywords: Microbiome
Peri-implantitis
T cell
Advisor: Glogauer, Michael
Targeting T-Cell Malignancies Using Allogeneic Double-Negative CAR-T Cells

Chimeric antigen receptor (CAR)-T cell therapies have achieved significant clinical success against B-cell malignancies. However, the application of CAR-T cell therapy for T-cell malignancies is challenging due to possible contamination of patient-derived T-cell products and fratricide of CAR-T cells targeting T-lineage antigens. Donor-derived CD3+CD4−CD8− double negative T cells (DNTs) have been shown to be safe as an off-the-shelf adoptive cell therapy and to be amendable for CAR transduction. CD4 is a T-cell lineage marker and an attractive candidate antigen for CAR-redirected targeting of T-cell malignancies. Incorporating CD4-CAR (CAR4) onto donor-derived DNTs would create a safe, fratricide-resistant product for T-cell malignancies. We transduced donor-derived DNTs with a third-generation CAR4 construct and evaluated their antitumor efficacy and mechanisms of action against T-cell malignancies using cytotoxicity assays and xenograft models. Our results demonstrate that CAR4-DNTs can effectively target T-cell malignancies and support the use of CAR4-DNTs as an adoptive cell therapy for T-cell malignancies.

Advisor: Zhang, Li
Optimizing and Streamlining the Study Abroad Process using Design Thinking Methodologies and UX Strategies

This thesis aims to assess the user experience of learning abroad programs and the corresponding funding applications, with the goal of reducing barriers for financially disadvantaged students in accessing funding for such programs. Using a design thinking approach, the study focused on conducting interviews and contextual inquiries with 24 students from the University of Toronto, ten learning abroad administrative staff from various universities worldwide, and eight stakeholders representing the Canadian Government or their funding distributors. This project takes into consideration the viewpoints of these participants who may be involved in funding a student's learning abroad journey. Based on the findings, the thesis proposes recommendations to enhance the user experience, with the goal of supporting more students in their learning abroad endeavours. Ultimately, the final objective of this research is to increase access to learning abroad programs for all students, regardless of their socio-economic background.

Keywords: Education
Global Citizenship
International
Learning Abroad
Scholarships
User Experience Design
Advisor: St-Cyr, Olivier
Interactions of Trihalomethanes (THMs) and Haloacetic Acids (HAAs) with PVC and PE Microplastics in Water

Microplastics (MPs) remaining after water treatment, along with those that are released from water distribution pipes, can interact with potentially toxic disinfection byproducts (DBPs) formed during chlorination and act as vectors, increasing the likelihood of their transport into the human body via consumption. In this study, lab-scale adsorption trials were conducted to evaluate the interactions of trihalomethanes (THMs) and haloacetic acids (HAAs) with virgin and weathered forms of polyvinyl chloride (PVC) and polyethylene (PE) MPs (125-250 µm) in three water matrices. The findings reveal that THMs tend to chemically adsorb onto PVC (up to 18 µg/g). Preliminary experiments showed little evidence for the adsorption of HAAs onto MPs, likely due to their hydrophilicity. For THMs, the Freundlich isotherm model provided the best fit indicating multilayer adsorption onto PVC; however, PE exhibited minimal adsorption. Overall, the adsorption behavior varied with the polymer type, degree of weathering, and water matrix.

Advisor: Andrews, Susan Dr.
Curating the Everyday: Taking Care in Exhibitions

While notions of care are fundamental in museum work, current museological care practices focus mainly on collections. In this thesis, I work to complicate existing care definitions by critically examining four case studies: Jason Lazarus’s Too Hard To Keep, The Glen Burnie Historic House renovation, The Family Camera Network project, and the exhibition, What Matters Most: Photographs of Black Life. Based on decolonial, Queer, feminist, and social justice ideals, my cumulative care definition is conceptualized as an entry point, not a prescriptive care model. My research questions are: How do personal and highly affective materials shape curatorial sensibilities towards care? And how has care been conceptualize operationalized, and received by exhibition participants and professionals in these case studies, and in what ways were these care practices made evident to audiences? By interviewing case study professionals, I gleaned their care definitions, while allowing me to examine the care practices I utilized in this research.

Keywords: Affect
Care
Curation
Gallery
Historic House
Photography
Advisor: Luka, Mary Elizabeth
Krmpotich, Cara
Movement in Museums: Towards an Embodied Dance Collection Practice

Traditional methods of preserving dance heritage, such as written records, filmed recordings,and collections of performance ephemera, fall short of capturing the embodied experience ofdance and fail to adequately safeguard movement itself. Drawing inspiration from intangiblecultural heritage practice and the work of Adrienne Kaeppler, this thesis asserts that the preservation of dance requires specialized care that prioritizes the experiential understanding of dancers. To explore this topic, the thesis offers a landscape survey of international dance heritage institutions and presents case studies of three exemplary institutions which model movement-oriented dance preservation practices: the Verdon Fosse Legacy Foundation, the Museo del Baile Flamenco, and Scenkonstmuseet. The research highlights the significance of embodied knowledge and interpersonal transmission in ensuring the continued vitality of dance and advocates for an expansion of collection strategies to incorporate community-oriented practice-based methods, as well as the adoption of heritage practices that prioritize dancers' firsthand expertise.

Keywords: collections
dance
embodied knowledge
intangible cultural heritage
museums
performance
Advisor: Krmpotich, Cara
Boye, Seika