VictorJuiz/thesis huggingface dataset:
A Combined Cell and Gene Therapy to Treat Retinitis Pigmentosa
Keywords: Allogeneic Cell Tolerance
Cell Therapy
Genome Engineering
Retinitis Pigmentosa
Vision Loss

Retinitis pigmentosa (RP) is an inherited retinal degenerative disease that causes severe vision loss or blindness. It is a genetically heterogeneous disease that is driven by any single deleterious mutation in over 70 identified genes. Gene therapy to prevent vision loss is showing promise in the clinic, but this therapeutic strategy poses risks of oncogenicity and genotoxicity. Moreover, developing new treatments to address each mutation is an infeasible approach. Cell therapy to restore vision, such as photoreceptor transplantation to replace those that have been lost, is hindered by poor cell survival. Also, the inadequate integration of cells into the neural retina severely diminishes its therapeutic potential. Alternatively, recombinant proteins can be used to prevent photoreceptor degeneration, but their short half-lives demand frequent redosing which may lead to complications of the eye. To address these limitations, I developed a combined cell and gene therapy that is expected to protect photoreceptors independent of the genetic cause. Human embryonic stem cells were genetically engineered to secrete soluble CX3CL1, a ligand that has been shown to preserve photoreceptors and their function in mouse models of RP by inhibiting microglia activation – a non-cell autonomous mechanism of photoreceptor degeneration. These cells were differentiated into eye-resident retinal pigment epithelium cells, which have been shown to be quiescent, long-lived, and safe in the human subretinal space. After the subretinal delivery of these cells into a mouse model of RP, I show that rod photoreceptors are protected in a local-acting manner within a two-week interval post-treatment. Finally, this thesis explores how genome editing can be used to ensure stable transgene expression in therapeutic cells, improve cell therapy safety, and prevent allogeneic cell rejection without systemic immunosuppression of the host. This novel therapeutic strategy could pave the way for the treatment of other neurodegenerative diseases, as exogenous CX3CL1 has been demonstrated to be an effective therapeutic in animal models of cerebral ischemia, Parkinson’s disease, and Alzheimer’s disease.
Geometry of Leaf Spaces of Singular Foliations
Keywords: Basic cohomology
Diffeology
Lie Groupoids
Quasifolds
Singular foliations

This thesis has three parts. First, we survey Stefan and Sussmann's work on singular foliations, highlighting diffeological objects that arise. We then propose a transverse equivalence of singular foliations, and show: equivalent foliations have diffeomorphic leaf spaces; the converse need not hold; and regular foliations with Hausdorff holonomy groupoid are transverse equivalent if and only if they are Morita equivalent. Second, we show that for a singular foliation (M,F), the quotient π : M → M/F induces an isomorphism π* : Ω*(M/F) → Ω*(M,F; b), where Ω*(M,F; b) denotes the complex of F-basic forms on M, when: F is regular; when the union of k-leaves is a diffeological submanifold, for all k; and when π* is an isomorphism if we excise the 0-leaves. Finally, we introduce diffeological quasifolds and quasifold groupoids. A quasifold is locally modelled by the affine action of countable groups Γ on ℝⁿ. When the Γ are finite, we recover orbifolds. We show that the categories of diffeological quasifolds and quasifold groupoids are equivalent, when we restrict the arrows to local diffeomorphisms and locally invertible bibundles, respectively.
Synthesis and Characterization of Electrodeposited Nanocrystalline Medium- and High-Entropy Alloys
Keywords: Electrodeposited
High-Entropy Alloys
Nanostructured

This thesis outlines the first systematic study on the feasibility of using electrodeposition to synthesize nanocrystalline medium- and high-entropy alloys (M/HEAs, alloys made up of 3–4 and 5+ elements, respectively), towards producing stronger and more thermally stable materials. A graduated three-stage experimental approach was employed to incrementally study and assess electroplating systems of increasing complexity, building from ternary (NiFeCo) to quaternary (NiFeCoW and NiFeCoMo), and finally quinary (NiFeCoMoW) systems. These candidate systems were identified from a novel set of material selection guidelines developed for the electrodeposition of M/HEAs. To this end, an ease of codeposition parameter and grading scheme was employed to examine alloy bases in existing literature. Fully dense, high-quality, near-equimolar deposits with nanocrystalline and/or amorphous structures were successfully synthesized in each system from aqueous electrolytes. Evaluating their thermal stability revealed incremental improvements with increasing alloy complexity, as compared to their binary and pure metal counterparts: from ~100°C in Ni and ~250°C in NiCo, to ~300°C in NiFeCo and ~500°C in NiFeCo(W/Mo). Heightened stability was also reflected by improvements in the activation energy for grain growth, measuring up to 3.1 eV in NiFeCoW, compared to 1.3 eV in nanocrystalline Ni. However, the theory of improved stability with increasing number of elements was not observed, as NiFeCoMoW displayed near identical performance to its quaternary subsets. Mechanical testing via nanoindentation revealed a regular-to-inverse Hall-Petch transition in each of the annealed M/HEAs, coupled with grain-boundary relaxation processes at low annealing temperatures (≤400°C). Again, improved performance with increasing alloy complexity was not observed, as the as-deposited hardness and elastic modulus of each electrodeposited M/HEA was comparable to those of less compositionally complex counterparts. However, the advantage of these M/HEAs was showcased in their post-processed performance, whereupon nanograin nucleation in the NiFeCo(W/Mo) alloys resulted in a ~60% improvement in hardness. From these results, it was concluded that electrodeposition is indeed an effective means to fabricate nanostructured HEAs with improved thermal stability and mechanical properties. In its first documented use, the graduated experimental approach that was employed herein proved valuable in providing a better understanding of the increasingly complex electroplating systems that were studied.
Setting the PACE for Learners: A Theory-Informed Approach for Supporting Learners’ Motivation, Self-Regulated Learning, and Achievement in Web-Based Environments
Keywords: Educational technology
Health professions education
Motivation
Self-regulation

Online instruction has the potential to add incredible value to health professions education (HPE). To achieve this potential, it must be designed and delivered in a manner that facilitates constructive learning interactions between learners and content, educators, and peers. A key determinant of such interactions in online environments is learners’ motivation. This dissertation focuses on the motivational design of online instruction: how it is designed and delivered to support, rather than thwart, learners’ motivation. We propose a novel, theoretically informed approach for designing motivating instruction in HPE, which we call the PACE model after its four key conditions: purpose, adaptability, confidence, and engrossment. The PACE model proposes that instruction can be designed to harness the motivational potential of the life goals that learners pursue through their career. The model predicts that, when learners frame their learning in terms of the life goal(s) it serves, when they can adapt an activity to best align with their life goals, when they are confident that they can attain their learning goal(s), and when they become engrossed with instruction because it affords interest-enhancing actions, instruction will best support learners’ deep engagement toward long-term retention and knowledge transfer. In an initial experimental study, we provide support for a predicted interaction between life goal framing and learners’ confidence. However, we fail to generate evidence that a life goal framing prompt is an effective motivational design strategy when embedded in an online module delivered to medical students. Then, we review the experimental literature on motivational design strategies for online instruction in HPE. We find that studies have overwhelmingly targeted the engrossment condition of the PACE model, relative to the other conditions, and thus the other conditions should receive future attention. Taken together, this dissertation provides the basis for a program of research to advance a theoretically informed and empirically substantiated approach for designing motivating instruction in HPE, including in online environments. When the PACE model is supported by additional evidence, it can provide educators with a source of needed knowledge to design motivating, engaging, and ultimately effective online instruction in HPE.
Non-vanishing and 1-level Density for Artin L-functions of D4 Fields
Keywords: 1-level density
Artin L-functions
Central values
Non-vanishing
Quartic dihedral fields

We study families of Artin L-functions associated to the 2-dimensional irreducible representations of the Galois group of D4 number fields, ordered by their conductors. We compute the first moment of the central values of these L-functions, and as a consequence prove that infinitely many L-functions in each family are non-vanishing at 1/2. In order to obtain these results, we prove asymptotic formulas with power saving error-terms for these families. As a consequence, we are also able to study the 1-level density of the low-lying zeros of the L-functions in these families and verify the Katz-Sarnak conjecture.
The Role of Cell Size Regulation in Embryonic Wound Repair
Keywords: cell volume
coordinated cell behaviours
epithelial morphogenesis
wound healing

Coordinated cell behaviours drive embryonic development and tissue repair, and also contribute to the spread of tumours. Therefore, understanding the mechanisms of collective cell behaviour in living animals will have important implications for the treatment of congenital disorders, chronic wounds or cancer metastasis. To investigate the cellular and molecular mechanisms of cell coordination in living embryos I took advantage of the embryonic wound healing response. Embryos repair wounds rapidly, with no inflammation or scarring, in a process driven by the collective movement of the cells around the wound. Using embryos of the fruit fly, Drosophila melanogaster, combined with genetic and pharmacological manipulations, five-dimensional time-lapse microscopy and image analysis, I demonstrated that contrary to the prevalent dogma, cytoskeletal rearrangements are not sufficient for rapid embryonic wound repair. Instead, I showed that for wounds to close fast, the cells adjacent to the wound must increase their volume. The swelling of the cells adjacent to the wound is driven by the damage-induced activation of the serine/threonine kinase p38 mitogen-activated protein kinase (MAPK). My results indicated that p38 activates the sodium/potassium/chloride cotransporter NKCC1 to promote an increase in volume in the cells adjacent to the wound that enables rapid coordinated cell movements. In addition, I demonstrated that another regulator of cell size, the mechanistic target of rapamycin complex 1 (mTORC1), is necessary for rapid wound healing. mTORC1 inhibition prevented cell swelling around embryonic wounds and slowed wound healing down. Catabolic processes, such as autophagy, can disrupt cell swelling. I demonstrate that the number of autophagosomes around wounds decreases as wound closure progresses, in a process that requires mTORC1 signalling. Inhibiting autophagy rescues the wound healing response in embryos with defective mTORC1 signalling, further indicating that mTORC1 suppresses autophagy to facilitate cell swelling and rapid wound repair. Together, my results show that p38-induced osmoregulation and mTORC1-controlled reduction of catabolic activity promote cell swelling to drive collective cell behaviours in vivo.
Determining the Significance of BORF2 Interaction with A3B and p53 in EBV Infection
Keywords: APOBEC3B
BORF2
Cell Cycle
EBV
Herpesvirus
p53

Epstein-Barr virus (EBV) is a human herpesvirus that infects over 90% of the world's population and is a causative agent of several types of cancers. EBV establishes lifelong infection in the host by alternating between latent and lytic infection. During the lytic phase of infection, the virus produces a cascade of ~70 proteins, many of which function to manipulate cellular processes to enable efficient production of virions. However, the functions of many of these proteins are poorly understood. In this study, I identified novel functions of the EBV lytic protein BORF2, that interacts with the cellular proteins APOBEC3B (A3B) and p53. A3B is a member of the APOBEC3 family of cytidine deaminases, which play a critical role in innate immune defense against viral infections by inducing hypermutation of viral genomes. p53 is a tumor suppressor protein that regulates the cell cycle and plays a critical role in G1/S arrest. Using affinity purification mass spectrometry (AP-MS), our lab discovered that BORF2 interacts with A3B and p53. I confirmed this interaction through proteomic and fluorescent microscopy experiments. My results also showed that BORF2 protects the viral genome by sequestering A3B away from the EBV replication compartment. Furthermore, we collaborated with the Harris lab at the University of Minnesota to perform infection assays which showed that BORF2 protects the EBV genome from A3B mutations. We also found that the interaction between BORF2 and A3B is conserved in KSHV with its viral protein ORF61, homologue of BORF2. In addition to its interaction with A3B, I showed that BORF2 induces p53 independently of A3B binding. My immunofluorescence microscopy experiments revealed that p53 bodies were juxtaposed to and not co-localized with BORF2-A3B bodies. However, in the absence of A3B, p53 co-localized with BORF2. My results suggest that A3B outcompetes p53 for the interaction with BORF2, leading us to propose a competition model where BORF2 can only induce G1/S through a p53-dependent manner in cells that express A3B. Therefore, my research has provided new insights into the mechanisms by which EBV protects its genome from A3B mutagenesis and contributes to G1/S arrest. The discovery of the mechanism by which EBV neutralizes A3B may provide opportunities for the development of therapeutic approaches against EBV as well as A3B-induced cancers.
Transport, Fate, and Effects of Microplastics in a Rapidly Changing Arctic
Keywords: Arctic Ecology
Ecotoxicology
Emerging Contaminants
Persistent Organic Chemicals
Plastic Additives
Plastic Pollution

Microplastics (<5 mm) have been deemed a contaminant of emerging Arctic concern. Microplastics are multi-dimensional in that they range in morphology, size, and chemical cocktail (e.g., additives, sorbed contaminants) and are hypothesized to serve as an important transport mechanism for chemical contaminants to and within northern ecosystems. While microplastics and plastic additives have been identified across Arctic ecosystems, there is a need to better understand the transport, fate, and effects of microplastics and their additive chemicals. Here, I explore these three themes through a series of field observations and laboratory experiments. First, in Chapter 2 of this dissertation, I show that while seabirds may be an important transport pathway of microplastics to the Arctic, there are other regional sources that need to be considered. In Chapters 3 and 4, I explored the role of long-range atmospheric transport of microplastics via atmospheric deposition. In Chapter 3, using a high-Arctic ice core, I show an increasing trend of microplastics over time. I also observed a positive relationship between microplastics and organophosphate esters (a plastic additive), suggesting microplastics may act as a long-range transport pathway. In Chapter 4, I sampled snow from five sites at increasing distances from a local community. I observed a change in microplastic and polymer composition in sites closer to the local community suggesting that local sources of microplastics may also be important. In Chapter 5, I investigated the presence of microplastics and additive chemicals in wild-caught Arctic char (Salvelinus alpinus) and their habitat. Here, I show elevated concentrations of microplastics in Arctic char and their summer feeding habitat compared to previously reported observations. I also demonstrate translocation of microplastics to Arctic char. And finally, in Chapter 6, informed by observations in the previous chapters, I exposed larval fish to polyurethane, with and without chemical additives to assess the mechanisms of toxicity. Here, I show that the physical and chemical components of polyurethane affect growth and development, and that the physical particles may facilitate the bioaccumulation of plastic additive chemicals. Throughout my thesis, I highlight the importance of evaluating microplastics as a multi-dimensional contaminant - the physical and chemical properties may influence their fate, transport, and biological effects.
MicroRNA Dysregulation in Hereditary Hemorrhagic Telangiectasia
Keywords: endothelial cells
epigenetics
hereditary hemorrhagic telangiectasia
microRNAs
rare disease
vascular biology

Hereditary hemorrhagic telangiectasia (HHT) is a rare, autosomal dominant genetic disease characterized by life threatening vascular malformations. Mutations in endoglin (ENG) and activin receptor-like kinase 1 (ACVRL1) account for ≈90% of HHT cases and disrupt the transforming growth factor β signalling pathway. This predominately results in endothelial cell (EC) and angiogenic dysfunction. HHT mouse models have revealed that the genetic mutations alone are necessary, but not sufficient to generate the observed vascular malformations, suggesting alternative biological factors must be at play. The role of microRNAs (miRNAs), small biomolecules (21-25 nucleotides) that regulate gene expression post-transcriptionally, has yet to be explored in HHT. I hypothesized that miRNA levels are abnormally altered in HHT. To address this gap in knowledge I sought to profile and characterize miRNAs in peripheral blood mononuclear cells (PBMCs) and myeloid angiogenic cells (MACs) derived from HHT patients, as well as in ENG-knockdown human umbilical vein ECs (HUVECs). PBMCs, comprised mostly of lymphocytes and monocytes, are dysfunctional in HHT. MACs, alternatively called early endothelial progenitor cells or circulating angiogenic cells, do not directly incorporate into developing blood vessels but augment angiogenesis in a paracrine manner. MAC dysfunction has been reported in HHT. PBMCs and MACs were isolated from HHT patients and age- and gender-matched healthy controls for comparative miRNA profiling. MiRs-28-5p and -361-3p were found to be significantly decreased in HHT PBMCs, while the mRNA levels of their putative target, insulin-like growth factor 1 (IGF1), were significantly elevated. IGF1 is a potent angiogenic factor and may be contributing to local angiogenic dysfunction. MiR-132-3p was found to be significantly decreased in HHT MACs and enriched in signalling pathways related to HHT pathogenesis that may in part explain HHT MAC dysfunction. ENG, responsible for ≈50% of HHT cases, was knocked down in HUVECs with short interfering RNA technology. MiRNA profiling of ENG-knockdown HUVECs revealed that miRs-139-5p and -454-3p were significantly downregulated. Most notably, inhibition of these miRNAs independently resulted in impaired HUVEC tube formation and their overexpression rescued ENG-knockdown-induced HUVEC dysfunction. These novel findings underscore the critical involvement of miRNA dysregulation in HHT that warrants further research.
Searching for Equity: A Holistic Analysis of East Asian International Student Experiences and Policy Implications – A Case Study of a Canadian University Engineering Program –
Keywords: Case study
East Asian international students
Equity policy
model minority myth

This study investigates experiences and perceptions of first year East Asian international students, faculty and staff members in the engineering program in a Canadian university and further identifies and discusses policy gaps affecting first year East Asian international students. This study used a case study approach with a document analysis and fourteen semi-structured qualitative interviews. The document analysis included university and departmental wide documents, such as University of Toronto Internationalization Strategy Document and Academic Planning as well as publicly available policy documents that were identified as gaps by the interview participants, such as Petitions and Mental Health support. The interview data were collected during the COVID-19 pandemic. All three interview groups, East Asian international students in their 1st year, faculty members and student services staff members addressed the need for more mental health support for the East Asian international students, and the faculty and staff group identified lack of culturally responsive interpretation of educational policy major gaps affecting the East Asian international students. This research used a sensemaking framework to analyze the data. In addition, the “Model Minority Myth” was used to interpret the East Asian international student experiences. In conclusion, I characterized the issues of East Asian international students as a “wicked problem” (Rittel & Weber, 1973), as the policy barriers and challenges they face are multifaceted and full of complexities. This study is significant because of the increasing number of East Asian international students in the Canadian higher education landscape. The voices of East Asian international students in scholarship have been limited and lacking, especially related to the policies affecting their experiences. University institutions and policy makers including policy implementers require a more culturally sensitive and nuanced approach in order to address the unique needs of East Asian international students and to ensure their academic and social successes in their institutions.
Lattice Point Counts in Teichmuller Space and Negative Curvature
Keywords: Counting in dynamics
Negative curvature
Teichmuller theory

In this thesis we present two different, but related, results; one in the setting of Teichmuller theory, and the other in the setting of negative curvature. For the first result, let $\gamma$ be a pseudo-Anosov homeomorphism of a compact orientable surface $S_g$, and let $L_\gamma$ denote the axis of the action of $\gamma$ on the Teichmuller space of $S_g$, denoted by $\mathcal{T}_g$. In Chapter 3 we obtain asymptotics for the number of translates of $L_\gamma$ that intersect a Teichmuller ball of radius $R$ centered at a fixed $X \in \mathcal{T}_g$, as $R \rightarrow \infty$. For the second result, let $M$ be a compact closed manifold of variable negative curvature. We fix two points $x, y$ in the universal cover $\widetilde{M}$ of $M$, fix an element $\mathrm{id} \neq \gamma$ in the fundamental group $\Gamma$ of $M$, and denote the set of elements in $\Gamma$ that are conjugate to $\gamma$ by $\mathrm{Conj}_\gamma$. In Chapter 4 we obtain asymptotics for the number of $\mathrm{Conj}_\gamma$--orbits of $y$ that lie in a ball of radius $R$ centered at $x$, as $R \rightarrow \infty$. If $M$ is two-dimensional, or of dimension $n \geq 3$ and curvature bounded above by $-1$ and below by $-(\frac{n-1}{n-2})^2$, we find a power saving error term for this count. Since the two results are written in different settings, their similarities might be hidden at first glance. This is why we included Chapter 2, in which we present a unified approach to both results in the setting of constant negative curvature. Writing the arguments in this simple setting helps us emphasize the similarities between the two results.