VictorJuiz/thesis huggingface dataset:
Algebraic Cycle Loci at the Integral Level

Let $f : X \to S$ be a smooth projective family defined over $\mathcal{O}_{K}[\mathcal{S}^{-1}]$, where $K \subset \mathbb{C}$ is a number field and $\mathcal{S}$ is a finite set of primes. For each prime $\mathfrak{p} \in \mathcal{O}_{K}[\mathcal{S}^{-1}]$ with residue field $\kappa(\mathfrak{p})$, we consider the algebraic loci in $S_{\overline{\kappa(\mathfrak{p})}}$ above which cohomological cycle conjectures predict the existence of non-trivial families of algebraic cycles, generalizing the Hodge loci of the generic fibre $S_{\overline{K}}$. We develop a technique for studying all such loci, together, at the integral level. As a consequence we give a non-Zariski density criterion for the union of non-trivial ordinary algebraic cycle loci in $S$. The criterion is quite general, depending only on the level of the Hodge flag in a fixed cohomological degree $w$ and the Zariski density of the associated geometric monodromy representation.

Advisor: Tsimerman, Jacob
From Exercise to Physical Literacy Measurement in Individuals with Intellectual Disabilities

Physical inactivity is prevalent among individuals with intellectual disabilities, which has significant negative health consequences for this population. Increasing physical activity is one strategy for improving health outcomes but to be active, one must have the competence, confidence and knowledge to be active for life; collectively, this has been called physical literacy. Unfortunately, there has been no research exploring how best to measure physical literacy in individuals with intellectual disabilities. The purpose of this dissertation was to investigate how to measure physical literacy in adults with intellectual disabilities. Study one was a systematic review and meta-analysis on the broader physical activity and exercise literature. This study served to identify current trends within the literature. The review found that exercise had the most significant impact on the psychological domain, specifically anxiety and depression (SMD=-3.07). While the review did serve to identify key areas lacking in terms of measurement of movement competencies, its primary purpose was to examine how exercise and physical activity impact the physical and psychological well-being of this population. Study two used Generalizability Theory to evaluate the measurement properties of PLAYable. PLAYable was the first movement assessment designed specifically for individuals with intellectual disabilities. Fourteen raters utilized the tool to score 368 video clips each depicting individuals with various intellectual disabilities performing one of the 23 movement skills included in the assessment. The study found that the variability in scores was primarily due to the participant (facet of measurement) performing the skill. Study three examined the feasibility of using the Physical Literacy for Children Questionnaire to measure perceived physical literacy adults with ID. A total of 12 individuals with intellectual disabilities completed the questionnaire while their parents served as a proxy and completed the PLAYparent questionnaire. Overall, the results illustrated that the Physical Literacy for Children Questionnaire was a feasible measure of perceived physical literacy adults with ID. Overall, the three studies from this dissertation provided vital evidence to support and justify the need to explore physical literacy in adults with intellectual disabilities. In addition, this dissertation presented two promising measures, which researchers could use successfully with this population.

Keywords: Adults
Exercise
Health
Intellectual Disability
Physical activity
Physical Literacy
Advisor: Cairney, John
Writing Skills and Students’ Aspirations to Pursue Post-Secondary Educational Opportunities

This study highlights potential positive impacts of tutoring writing to marginalized youth at a community service after-school programme. Although many secondary school students possess language fluency and competency, youths from low-income and/or minority cultures may experience unequal access to essential writing instruction in school. Students’ potential for academic advancement depends on the procurement of written language “codes” necessary to familiarize them with the manners, culture and language of power. Writing tutoring responds to the individual learning needs of youth at-risk; tutoring programmes are effective in supporting the advancement of their goals and values and for their integration into society. Interview data from nine students, staff and tutors at Pathways, Lawrence Heights and observations, field notes and journal entries from my position as researcher and volunteer tutor, reveal that the dialogic nature of tutoring facilitates an unconstrained interchange of ideas, which generates knowledge applicable to the students’ particular needs, and fosters a bond between the tutor and tutee unlike the teacher/student relationship experienced in the school context. My investigations explore how one-to-one tutoring for teaching writing skills to youth at-risk might be especially conducive to improving writing effectiveness because the tutor’s non-evaluative and non-autocratic responses are personalized to the contexts, situational needs and nuances of each student. By acknowledging the unequal distribution of writing proficiency among Ontario’s students and the inequities within the system, educators and policymakers may look for occasions in the writing curriculum that address students’ perceptions of themselves as thinkers and learners. With a broadened appreciation for the impact of tutoring programmes and their relevance to students’ pursuit of post-secondary opportunities, collaboration between researchers, schools and their communities, a thoughtfully developed educational agenda that supports our students is possible.

Keywords: Lawrence Heights
marginalized
Pathways
tutor
volunteer
writing
Advisor: Cooper, Karyn
Investigating the Cardiac Immune Response in Viral Myocarditis

Heart failure (HF) is a growing global epidemic affecting people of all demographics. Non-ischemic cardiomyopathies (NICM) accounts for up to 40% of HF patients. Myocarditis, inflammation of the myocardium is the underlying cause of NICM in 9-16% of patients. The most common cause of myocarditis is due to viral infection, known as viral myocarditis. The immune response is critical in mitigating cardiac injury due to viral infection; however, it can also be pathological due to the cytotoxic effects of certain innate and adaptive immune cells. Conventional or classical dendritic cells (cDCs) are important antigen presenting cells linking the innate and adaptive immune response. Type 1 cDCs (cDC1) are critical for initiating an antigen-specific CD8+ T cell response during viral myocarditis. Mice lacking cDC1s have increased cardiac injury and dysfunction following viral myocarditis, indicating their importance in mitigating cardiac injury. The transcription factor (TF) BATF3 is necessary for the development of cDC1s. Batf3-/- mice lack cardiac cDC1s at steady state. However, during viral infection, cDC1s develop in a BATF3-independent pathway. In this thesis we investigate the BATF3-indepdent development of cardiac cDC1s during viral myocarditis. Cardiac cDC1s from Batf3-/- mice are transcriptionally similar to those from wildtype mice at 7dpi by single cell RNA-sequencing. We have shown that the cytokine GM-CSF is essential for the compensatory cDC1 development while IFNγ is partially involved. Interestingly, these compensatory cDC1s are present in the heart after inflammation has resolved and their continued presence is due to tissue-specific changes that support their persistence. We also explore sex differences in young mice (5-weeks of age) in both susceptibility and immune response to viral myocarditis. We show that young male mice have increased mortality and cardiac injury post-infection in comparison to female littermates. Importantly, we found there is a delayed response of type I interferon (IFN-I) by 12 hours in the young males have a compared to females. This thesis increases our knowledge about the BATF3-independent cDC1 development in peripheral tissues, specifically cardiac cDC1s, during both acute and resolved inflammation. More broadly, we also examine sex differences in viral myocarditis identifying IFN-I as a potential therapeutic target in early viral myocarditis.

Keywords: BATF3
Dendritic cell
Advisor: Epelman, Slava
Development of Orthogonal and Cooperative Catalytic Processes via Dual Metal Catalysis

In this thesis, the concept of dual metal catalysis will be explored in different contexts: one-pot orthogonal catalysis where both metal catalysts act sequentially and cooperative tandem catalysis where the two metal catalysts act in a synergistic fashion. In Chapter 1, a rhodium-catalyzed tandem isomerization-allylation of unsymmetrical diallyl carbonates enables the synthesis of α-quaternary allylated aldehydes. Notably, the rhodium catalyst can discriminate between two allyl groups of the unsymmetrical diallyl carbonate via a selective oxidative addition. Reaction progress kinetic analysis (RPKA) of this reaction uncovered second order kinetics with respect to rhodium, suggesting a bimetallic rate-determining step. In Chapter 2, the tandem isomerization-allylation of unsymmetrical carbonates is re-investigated from a dual metal perspective. A novel variant of this catalytic reaction is developed where a Pd(0) catalyst forms the electrophilic π-allyl species and a Rh(I) catalyst mediates the isomerization to form the enolate nucleophile. This dual metal approach was found to be more efficient and enables access to a large variety of α-quaternary allylated ketones. In Chapter 3, a one-pot reaction featuring two orthogonal transition metal-catalyzed asymmetric transformations is disclosed. The one-pot reaction combines a Pd-catalyzed asymmetric allylic alkylation and a Rh-catalyzed Miyaura-Hayashi reaction, converting allyl enol carbonates or allyl β-keto esters into enantioenriched cyclic ketones with two non-contiguous stereocenters. The process is enantio- and diastereodivergent and the major diastereomer is formed in excellent enantiopurity, owing to the Horeau principle.

Keywords: catalysis
palladium
rhodium
transition metal
Advisor: Lautens, Mark
Transition Metal Hydride Complexes: From Computation to Catalysis and Everything in Between

Computational methods were used to investigate transition metal hydride complexes both in the ground state and as reactive intermediates. Chapter 2 investigates an interesting phenomenon concerning the reversal of the relative position of the antisymmetric and symmetric vibrational modes of trans-dihydrides of transition metals and main group elements. These findings were used to show the different modes of hydride attack on CO2 by a transition metal and main group porphyrinate trans-dihydride complex. Chapter 3 details both an experimental and computational study on the catalytic transfer hydrogenation of aryl ketones with basic iso-propanol by a ruthenium hydride complex with a protic N-heterocyclic carbene ligand. The bifunctional character of the protic N-heterocyclic carbene moiety was determined to play a crucial role in the mechanism of the inner-sphere hydride transfer to acetophenone in a computational study. Chapter 4 describes the synthesis of an iridium(III) azolato complex through rearrangement of a tethered C8-iodinated theophylline fragment. The rearrangement proceeds through an unusual seven-coordinate cationic iridium(V) hydride intermediate which is supported by computational analysis. Finally, chapter 5 concerns the development of an undergraduate laboratory experiment in which an iron carbonyl complex is synthesized to investigate its catalytic activity in the transfer hydrogenation of acetophenone.

Keywords: Density functional theory
Hydride
Hydrogenation
N-heterocyclic carbene
Transition metal
Advisor: Morris, Robert
Prescriptive Partnerships: Black Mothers of Disabled Children and Educators in Ontario's Public School System

This study draws on key teachings and principles of Critical Race Theory to examine the experiences of seven Black mothers as they perform as agents on behalf of their children who are enrolled in the special education environments in elementary schools across the Greater Toronto Area of Ontario, Canada. This qualitative study uses techniques of constructivism and bricolage as it disrupts normalized, hegemonic approaches to parental engagement. The Black mothers’ voices are foregrounded as they share their experiences of engagement with, and disengagement by, members of the in-school team (including educators and health professionals). Critical policy analysis was employed to analyze two Ontario educational policies: (1) parent engagement and (2) special education.This study presents a multi-layered analysis of seven Black mothers as they fight to access special education services; advocate on behalf of their children to get teacher feedback and classwork samples; and negotiate with educators to ensure their children receive timely access to the Ontario curriculum. Notions of power relations between home and school are explored. Black mothers have significantly less power than educators who are all backed by the powerful master legislation, the Education Act of Ontario. This dissertation reveals that educators’ responses to Black students and their parents will vary based upon educator’s values and attitudes, their levels of professionalism, the local school culture as well as the expectations of the district school board and the Ontario Ministry of Education. This study is unique in that through a brief, selective history of Ontario’s general and special education, it investigates the impact of race and racism on Black mothering and mother-work within the special education environment in public elementary schools. Also, by weaving the experiences and perspectives of the seven Black mothers into the analysis of Ontario’s current educational policies, this dissertation shows further how it stands apart: this unique study looks at the role that race and racism play within the discourse of (and discursive practice inherent to) parental engagement within special education environments in elementary public schools in the Greater Toronto Area (GTA) of Ontario.

Keywords: critical race theory
disability studies
education policy
mother
parental engagement
special education
Advisor: Bascia, Nina
Population Dynamics of CRISPR Adaptive Immunity in Communities of Bacteria and Phages: a Window into Another World

Adaptive immunity shapes organisms at all scales of life, from bacteria to humans, allowing organisms to learn from past exposure to pathogens by storing specific immune memories. In humans and other vertebrates, these memories are contained in a diverse pool of specialized cells that express a range of unique immune receptors, while bacteria and archaea store immune memories using the CRISPR-Cas system. Bacteria incorporate small samples of phage DNA, called spacers, into their own genome, using this genetic memory to recognize and destroy future phage infections. Experiments have revealed high spacer diversity on the level of populations, dynamic gain and loss of immunity in bacteria, and phage evolution under pressure from CRISPR targeting, all of which is accessible through DNA sequencing. In both vertebrate and CRISPR adaptive immunity, many biological processes overlap to produce observed outcomes, but by simplifying these complicated systems, phenomenological models have the potential to reveal intuitive patterns. This thesis is about using simple phenomenological models to understand adaptive immunity in bacteria. Starting with basic bacteria and phage interactions with CRISPR immunity, I find remarkable emergent complexity that provides new but simple ways to interpret data. First, I show that stochastic bacteria-phage interactions lead to broad spacer abundance distributions that are stable in time, matching experimental data. Next, I add phage evolution in response to CRISPR targeting. I show that phage mutations and CRISPR immunity drive the emergence of stable genetic diversity and that new phage mutants experience strong positive selection. This model also provides insight into the timescale of immune memories through the summary parameter average immunity which can be calculated from whole-genome sequencing data. Finally, I show that cross-reactivity between spacers and phage genomes leads to fundamentally different regimes of evolution that are analogous to regimes appearing in models of vertebrate adaptive immunity, highlighting shared features in these very different systems. My work is a step forward in the theoretical understanding of both bacterial communities and adaptive immunity in general and illustrates the power of simple models to build intuition about complex phenomena.

Keywords: adaptive immunity
CRISPR
model
simulation
Advisor: Goyal, Sidhartha
Fast Algorithms for $\ell_p$-Regression and Other Problems

Regression in $\ell_p$-norm is a canonical problem in optimization, machine learning and theoretical computer science which asks for a vector with minimum $\ell_p$-norm in a linear subspace. In this thesis, we give fast, high-accuracy algorithms for $\ell_p$ regression for all $p\geq 2$. Our algorithms are built on novel techniques including {\it iterative refinement for $\ell_p$-norms}, and a fast {\it width-reduced} multiplicative weight update routine among others. Furthermore, via a new {\it inverse maintenance} scheme, we can solve $\ell_p$-regression almost as fast as linear regression for all $p>2$. For graph instances, where the goal is to optimize $\ell_p$-norm objectives (flow or voltages), our algorithms incorporate sparsification routines that preserve such objectives, to obtain {\it near-linear-time} algorithms. As a consequence, we also obtain a fast algorithm for the maximum flow problem in unweighted graphs. A popular approach to fast algorithms for $\ell_p$-regression in practice is via empirical modifications of the {Iteratively Reweighted Least Squares (IRLS)} algorithm since the basic version of IRLS is known to converge only for $p \in (1, 3)$ and diverge even for moderate $p$ (e.g., $p > 3.5$). We give the first IRLS algorithm that provably converges to a high accuracy solution in a few iterations. Our algorithm has shown exemplary practical performance as well beating standard MATLAB CVX implementations by 10-50x. We further extend our techniques to obtain fast algorithms for {\it Quasi-self-concordant (QSC)} functions, which includes $\ell_p$-regression, softmax regression, and logistic regression among others. We show how iterative refinement and width reduction techniques extend and give fast rates of convergence for all QSC functions.

Keywords: Optimization
Regression
Theoretical Computer Science
Advisor: Sachdeva, Sushant
Renegades and Inquisitions: Sense, Interiority, and Conversion to Catholic Subjecthood in Early Modern Italy

In the sixteenth and seventeenth centuries, hundreds of penitent renegades—Christian converts to Islam who sought to become Catholic—approached local tribunals of the Roman Inquisition for absolution in the Italian peninsula. This dissertation examines 240 renegade reconciliations from the cities of Rome, Naples, and Livorno in the years 1552-1697 to explore how inquisition officials adjudicated these conversions. The study challenges much of the literature on renegades and early modern religious conversion by arguing that renegades’ “identity” or sense of self was not at stake in depositions and sentencing. What was at stake—what was, in fact, changing in these rituals—was the nature of the renegade’s membership or belonging with the Catholic communion. The foundation of that belonging lay in the renegade’s ability to perform, publicly and before the local inquisition, as an obedient juridical subject of the Catholic Church. After sketching the local historical contexts and personnel for the three Inquisition tribunals, the dissertation compares how each engaged sensory behaviours (Chapters Three and Four) and interiority (Chapter Five) to demonstrate how expectations for that performance intensified over time in Naples and Livorno but not in Rome. While Roman officials consistently required only a perfunctory statement affirming Church teachings on apostasy, Neapolitan inquisitors increasingly emphasized bathing, dietary, and praying habits, and tied them to matters of intention, at the turn of the century. In its later cases, tribunal leaders focused on eliciting affirmations of Catholicism’s exclusive salvific worth. Livorno’s officials, on the other hand, stressed Catholic speech and dietary regimens in the tribunal’s early years and demanded renegades acknowledge links between action and belief in its later ones The dissertation explores how local leadership, religious dynamics, and regional geo-political conflicts may have shaped these varied approaches to addressing a shared goal: molding converts into obedient Catholics whose conduct was unlikely to cause public scandal. It makes original contributions to scholarly discussion of early modern religious conversions and inquisitions, and argues that centring inquisitions’ pragmatism toward “voluntary” penitents rather than the institutions’ repressiveness can help scholars write broader histories of social discipline that make room for local particularity.

Keywords: Catholicism
conversion
Inquisition
interiority
Islam
sensory history
Advisor: Terpstra, Nicholas
Fast Radio Burst Localization with very Long Baseline Interferometry

This thesis covers the development of Very Long Baseline Interferometry (VLBI) localization techniques for Fast Radio Bursts (FRBs). FRBs were discovered only in the 2000s and have revolutionized the radio transient field due to their unknown and complex emission mechanisms, their brightness, and the potential use as probes of the Universe's cosmology. The aim of this thesis project is to enhance the localization potential of Canadian Hydrogen Intensity Mapping Experiment (CHIME) in order to identify galactic hosts, which are necessary to precisely measure redshifts of FRBs. The VLBI prototype station chosen, was the Algonquin Radio Observatory (ARO) 10-m telescope a decommissioned radio dish from the 1960s. During the first two years of PhD studies, a complete refurbishment of the system was done, which included an update on the analog signal chain and a new acquisition system. While upgrades were on their way, CHIME Fast Radio Burst Project (CHIME/FRB) detected its first FRB in 2018, and today more than thousand have been observed. The ARO 10-m telescope has proved to be robust and stable over the years, with scientific results since its functioning on 2019 until the completion of this thesis (February 15th, 2022). Observations of at least three bright radio bursts have been recorded and analyzed at the ARO 10-m telescope, which have paved the way for the upcoming CHIME/FRB Outriggers project. A VLBI study has been carried out with the ARO testbed, including a new fringe fitting correlator model and a new method to phase calibrate using pulsars, particularity developed for the 400--800 MHz low frequency bandpass. The upcoming CHIME/FRB Outriggers project will have multiple baselines across North America in order to localized thousands of FRBs in the next years, to 50 mas precision, which no other experiment has been able to accomplish. Therefore, these results will open a new era in transient astronomy and unlock the unknown matter content of the Universe.

Keywords: Fast Radio Bursts
Radio astronomy
Radio instrumentation
Radio interferometry
Radio transients
Very Long Baseline Interferometry
Advisor: Vanderlinde, Keith