VictorJuiz/thesis huggingface dataset:
Schools, Summers, and Educational Inequality

Sociologists have claimed that summer vacations widen inequality in academic achievement because, during the summer, students with access to learning opportunities at home continue to learn while students with limited access forget much of what they learned the previous school year. Part I of this dissertation argues that this claim is premised on the assumption that, summer after summer, the same lowest-achieving students fall further and further behind in all school subjects and the same highest-achieving students pull further and further ahead in all school subjects. I test the tenability of this assumption, which I term the assumption of within-student stability in learning across time and school subjects. I fit univariate-outcome and multivariate-outcome multilevel piecewise growth models to the math and reading achievement of 19,524 students in the United States between kindergarten and grade 5. Some of the results support the assumption of within-student stability, and others undermine it. I show that the growth models that have been informing theories of summer learning are sensitive to analytic choices. I offer avenues for advancing sociological theories of educational inequality and for improving the analytic methods that are used in research on educational inequality. In Canada and the United States, the provision of free summer learning programs is among primary strategies for improving student achievement and narrowing achievement gaps. However, research on their effectiveness is inconclusive. Part II of this dissertation argues that evaluations of summer learning programs can be strengthened by using analytic methods that are appropriate for the evaluation of time-varying treatments that may operate indirectly through time-varying characteristics of students. I fit regression-with-residuals models to the math and reading achievement of 2,111 students in Ontario, Canada, between grades 1 and 3. Results suggest that summer learning programs raise student achievement more when students attend a program in multiple summers rather than in a single summer. Results also suggest that the effects of summer learning programs vary significantly between students. However, estimates are noisy. I propose ways to increase capacity for rigorous evaluations of summer learning programs.

Advisor: Davies, Scott
Communication Over Nonlinear Optical Fiber Channels

A nondispersive model for optical fibers is considered. The nonlinear interaction between signal and noise is formulated as a reachability problem. A bounded-noise model for the nondispersive optical fiber channel is introduced. The new model is based on the so-called split-step model and is meant to facilitate understanding of capacity limitations caused by nonlinear signal-noise interactions in optical fiber. Some characteristics of the noise balls pertaining to this new model are discussed and, accordingly, upper and lower bounds on the zero-error capacity of this channel are found. By relaxing the assumption on boundedness of the noise, the problem of finding the minimum amount of noise energy that can render two different input points indistinguishable is formulated. This minimum noise energy is then taken as a measure of distance between the points in the input alphabet. Using the machinery of optimal control theory, necessary conditions that describe the minimum-energy noise trajectories are stated as a system of nonlinear differential equations. It is shown how to find the distance between two input points by solving this system of differential equations. The problem of designing signal constellations with the largest minimum distance subject to a peak power constraint is formulated as a clique-finding problem. As an example, a 16-point constellation is designed and compared with conventional quadrature amplitude modulation. A computationally efficient approximation for the proposed distance measure is provided. It is shown how to use this approximation to design large constellations with large minimum distances. Based on the control-theoretic viewpoint of this paper, a new decoding scheme for such nonlinear channels is proposed. A time-domain perturbation model of the nonlinear Schrodinger equation is used to study wave-length-division multiplexed communication over a single polarization. The model explains (a) why constant-composition codes offer an improvement in signal-to-noise ratio compared with independent and uniform selection of constellation points and (b) why similar gains are obtained using carrier recovery algorithms even without using constant-composition codes. It is shown that the more general class of spherical codes, which encompass constant-composition codes, have the potential to reduce cross-phase modulation, as long as their blocklength is not too long.

Advisor: Kschischang, Frank R
Molecular Mechanisms of Mechanically Regulated Aortic Valve Disease: A Focus on the Wnt Signaling Pathway

Calcific aortic valve disease (CAVD) is characterized by the thickening and calcification of aortic valve leaflets. CAVD is a multifaceted disease caused by aberrant differentiation of valvular endothelial cells (VECs) and valvular interstitial cells (VICs) in response to changes in physiological mechanical environments. VECs can undergo endothelial-to-mesenchymal transition (EndMT) and contribute to the resident pool of fibroblast cells (VICs) within the aortic valve and upon stimulation, VICs can differentiate into myofibroblast- or osteoblast-like cells. The Wnt/β-catenin signaling pathway has been implicated in CAVD, VIC myofibrogenic, and osteogenic differentiation, however, its roles in mechanically-regulated EndMT and VIC osteogenic differentiation have not been investigated. The first part of this thesis examines the role of matrix stiffness and β-catenin in EndMT of VECs and found that TGF-β1 induced EndMT in a stiffness- and β-catenin-dependent manner. Notably, the initiation of EndMT (disruption of cell morphology and membrane VE-cadherin expression) was insensitive to matrix stiffness, but α-SMA fiber formation and nuclear translocation of β-catenin both increased on stiff substrate. Endostatin treatment revealed that β-catenin was necessary for TGF-β1-induced transformation of VECs to α-SMA positive myofibroblasts, and this association was confirmed by immunofluorescent staining of sclerotic aortic valves. The second part of the thesis analyzed the role of β-catenin, FoxO1, and cyclic stretch on VIC osteogenic differentiation. We demonstrated for the first time that FoxO1 expression is increased and co-localized with Runx2 in calcified region of diseased human aortic valve using immunostaining. In vitro experiments using siRNA knockdown and exogenous overexpression confirmed the causal effect of FoxO1 on the expression of osteogenic genes RUNX2, ENPP1, and SPP1 in VICs. Surprisingly, β-catenin knockdown had no effect on VIC osteogenic gene expression and thus was unlikely to be a co-factor of FoxO1 in regulating VIC osteogenic differentiation. Although short-term mechanical stretch had no effect on FoxO1, β-catenin, and osteogenic gene expression, long-term stretch promoted dystrophic calcific nodule formation. The findings in this thesis characterized the role of Wnt/β-catenin signaling pathway in mechanically-regulated EndMT and VIC osteogenic differentiation, identified FoxO1 as a novel mediator of VIC osteogenic differentiation, and provided insights into the molecular mechanisms behind CAVD pathogenesis and potential therapeutic targets.

Keywords: Aortic valve stenosis
Calcific aortic valve disease
FoxO1
Mechanobiology
Wnt/b-catenin signaling pathway
Advisor: Simmons, Craig A
Protein Requirements and Amino Acid Metabolism following Endurance Exercise

Sex and diet [e.g. amino acid (AA) ingestion] can impact whole-body protein turnover following intense endurance exercise, ultimately influencing protein recommendations to enhance performance. This thesis examined sex-based differences in protein requirements and the impact of protein intake on plasma AA concentrations and markers of myofibrillar protein breakdown [3-methylhistidine (3MH)] in endurance athletes. Study one utilized a modified indicator amino acid oxidation (IAAO) 3-point curve to assess protein requirements in male and female endurance athletes. Following 2-d of controlled diet and training, participants completed an IAAO trial following a 20km outdoor run from home on three occasions testing variable protein intakes (0.2, 1.2 or 2.0g⋅kg−1⋅d-1). Oral[1-13C]Phenylalanine was used to generate a biphasic linear regression of 13CO2 excretion (F13CO2) and phenylalanine oxidation (PheOx; the reciprocal of whole-body protein synthesis) with the mean breakpoint per group serving as the estimated average requirement (EAR). Results indicated a PheOx EAR of ~1.60g·kg-1·d-1 and safe intake of ~1.85g·kg-1·d-1 with no difference (P=0.94) between sexes. The EAR and safe intake were not different from those previously determined using traditional lab-based IAAO in males, suggesting the modified 3-point IAAO is effective at determining AA requirements, and recommendations are similar whether the run is performed on an automated treadmill or in the real-world environment. Study 2 was a subset of previous research in which urine and blood samples of endurance trained males were examined to determine the effect of three different protein intakes (0.94, 1.20 or 1.83g·kg-1·d-1) following a controlled running protocol on plasma AA and plasma and urinary 3MH. Plasma results demonstrated significantly greater essential AA and branched chain AA as well as reduced 3MH with 1.83 compared to 0.94 or 1.2g⋅kg-1⋅d-1. This may indicate less myofibrillar protein breakdown is required to maintain plasma AA with an intake of 1.83g⋅kg-1⋅d-1. In conclusion, future research should consider the time-efficient modified 3-point IAAO and the home-based protocol we have developed to examine protein requirements in other populations. A protein intake of 1.85g⋅kg-1⋅d-1 maximizes whole-body protein synthesis and may reduce myofibrillar catabolism. On this basis, we recommend that endurance athletes consume towards the upper end of current consensus statement protein recommendations (1.2-2.0g⋅kg-1⋅d-1) regardless of sex.

Keywords: Dietary Protein
Endurance
Protein Breakdown
Protein Synthesis
Recovery
Sexual Dimorphism
Advisor: Moore, Daniel R
Macrophage Migration Inhibitory Factor as a Critical Disease Driver and Novel Therapeutic Target in Spondyloarthritis

Spondyloarthritis (SpA) is a rheumatic disease characterized by inflammation and new bone formation (NBF). Although current treatments including anti-tumor necrosis factor (TNF) and anti-interleukin-17 (IL-17)-targeted therapies are available, up to 40% of SpA patients do not adequately respond to any treatment modalities. Therefore, better understandings of the disease pathogenesis and discoveries of novel therapeutic targets are warranted in SpA. Our group previously found that the concentration and expression of macrophage migration inhibitory factor (MIF), a proinflammatory mediator, in serum and target tissues are increased in SpA patients compared to healthy volunteers or osteoarthritis patients (disease controls). However, the specific roles of MIF in the pathogenesis of SpA remain elusive. Chapter 1 describes the overview of current understandings of the pathogenesis of SpA, extensively covering contributions of genetic and environmental factors, immune activation leading to inflammation, and NBF associated with SpA. Chapter 2 describes the specific roles of MIF in the immunopathology of SpA. The data shown here incorporates experimental results obtained from a well-established SpA mouse model (curdlan-SKG mice) and SpA patient samples. I identified that among major immune cell lineages, neutrophils are the primary cells producing and secreting high amounts of MIF in both the mouse model and SpA patients. Pre-clinical testing shows that both MIF- and neutrophils-targeted therapies are effective in decreasing inflammation and NBF in SpA. Mechanistically, MIF boosts type 3 immunity by enhancing the acquisition of a T-helper 17 cell (Th17) phenotype in both mouse and human regulatory T cells. The data shown in this chapter was published in Science Translational Medicine. Chapter 3 outlines the potential role of MIF on the development of NBF in SpA. During endochondral ossification, a common process of NBF in SpA, MIF increases the expression of chondrogenesis and cartilage extracellular matrices markers by activating STAT3 and mitochondrial energy potentials. Chapter 4 proposes future directions for MIF-related research and therapies. My findings expand the current understanding of the pathogenesis of SpA and demonstrate the potential of MIF-targeted therapies to attenuate the development of inflammation and NBF in SpA. Future clinical trials testing the efficacy and safety of MIF-targeted therapies are warranted.

Keywords: Ankylosing spondylitis
CD74
Macrophage migration inhibitory factor
New bone formation
spondyloarthritis
type 3 immunity
Advisor: Haroon, Nigil
Seeking a Right to the City in Toronto: Youth, Pedagogy, Pandemic, and Performance

This drama-based ethnographic research study asks how youth in Toronto, Canada, negotiate a right to the city in these times of pandemic and climate crisis. It also examines the affordances of using drama-based methodologies to study Toronto youth’s right to the city. It engages with three online drama classrooms in the Toronto District School Board: one middle school (12-14 years old) and two high schools (14-18 years old). In these drama classrooms, auto-topography (Heddon, 2007) is mobilized as a methodological and pedagogical tool to engage the city as an oeuvre (Lefebvre, 1996) that integrates both physical and virtual space. Amin’s (2012) ‘urban feelings,’ Ahmed’s (2004/2014) ‘cultural politics of emotion’ and Massumi’s (2015) ‘politics of affect’ conceptually guide this study. ‘Diffracted reflexivity’ (Serra Undurraga, 2021) is adopted as an analytical approach that attends to the sensory and embodied qualities of the data, and the broader forces of power, history and identity in which they are entangled. The findings align with Deleuze and Guattari’s (1985) concept of ‘the minor’ in that the youth’s auto-topographical performances contest majoritarian narratives of belonging, exclusion, nature, culture, and participation in Toronto in these times. Auto-topography gestures to how emotional flows of shame, disgust, fear, nostalgia, longing and joy serve to ‘deterritorialize’ and ‘reterritorialize’ youth in the context of gentrification (Deleuze and Guattari, 1987). Auto-topography confronts the capitalist and anthropocentric city, enlivening the enchanted materialism (Bennett, 2001) and ‘ecological anthropomorphism’ (Woynarksi, 2015) of parks, libraries, valleys, animals, and streets. Further, ‘participation’ – as foundational to the formation of the urban citizen – is problematized amid the changing stakes of ‘trust’ and ‘risk’ during the COVID pandemic. Hospitality and intimacy emerge as concepts for advancing a right to the city that integrates the public and private spheres. The dissertation closes with a consideration of a ‘theatre of little changes’ (Balfour, 2009) for the conceiving of a right to the city via a politics of co-flourishing.

Keywords: Drama Education
Pedagogy
Performing Arts
Qualitative methodology
Urban
Youth
Advisor: Gallagher, Kathleen M
Investigating Human Neutrophil Phenotypes that Associate with Neisseria gonorrhoeae

The human-specific pathogen Neisseria gonorrhoeae (Ngo) causes the sexually transmitted disease gonorrhea, an oppressive public health burden due both the recent emergence of multidrug-resistant ‘superbug’ strains and the ability of untreated infections to cause inflammation-induced scarring of the maternal reproductive tract and blindness in children born from infected mothers. The hallmark of gonococcal infection is a massive influx of neutrophils that do not seem to clear the infection. Primary human and murine neutrophil-based studies demonstrate that opsonin-independent binding and engulfment of Ngo is driven by bacterial Opa protein adhesins binding to CD66 glycoproteins expressed on the neutrophil surface. A growing awareness that multiple neutrophil phenotypes exist prompted us to hypothesize that these neutrophil populations may differentially respond to Ngo. If true, then we must revisit the potential roles for neutrophils in gonococcal immunity and the immunopathogenesis of infection. The specific objective of this work is to develop a model to study the interaction between Ngo and different neutrophil subsets, to define and characterize the subpopulations of neutrophils that respond to Ngo infection, and to understand the specific response of each neutrophil phenotype to this infection. My studies to date reveal substantial differences in the phenotypes of neutrophils recovered by standard purification methods (such as Ficoll-isolation and MACSpress negative isolation beads) and whole-blood neutrophils, and my results have been compiled in a manuscript. Using a whole blood infection model, I performed a high-throughput flow cytometry-based analysis of 355 different cluster of differentiation (CD) antigens to reveal those expressed by Ngo-infected neutrophils. After identifying the most frequent CD antigens present, I generated customized HTS plates with our top 20 hits to identify antigens expressed on neutrophils that bound Ngo. I found that expression of CD11b, CD63, CD66c, CD256, CD277 and CD288 identify neutrophil phenotypes that are more likely to bind Ngo. My ongoing research aims to further understand how these different populations contribute to immunity versus immunopathogenesis against this devastating pathogen.

Keywords: CEACAM
infection
Neisseria gonorrhoeae
neutrophil
pathogen
phenotypes
Advisor: Gray-Owen, Scott D
The Positional Logic of Technological Innovation in the Canadian Bioenergy Sector

For almost fifty years, OECD governments have sought to increase the rate of technological innovation in the energy sector to resolve price-supply risks, improve economic performance, and address environmental concerns. Policy and innovation effort has been concentrated within the transportation, electricity, and industrial sectors; fewer resources have been allocated to support the innovation of alternative energy technologies applicable to non-industrial buildings. Small European nations and many subnational jurisdictions are important exceptions to this general tendency. This dissertation presents an integrative theoretical approach to understanding these patterns that begins explanation with the power-distributional effects of material reality and then considers the power-distributional effects of institutions that do not logically derive from material reality. The explanation is improved through attention to temporal processes (path dependence and positive feedback). Areas of the political economy that are prone to oligopoly and vertical/horizontal integration (that are ”centralized”) and that involve complex technologies are more likely to receive resource allocations owing to greater institutional development (organizations and rules). The development of institutions in areas of the political economy that are less centralized and associated with less complex technologies functions to expand the scope of policy and innovation effort. The approach is tested using the example of clean technology innovation in the Canadian bioenergy field. In Chapter 2, federal policy and sectoral developments since the 1970s demonstrate that the transport sector – a highly centralized area of the economy involving the innovation of complex technologies – has been the principal emphasis of policy and innovation effort. The lack of federal policy effort in the non-industrial heating sector is attributed to its decentralized and low-tech nature. In Chapter 3, a comparison of the development of recent non-industrial heating policies in the bioenergy fields of Ontario and Quebec provides evidence supporting the proposition that institutionally complex jurisdictions function to increase resource allocations in decentralized, low-tech areas of the economy. Chapter 4 presents a method of technical and policy model parameterization that is designed to mitigate overconfidence, a plausible mechanism of positive feedback. The final chapter summarizes the findings and discusses implications for clean energy transitions and comparative political economy scholarship.

Keywords: Clean Energy
Climate Change
Comparative Political Economy
Varieties of Capitalism
Advisor: Caspersen, John P
Three Essays in Public Economics

This thesis collects three papers on topics in public economics. In the first two chapters, I consider the relationships between political and economic effects at the US state-level. Chapters 2 and 3 both have ramifications for contemporary policy debates, and highlight features of tax and intellectual property systems which have been understudied. The first chapter examines the relationship between economic growth and the outcomes of US presidential elections. Contemporary US politics has been marked by substantial increases in political polarization and a decline in swing voting, which we might expect would reduce the effect of economic growth on election outcomes. Using a Bartik-type instrument and state-level and individual-level data, I find that the effect of state economic growth on incumbent vote share is smaller when state-level polarization or individual partisanship is stronger. I also show that swing voting and economic voting are closely linked. The second chapter studies how tax systems reflect different social preferences about taxing income groups. I apply the inverse-optimum income tax method to quantify these preferences by calculating the implied weights for every US state. To capture major features of state taxation, I extend the theory underlying the inverse-optimum method to include sales taxes, property taxes, and state income taxes. Using IRS data, I calculate effective tax rates for each state, and find the weights for both single and joint filers across incomes in every US state. I find that the weights vary substantially across states, and do not decrease monotonically as might be expected from most theories of social welfare. The third chapter examines the effect of a different public policy: Canada's protection of a specialized form of intellectual property, industrial designs (IDs). Estimating the effect of holding IDs with nearest-neighbour matching, I find a 19% total treatment effect in revenue for Canadian firms holding IDs. To determine the marginal effect of each additional ID held, a regression with fixed effects finds that a 1% increase in the stock of IDs increases revenue by 0.14%. This shows the importance of design protection in Canada's IP policy.

Keywords: Political economy
Presidential elections
Public economics
Tax policy
Advisor: Eli, Shari