VictorJuiz/thesis huggingface dataset:
The Role of Peroxisome Proliferator-activated Receptor Alpha in the Regulation of Sex Differences in T Helper 1 Immunity

It is reported that female CD4+ T cells are biased towards T helper (Th) 1 cytokine production, whereas male CD4+ T cells are biased towards Th2. It has been suggested that the female bias in Th1 immunity is the reason why females not only generate enhanced anti-viral and anti-tumour responses, but also are more likely to develop certain autoimmune diseases than males. Our group previously reported that the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARα) has a sex-specific role in negatively regulating Th1 immunity in mice. The objective of the thesis is to further explore the roles of PPARα in the regulation of sex differences in Th immunity. We first investigated sex differences in Th cytokine production in SJL mice and human primary CD4+ T cells. We observed that female CD4+ T cells of both species produced higher levels of interferon (IFN)-γ and lower levels of IL-17 than male counterparts. Furthermore, we showed that this sex bias in Th immunity was controlled by androgens. The effects of androgens in suppressing Th1 immunity were shown to be mediated through PPARα. Moreover, we showed that PPARα activity negatively correlated with IFN-γ production by CD4+ T cells. Subsequent studies in mice identified IFN-γ as the gene repressed by PPARα. We showed that this repression was mediated through the recruitment of PPARα and the nuclear receptor co-repressor 1(NCOR)-containing co-repressor complex to certain conserved non-coding sequences (CNS) at the Ifng locus in male T cells. Conversely, repressing PPARα activity with the antagonist NXT-1120 lead to global derepression at the Ifng locus and increased IFN-γ production. This control of IFN-γ production by PPARα in male T cells also extended to natural killer (NK) T cells and CD8+ T cells. On the other hand, we found that the sex difference in Th17 immunity was regulated by PPARγ. Androgens decreased PPARγ mRNAs in murine and human CD4+ T cells. Furthermore, knocking down PPARγ expression using siRNAs was associated with higher IL-17 production by female CD4+ T cells. Taken together, these findings have furthered the understanding of sex differences in Th immunity.

Keywords: Histone modification
Nuclear receptor
Sex difference
T cells
Transcription factor
Advisor: Dunn, Shannon
Regeneration in Recall and Verb Phrase Ellipsis

In this thesis, I propose the Ellipsis Regeneration Hypothesis, whereby resolution of verb phrase ellipsis (VPE) involves accessing a conceptual/propositional representation of the antecedent, and regenerating structure using recently activated lexical items. This hypothesis pulls together strands from two independent areas of research: anaphor resolution and recall. Previous research on the processing of VPE constructions has demonstrated that the linguistic structure of the antecedent appears to be accessed and reactivated during resolution. At the same time, in a series of experiments investigating immediate recall, Potter and Lombardi (1992, 1998) and Lombardi and Potter (1992) argue that such linguistic representations do not persist in memory. Under their view, immediate recall (which is normally highly accurate) entails access to a conceptual (rather than linguistic) representation of the target and regeneration of structure using recently activated, but unordered, lexical items. The primary piece of evidence for this hypothesis is lure intrusion: if recall consults a surface representation of the target, then it should not be possible to induce changes to lexical items or structure. And yet, Potter and Lombardi show that when subjects are presented with synonyms (lures) to a word in the target, they will sometimes select the synonym in recall. Moreover, if that synonym is a verb (e.g., donate) that requires a different structure to that of the target (e.g., give), subjects will make the appropriate structural changes in recall. Bringing the two strands together, one comes to an intriguing possibility: that VPE does not access a linguistic representation of the antecedent but rather, like recall, accesses a conceptual representation and regenerates using recently activated lexical items. Taking lure intrusion to be a hallmark of regeneration, three experiments were designed to determine whether the lure intrusion effect would obtain: a recall study, an ellipsis study, and a study using 'do it'. The prediction of the current thesis is that lure intrusion should occur with both recall and ellipsis, but not with 'do it'.. Evidence from the three experiments supports the hypothesis that the structural output of VPE is, like recall, not accessed, but regenerated.

Keywords: anaphora
ellipsis
recall
regeneration
Advisor: Smyth, Ronald
Applications of Quasi-fixed-Frequency Current-mode Power Converters

This thesis presents the small-signal analysis and implementations of two Quasi-Fixed Frequency (QFF) Current-Mode Control (CMC) schemes: 1) ripple Hysteretic CMC (HCMC) with frequency regulation and 2) Peak CMC (PCMC) with controlled off-time. The QFF CMC schemes eliminate the need for slope compensation and its negative impact on the converter stability; therefore, offering reduced compensator complexity and suitability for applications with wide input and output voltage range. The two QFF CMC schemes with different implementation complexities are applied in three emerging applications: 1) Hybrid Energy-Storage System (HESS) for Internet of Things (IoT) applications, 2) cell-level differential power processing in Concentrating-PV (CPV) system, and 3) applications of high-voltage Gallium-Nitride (GaN) High-Electron-Mobility Transistors (HEMTs). In addition to the practical implementations of the QFF CMC schemes, efficiency/power-density improvements and integration issues are also addressed. In particular, a cell-level Power Management Integrated Circuit (PMIC) operating at 3.6 MHz is the first on-chip realization of ripple HCMC with frequency regulation using a Phase-Locked Loop (PLL). With light-load operating modes, integrated driver and controller supplies, and low-voltage start-up capability, the low-cost PMIC can increase the power output of a CPV system by over 10%. A dual-mode driver/controller IC is designed for a depletion-mode HEMT, with monolithic negative gate-drive capability and digitally programmable slope control. PCMC with controlled off-time is used to simplify the current sensing. The co-packaged driver/controller IC with a customized high-voltage GaN HEMT were operated at 1 MHz in a 35W boost converter prototype.

Keywords: Current Mode Control
Integrated Circuit
Power Converter
Power Management
Advisor: Trescases, Olivier
The Effect of Material Properties on Dynamo Generation in Planets

In this thesis I use a three dimensional numerical dynamo model to explore the effect of novel material properties and core states on magnetic field generation in the planet Mercury, and in rocky extra-solar planets. In the first part of this work I focus on the recent evidence of pressure induced metallisation in materials which commonly comprise planetary mantles. In this scenario the materials which make up the lower mantle of a planet conduct electricity with a conductivity similar to that of iron. I show that a metallised mantle changes the way in which magnetic field is generated by providing a new source of magnetic shear between the fluid outer core and the solid mantle. I then show that this has the effect of making planetary magnetic fields more difficult to observe from Earth. The second and third parts of this work focus on the planet Mercury. First, I incorporate recent evidence of buoyancy sources mid-way through Mercury’s liquid core (known as “snow zones”) to show that they can explain the weak observed magnetic field of Mercury. In a second project on Mercury I test whether recent evidence of a dense solid layer at the top of Mercury’s core, attributed to a solid, electrically conducting layer of FeS, could help explain Mercury’s weak magnetic field. I find that the addition of this layer causes the dynamo to generate a strong, dipolar magnetic field, which does not match the observations made by the MESSENGER spacecraft.

Keywords: Dynamo
Exoplanet
Magnetic Field
Mercury
Planet
Super Earth
Advisor: Stanley, Sabine
Analyzing Phenotypes in High-content Screening with Machine Learning

High-content screening (HCS) uses computational analysis on large collections of unlabeled biological image data to make discoveries in cell biology. While biological images have historically been analyzed by inspection, advances in the automation of sample preparation and delivery, coupled with advances in microscopy and data storage, have resulted in a massive increase in both the number and resolution of images produced per study. These advances have facilitated genome-scale imaging studies, which are increasingly frequent. Although the sheer volume of data involved strongly favours computational analysis, many assays continue to be scored by eye. As a scoring method, visual inspection limits the rate at which data may be analyzed, at increased cost and decreased reproducibility. In this thesis, we propose computational methods for data analysis of HCS data. We begin with feature data derived from confocal microscopy fluorescence images of yeast cell populations. We use machine learning methods trained on a small labeled subset of that feature data to robustly score each population with respect to a DNA damage focus phenotype. We then introduce a method for using deep autoencoders trained using a label-free objective to perform dimensionality reduction. This allows us to model the non-linear relations between features in high-dimensional data. The computational complexity of our approach scales linearly with the number of examples, allowing us to train on a much larger number of samples. Finally, we propose an outlier detection method for discovering populations that present significantly different distributions of cellular phenotypes as com- pared to wild-type using nonparametric Bayesian clustering on the low-dimensional data. We evaluate our methods against comparable alternatives and show that they either meet or exceed the level of top performers.

Keywords: Bioinformatics
High Content Screening
Machine Learning
Advisor: Zhang, Zhaolei
Effects of Landscape Spatial Heterogeneity on Host-Parasite Ecology

Landscape spatial heterogeneity interacts with ecological processes that influence pathogen emergence and infectious disease spread. Modification of landscape composition and configuration is hypothesized to alter host densities, frequency of host-parasite interactions, host community assembly processes, and dispersal processes of host, vector, and parasite populations. Understanding the spatial and environmental dependence on host-parasite interactions is, therefore, critical in predicting the response of disease dynamics to widespread habitat modification. I combine wildlife disease ecology with landscape ecological concepts and varied modeling techniques (i.e., multivariate redundancy analyses, network connectivity models, bipartite mutualistic networks, beta diversity analyses) to test the mediating role of landscape spatial heterogeneity on the spread of a vector-borne disease system (chapter 2), and the effect of urban landscape spatial heterogeneity on host exposure to parasitism (chapter 3), host-parasite interaction structure (chapter 4), and host-parasite beta diversity (chapter 5). My results demonstrate that landscape spatial heterogeneity has a differential influence on tick dispersal than pathogen dispersal by the movement of a host community, most critically mediated by stepping-stone habitat. I also provide evidence that urban landscape spatial heterogeneity affects the exposure likelihood of a single host population, the structure of host-parasite interactions in multiple host populations, and the spatial contributions of host and parasite beta diversity. My work demonstrates that landscape spatial heterogeneity has a mediating role in multiple disease systems whereby spatial and environmental factors play a critical role in the likelihood of short- and long-distance pathogen invasion, the persistence of environmentally-mediated parasites, and the selection of generalist host and parasite species in urbanized habitat. Overall my research contributes to our theoretical understanding of the multi-scalar ecological interactions between landscape change and disease dynamics and our applied understanding of the role of landscape in the emergence of infectious diseases.

Keywords: bipartite networks
disease ecology
landscape connectivity
Lyme disease
spatial epidemiology
urban ecology
Advisor: Fortin, Marie-Josee
K-12 Education as a Hermeneutic Adventurous Endeavor: Theorizing the Instrumental Approach, Education as a Sovereign Agent for Humanity, and the Relationships with Philosophy

This work introduces and discusses my vision for education as a response to a dominant instrumental approach to education. Situated within a broader discussion of the place and role of public education and education research in our lives and in society, I touch upon several key components of foundations of education in order to point at what I consider a problematic and dangerous approach to education as a social and political instrument. This approach, which has become prevalent and taken for granted, divorces education from its deep human capacities and as a result damages students’ humanity and humanity as a whole. From theorizing the instrumental approach I argue for the need for stronger statements about public K-12 education and to the necessity to protect it, and propose a shift in perceiving its role from a social servant to an agent for humanity based on the guideline that we are all human beings. This characterization is meant to make schooling an adventurous endeavor, both for teachers and students, that enables and encourages imagining alternative ways of life and alternative social arrangements. To support this kind of education, I propose to incorporate basic human features alongside the curriculum, namely experiences, understandings, and meanings. As a step towards restoring education’s agency I propose to establish a sovereign education that will depoliticize schooling and will reconsider its associations with other spheres. Particularly, I examine education’s ties with philosophy and argue for non-committal relationships between them in the form of distilling educative ideas from philosophical discussions. Practical measures and policy implications, as well as several expected objections, are discussed and comparisons are made to other views and educational programs, especially to Dewey’s. By way of conclusion, this work offers several ideas about school as a social organization and about public education as human enterprise.

Keywords: adventurous education
humanity
instrumentalism
philosophy of education
public education
sovereign education
Advisor: Portelli, John P.
Bialystok, Lauren
Integrated Microfluidics for Targeted Applications Including Polymerization, Carbon Dioxide Sequestration and Gas Separation

The work presented in this thesis explores the utilization of microfluidic (MF) reactors fabricated in different materials for targeted applications and capitalizes on various fundamental advantages inherent to MFs for studying chemical reactions. In Chapter 3, we describe MF reactor fabrication in polymer materials, including polycarbonate, cyclic olefin polymer, acrylic polymer, polyethylene, poly(vinyl chloride), and polystyrene to address the previous lack of MF reactor materials that are chemically stable in polar and nonpolar solvents, have gas impermeability, are cost-efficient, and biocompatible. We investigated polymer performance under specific conditions and optimized fabrication conditions of MF reactors following well-defined requirements. Chapter 4 explores development and utilization of a MF platform with integrated online attenuated total reflection Fourier infrared spectroscopic characterization for studying kinetics of an exemplary reaction, namely, polymerization of N-isopropyl acrylamide in the presence of accelerator N’,N’,N,N–tetramethylethylenediamine, and initiator ammonium persulfate. The polymerization was studied in flow in a high-throughput manner at various reagent concentrations and pH values. Monitoring the rate of disappearance of the monomer IR band vs. time, we obtained reaction orders with respect to reagents and found good correlation to values reported in the literature. In Chapter 5, we utilized MF reactors by generating segmented flow of CO2 gas and solvent (bromobenzene) to investigate fundamental information, such as thermodynamics and reaction efficiency, of the reaction involving CO2 gas and Frustrated Lewis pairs (FLPs). We developed a method to overcome the challenges inherent in batch processes and successfully obtained ΔG, ΔH, ΔS, and enhancement factors, in the temperature range from 0 °C to 40 °C. This information is vital for future optimization and development of FLPs. Finally, Chapter 6 explores the use of FLPs to effectively separate gases by extracting one gas in a reactive solvent phase. We used MFs to assess the efficiency of the separation of ethylene from its mixture with ethane, due to the chemical reaction of ethylene with FLP. Increasing the FLP concentration and reducing the temperature from 25 to 0 °C, led to significant increase separation of ethylene. The resultant separation factor for ethylene was 7.3 with an ethylene purity of 88%.

Keywords: microfabrication
microfluidics
polymerization
Advisor: Kumacheva, Eugenia
Cultivating Conformity and Safeguarding Catholicism: The Christian Brothers and their Schools in Ontario, 1851-1962

This dissertation discusses the evolving educational apostolate of the Institute of the Brothers of the Christian Schools in Ontario from their 1851 arrival to the province through to the Second Vatican Council in 1962. Through a careful examination of the Brothers’ rulebooks, memorials, letters, and community annals, alongside Church, state, and school board records from archives in Toronto, Montréal, Ottawa, and Rome, this study explores the secular and sacred aims of this Roman Catholic teaching congregation – commonly referred to as the Christian Brothers – within the province’s social, educational, political, and religious contexts. Successive generations of Brothers pragmatically transformed their membership, philosophy, and services in order to integrate into the larger social and educational world in which they lived and thereby live out their apostolic mission and perpetuate the faith to their all-male student body. They overwhelmingly advocated for English-language institutions and greater local control over congregational life; they underwent significant pedagogical training and recognized that improving their qualifications enhanced their professional standing; and they established a more comprehensive array of schooling options (i.e., commercial, secondary, and industrial schools) and altered the curricula therein to accommodate to Ontario’s increasingly dynamic social and economic context. These strategies of conformity – anglicization, professionalization, and curricular adaptations – had the cumulative effect of firmly positioning their congregation in Ontario. Their history acts as a gateway to explore the vital connections between religious and secular society and challenges the often-accepted notion of antipathy between Catholic orders and modern life. By complying with societal norms and the provincial government’s educational standards, the Christian Brothers built up their membership and expanded their educational reach. In so doing, they became crucial players in the consolidation and expansion of a controversial publically funded Catholic separate school system in Ontario that still endures today. Ironically, the greater the Brothers’ integration, the more they were concerned about their status and security in the face of moral, financial, administrative, and educative tensions and scandals. Numeric expansion and a growing confidence in their position as Catholic educators existed alongside deep uncertainty about the permanent viability of their mission. Put simply, conformity did not lead to comfortability.

Advisor: McGowan, Mark G
Vapours Adsorption on Non-porous or Porous Solids: Zeta Adsorption Isotherm Approach

The Zeta adsorption isotherm, ZAI, has been extended so it may now be applied to describe the adsorption of molecularly adsorbed gases, of dissociatively adsorbed gases, and of vapours. This isotherm assumes, as a hypothesis to be tested, that the adsorbates consist of differently sized clusters. The ZAI theory is used to derive an expression for predicting the cluster distributions in the adsorbed phase. Cluster distribution predictions are a unique feature of ZAI and they are not available from other adsorption isotherms. For vapours, this isotherm supposes that an adsorbate at pressures less than the saturation-vapour pressure, P_s (T), consists of molecular clusters with 1, 2, 3••• up to a limited maximum value of ζ_m molecules. Since ζ_m is bounded, we show that ZAI has no singularities for any pressure. This allows the adsorption of vapours at pressures greater than P_s to be investigated. The cluster distribution predicts the formation of an adsorbed film at a vapour phase pressure greater than P_s. Further, the ZAI is combined with Gibbsian thermodynamics to obtain an expression for the surface tension at the solid-vapour interface, and a method has been proposed for determining the conditions at which an adsorbed vapour becomes an adsorbed liquid. For molecularly gas adsorption, the same procedure is applied; it is found that ζ_m is unity, meaning there is no clustering. When the same procedure is applied for dissociative gas adsorption, namely for hydrogen adsorbing on metals, ζ_m is found to be two, meaning the adsorbates consist of both adsorbed atoms and molecules and the mole fraction of the adsorbed molecules and atoms are predicted. For porous materials, we present a method by which the values of the pore structure may be determined from the ZAI combined with the necessary conditions for thermodynamic equilibrium. The consistency of the proposed method is evaluated by comparing the values of the material properties obtained by different vapours. These results also agree closely with the TEM images. A total of 27 different fluid-solid systems have been examined successfully with the Zeta adsorption isotherm. ZAI is also used to determine the surface properties of two mesoporous silica templates (MCM-41 and SBA-15) and a highly porous shale.

Keywords: Adsorption
contact angle
Porous
Surface tension
Thermodynamics
Advisor: Ward, Charles