VictorJuiz/thesis huggingface dataset:
A flexible summary statistics-based colocalization method to integrate omics data
Keywords: colocalization
composite null hypothesis
cystic fibrosis
lung disease
meta-analysis
Simple Sum 2

Colocalization methods that integrate omics data can help define the mechanism by which Genome-wide association study (GWAS) loci contribute to disease. Contemporary colocalization analytical tools must be valid and powerful under several complex scenarios such as for summary statistics calculated from meta-analyses or using related or overlapping samples; in the presence of a composite null hypothesis; and in regions with high linkage equilibrium (correlation between genetic markers) and/or allelic heterogeneity. In this thesis, we develop colocalization methods and tools to address these complex scenarios through a frequentist and summary statistics-based approach. The proposed methods could assess colocalization, for example, between a primary phenotype and gene expression, or between other omic-data including DNA methylation (meQTLs), protein QTLs (pQTLs) or metabolites (metQTLs). Chapter 1 provides the scientific motivation and genetic background for calculating the summary statistics. Chapter 2 focuses on the development of the Simple Sum (SS) colocalization framework, which is powerful in regions with high linkage disequilibrium and allelic heterogeneity. However, the SS is restricted to implementation in regions with sufficient eQTL evidence to achieve type I error rate control. This inspired the work of Chapter 3 where we develop a more flexible procedure based on the SS (SS2), which avoids a priori eQTL assumptions. We advance the utility of the method to complex scenarios, such as correcting for multiple hypothesis testing in the presence of a composite null hypothesis, analyzing meta-analysis summary statistics with and without related individuals, and adjusting for overlapping samples between studies. Chapter 4 describes the implementation of the SS2 methodology in a web-based tool, LocusFocus, with extended R functions. Currently LocusFocus is used by over 100 new users per month according to Google Analytics. Chapter 5 concludes with a discussion of the impact and limitations of the work in this thesis, and describes some concrete steps that have been taken towards future work.
How to Be a Pragmatist in the End: Objectivity, Skepticism, and the Demands of Agency
Keywords: American Philosophy
C. I. Lewis
Charles Sanders Peirce
History of Analytic Philosophy
Pragmatism
Wilfrid Sellars

Pragmatists face serious difficulties in accounting for the objectivity of truth and knowledge. For they clarify our beliefs’ meaning and truth by appeal to their practical success, and practical success seems relative to particular contexts, or even particular believers. Some pragmatists verge on simply accepting this consequence, but others attempt to secure objective standards of truth and justification. My dissertation interprets and evaluates this objective pragmatist tradition. I argue for three key claims. First, there are two conceptions of objectivity prominent within this tradition, which stand in serious mutual tension: an empiricist conception, on which objective constraints on belief are provided by possible experiences, and a realist-causal conception, on which they are provided by causal interaction with the mind-independent natural world. These conceptions dominate in different historical periods, marking the transition from classical pragmatism to neo-pragmatism. The classical pragmatists most concerned with objectivity, C. S. Peirce & C. I. Lewis, opt for the former conception (notwithstanding apparent realist-causal sympathies in Peirce’s work that ultimately explain the emergence of the latter). Neo-pragmatists who preserve objectivity, like Wilfrid Sellars, opt for the latter. Second, neither camp effectively deploys its conception to provide an adequate account of the epistemic objectivity of our beliefs and assertions: the former camp falls prey to phenomenalism (and so, among other problems, fails to accommodate other minds satisfactorily), while the latter fails in its effort to leverage semantic externalism into an adequate response to skepticism. Finally and in consequence, pragmatism's most fruitful contribution to thinking about objectivity turns out not to lie in its treatments of meaning and truth, but in its independent epistemology: specifically, in Peirce’s and Sellars’s arguments that our right to accept our basic empirical beliefs is a pragmatic warrant. I develop this stance by arguing that our warrant to accept that our perceptual beliefs are likely to be true derives from our commitment to being effective agents and, ultimately, from the value of control over our empirical circumstances.
Data-driven Modelling and Control of Hospital Blood Inventory
Keywords: approximate dynamic programming
blood supply chain management
empirical risk minimization
perishable inventory management
robust optimization

Determining order quantities for platelet and Red Blood Cell (RBC) units at hospitals is a challenging task since they are perishable and their usage is subject to high uncertainty. In this thesis, we develop data-driven models and methods for determining order quantities for hospitals that order their required units from a central supplier such as Canadian Blood Services (CBS). An important characteristic of the problem in the case of such hospitals is that the remaining age of received units is also subject to uncertainty, a factor that has been generally ignored in the literature. We use data from a network of hospitals in Hamilton, ON, to develop and test our proposed models. We study a periodic-review perishable inventory problem with zero lead-time that operates under the Oldest-Unit, First-Out (OUFO) allocation policy. In Chapter 4, we propose a data-driven approach for determining daily order quantities for platelets. Our approach can be viewed as a demand prediction model that is equipped with a new loss function. Specifically, we assume the required inventory (base-stock) level for each period is a linear function of a set of observed features in that period and optimize coefficients of the linear model by minimizing an approximate measure of the inventory costs comprised of expiry and shortage costs. Our first model assumes a fixed remaining age tuned using cross validation while our second model explicitly accounts for the remaining age variability through a robust optimization approach. In Chapter 5, we introduce two extensions of our first model to account for holding costs, particularly tailored for ordering RBCs that have a longer shelf-life. Our data-driven approach however does not account for fixed ordering costs and therefore is appropriate for larger hospitals relying on daily deliveries. In Chapter 6, we consider a dynamic programming (DP) approach using parametric models of demand and remaining age uncertainty and propose a simulation-based Approximate Dynamic Programming (ADP) for general stochastic perishable inventory problems with fixed ordering costs and decision-dependent remaining age uncertainty. We leverage ADP-based policies to investigate the value of accounting for (decision-dependent) uncertainty in the shelf-life of units when making ordering decisions.
Atomic Structure of Thin Films in the Cesium-Lead-Bromine System
Keywords: CsBr
PbBr2
Perovskite
Physical Vapor Deposition
STM
Thin Films

Cesium lead bromide (CsPbBr3) perovskite nanocrystals have a promising future in the field of optoelectronics. Their potential applications are primarily in improving the efficiency of solar cells and light emitting diodes (LEDs). However, it remains a great challenge to fabricate halide perovskite nanodevices using traditional methods as they dissolve in polar solvents used in the fabrication of the devices. The available research regarding CsPbBr3 crystals is insufficient, particularly in the area of growth by solid phase evaporation. Therefore, the growing interest in perovskite crystals motivated us as to study the growth of the two binary constituents, Cesium bromide (CsBr) and Lead bromide (PbBr2) on a metallic substrate, as well as the results of co-deposition. In this study, ultra-thin films have been grown using thermal evaporation, studied using low energy electron diffraction (LEED), scanning tunnelling microscopy (STM) and density functional theory (DFT). The growth of CsBr on Ag (111) has been observed in the coverage range 2.5 to 5 ML. Analysis of atomically resolved images show that the thin films have the NaCl structure. At higher coverages, significant mobility is seen in the films imaged at room temperature. The growth of PbBr2 epitaxial layers in the coverage of ~ 0.05 to ~ 1 ML results in the decomposition of PbBr2 to Pb and mobile Br atoms and later their recombination to form PbBr2. Co-deposition of these binary components shows the evidence of formation of the cubic and the orthorhombic phases of CsPbBr3 perovskites thin films. Finally, a study on the phase control as a function of molar deposition ratio has been performed which will lead to better control of the quality of perovskite thin films.
Humanities and Learning Outcomes in Ontario Higher Education
Keywords: Capability Approach
Higher Education
Humanities
Learning Outcomes
New Institutionalism
New Public Management

Governments in western liberal economies, such as Ontario, are shifting to outcomes-based systems that ‘tune’ higher education curriculum to stakeholder interests. Globally, governments are using learning outcomes for quality assurance, to modernize curriculum for societal interests, and to apply government and market influence upon the curriculum. This thesis applies new institutionalism and the capability approach to examine how humanities leaders in Ontario higher education perceive and react to the new administrative layer of learning outcomes. According to institutional theory, responses may include superficial strategies for compliance, non-compliance, or the layering of new policies among existing traditions. The research asks, “How do Ontario university leaders in the humanities perceive and implement the shift to learning outcomes?” The study aims to understand to what extent an outcomes-based system aligns with the curricular priorities of the humanities in higher education. Narratives of 19 university humanities leaders were analyzed through qualitative interviews within 10 Ontario universities. The data was reviewed using thematic analysis, inductive and deductive analysis, and compared within the context of the outcomes-based education literature. The overarching narrative of participants indicated that learning outcomes were both an innovative opportunity for pedagogical reflection and a new burdensome administrative layer. The process of tuning the humanities curriculum with administrative pursuits, targeted government funding, and specified career outcomes was not widely accepted by the participants in the study. The approach of passive compliance with learning outcomes became more evident when asking about the consistency, and verifiability of outcomes achieved. Participants shared political challenges and chronological alignments with program restructuring, displaced curriculum, and in some cases program cancellations. Participants said that students were generally unfamiliar with learning outcomes. When discussing opportunities of learning outcomes, participants said that they were an effective discussion tool to envision curricular strategies for enrolment management, experiential learning, interdisciplinary programs, and large elective courses. The study adds to the literature by providing an in-depth view of the agency of department heads to manage the curriculum in the humanities, an understanding of the implementation of Ontario’s learning outcomes policy, and the political positioning of the humanities in Ontario’s higher education system. Key Words: Learning Outcomes, Ontario, Higher Education, New Institutionalism, New Public Management, Neoliberalism, Humanities, Capability Approach, High Participation System.
Mitigating Model Errors in Chemical Data Assimilation: Application of New Data Assimilation and Machine Learning Approaches
Keywords: Air quality
Data assimilation
Deep learning
Nitrogen oxides
Ozone
Remote sensing

Ozone (O3), nitrogen oxides (NOx = NO + NO2) and carbon monoxide (CO) are air pollutants that impact global mortality. Accurate estimates of the emissions of NOx, CO, and other O3 precursors are crucial for improving air quality. A widely used means of estimating these emissions is through data assimilation, which relies on imperfect atmospheric models. This thesis explores the potential of mitigating the impact of model errors on chemical data assimilation from three approaches: improving conventional data assimilation systems, reducing model errors, and the use of a new machine learning approach. A new weak constraint (WC) four-dimensional variational (4D-Var) data assimilation approach was evaluated for assimilating CO and mitigating model errors using the GEOS-Chem model. The performance of the WC 4D-Var system was assessed using Observing System Simulation Experiments and the results showed that the system is able to mitigate biases associated with convective transport. Vertical transport in GEOS-Chem was previously found to be too weak, thus we investigated the use of recomputing convective mass fluxes online in GEOS-Chem to mitigate some of the transport bias. The physical parameters in the convection scheme were optimized using a statistical approach and the impact of the new online convective was investigated using observations of Rn222, Be7, and SF6. The results showed that the new system reduces bias in the model. To go beyond traditional modeling and data assimilation approaches, a deep learning (DL) model was developed and used for predicting summertime O3 in the United States. The DL model exhibited good predictive skill in capturing long-term and short-term variability in O3. The model was then used to evaluate trends in US anthropogenic NOx emissions, confirming that satellite-derived trends reflect a mix of anthropogenic and background influences on NOx. A second application of the DL architecture was focused on integrating a satellite-derived chemical reanalysis with in situ measurements of surface NO2 to quantify emissions of NOx from China. The DL model suggested slightly higher emissions for central and eastern China and was better able to capture rapid changes in NOx emissions, such as those associated with the Chinese New Year holidays.
Interacting Electronic Orders in Cuprate Heterostructures and Praseodymium-doped Cuprate Thin Films
Keywords: charge order
cuprate
epitaxial strain
heterostructure
superconductor
thin film

The REBa2Cu3O7 – δ (REBCO) family of cuprates (RE = Y or rare earth) has an electronic phase diagram with superconductivity, charge order, and a pseudogap existing at different temperature and doping regions. This thesis explores the effects of RE-site substitution by Pr and heterostructuring with the ferromagnetic La2/3Ca1/3MnO3 (LCMO) on these orders. First, we explore the extent strain-induced deoxygenation of YBCO is responsible for the observed Tc attenuation in LCMO/YBCO multilayers, where a long-range ferromagnetic/superconductor proximity effect is proposed to exist. We compare changes to the Tc in oxygen-underdoped perovskite/YBCO/perovskite trilayers with perovskite layers of ferromagnetic LCMO, paramagnetic LaNiO3 (LNO), and orthorhombic PrBa2Cu3O7 – δ (PBCO). We find that LCMO and LNO trilayers show similar Tc attenuation in response to decreasing annealing pressure. We also use x-ray absorption spectroscopy to gauge the Tc vs. hole concentration (p) relationship in LCMO trilayers. We find this relationship to be the same as what is seen in bulk YBCO. These results indicate that the superconductivity in LCMO/YBCO multilayers is similar to that of YBCO and that strain-induced deoxygenation by itself can account for the observed Tc attenuation. Second, we examine the role of epitaxial strain on a previously observed enhancement of the charge order in LCMO/YBCO multilayers. We use resonant x-ray scattering to measure changes in the onset temperature of the charge order (TCO) of LCMO/YBCO/LCMO trilayers with different YBCO thicknesses and doping levels. We find higher TCOs in LCMO trilayers with thinner YBCO even after accounting for strain-induced deoxygenation of the YBCO layer. Our results indicate that the charge order in LCMO/YBCO multilayers is additionally enhanced by the epitaxial strain on the YBCO. Finally, we report the observation of a bulk charge order in the Mott limit of a REBCO compound. In PBCO thin films, we find a charge order with a double-peak structure in momentum space. This charge order resonates at both the Cu-L3 and Pr-M5 edges, which provides strong evidence for the Pr-CuO2 Fehrenbacher-Rice state. This charge order is also the first to be found in the Mott limit of a cuprate and provides strong evidence for the real-space scenario of charge order formation inREBCO.
The Self-care of Older Adult Iranian Immigrants with Diabetes: Implications for Identity and Social Justice
Keywords: Care ethics
Diabetes
Healthism
Immigrants
Self-care

Self-care has become a central focus in health care policies and practices over the past few decades. Under the neoliberal construction of responsible citizenship, individuals are considered autonomous agents who are expected to be self-reliant and to assume responsibility for their health with the goal of reducing healthcare costs and increasing efficiency. While this might seem to be beneficial to people and healthcare systems, there is a systemic lack of interest in the structural, social, and economic inequities that impact the ability of underprivileged groups to practice self-care. People’s inability to meet the required expectations of self-care may not only have consequences for their health but may also negatively affect their identities and undermine their sense of agency. Little is known about the impact of current self-care directives on the identities of patients with chronic illnesses living in marginal social locations. The purpose of this study was to explore how older adult Iranian immigrants with diabetes understand and negotiate their identities in the context of diabetes self-care demands. This group was chosen because immigrant Iranian older adults may face additional constraints in practicing self-care due to their marginal social location. A feminist ethics framework informed by the works of Hilde Lindemann, Joan Tronto, and Iris Young guided this study. Using a critical qualitative narrative methodology, 15 older adult Iranian immigrants with diabetes living in the Greater Toronto Area were interviewed. Four key findings resulted from this study. First, the moralization and responsibilization of health, with little regard to the structural and relational constraints of people’s lives, can damage people’s identities and sense of agency. Second, the language of control, compliance, and dependency has a negative impact on people’s identities. Third, medicalization and corporatization of healthcare contribute to the marginality of care receivers. Finally, experiencing racialization inside and outside of the healthcare system and biased self-care directives constrain immigrants’ self-care practices. This research suggests that current self-care directives can damage the identities of chronically ill older adults and widen existing social inequalities by legitimizing unjust health disparities. This thesis is a call to move away from individualistic solutions for care by acknowledging our shared interdependence and vulnerabilities.
Trends in Resin Composite versus Amalgam Restorations Placed in North American Dental Schools
Keywords: Amalgam
Dental schools
North America
Resin composite
Teaching policies

Many surveys have been conducted to determine the approach in teaching posterior composite in dental schools in North America. However, none of these surveys have correlated the numbers of posterior restorations placed by students in North American dental schools’ clinics with their teaching policies. In this thesis, three studies have been conducted to investigate the trends of posterior composites and amalgam restorations placed in North American dental schools. The first study investigated the latest teaching policies of posterior composite placement versus amalgam and determined the actual numbers of posterior composites versus amalgam restorations placed in Canadian dental schools from 2008 to 2018. Results revealed a clear trend toward an increase in posterior composite restorations placement and a decrease in the number of amalgam restorations placed. However, the teaching time assigned for the posterior composite is not aligned with the quantity placed. The second study investigated the latest teaching policies of posterior composite placement versus amalgam and determined the actual numbers of posterior composites versus amalgam restorations placed in U.S. dental schools from 2008 to 2018. Results indicated a definite trend toward an increase in the placement of posterior composite restorations and a decline in the placement of amalgam restorations, suggesting a misalignment between the amount of time assigned to teach each restorative material with the number of posterior restorations placed in U.S. schools’ clinics. The third study compared the trends of posterior resin composites and amalgam restorations placed in Canadian dental schools to their counterpart in U.S. dental schools. Results suggested that Canadian dental schools’ conduct toward posterior resin composite teaching is relatively conservative compared to U.S. dental schools. Furthermore, there was no consensus on posterior resin composite preparation techniques or contraindications among Canadian and U.S. dental schools. Based on the findings of these studies, it is suggested that the time devoted to teaching each restorative material in preclinical courses among North American dental schools should be revised and adjusted. In addition, clear, unified guidelines pertaining to resin composite teaching policies should be readily available among North American dental schools.