VictorJuiz/thesis huggingface dataset:
An Examination of Factors Affecting the Labour Supply of Personal Support Workers in Canada
Keywords: Health Economics
Health Human Resources
Health Services Research
Home care
Labour Supply
Personal Support Workers

Despite rising concern over Personal Support Worker (PSW) supply, relatively little literature is available that describes the PSW workforce and addresses issues of PSW labour supply. This thesis provides an overview of the current PSW labour supply literature, followed by four analytical chapters all based on analyses of the Statistics Canada longitudinal Survey of Labour and Income Dynamics (SLID). The first empirical chapter, chapter 4, provides a comprehensive descriptive analysis of socio-demographic, family and household, health, and education characteristics of the PSW labour force with a focus on sector-specific findings across Canada. Chapter 5 examines hours worked, employment history, unionization, pensions, and wages as well as employing non-parametric techniques to understand the distributional changes in PSW wages across sectors. Chapter 6 estimates a two-part selection model to investigate the determinants of PSW wages. Chapter 7 applies a multi-nomial fixed effects model to investigate the factors which affect PSWs’ choice of care sector of employment, treating wage as endogenous to sector choice. Descriptive analyses reveal that the PSW workforce varies significantly across the sectors by many socio-demographic and job characteristics (proportions of women, older individuals, immigrants, and those belonging to visible minority groups). Wage differences by care sector were identified through both averages and non-parametric relative distribution analyses. In the econometric analyses, PSW wages were positively and significantly associated with a variety of factors, including unionization and employment in the hospital sector. Multiple variables had a significant effect on employment in one sector versus another, e.g., being female, older age, and being an informal caregiver were found to have a significant and positive effect on the decision to work in the home and community sector. Understanding factors influencing PSW labour supply outcomes such as wages and sector choice is of particular relevance when designing policies aimed at improving PSW recruitment and retention. PSW labour policies should give due consideration to the implications for existing disparities between PSWs by sector, the inter-connectedness of care sectors and the connection between PSWs and opportunities for these workers in labour markets outside of health care.
Chromatin Architecture Aberrations Contribute and Acute Lymphoblastic Leukemia Relapse
Keywords: B-cell acute lymphoblastic leukemia
cancer
chromatin
computational biology
epigenetics
prostate cancer

Cancer results from aberrations at the molecular level that enable biological hallmarks. These aberrations can be found within the chromatin architecture of cancer cells that includes the genome, molecular modifications to the genome, and the three-dimensional organization of the chromatin fiber. The majority of genetic variants target non-coding regions of the genome and many genes affected by genetic and epigenetic variants have important roles in chromatin remodelling and maintenance. Thus, understanding the origins of cancer progression requires investigating the targets of these aberrations and how they impact the chromatin architecture. First, I investigated the impact of non-coding single nucleotide variants that converge on cis-regulatory elements for the FOXA1 gene in primary prostate tumours. We found that deletion and repression of these cis-regulatory elements significantly decreases FOXA1 expression and prostate cancer cell growth by altering the potential of transcription factors to bind at these loci. These results identify cis-regulatory elements that control FOXA1 expression in primary prostate cancer as potential targets for therapeutic intervention. Secondly, I used chromatin conformation capture of 12 primary prostate cancer tumours and 5 benign prostate tissues to characterize the three-dimensional genome organization. We found that large-scale organization, including topologically associated domains and compartments, is largely stable over oncogenesis but that small-scale focal chromatin interactions change between benign and tumour tissue. We also investigated the impact of structural variants on chromatin organization and identify novel enhancer hijacking events. These results indicate that enhancer hijacking of prostate cancer oncogenes may be a more common driver of disease than previously recognized. Then, I developed a statistical framework for differential gene expression analysis to address the impact of non-recurrent structural variants in our primary prostate tumour cohort. This method improves on conventional gene expression fold change estimates in these unbalanced experimental designs. Finally, I investigated the genetic and epigenetic changes that underlie B-cell acute lymphoblastic leukemia relapse. I found recurrent loss of DNA methylation in patient-matched relapse samples that indicate a more stem-like chromatin state. Together, my work investigates the relationship between multiple components of the chromatin architecture, and how aberrations to this architecture connects oncogenesis, disease progression, and relapse.
Inferring RNA Sequence Specificities from Protein Sequences to Characterize Post-transcriptional Regulation in Eukaryotes
Keywords: Post-transcriptional regulation
Protein-RNA interactions
RNA sequence specificity
RNA-binding proteins

Most RNA-binding proteins (RBPs) find their targets through unique binding preferences towards specific RNA sequence or RNA sequence-structure patterns, called specificities. Recently, we used RNAcompete, an in vitro binding assay, to measure the RNA sequence specificities of 174 RBPs. Combined with previous measurements, we established the largest collection of RBP sequence specificities to date, containing 381 RBPs from 33 eukaryotes, from protists to humans. RNA sequence specificities are nearly always conserved if RBP sequences share more than 70% identity in their binding regions (70%-rule). However, only half of the RBPs sharing between 30% and 70% sequence identity recognize similar RNA, limiting the confidence in predictions from sequence identity. To increase the number of RBPs with a confidently inferred specificity from our measured data, I developed a computational method, called joint protein-ligand embedding (JPLE), which jointly embeds amino acid 5-mers and RNA sequence specificities into a joint latent space. The joint latent embedding of an RBP sequence can be approximated from protein sequence features alone and enables reconstructions of RNA sequence specificity, prediction of RNA binding similarity, and identification of important binding regions in the protein sequence. JPLE doubles the number of RBPs with confidently inferred RNA sequence specificities compared to predictions with the 70%-rule. I embed RBPs from 690 eukaryotes in JPLE’s latent space, confidently reconstruct specificities for 29,000 RBPs, and cluster RNA sequence specificity groups (RSSGs). I use these RSSGs to estimate the number of distinct RSSGs for all eukaryotic RBPs with RRM and KH domains. I confirm that RRM containing RBPs recognize highly diverse sequences, covering every possible 7-mer, while KH containing RBPs recognize only 40% of all possible 7-mer sequences. Moreover, I determine the last common ancestor of the RBPs in an RSSG and derive the evolutionary rate with which new RNA sequence specificities evolve in different eukaryotic clades. Lastly, to demonstrate the utility of this new resource to investigate post-transcriptional regulation, I combine 101 inferred RNA sequence specificities from Arabidopsis thaliana with RNA-seq from 69 plant tissues and I identify RBPs that regulate mRNA stability through interactions with the 3’UTR.
Ultra-narrowband Imaging with the Dragonfly Telephoto Array: Toward the Cosmic Web
Keywords: circumgalactic medium
galaxy evolution
instrumentation
intergalactic medium
narrow-band imaging

The circumgalactic and intergalactic medium (CGM and IGM), are arguably the most important baryonic components of the Universe, yet are poorly understood. The CGM and IGM contain the majority of baryons in the Universe and play vital roles in galaxy formation and evolution, but due to their diffuse nature they are extremely hard to detect. At high redshift, recent technological developments in integral-field spectroscopy have yielded success in detecting emission from the CGM and IGM, but an alternative method is needed to extend this accomplishment to low redshift. This thesis presents a novel method for investigating the line emission from the CGM and IGM in the local Universe: a narrow-band imaging extension to the Dragonfly Telephoto Array designed to target diffuse visible-wavelength line emission. In Chapter 1, the current status of the field and an introduction to line absorption and emission studies is presented, along with an introduction to narrowband imaging and the Dragonfly Telephoto Array (Dragonfly, hereafter). Chapter 2 presents an analysis of cosmological hydrodynamical simulations from the EAGLE project to predict whether visible-wavelength line emission from the local CGM and IGM would be detectable. The result of this analysis is that observations taken by Dragonfly with ultra-narrow bandpass filters would be able to detect the CGM in exposure times as little as ~10 hours. Based on these predictions, the following Chapter presents the design and lab-based testing of instrumentation that implements ultra-narrow bandpass imaging capability on Dragonfly, the “Filter-Tilter”. Chapter 4 presents the first scientific observations taken by a pathfinder Dragonfly Narrowband imager (a 3-lens version of Dragonfly with Filter-Tilter instrumentation), the main result of which is the discovery of a giant ionized gas cloud in the CGM of the starburst galaxy M82. Chapter 5 reports on the current status and work towards a 120-lens full-scale Dragonfly Narrowband imaging upgrade, which is currently under construction and is based on the pathfinder. Finally, Chapter 6 gives a summary of this thesis and plans for future work, the bulk of which is a survey of the CGM of local galaxies with the Dragonfly Narrowband imaging upgrade.
Nursing Students’ Self-efficacy to Care for Older Adults in Acute Care Settings in Ghana: A Mixed Method Study
Keywords: Attitudes
Gerontological nursing
Knowledge
Nursing students
Older adults
Self-efficacy

Self-efficacy has been reported to serve as a motivator for goal achievement and to impact care quality and career development choices. Understanding nursing students’ self-efficacy to care for older adults can provide an opportunity to identify gaps and develop strategies to shape nursing students’ interest in caring for older adults. This study sought to identify the relationship between nursing students’ knowledge about, attitudes towards, and self-efficacy to care for older adults and explored nursing students’ understanding of their self-efficacy to care for older adults. The study also examined stakeholders’ perceptions about nursing students’ self-efficacy to care for older adults and how these views shape gerontological nursing education and practice in Ghana. Bandura’s self-efficacy theory guided this study. Results of this sequential explanatory mixed-method study showed that nursing students’ age and attitudes towards older adults were associated with their self-efficacy to care for older adults. Content knowledge about gerontology was not associated with self-efficacy. Nursing students suggested their self-efficacy to care for older adults was based on their perceived competency in routine procedural nursing care, the impact of the general nursing education program, and the sociocultural norms of caring for older adults in Ghana. Stakeholders indicated that nursing students were well prepared and confident to care for older adults and that the general nursing education program and sociocultural norms of caring for older adults enhanced nursing students’ self-efficacy to care for older adults; however, they also acknowledged the need for gerontological clinical placements for nursing students and the challenges of the gerontology curriculum in the general nursing program. Findings suggest a need for a larger study encompassing different nursing training institutions to determine the extent of revisions needed in gerontological nursing curricula. Findings also indicate a need for gerontological nursing clinical placements to enhance students’ gerontological skills development, for capacity building of faculty, and for the government’s commitment to invest in gerontology education and practice.
Causal Inference Methods for Secondary Analysis of Randomized Screening Trials
Keywords: Causal inference
Instrumental variable estimator
Multi-state model
Randomized screening trials

The primary objective of randomized trials is usually pre-specified in the protocol and typically adheres to the intention-to-treat (ITT) principle, allowing for simple comparisons between intervention arms. However, trials often collect high-quality data that can be utilized for secondary analysis. This thesis is focused on randomized screening trials where asymptomatic individuals are assigned to receive a series of screening examinations or standard care and subsequently followed for a pre-specified period. While the primary analysis in randomized screening trials estimates the effect of intention-to-screen (ITS) on cancer-specific mortality, among the screening-detectable subgroup we might also be interested in the causal effect of early (screening-induced) treatments compared to delayed treatments in the absence of screening. The first objective of this thesis is to develop estimators for the effect of early versus delayed cancer treatments among the screening-detectable subgroup. Using the framework of Rubin’s causal model, we consider two alternative measures, proportional and absolute mortality reductions in the subgroup. We propose estimators for these using the instrumental variable principle as well as outline their identifying assumptions. These estimators generalize existing IV estimators to allow for time-dependent exposure/latent subgroup. The existing models for screening trials, primarily proposed for planning future trials with adequate power for the ITS analysis, are unnecessarily complex for defining and estimating the causal effect of screening-induced early treatments. To address this, we formulate a simplified structural multi-state model, in which the causal effect of early treatments is summarized using a time-invariant, cause-specific structural hazard ratio. For estimating the hazard ratio, we propose two methods, based on an estimating equation and a likelihood expression. Finally, with the aim to generalize the IV methods outside of the trial setting and to allow for covariate-dependent censoring, we introduce covariate adjustment into the estimation. We consider both parametric and non-parametric covariate adjustment using hazard regression models and machine learning algorithms. For the latter, we propose a sub-sampling approach to avoid large-counting process datasets. The performance of all the proposed estimators in this thesis are illustrated through simulation studies and real data examples.
Essays in Environmental and Energy Economics
Keywords: Corporate Social Responsibility
Corporate Sustainability
Energy Economics
Environmental Economics
Event Studies
NGOs

This thesis contains three chapters associated with the study of environmental and energy economics. The first chapter studies the impact of activism by non-governmental organizations (NGOs) on the stock returns of the firms they target, measured through their cumulative abnormal returns (CARs). I find that campaign events on environmental concerns substantially reduce CARs, and that there is no significant effect on campaigns related to non-environmental issues. I additionally test whether NGOs strategically time their campaigning activities and find evidence that NGOs avoid days with newsworthy events that may shift public attention away from their activity. Taken together, the results of this paper provide comprehensive evidence of the effectiveness of activism by NGOs in impacting firms. The second chapter investigates trends in energy use in Canada, relating them to economic output using a key metric: energy intensity. We first derive the major determinants of energy intensity in Canada between 1997 and 2017 using a traditional decomposition framework, namely the activity and efficiency indices. We then find through a non-parametric estimation framework that energy intensity trends downwards, with an average reduction of 1.5% per year, and improvements in efficiency of roughly 1% per year. Our results demonstrate that non-parametric estimation methods are effective in analyzing improvements in energy intensity. The third chapter models the interaction and strategic decision-making between activist NGOs and the firms they target. Firms respond to pressure from NGOs by choosing "green" or "brown" technologies, or by window-dressing; engaging in costly deception to avoid paying the full cost of complying to green technology. I examine how NGOs and firms interact in a monopolistically competitive environment. I derive an NGO-firm game in which firms can choose their technology in response to NGO activism, and the NGO chooses its monitoring intensity. I find that increases in payoffs to the NGO's arm that monitors the use of brown technology lead to an increase in window-dressing. Meanwhile, increases in payoffs to the arm that monitors window-dressing cause a rise in brown technology adoption.
Mirrors and Reflections: Perceptions of Muslim Immigrant Women in Toronto
Keywords: Islamophobia
Microaggression
Mixed Methodology
Muslim immigrant
Orientalism
Women

This study addresses the perceptions that Muslim immigrant women in Canada have about themselves, as self-perception, while also speaking to how they perceive others’ views that affect their lives. Drawing on the experiences and perceptions of self-identified Muslim immigrant women in Toronto, who are English language learners, this study aims to understand Muslim immigrant women’s self-esteem. The study seeks to understand how they perceive themselves, how they simultaneously perceive how others see them in Canada, and the impact of such a double reflexive process. The study examines the cultural and religious impacts on immigrant Muslim women that lead them to deal with a certain “double consciousness” (Du Bois, 1968) to fit into a dominant Canadian culture shaped by colonialism, patriarchy and anti-Muslim racism. Specifically, the study investigates the challenges and needs encountered by Muslim immigrant women in Canada due to existing Orientalist stereotypes and biases about the Muslim community, and how they navigate these challenges. This study adopts a mixed methodology grounded in autoethnography, interviews and a focus group, reflexivity and poetry expression, and creative imagination and visualization. While the study is based on a limited sample, results revealed that Muslim immigrant women’s response to the racist and patriarchal gaze does not diminish their self-esteem; instead, the key finding is that their sense of themselves as agentic, confident women is strong, and this self-perception is not lowered by the perceptions of others.
Diversification and Evolution of Leech (Hirudinida) Anticoagulants with Emphasis on Antistasin-like Proteins
Keywords: Anticoagulants
Antistasin
Leeches
Phylogenetics
Protein evolution

Bloodfeeding is a common feeding behavior among animals and it requires several adaptions for individuals to feed efficiently. Molecular mechanisms of hemostasis inhibition are common adaptations of bloodfeeding species, and it is essential to allow the parasite to feed for a longer time. The diversity of anticoagulants secreted by these animals is noticeable by many cases of functional convergence and divergence within and between protein families. Leeches are an ecologically diverse group of annelids that are closely related to earthworms and other clitellates. They are known for their bloodfeeding behavior that has attracted great attention during human history, because of the medical properties attributed to leech saliva.This thesis aims to (1) test previous orthology hypothesis between archetypal anticoagulants (2) identify the origin of main orthologous groups (3) seek for putative anticoagulants in non-bloodfeeding leech species and (4) understand the contribution of gene duplication and alternative splicing in the diversification of leech anticoagulants. The results presented here contribute to the expansion of leech salivary transcriptome sampling and orthology determination of several anticoagulants. Moreover, we identify putative homologs of many anticoagulants in non-leech clitellates, helping to clarify the origin of these proteins, which can be traced back to before the origin of extant leeches. The presence of ii anticoagulants in non-predatory species suggests that many of these anticoagulants may be involved in other functions. Finally, we found several splicing isoforms that may contribute to a local exploration of protein sequence space. These results have a high impact on our understanding of leech anticoagulant evolution and suggest that the ancestral leech was probably capable of inhibiting factor Xa. However, important thrombin inhibitors such as Hirudin, seem to be an innovation of Hirudiniforms.
Rheology and Microstructure of Aqueous Clay Suspensions
Keywords: Clays
Neutron Scattering
Physical Aging
Rheology
Scattering
Thixotropy

The clay minerals kaolinite and montmorillonite are ubiquitous and abundant and have therefore been the focus of research since the early 20th century when Eugene C. Bingham used aqueous kaolinite suspensions in his seminal work that introduced the concept of yield stress, and Irving Langmuir used aqueous montmorillonite suspensions in his seminal work that laid the foundation of Onsager’s theory of the isotropic–nematic liquid crystal transition. Since then, an enormous amount of work has been carried out on the microstructure and rheological behaviour of these two clay minerals. However, the true microstructure and associated rheological response remain poorly understood. The present work focuses on understanding the microstructure of kaolinite and montmorillonite suspensions and their associated rheological behaviour. The microstructure of kaolinite suspensions was investigated as a function of pH and concentration using scattering and rheology experiments. The microstructure at pH 10—far above the iso-electric point (IEP) of the alumina basal plane—showed the absence of aggregation up to a clay concentration of 55 wt.%. Increasing the concentration further led to aggregation to form entities larger than 20 µm in size. The microstructure at pH values below and above the edge IEP did not change except in terms of attraction strength, signifying that the silica-alumina basal plane interaction was the main mode of aggregation. For montmorillonite, scattering experiments revealed objects in the microstructure that were at least an order larger than individual particles, along with the presence of order. Cryo-electron microscopy complemented the scattering results, showing the presence of domains having strong particle-particle ordering as well as regions of particle-particle aggregation. Thus, the presence of an assembly of particles was confirmed, which refuted a widely accepted model for a purely repulsive nature. The presence of nematic domains refuted a widely accepted model for a purely attractive nature. Rheology experiments revealed a pH-driven aging bifurcation. Furthermore, low ionic strength suspensions at clay concentrations above the sol–gel transition were shown to exhibit features of physical aging and thixotropy, suggesting an out-of-equilibrium behaviour, even within the limit of low ionic strength.