VictorJuiz/thesis huggingface dataset:
Evaluation of Genetic Service Utilization and Patient Psychological Response to the Implementation of Reflex BRCA1/2 Tumour Genetic Testing for Ovarian Cancer

Background: Reflex (automatic) BRCA1/2 tumour genetic testing of all newly diagnosed high-grade serous ovarian cancer (HGSOC) was implemented in the province of Ontario, without data regarding potential impacts on germline genetic testing rates or patient psychological outcomes. This thesis aimed to identify changes in genetic service utilization and measure the psychological impact reported by HGSOC patients following reflex BRCA1/2 tumour genetic testing. Methods: A scoping review identified measures evaluating alternative models of genetic service delivery for cancer patients. A retrospective review compared rates of genetic counselling referral, attendance, and patient uptake of germline genetic testing before and after implementation of BRCA1/2 reflex tumour genetic testing. A cross-sectional patient survey study collected patient reported outcomes after receiving reflex BRCA1/2 tumour genetic test results. Results: Evaluations of alternative genetic service delivery models reported on genetic service use (rate of genetic counselling referral, attendance for genetic counselling, and uptake of genetic testing) and patient outcomes (satisfaction, knowledge, and psychological outcomes). There was an absence of studies involving reflex tumour genetic testing. Following implementation of reflex BRCA1/2 tumour genetic testing at the Princess Margaret Cancer Centre, genetics referral rates increased (IRR=1.60, 95% CI: 1.07-2.42) and the median time from diagnosis to referral decreased (59 days pre- vs 33 days post-implementation; p=0.04). Once referred, most patients attended genetic counseling and pursued germline testing. Among HGSOC patients surveyed, 41% could not accurately recall their tumour genetic test results, but 85% were satisfied with having reflex BRCA1/2 tumour genetic testing completed as part of their cancer care. Higher cancer-related distress was associated with a higher psychological impact of tumour genetic testing (p

Keywords: BRCA
genetic testing
health service
ovarian cancer
psychological
tumour testing
Advisor: Metcalfe, Kelly A
The 2014 Mount Polley Mine Disaster: Environmental Injustice, Antirelationality, and Dreams of Unconstrained Futures

On August 4, 2014, within Secwépemc territory in the interior of British Columbia, a failing retainment wall of an over-burdened tailings storage facility released ~25,000,000 m3 of industrial waste into adjacent ecosystems culminating in what is now known as the Mount Polley Mine Disaster (MPMD). This dissertation takes the MPMD as a stepping off point to analyze how the disaster is relationally connected to larger patterns of socio-ecological disruption in the context of British Columbia’s colonial history. Drawing from Ruth Wilson Gilmore’s idea of antirelationality, I raise questions about the underlying logics that enabled the disaster and how this disaster fits within broader historical patterns of violent disruption. My research employs qualitative research methods that include historical archival research, interviews, participant observation, as well as document and media analyses to support a central overarching argument. Here I argue that, while the MPMD is commonly viewed as a representation of state or industry failure, looking instead to the history of British Columbia reveals that mass socio-ecological disruption from industrial mining have not been failures at all. Instead, mass socio-ecological destruction has been an inherent part of the entirety British Columbia’s complex and evolving project of modern settler colonial state-building.

Keywords: antirelationality
British Columbia history
environmental injustice
settler colonialism
socio-ecological disruption
the Mount Polley Mine disaster
Advisor: Ruddick, Sue
Bayesian Optimal Allocation of Search Effort in Archaeological Survey: Seeking the Late Neolithic in Wadi Qusaybah, Northern Jordan

This dissertation explores the use of predictive modelling and optimal allocation in an archaeological survey designed to optimize the allocation of effort in the search for evidence of Late Neolithic activity in Wadi Qusaybah, northern Jordan. The allocation algorithm assigns daily effort to discrete survey units delineated in a Geographic Information System (GIS). These units are landscape elements that are likely fragments of early Holocene land surfaces that have survived millennia of erosion, sedimentation, and anthropogenic alteration. Demarcation of these landscape elements is the first in a two-step predictive model. The second step involves eliciting probabilities of detecting Late Neolithic remains in each search space from experts on the Late Neolithic of the southern Levant and especially northern Jordan. These a priori estimates are updated iteratively in a Bayesian framework as each day’s survey provides new information. New information comes in the form of estimated coverage for each space, as determined by multiplying “sweep widths” by the total length of surveyors’ search paths, coupled with either discovery or non-discovery of Late Neolithic artifacts. These Bayesian updates result in posterior probabilities that serve as new priors for the following iteration and are used by the optimal allocation algorithm to determine how much effort, if any, the survey team should expend in each search space on the next day’s survey. Use of this method in Wadi Qusaybah led to the discovery of several certain and several candidate Late Neolithic sites. As these sites are often small, ephemeral, and difficult for conventional surveys to detect, this approach allows us to evaluate hypotheses about a Late Neolithic settlement system, while also demonstrating that conventional archaeological surveys are likely overestimating their thoroughness.

Keywords: Allocation
Neolithic
Optimal
Survey
Advisor: Banning, Edward B
Variable-centered and Person-centered Approaches to Understanding a Satisfying Single Life: A Focus on Singles’ Social Lives

Despite the worldwide increase in the unpartnered population, little research has examined what factors contribute to a satisfying single life. This is an important gap in the literature as the degree to which one is satisfied with one’s relationship status has been shown to be a more important determinant of well-being than relationship status per se. In the present research, I examined situational (Studies 1-3) and individual factors (Studies 4-6B) related to a satisfying single life, with a focus on single individuals’ social experiences. In the first three studies (N = 3,890), I examined if and how having satisfying relationships with family and friends or having a satisfying sexual life is associated with single individuals’ satisfaction with singlehood. Results showed that having satisfying friendships and a sexually satisfying life were both associated with single individuals’ feelings of satisfaction about being single. In the next four studies (N = 3,195), I drew on the Fundamental Social Motives Framework to examine single individuals’ motivations to pursue different types of social experiences in relation to satisfaction with singlehood. Across two Western samples (primarily European and American) and one Korean sample (collected during the COVID-19 pandemic in 2020-2021), I identified three different configurations of motives that exist within the single population. Importantly, the profile characterized by high independence motives in combination with low affiliation and mating motives seemed to be associated with greater satisfaction with singlehood compared to the profile characterized by strong interest in self-protection and social connections as well as the profile characterized by little interest in self-protection but moderate interest in affiliation. Despite considerable consistency, these profile features did not perfectly replicate in a smaller sample collected before the pandemic, highlighting the need to interpret the data with the historical background in mind. Overall, the present research provides novel evidence that maintaining satisfying friendships and sexual lives may contribute to a satisfying single life; at the same time, individuals oriented towards independence in the absence of strong interest in affiliation or romantic partnership may be prone to experiencing singlehood as more satisfying.

Advisor: MacDonald, Geoff
Impett, Emily A
Life Cycle Assessment Based Greenhouse Gas Emission Reductions, Cross Country Analysis and Algorithm Aided Prediction for Lightweighted Composite Auto Parts

Algorithms made our life simpler and enables Machine to learn and predict and seems like a promising revolutionary science of the future. Even though this has been a hotspot in many aspects of science; there are some areas still behind. One of these areas is the Environmental and lifecycle assessments (LCA). The main problem with these areas is that the collected data are not comparable as every research has its own unique details even though LCA has a standard set of guidelines to perform. The second main problem is that we have very limited data avail-able for machines to be able to use in these areas. Here in this thesis, several normalization methods and a coefficient were used to make these data comparable. Also, because we had lim-ited data available, we performed several LCA studies to generate more data to be able to use it in Machine learning algorithms for the purpose of testing, validation and training. One of the advantages of having limited data here was that it enabled us to implement several machine learning algorithms and methods to compare their performances. The results of this study created a powerful tool that can help researchers, original equipment manufacturers, policymakers and automotive companies to make better environmental decisions prior to any design stages just by knowing the percentage of lightweighted automotive parts. This tool is specifically created to work with lightweighting that is resulted from replacing a glass fibre automotive part with natural fibre-reinforced composites. Also, with the developed coefficient of countries, one can transfer the LCA data from one country to another by using a simple equation. These coefficients were developed by using the countries posted total primary energy supply and electricity grid mix. By using these tools, we will have a better understanding of our emissions prior to any design with relatively high accuracy.

Keywords: automotive
Cross country
Ghg
LCA
lightweighting
machine learning
Advisor: Sain, Mohini
Tjong, Jimi
The Animal-industrial Complex and the Politics of Resistance: A Critical Discourse Analysis of White Veganism

Using the theoretical dimensions of critical animal studies (CAS) and the methodological field of critical discourse analysis (CDA), this project examined how the logic that produced and maintains the current system of animal agriculture in Canada and the United States is re-inscribed and/or challenged in online vegan advocacy. Data were collected from 10 online Facebook pages dedicated to vegan advocacy and included entries posted by the page administrator(s) within a 6-month period, as well as the top 5 user comments left on each of these entries. Across all 10 vegan advocacy groups, the total number of posts analyzed was 3,071 and the total number of user comments analyzed was 8,313. Overall, the analysis highlighted the ways in which White privilege and capitalist logic are reproduced and/or contested in online spaces of vegan advocacy. More specifically, CDA revealed the following themes in the data: commodity fetishism and “removing the veil”; conceptualization of animals; varying socio-political context; and relationship to other social justice causes. Drawing on these four themes, this project provides insight into the possibilities and limitations of vegan advocacy and emphasizes strategies for building solidarity across various social justice movements.

Advisor: Bialystok, Lauren
An Examination of Factors Affecting the Labour Supply of Personal Support Workers in Canada

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.

Keywords: Health Economics
Health Human Resources
Health Services Research
Home care
Labour Supply
Personal Support Workers
Advisor: Laporte, Audrey
Chromatin Architecture Aberrations Contribute and Acute Lymphoblastic Leukemia Relapse

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.

Keywords: B-cell acute lymphoblastic leukemia
cancer
chromatin
computational biology
epigenetics
prostate cancer
Advisor: Lupien, Mathieu
Inferring RNA Sequence Specificities from Protein Sequences to Characterize Post-transcriptional Regulation in Eukaryotes

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.

Keywords: Post-transcriptional regulation
Protein-RNA interactions
RNA sequence specificity
RNA-binding proteins
Advisor: Morris, Quaid D.
Ultra-narrowband Imaging with the Dragonfly Telephoto Array: Toward the Cosmic Web

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.

Keywords: circumgalactic medium
galaxy evolution
instrumentation
intergalactic medium
narrow-band imaging
Advisor: Abraham, Roberto G