VictorJuiz/thesis huggingface dataset:
Lived Experiences of Chronic Pain among Immigrant Indian Women in Canada

Chronic pain affects an estimated 1.5 million people in Canada (Canadian Pain Task Force, 2019). As recent immigrant status is a risk factor for the development and progression of chronic pain (Cimmino, Ferrone Cutolo, 2011), it is a particular concern for Canadian immigrant communities. Currently, the Indian population is the fastest growing immigrant group in the country (Statistics Canada, 2014). This makes them an important community in which to understand chronic pain – both its manifestations and its meaning – to ensure culturally-sensitive pain management (Weerasinghe Numer, 2010). As elsewhere in the world, the prevalence of chronic pain is higher among Indian women than men, with women also reporting more severe pain (Dureja et al., 2013). In countries other than India, Indian women also report more pain than non-Indian women (Chia et al., 2016; Allison et al., 2002). However, little is known about their lived experiences of chronic pain or the context in which their pain occurs. In order to fill these gaps, the current qualitative study explores: (1) Canadian immigrant Indian women’s lived experiences of chronic pain, and (2) the role culture plays in these experiences. Thirteen immigrant Indian women with chronic, non-cancer pain participated in this study. Women’s experiences were gathered using one-on-one interviews and photovoice methods. interviews and photographs were analyzed using van Manen’s (1990) phenomenological thematic analysis and Oliffe, Bottorff, Kelly and Halpin’s (2008) photograph analysis. Findings revealed the multidimensional nature of Indian women’s chronic pain, as well as the influence of the larger contexts of gender and immigration on their pain experiences. In particular, women discussed pain in relation to gendered roles and expectations. They also described the process of emigrating to a new country, adapting a new way of life, and adjusting to shifting roles as key factors affecting their pain experiences. These valuable insights have practical, as well as theoretical implications; they not only inform our current knowledge of pain within this understudied population, but also expand our understanding of pain’s biocultural components to include gender and immigration.

Keywords: Chronic Pain
Immigration
Indian Women
Pain Experiences
Socio-Cultural Context
Advisor: Einstein, Gillian
Structure and Functional Characterization of ERG and SPOP

Deregulation of protein homeostasis is a hallmark of cancer and diseases such as prostate cancer and leukemia. ERG is transcription factor that is aberrantly overexpressed in the majority of prostate cancers patients in North America. The second major cause are missense mutations in the Cul3 E3 ligase substrate receptor SPOP. It was previously reported that SPOP targets ERG for degradation in prostate epithelial cells and deregulation of this process drives prostate cancer progression. However, their proposed mechanism is inconsistent with other established biophysical studies. Here, we demonstrate that SPOP interacts with ERG using the canonical binding mechanism and that phosphorylation of S37 abolishes the interaction. Prostate cancer mutations in the MATH domain on SPOP impair ERG binding. However, we did not find sufficient evidence to support the previous findings that SPOP targets ERG for ubiquitination in vitro or subsequent degradation in vivo. ERG overexpression is also associate with leukemia. Our collaborators have fortuitously discovered a P199L mutation in the PNT domain that impairs ERG mediated leukemogenesis. We find that the mutation does not affect the structure, stability or localization of ERG in vitro or in vivo. Using BioID and RNAseq we found that ERG associates with several histone modifying complexes such as HDAC3 and the BAF complex to repress genes involved myeloid differentiation. The mutation appears to impair association with these transcription factor complexes and derepresses myeloid differentiation. Furthermore, using an HDAC3 inhibitor we observed a reversal of ERG mediated leukemic transcriptional programming. Together this thesis provides insights on the nature of the SPOP and ERG interaction in prostate cancer and provide a foundation for developing a therapeutic strategy for treating leukemia.

Keywords: ERG
Leukemia
Prostate Cancer
SPOP
Structure
Ubiquitin
Advisor: Privé, Gilbert G.
On the Molecular Counting and Clustering Problems in Single-molecule Quantitative Nanoscopy

The advent of single-molecule localization microscopy (SMLM) revealed the nanoscopic domain of cellular and molecular biology beyond the diffraction-limit of light. Since its inception, much effort has been focused on the continued improvement of SMLM as a qualitative tool for the study of biological systems that were previously out of reach by fluorescence microscopy. However, a complete understanding of these systems also requires the development of techniques that can extract quantitative information to complement the imaging capabilities of SMLM. This thesis presents the development of a molecular counting technique based on a Bayesian analysis of the blinking statistics of fluorophores in SMLM. This method considers labeling distributions which result from tagging techniques used to attach fluorophores to biomolecules. This framework also allows for a threshold-free measurement of the number of blinks that addresses the important issue of undercounting due to missed blinks that has been ignored by the community. The applicability of the counting technique is explored with numerical simulations that imitate the acquisition pipeline of a typical experiment. The accuracy of the technique in determining molecule copy numbers and protein stoichiometry is then experimentally demonstrated using two constructs of DNA origami grids to mimic biomolecules of interest. In particular, this work revealed difficulties in calibrating for the blinking behaviour of fluorophores and the effects of imposing an intensity threshold on undercounting blinks. These suggest that applications of other counting methods which did not consider these particularities are likely inaccurate. The dynamic range of counting methods based on SMLM is examined with numerical simulations. From these, it is concluded that densities on the order of hundreds of fluorophores in a diffraction-limited area are compatible with the molecular counting framework developed. Additionally, the development of a density-based three-dimensional cluster analysis algorithm (FOCAL3D) for SMLM is outlined. FOCAL3D scans for optimal values of its parameters via a semi-supervised, data-driven pipeline, and is able to perform fast and accurate identification of clusters better than many existing clustering algorithms, most notably the popular DBSCAN algorithm. These contributions provide new tools for the extraction of quantitative information from biological systems imaged by SMLM.

Keywords: Cluster analysis
Molecular counting
Quantitative nanoscopy
Single-molecule localization microscopy
Advisor: Milstein, Joshua N
Indoor Particles: Airborne Measurements and Quantitative Filter Forensics

Filters installed in residential heating, ventilation, and air-conditioning (HVAC) systems are primarily used for air-cleaning of indoor particles. Besides, HVAC filters serve to sample particles from a large volume of indoor air. The analysis of dust particles on HVAC filters, filter forensics, along with the HVAC metadata measurements such as airflow, filter efficiency, and system runtime helps to quantify the concentration, composition, and size distribution of indoor airborne particles averaged over the HVAC filter lifetime. This sampling method is referred to as quantitative filter forensics (QFF). In this dissertation, I explore the dual air-cleaning and sampling roles of HVAC filters for particles and trace metals. The air-cleaning results in an old single-family house indicated that the filtration by a relatively high-efficiency filter is not always effective as continuous HVAC operations (100% runtime) did not consistently reduce airborne concentrations relative to conditioning-based operations (with

Keywords: Dust
Filtration
Indoor Air
Laser Diffraction
Particles
Trace Metals
Advisor: Siegel, Jeffrey A
Considerations Regarding Puberty Assessment Methodology and the Relationship between Undernutrition and Puberty among Adolescents Living in Pakistan

Background: Knowledge regarding the timing of pubertal milestones among those living in Pakistan is sparse. Additionally, an accurate methodology for pubertal self-assessment is key to develop a more comprehensive understanding of sexual maturation on adolescent health. Such research is lacking among those living in low-and middle-income countries (LMIC) and especially for males. Objectives: The first objective of this thesis was to assess the accuracy of pubertal self-assessment. The second objective was to determine the relationships between undernutrition and the timing of pubertal milestones among adolescents living in two different settings in Pakistan – rural Matiari and an urban slum in Karachi. Methods: A systematic review with meta-analysis was conducted to assess the level of agreement between self-assessment using Tanner Stages images and clinician-based assessment. Among youth living in rural Pakistan, the level of agreement between self-assessment using a questionnaire-based tool without images with physician assessment was determined. Next, the relationship between the timing of all pubertal milestones and undernutrition among youth living in Matiari, a rural district in Pakistan was determined using cross-sectional data. Lastly, the relationship between the timing of pubertal onset and undernutrition among youth living in an urban slum in Pakistan was determined using longitudinal data. Results: Participants in rural Matiari and the Karachi slum were able to assess their pubertal development reasonably well when mapped to a three-point classification. However, when the subtitles of the five-point Tanner Stages are of interest, clinician-based assessments were superior. Participants in rural Matiari and the Karachi slum who weren’t impacted by stunting, experienced pubertal milestones consistent with LMIC estimates. However, those with stunting or thinness experienced delays in attaining pubertal milestones. A high prevalence of anemia and nutrient deficiencies were observed in both settings. Conclusions: Integrating self-assessment puberty measures into adolescent research may reveal the interconnectivity of nutrition, health, and well-being. The body of research in this thesis highlights the nutritional vulnerability of adolescents in LMIC as demonstrated by delays in puberty in stunted youth and high levels of hidden hunger.

Keywords: malnutrition
puberty
self-assessment
Advisor: Bhutta, Zulfiqar A
Investigating the Synthesis and Reactivity of Boron Carbonyl Compounds

In the context of small molecule synthesis, boron-containing building blocks have proven to be indispensable tools. Therefore, efforts to develop novel molecules with boron at strategic positions is an important research objective. As part of an ongoing study in the area of amphoteric reactivity, our goal has been to generate molecules wherein the boronate functionality is nearby or bound to the carbonyl functional group. This is challenging due to the known instability of boron in heteroatom-rich environments, but the use of the N-methyliminodiacetic acid (MIDA) ligand has shown to mitigate the propensity of boron to migrate from carbon to oxygen or nitrogen. This dissertation explores the synthesis of novel boron carbonyl compounds and demonstrates that the selective manipulation of the carbonyl moiety extends the scope of accessible boron-containing molecules. Chapter 1 provides an overview of the unique chemical and physical characteristics of MIDA boronates and our previous contributions to the chemistry of boryl carbonyl compounds. Chapter 2 outlines two distinct approaches to achieve the oxidative functionalization of alkenyl MIDA boronates, providing facile access to oxalyl boronates and alpha-borylated ketones. Application of these compounds towards the synthesis of borylated heterocycles is also explored. Chapter 3 reports the chemistry of boryl oximes, which are derived from alpha-boryl aldehydes or acylboronates. Applications in the context of nitrile oxide chemistry, bioconjugation and the Beckmann rearrangement are discussed. Chapter 4 details the identification of the unprecedented C1 building block, carboxyboronate, which can participate in a range of polar transformations. In the process of evaluating the reactivity of carboxyboronate, its ability to react with nucleophiles at both carbon and boron atoms was discovered. Reactions at the boron atom were found to be coupled with the release of carbon monoxide, a property that was applied in carbonylative coupling chemistry. In Chapter 5, the potential of acylboronates to function as acyl anion surrogates is discussed in the context of the Suzuki-Miyaura reaction. Optimal reaction conditions were identified, providing the corresponding ketones in good yields.

Advisor: Yudin, Andrei K.
Maternal Metabolic, Obstetrical and Dietary Characteristics are Associated with the Microbiota and Oligosaccharides in Human Milk at Three Months Postpartum

Background: The association between maternal demographic, metabolic, obstetrical and nutritional parameters on the human milk microbiota and human milk oligosaccharide (HMO) composition remains poorly understood. Objectives: To determine if: (1) maternal BMI, gestational glucose tolerance, mode of delivery and ethnicity are associated with human milk microbial composition and predicted function, (2) if maternal diet and infant feeding practices are associated with the human milk microbiota composition and predicted function, and (3) if maternal characteristics are associated with HMO composition and ii) if HMOs are associated with milk microbiota community structure and predicted function. Methods: Mature milk samples (n= 113) along with demographic, anthropometric, obstetrical and maternal and infant dietary data were collected at three months postpartum. V4-16S rRNA gene sequencing of the human milk microbiota was conducted and rapid high-throughput high performance liquid chromatography of milk samples was performed to analyze HMO composition. Results: Pre-pregnancy BMI was most consistently associated with a number of parameters of the milk microbiota including beta-diversity (Bray-Curtis R2=0.037, P=0.031) and a functional gene inference pathway (biosynthesis of secondary metabolites; coefficient=0.0024, PFDR

Keywords: Bacteria
Body mass index
Gestational diabetes
Human milk
Human milk oligosaccharides
Microbiota
Advisor: O'Connor, Dr. Deborah L.
Modeling Human Yolk Sac Hematopoiesis with Pluripotent Stem Cells

Embryonic hematopoiesis in the mouse consists of distinct programs that differ in their lineage potential and spatiotemporal organization. Prior to the generation of hematopoietic stem cells, the yolk sac initiates three programs, known as the primitive, erythro-myeloid progenitor (EMP) and lymphoid-primed multipotent progenitor (LMP) programs. While these programs do not contribute to long-term, multilineage hematopoiesis, their innate immune cell progeny seed and persist in the tissues throughout development and adult life. These populations execute organ-specific functions to maintain homeostasis. Given the transient nature of their progenitors and their emergence at early stages of development, the identification and study of these programs has not been possible in the human embryo. To overcome this hurdle and access these progenitor populations, I established a developmental biology-guided protocol to generate the yolk sac hematopoietic programs from human pluripotent stem cells (hPSCs) in vitro. Using this strategy, I show that the human primitive hematopoietic program transitions through a NOTCH-dependent progenitor, known as the hemogenic endothelial cell (HEC), prior to the generation of the first hematopoietic cells. Coincident with the emergence of primitive hematopoietic cells, I demonstrate that a second population of HECs gives rise to the progenitors of the EMP program. This second ﻿HEC population also harbours T lymphoid potential indicative of the development of the LMP program. Clonal analyses revealed that the EMP and LMP programs derive from a common hematopoietic progenitor, defining in the human, a unified yolk sac program that develops from a multipotent cell. Together, the findings from my PhD project outline the architecture of the equivalent of the developing human yolk sac hematopoietic system and in doing so, offers a progenitor source for the study of the function of tissue-resident immune cells and their role in disease.

Keywords: developmental hematopoiesis
hemogenic endothelial cells
human pluripotent stem cells
mesoderm
model of embryonic development
yolk sac hematopoiesis
Advisor: Keller, Gordon M
From Bike Lanes to Highway Trucks, Assessing the Impact of Transportation Policies on Air Pollution Exposure at Local and Regional Scales

In a context of increasing concern for population exposure to ambient air pollution, it is crucial to develop tools to assist urban policies tackling air quality. In this thesis, techniques to investigate air quality at local and regional scales were developed and applied to analyze the impact of transportation policies on population exposure and health. The first part of this thesis consists in a large data collection campaign involving short-term stationary and mobile measurements of air pollutant concentrations in Toronto. Land-use regression (LUR) models based on the two data collection protocols are developed and compared with data from a panel study. Recommendations are provided for the design of short-term monitoring campaigns. In the second part of this thesis, we set-up a chemical transport model (CTM) and a plume-in-grid (PinG) model for the Greater Toronto and Hamilton Area (GTHA) to simulate the levels of various air contaminants at a scale of 1 km2. These models are based on a detailed traffic emission inventory and enable a refined analysis of population exposure to traffic-related air pollution. The CTM is combined with a health impact assessment tool to investigate the benefits of greening freight movements on urban air quality and health. In the third module, we use our LUR and air quality models to analyze the impact of transportation policies on population exposure and health. The fine spatial resolution of the LUR exposure surfaces is optimal to assess a major urban planning strategy of the City of Toronto: the installation of new bike facilities. We use our CTM to investigate the health and climate benefits of renewing the fleets of private household vehicles, transit buses and commercial vehicles. While we recommend the use of detailed air pollutant maps such as those obtained from LUR models to assist local policy making, spatially refined CTMs supplemented by comprehensive emission inventories are outstanding tools to assess and compare the benefits of transportation policies at a regional scale.

Advisor: Hatzopoulou, Marianne
Theoretical Considerations of High-frequency Air Temperature Variations and Their Application to the Identification of Physical Heterogeneities in Canadian Temperature Time Series

Theoretical considerations of high-frequency air temperature variations primarily address the representativeness of diurnal temperature extrema in climatological analysis and application and ask the questions related to extrema characterization, causes of systematic temperature biases, and presence of physically based heterogeneities in Canadian temperature time series. The main objective of this thesis is to lay the theoretical foundation for the study of physical heterogeneities in air temperature samples and to offer a practical algorithmic solution for the separation of temperature time series into the radiative and advective temperature components. The initial research question was, Is diurnal air temperature variation accurately represented by the average of daily temperature extrema, and what are the implications of using such averages in the estimation of temperature-related quantities? The answers led to more questions: Can observing windows bias air temperature observations, and which observing window is the most suitable for identification of diurnal mathematical extrema of the temperature-time function? What can improve the representation of diurnal temperature variation? The final question, and a confluence of all previous ones, was, Is high-frequency air temperature sample from northern midlatitudes physically heterogeneous, and if it is, what is the relationship between its components? The results indicate that: (i) Modification of the degree-day formula significantly improves the prediction accuracy of temperature-related quantities. (ii) An improved climatological observing window identifies correctly radiatively driven diurnal minima and remedies the “cold bias” in Canadian temperature observations. (iii) The critical element to an improved representation of diurnal air temperature variation is diurnal extrema timing. (iv) Separation of Canadian air temperature time series into physically distinct populations yields homogeneous radiative and advective air temperature components. The findings suggest that inattention to the physical make up of the air temperature sample can potentially lead to a significant underestimation of the radiatively driven air temperature signal. Finally, the information on the position of diurnal temperature extrema is a key to a plethora of climatological applications, few of which are the main subjects of this thesis.

Keywords: air temperature extrema
air temperature heterogeneity
climatological observing window
degree-day method
diurnal extrema timing
diurnal temperature pattern
Advisor: Gough, William A
Comparative Genomics Identifies DDX56 as a Highly Conserved Stemness Regulator in Normal and Cancer Stem Cells

In all animals, development and homeostasis is ultimately regulated by stem cell proliferation, differentiation, and self-renewal. Aberrant activation of “stemness” programs is deleterious at both the cellular and organismal level and is commonly observed in human cancers. However, identifying key stemness genes directly in humans is challenging. Here, I use the power of model systems and comparative genomics to identify and functionally screen 76 highly conserved, putative stemness regulators in vivo that are also candidate drivers of stemness in human glioblastoma, a highly aggressive, stem-cell driven cancer with limited treatment options. I then closely characterize the DEAD-box RNA helicase DDX56, which is conserved across evolution as a single gene, and its upregulation is prognostic of a poor clinical outcome in glioblastoma. I demonstrate that DDX56 is essential for stem cell maintenance in planarians and is required for survival and proliferation of radial glial stem cells in the developing murine cortex. In glioma neural stem cells, I show that DDX56 is required for normal growth kinetics and sphere forming ability in vitro. Finally, in a Drosophila glioblastoma model, I show that DDX56 is required for tumourigenesis in vivo. In summary, my thesis work supports that underlying programs governing stemness have been conserved across evolution and demonstrates the utility of taking a comparative genomics approach in identifying stemness genes that are key players in an incurable, stem cell-driven, human cancer.

Keywords: comparative genomics
evolution
glioblastoma
planarians
stemness
Advisor: Pearson, Bret J