VictorJuiz/thesis huggingface dataset:
Lived Experiences of Chronic Pain among Immigrant Indian Women in Canada
Keywords: Chronic Pain
Immigration
Indian Women
Pain Experiences
Socio-Cultural Context

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.
Structure and Functional Characterization of ERG and SPOP
Keywords: ERG
Leukemia
Prostate Cancer
SPOP
Structure
Ubiquitin

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.
On the Molecular Counting and Clustering Problems in Single-molecule Quantitative Nanoscopy
Keywords: Cluster analysis
Molecular counting
Quantitative nanoscopy
Single-molecule localization microscopy

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.
Indoor Particles: Airborne Measurements and Quantitative Filter Forensics
Keywords: Dust
Filtration
Indoor Air
Laser Diffraction
Particles
Trace Metals

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
Considerations Regarding Puberty Assessment Methodology and the Relationship between Undernutrition and Puberty among Adolescents Living in Pakistan
Keywords: malnutrition
puberty
self-assessment

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.
Maternal Metabolic, Obstetrical and Dietary Characteristics are Associated with the Microbiota and Oligosaccharides in Human Milk at Three Months Postpartum
Keywords: Bacteria
Body mass index
Gestational diabetes
Human milk
Human milk oligosaccharides
Microbiota

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
Modeling Human Yolk Sac Hematopoiesis with Pluripotent Stem Cells
Keywords: developmental hematopoiesis
hemogenic endothelial cells
human pluripotent stem cells
mesoderm
model of embryonic development
yolk sac hematopoiesis

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.
Theoretical Considerations of High-frequency Air Temperature Variations and Their Application to the Identification of Physical Heterogeneities in Canadian Temperature Time Series
Keywords: air temperature extrema
air temperature heterogeneity
climatological observing window
degree-day method
diurnal extrema timing
diurnal temperature pattern

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.
Comparative Genomics Identifies DDX56 as a Highly Conserved Stemness Regulator in Normal and Cancer Stem Cells
Keywords: comparative genomics
evolution
glioblastoma
planarians
stemness

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.
Constrained Care: Doula Practice and Hospital Birth
Keywords: Care work
Childbirth
Doula
Emotional labour
Maternity care
Medicalization

Doulas offer emotional, physical, and informational support to women during pregnancy, childbirth, and the early postpartum period. Their model of practice is based on providing continuity of care and helping clients feel well supported regardless of how their birth proceeds. In hospitals, these efforts are complicated by doulas’ lack of formal status in the health care system and by the medical model of birth, which views childbirth as a clinical event rather than one that requires support and encouragement. Presently, little is known about how these “complications” shape doulas’ work in hospitals. As more women train and practice as doulas, it is critical to understand the nature of their working conditions and their capacity to deliver their ideal model of care. I asked: How do doulas accomplish their work in hospitals? To explore this question, I conducted interviews with 26 doulas working in Toronto, Canada. I invited participants to describe the work involved in providing client support, their interactions with hospital staff, the overall demands of their role, and their level of satisfaction with doula practice. My analysis brought together data about the particularities of doulas’ work practices with feminist critiques of medicalized childbirth and the gendered organization of care work. I found that doulas’ position in hospitals created several challenges. Many participants reported an inability to perform their ideal model of care without tiptoeing around staff, a need to show deference to medical authority and appear as if they were not challenging the medical model of birth (even if that was their aim), and an implicit obligation to perform work outside of their scope of practice to assist busy nurses and ensure that their clients received adequate care. These demands were in addition to the considerable challenge of providing women with comfort and support during childbirth – a task that required a great deal of emotional labour – and the commitment involved in providing continuity of care. My findings suggest that the current model of doula practice is unsustainable and the challenges doulas face in hospitals highlight broader deficiencies in the organization and delivery of maternity care.
Robotic Micromanipulation of Cellular and Intracellular Structure
Keywords: cancer biophysics
cell mechanics
magnetic tweezers
micromanipulation
microrobotics

The development of magnetic micromanipulation systems, using electromagnets or permanent magnets, has enabled a multitude of applications for cellular and intracellular measurement and stimulation. Controlled by different configurations of magnetic field generation systems, magnetic particles and different types of microrobots have been actuated by an external magnetic field to exert forces/torques and perform mechanical measurements on the intracellular structures. Magnetically controlled particles and microrobots have also been controlled to apply mechanical stimulations, generate aggregations to trigger cell signaling pathways, and produce heat to cause cancer cell apoptosis for hyperthermia treatment. This thesis presents a multi-pole magnetic tweezers system for micromanipulation involving sub-micrometer position control and picoNewton force control of a sub-micron magnetic bead inside a single cell for measurement on different locations (spatial) and different time points (temporal). The average positioning error was quantified to be 0.4 µm. The system is also capable of applying a force up to 60 pN with a resolution of 4 pN for a period of time longer than 30 mins. The system was applied for revealing nuclear mechanics in migrating cells, and intra-embryonic mechanical properties. The thesis also presents magnetic micromanipulation as a tumour treatment approach for glioblastoma, the most common and aggressive brain cancer in adults. Transmission Electron Microscopy images and histology results showed that the glioblastoma cells are able to internalize the carbon nanotubes within the cytoplasm, endosome, and lysosome. Through controlling the torque generation on magnetic carbon nanotubes, the results showed that the magnetic treatment is able to induce cell death on petri dish, and extend the survival time of tumour mice significantly from median survival of 22 days to 26 days. The treatment relies on physically tearing cellular structures without suppressing a specific cancer cell growth as in chemotherapy drugs, potentially circumvent the chemotherapy-resistance and provide an alternative or combinatory treatment approach for glioblastoma.