VictorJuiz/thesis huggingface dataset:
Engineering the Fractal Properties of Podocytes

Nature efficiently self-organizes cells and tissues into complex fractal forms, where fractal structures have cascading features that are statistically similar to the whole. While fractality of a tissue’s structure has been associated with healthy or pathological state, an understanding of whether fractal patterning of the native milieu contributes functionally to tissue maturation, and how cells interpret such shape cues, is not well understood. This thesis uses kidney podocytes as a model system to study the role of fractal patterning of shape cues in tissue development and function in vitro. Podocytes are a major component of the glomerular filtration barrier and exhibit a complex, sieve-like, branching cell architecture. Disruption of podocyte architecture is involved in many kidney diseases, yet is poorly understood. New lab-based approaches are thus needed to accelerate kidney research. However, podocytes are difficult to cultivate in vitro. Here, out-of-plane microscale curved shape cues, biomimetic of glomerular capillaries, were developed as a 2½-D topographic organ-on-a-chip surface and augmented with low and high extents of fractality, to study the role of microenvironment shape in podocyte development in vitro. It was discovered that the micron-scale curvature of polydimethyl siloxane scaffolds exhibited differential surface charge density compared to flat regions, which was correlated with extracellular matrix organization that led to assembly of cell structures and hierarchical cell branching in vitro, delineated using a novel fluorescent “Mosaic” assaying technique. Fractally stimulated cells reflected biological complexity more completely than flat cultures in applications of drug testing, coronavirus infection, and a cells-as-sensors approach to patient serum diagnostics, supporting overall podocyte maturation. RNA-sequencing confirmed maturation and further identified a signature of genes and pathways enhanced uniquely by shape stimulation. This thesis contributed to the understanding of the unique role of fractally-patterned shape cues in supporting podocyte maturation in vitro, and harnessed this knowledge to develop advanced laboratory tissue modeling tools. This work thereby addressed some challenges of cultivating podocytes in vitro, and sets a precedent for how fractal frameworks may support higher-fidelity bioengineering that may extend to other tissue engineering and regenerative medicine applications broadly.

Keywords: Biomaterials
Fractals
Kidney Podocytes
Organ-on-a-chip Engineering
Shape Cues
Tissue Engineering
Advisor: Radisic, Milica
Exploring Novel Drug Targets and Combination Therapies to Extend the Life of Current Antifungal Agents

Fungal infections are a relatively unacknowledged contributor to human disease, despite global mortality rates being on par with well-known diseases such as malaria or tuberculosis. This growing threat has been met with the prophylactic overuse of a limited arsenal of antifungals, leading to the rapid emergence of multidrug-resistant pathogenic fungi. The rate at which resistance continues to emerge is greatly outpacing the rate of antifungal discovery, highlighting the urgent need for novel therapeutic strategies. My research aims to define the genetic circuitry underpinning antifungal drug resistance and to devise therapeutic strategies to abrogate resistance in human fungal pathogens. To identify new genes involved in tolerance and resistance to the azole antifungals, we screened a homozygous deletion library, covering ~11% of the Candida albicans genome, in the presence of fluconazole. We identified 13 genes for which deletion enhanced susceptibility to the azoles, two of which were also important for azole resistance acquired by diverse mechanisms. Mechanistic studies of the retromer component, Pep8, and RHO-GTPase activating protein, Rgd1, highlighted the central role of stress response signaling and genome plasticity in antifungal resistance. Taking a multi-pronged, chemical biology approach, we aimed to identify novel chemical scaffolds with antifungal activity against diverse fungal pathogens. By profiling a targeted set of synthesized macrocyclic peptides, we identified several molecules that enhanced fluconazole activity against diverse Candida species, including the drug-resistant pathogens Candida glabrata and Candida auris. We also leveraged the RIKEN NPDepo collection to perform multiple high-throughput screens against four prominent human fungal pathogens, both in the absence and presence of fluconazole. From this, we identified a broad-spectrum inhibitor, NPD6433, that targets fatty acid synthase, and an azole-potentiating compound, NPD827, that disrupts membrane homeostasis through interactions with sterols. Further, we demonstrated that both molecules circumvent biofilm formation in a rat catheter model of candidiasis that mimics central venous catheters in patients. Collectively, this research unlocks new opportunities for antifungal drug development and provides insight into adaptive mechanisms governing antifungal drug resistance.

Keywords: Antifungal
Candida
Drug Discovery
Drug Resistance
Fungi
Molecular Genetics
Advisor: Cowen, Leah E
Healthy Ageing in a Foreign Land? Examining Health Care Inequities Faced by Older Racialized Immigrants in the Canadian Community Health Survey (2015-2018)

Background: Canada's demographic landscape has transformed to be more multicultural and multi-ethnic, resulting from an increasing inflow of racialized immigrant populations from the Global South, made possible by the abolition of racially discriminatory immigration policy in the 1970s. Although there is a significant body of Canadian research examining immigrants’ access to care, contemporary immigration scholarship has typically examined immigrants as a monolithic population while the intersecting lens of “race” and “immigration” has been largely overlooked. The invisibility of racialization in immigrant research has been criticized for its European-centric worldview. Therefore, this three-paper dissertation aims to make racialized immigrants’ ageing experiences visible through a racial-nativity lens in health equity and health care equity. Methods: A combined dataset was generated to pool over four annual circles (2015-2018) from the Canadian Community Health Survey (CCHS). Statistical methods including Chi-square tests, binary logistic regression, multinomial logistic regression and classification and regression tree analysis (CART) were used. Results: Racialized immigrant older adults systematically bear an excess burden of compromised conditions in physical and mental health consequences, including undiagnosed depressive symptoms (Chapter 2, C#2), unrecognized depressive symptoms (Chapter 2, C#2), poor-fair self-rated mental health (C#3), perceived stressful life (C#3), co-morbidity of mood and anxiety disorders (C#3), poor-fair self-rated health (C#4), and multiple chronic conditions (C#4), compared to the dominant Canadian-born White populations. Moreover, racialized immigrant older adults experienced inequities in access to various types of care across different settings, including depression diagnosis (C#2), mental health consultations from family doctors, psychologists, and social workers (C#3), unmet healthcare needs due to affordability and acceptability barriers (C#4), and unmet needs for treatment of chronic physical conditions (C#4), compared to the dominant Canadian-born White populations. Conclusion: These systematic differences in health conditions and differential patterns of accessing necessary health care services, by race-nativity status, are judged to be unfair in a way that undermine Canada's mandate of universal health coverage. These health and health care inequities are also remediable which warrant interventions to address problems with provisions of health care resources to racialized immigrants at interpersonal, organizational, and policy levels.

Keywords: Health Care Access
Immigrant
Minority Ageing
Racial Minority
Social Determinants of Health Inequality
Social Epidemiology
Advisor: Fang, Lin
An Evaluation of Primary Biliary Cholangitis as a Lifelong Disease: Insights from Canadian Cohort Studies

Primary Biliary Cholangitis (PBC) is a rare chronic autoimmune liver disease that results in morbidity, mortality, and quality of life impairment. This thesis includes four projects designed to inform our understanding of the progression of a patient’s journey with PBC and contribute new knowledge that may inform clinical decision making and advance clinical research. The first study investigated patterns of biochemical response to long-term ursodeoxycholic acid treatment. This study found that achievement of adequate biochemical response was associated with improved liver transplant-free survival regardless of prior history of inadequate response, highlighting response as an important longitudinal treatment goal. The second study aimed to evaluate the real-world effectiveness of obeticholic acid (OCA), a new second-line therapy. This study found that OCA was associated with improvements in biochemical surrogates of outcome and was well tolerated. The third study investigated associations between ethnicity and disease severity, quality of life, and survival. This study found that Indigenous Canadians presented with more advanced disease, had impaired quality of life, and worse liver transplant-free survival compared to White patients. The fourth study investigated the in-hospital burden of liver disease and compared the burden of PBC to other common liver diseases. This study found that liver disease inpatients had premature morbidity, mortality, and high resource use and that PBC inpatients represented a similar resource burden to other common liver diseases. These findings provide evidence to support clinical decision making for patients with PBC and contribute to a growing body of literature.

Keywords: Liver Disease
National Study
Observational Study
Primary Biliary Cholangitis
Registry
Advisor: Hansen, Bettina E
An Investigation into the World Health Organization’s Discussion of Health Equity and Resulting Operationalization to Policy and Practice

The World Health Organization (WHO) is the most prominent global health institution as a specialized agency of the United Nations, whose key objective is “the attainment by all peoples of the highest possible level of health.” As a part of its constitution and work, over the last several decades, the WHO has expressed concern for health equity. However, there is a lack of clarity around the WHO’s fundamental definition and conceptualization of equity. This research asked “how does the WHO conceptualize equity in key texts about health promotion, the social determinants of health (SDH), and urban health, and how does this translate into policy, particularly in Urban HEART?” Urban HEART, the Urban Health Equity Assessment and Response Tool, is a WHO tool for cities to address health inequities through assessing indicators and responding with interventions. The research involved (i) a scoping review to understand how the WHO’s conceptualization of equity is discussed in the scholarly literature; (ii) an examination of WHO key texts about health promotion, SDH, and urban health, to provide an in-depth analysis of how health equity is conceptualized and how it maps against contradictions from study (i); and (iii) an analysis of Urban HEART as an illustrative case, based on interviews with key informants, to determine how key informants understand equity and to assess if discourses from key texts parallel the WHO Urban HEART’s work in practice. While these analyses led to a host of results, one of the main findings is that discourses in WHO texts have and have not paralleled practice through Urban HEART. Specifically, in terms of the outlined approaches for tackling health inequity, while the WHO outlines “three main approaches,” there are seven approaches that emerge through analyzing discourses in WHO texts, and Urban HEART aligns with two of these specified approaches and two unspecified approaches. This work contributed two key things: (i) it shed light on definitions to improve health equity, and (ii) elucidated disconnects between policy and practice.

Advisor: O'Campo, Patricia
Enright, Theresa
Diagnostic Applications of Circulating Endothelial-centric Biomarkers in Cardiovascular Diseases

The endothelial lining of blood vessels is a critical determinant of cardiovascular homeostasis. Endothelial dysfunction, characterized by an imbalanced release of vasomodulatory factors, pro-inflammatory molecules, and induction of reactive oxygen species, has been recognized as a major contributor to a plethora of cardiovascular (CV) ailments. Recently, novel circulating factors, including endothelial-enriched proteins, microRNAs (miRNA), and extracellular vesicles (EVs) have been suggested as a more informative and specific means of not only diagnosing CV diseases but also predicting outcomes. However, it remains unknown whether these novel circulating markers (i) accurately reflect endothelial dysfunction, (ii) provide incremental biological insights over existing markers, and (iii) have clinical utility. To address these lingering questions, this thesis reports a combination of in vitro and clinical studies to assess (i) endothelial-centric biomarkers, (ii) circulating miRNAs, and (iii) EV characteristics. To this end, chapter one highlighted the association of endothelial-centric markers (e.g., angiopoietin-2 [Ang-2], endothelin-1, and myeloperoxidase [MPO]) with mortality during SARS-CoV-2 infection while whole plasma transcriptomics revealed pathways for endothelial-focused intervention. Subsequent in vitro testing of endothelial barrier stabilizing treatments (e.g., angiopoietin-1 mimetics and Slit2-N) abrogated COVID-19 induced endothelial permeability. Extending these concepts to the context of cancer therapy, chapter two revealed how tyrosine kinase inhibitor therapy during chronic myelogenous leukemia differentially modulated the expression profiles of endothelial-centric biomarkers (e.g., increased vascular cell adhesion molecule and Ang-2) while not affecting high-sensitivity C-reactive protein; a commonly used inflammatory marker. Finally, chapter three looked at endothelial dysfunction in the context of cancer-therapy related cardiac dysfunction (CTRCD) during breast cancer therapy. These studies revealed that underlying inflammation (i.e., heightened expression of MPO), as well as endothelial-activation (i.e., increased Ang-2) prior to cancer treatment, may be associated with CTRCD. Whole plasma and EV transcriptomics further highlighted the potential of miRNAs to act as not only biomarkers but elucidate complex disease pathways, the latter of which included cellular senescence and apoptosis. In the broader context, these studies highlight the central role of endothelial activation/dysfunction in CV diseases and emphasize the utility of multi-omics datasets in diagnosis and prognostication.

Keywords: Biomarkers
Cardiotoxicity
Endothelial Cells
Endothelium
MicroRNAs
SARS-CoV-2
Advisor: Fish, Jason E
Integrating Qualitative and Geospatial Data to Understand Environmental Change in a Diverse Cambodian Landscape

A surge of anthropogenic activities has led to irreversible, destabilizing environmental conditions in recent years. Increased calls for stronger management and policy regulations on land use, climate change, and water resources have reached paramount levels globally, as citizens and governments reframe their role in this call to action. Research on these topics: land use, climate change, and water resources span across the world, highlighting the severity and urgency in every country and region. This research focuses on a case study in the Global South, which has undergone significant social, ecological, and economic shifts that have resulted in both positive and negative impacts on the environment and human well-being. In examining these impacts, this research examines how systematic changes in lifestyle and policy have impacted people and their environments and what reform needs to be put in place to ensure environmental sustainability for the future. In doing so, in this research project, I engage in an exploratory study that combines geospatial data (remote sensing/GIS) to analyze system level spatiotemporal changes and semi-structured interviews with residents to analyze local level individual experiences. Together the integration of these two methods helps to address the scalar challenges of environmental research and offers adequate consideration to the interconnection of people and their environment and where future work and policy needs to be focused. Results reveal the processes occurring across the landscape and highlight land transitions, temperature changes, and water resource shortages that are important for understanding broader evolving patterns, while interviews reveal uneven experiences, not just across different land types (rural mountain, rural agricultural lowlands, urban) but also within communities, drawing out issues pertaining to access, distribution, adaptive capacity, and education that all need to be improved. Within geography, planning, and environmental studies, this research offers critical insight regarding the underlying processes and experiences that drive environmental change, the impacts of those changes on humans, and where more research and attention needs to be directed when planning for the future.

Keywords: Climate Change
Environmental Change
Interviews
Land Use
Remote Sensing
Water Resources
Advisor: Daniere, Amrita
He, Yuhong
Amorphous Ni-based Alloys as Alkaline Oxygen Evolution Electrocatalysts

The overall efficiency of many electrochemical conversion and storage technologies, such as water electrolysis and CO2 conversion, is hindered by sluggish oxygen evolution reaction (OER) kinetics. Amorphous alloys display enhanced OER kinetics and stability over their crystalline counterparts but traditionally have had limited geometries (ribbons, flakes) due to material processing requirements tied to rapid solidification. These geometric constraints have restricted amorphous alloys from being explored and integrated into membrane systems. In this work, a two-stage ball milling process was developed and implemented to synthesize high surface area amorphous Ni-based nanoparticles. This process allowed for a broad range of novel compositions to be explored and not be limited to deep eutectic compositions, as most amorphous alloys are. The amorphous Ni-based alloys produced through ball milling were studied as OER electrocatalysts and displayed enhanced activity over their crystalline counterparts on an intrinsic and geometric basis. Various techniques were employed to study surface, electronic, and structural properties of amorphous Ni-based alloys to elucidate why amorphous alloys are more electrocatalytically active. These techniques revealed that the studied amorphous alloys' increased hydration was particularly beneficial for improving activity and stability. The increased hydration, along with minor additions of Co, led to the favourable formation of stable β-NiOOH. The integration of Y into β-NiOOH provided catalytic synergy by participating in proton-coupled electron transfer processes that assisted with removing electrons generated during polarization to facilitate the formation of β-NiOOH and prevent overcharging to form Γ-NiOOH. The absence of observed surface overcharging in amorphous Ni-based electrocatalysts resulted in long-term durability for both cyclic and steady-state polarization conditions. These results demonstrated that amorphous Ni-based alloys are promising candidates as oxygen evolution electrocatalysts, and producing them in the form of nanoparticles facilitates their use for commercial application. Additionally, ball milling was shown to be a valuable process for generating and scaling the synthesis of amorphous nanoparticles while allowing new chemistries to be explored to enhance the OER kinetics further.

Keywords: AEM
Amorphous
OER
Advisor: Thorpe, Steven J
Kirk, Donald W
Geography as a Determinant of HIV Health Outcomes for Individuals Living in Rural, Remote, and Northern Canada

Individuals in rural and remote areas face significant barriers to chronic disease care, including HIV. Challenges in defining and conceptualizing rurality and the lack of appropriate community engagement are ongoing limitations of rural health research. The objectives of this thesis are to: reflect on the importance of developing meaningful community relationships when engaging in rural health research impacting Indigenous peoples, engage with Indigenous community members to explore how distance to HIV care impacts quality of HIV care and, explore how different definitions of rural and northern impact the health outcome, HIV virologic suppression. This thesis explores my relationships as a settler physician engaging with Indigenous communities through a Two-Eyed Seeing approach. It focuses on co-writing methodologies to include perspectives from Indigenous and settler team members. Cohort data from the Canadian Observational HIV Cohort were used to explore the impact of distance to HIV care on markers of quality HIV care in Saskatchewan, as measured by the Positive Partnership Score. The Positive Partnership Score is a composite metric measuring quality of HIV care and includes frequency of viral load and CD4 measurements, baseline CD4 count, antiretroviral medication regimen, and virologic suppression. Cohort data from the British Columbia Comparative Outcomes And Service Utilization Trends cohort were used to explore the impact of different definitions of rurality on HIV virologic suppression. In Saskatchewan, living further from HIV specialist care or from a site of research enrollment was associated with lower Positive Partnership Scores. In British Columbia, rurality defined by Statistical Area Classification but not by Forward Sortation Address was associated with lower odds of virologic suppression. Northern Health Authority was associated with the lowest odds of virologic suppression. Rural health discrepancies have been frequently reported across many health conditions. Greater efforts are needed to address geographic health disparities in Canada. More significantly, this thesis demonstrates several lessons for how rural research should be conducted: careful consideration is needed to ensure geographic variable selection is conceptually appropriate for the research question and community members, such as Indigenous people living with HIV can enrich rural health research and should be included as team members.

Keywords: community engagement
HIV
Indigenous-settler relationships
northern health
rural health
Advisor: Loutfy, Mona