VictorJuiz/thesis huggingface dataset:
Exploring the Yse of Ligand.BirA* Constructs for Cell Surface Receptor Discovery

Antibodies directed at blocking immune checkpoint targets such as CTLA-4 and PD-1, referred to as immune checkpoint inhibitors, have had a remarkable impact in treating cancer patients. One needs to explore the use of agents targeting new immune checkpoint targets for the purpose of developing more effective and longer lasting mono or combination therapies. Some of these new attractive targets include members of the B7 family, B7-H3, B7-H4 and B7-H5, which act as natural inhibitory ligands to unknown immune checkpoints. Presently, the most commonly used techniques to study unknown protein protein interactions on the surface of cells include TAP, LRC-TRICEPS or genome-scale CRISPR/Cas9 genetic screens. An unmet need in this field is the development of a direct and specific labeling technique of unknown cell surface receptors involved in weak/transient interactions, also providing a snapshot of any proximally associated proteins.The main theme of my thesis was to explore the use of Ligand.BirA* constructs to identify unknown interactions on the surface of cells. As a proof-of-concept, two Affibody.BirA* fusion constructs were designed, expressed, purified and functionally characterized to demonstrate that they retain their biotinylation and binding function to their respective targets (Chapter 2). These 2 constructs successfully biotinylated their targets on the surface of cells. In Chapter 3, we tested if there is a distance limitation of BirA* constructs in terms of biotinylating surface antigens using antibodies. As such, an anti-CEA-mAb.BirA* conjugate and more generically applicable Protein G.BirA* constructs were built, functionally characterized and the extent of their biotinylation range monitored. Both constructs did not label their protein targets, suggesting their large molecular size of mAbs and of mAb-Protein G complexes exceed the biotinylation radius of BirA* (~10nm). In Chapter 4, I describe the design, and expression of a high valency form of the extracellular domain of the human ligand B7-H4, hB7-H4.COMP. hB7-H4.COMP was able to bind to activated murine CD4+ T cells and suppress their proliferation and cytokine secretion. A future goal will be to insert BirA* into B7-H4 with a view to biotinylate cell surface proximal targets on T cells and identify the putative B7-H4 receptor.

Advisor: Gariepy, Jean
“No one can decide for us…the solutions are within us”: Rhetoric and Reality of Youth Participation and Power in Sexual and Reproductive Health Decision-making in Malawi

Ensuring active and meaningful participation of youth in decisions that affect their health and wellbeing has been recognized increasingly by the global health community as a critical strategy to meet young people’s unique sexual and reproductive health needs and rights. Despite aspirational global and national rhetoric promoting youth engagement and sexual and reproductive health (SRH), there is a dearth of scholarship on young people’s everyday realities of participating in SRH decision-making. This critical qualitative study, conducted in Malawi, examined young people’s lived experiences of engaging in SRH decision-making and the underlying structural and societal forces shaping their active and meaningful participation therein. Informed by postcolonial feminist and difference-centred citizenship theories, this study adopts a focused critical ethnographic approach to challenge normative, gendered, racialized and adultist assumptions of young people’s engagement in SRH decision-making. Data was generated from October 2017 to May 2018, using: document analysis, moderate participant observation of SRH policy meetings/events, six focus group discussions with 46 young people, 30 semi-structured interviews and open-ended drawing exercises with youth, 32 semi-structured interviews with key informants (including national/district policymakers, community leaders, non-governmental and civil society organizations, and multi- and bilateral donors) and a reflexive fieldwork journal. Reflexive thematic analysis, and document and visual analyses were employed to produce an understanding of young people’s experiences of participation in SRH decision-making. Findings reveal that despite progressive youth and SRH policies in Malawi, and the establishment of youth participatory mechanisms, young people’s authentic engagement in SRH decision-making remains limited. This study generates insights into young people’s efforts to realize their SRH and participatory rights within a postcolonial context, gerontocratic structures, and policymaking processes dominated by foreign donors and national government. It also exposes the disconnect between the global discourse on youth participation, citizenship, gender equality, and young people’s political, cultural, economic and social realities in practice. The conceptualization of “youth lived SRH citizenship” acknowledges young people’s agency and everyday acts or practices of citizenship. By recognizing youth, including girls and young women, as ardent participants and agents of SRH change within their community and country, this study explores the underlying structural and societal determinants that impede youth from meeting their SRH and participatory rights.

Keywords: Decision-making
Focused critical ethnography
Lived citizenship
Malawi
Sexual and reproductive health
Youth participation
Advisor: Birn, Anne-Emanuelle
Strengthening Families through Responsive Caregiving: How to Target and Design Programs to Achieve Impact at Scale

Experiencing more responsive interactions with caregivers during early development is associated with better mental well-being, physical health, educational attainment, and employment outcomes over the life course. Programs that support caregivers to provide more responsive care to young children improve both parenting practices and child outcomes; nonetheless, these programs and their benefits currently only reach a small fraction of families. This dissertation uses three empirical studies to identify possible targets, teaching strategies, and approaches to program delivery that can be leveraged to increase the effectiveness, efficiency, and reach of such programs. A social relations analysis presented in study one underscores the important role parental responsivity and financial status play in shaping family interactions. Findings from study two—a network meta-analysis of 120 randomized trials—suggest that responsive caregiving programs are most effective when they give parents opportunities to observe models of responsive caregiving, have a narrow focus, use researchers as facilitators, and instruct parents to practice skills at home. Notably, effectiveness is no higher, on average, in programs that use individualized instruction, more sessions, home visits, or video-feedback. Finally, the results of a randomized controlled trial presented in study three demonstrate that it is both feasible and effective to provide online, professional development on responsive caregiving to practitioners working in remote, low-income settings. Together, these findings highlight ways to expand access to and impact of responsivity programs for parents and practitioners, as well as the importance of targeting such efforts towards equity-deserving groups to reduce intergenerational sources of inequality.

Keywords: family systems
network meta-analysis
professional development
program evaluation
responsive caregiving
Advisor: Jenkins, Jennifer M
The Development of High-fidelity In Vitro Cardiomyocyte Models for Physiological Investigation and Pharmaceutical Testing

Cardiomyopathies, heart failure, and arrhythmias or conduction blockages impact millions of patients worldwide and are associated with marked increases in sudden cardiac death, decreased quality of life, and sequelae or complications. These pathologies stem from dysfunction in the contractile or conductive properties of the cardiomyocyte (CM), which is a focus of fundamental investigation, drug discovery, and therapeutic development. Separate from direct disease impact, pharmaceutical cardiotoxicity or lack of efficacy during both clinical trials and marketing is a leading reason for clinical trial failure or post-release drug recalls, ostensibly due to inadequate predictivity by existing animal or in vitro models. In terms of in vitro models, both animals and pluripotent stem cells offer sources of cardiomyocytes for such specific applications. Murine adult cardiomyocytes are a workhorse model for basic science but are physiologically delicate and degrade rapidly in culture; pluripotent stem cell-derived cardiomyocytes (PSC-CMs) offer an inexhaustible source of human CMs but are immature in all aspects of functional physiology. Furthermore, with the advent of engineered tissues and lab-on-a-chip systems, certain well-established experimental workflows to address advanced or emergent physiology in situ or ex vivo have yet to be adapted to high-throughput or microfluidic applications.

Advisor: Simmons, Craig A
Santerre, Paul
Intraspecific Shape Variation in the Bony Labyrinth

Intraspecific shape variation of the Homo sapiens bony labyrinth, or inner ear, has been previously explored in relation to its association with body size, sexual dimorphism, and genetic between-group differences. While studies of the influence of extrinsic and lifelong factors on labyrinthine shape variation have received less attention, they have the potential to further our understanding of functional and non-functional shape differences between the labyrinths of recent humans and our close relatives, such as Neanderthals. Research presented here uses sliding semilandmarks and three-dimensional geometric morphometrics to quantify bony labyrinth shape in both humans and model organisms, for the purpose of assessing the impact of extrinsic and lifelong variables throughout ontogeny.The first chapter of this dissertation investigates the effect of maternal malnutrition on rats exposed to a protein restricted diet through gestation and suckling. No changes in either labyrinthine shape or levels of fluctuating asymmetry were identified, despite a significantly smaller body mass in the experimental group. The second chapter focuses on assessing the effect of climate and subsistence strategy on a global sample of 262 recent humans from archaeological and morgue collections. Climate and subsistence strategy were found to be associated with 7% of overall shape variation each, with temperature being the primary climate variable associated with climate-related labyrinthine shape variation. Finally, in the third chapter, the effect of estrogen- induced osteoporosis is explored with an ovariectomized rat sample. No shape differences were identified between the experimental and control group. Although the low-estrogen group did exhibit higher morphological disparity, this difference was not statistically significant. Overall, extrinsic and lifelong variables, while minimal, were found to have an impact on intraspecific bony labyrinth shape variation at several life stages. These sources of variation should be considered when assessing labyrinth functional and phylogenetic differences at the taxonomic level, particularly when comparing hominins. These findings also suggest that it is important to use representative, large, and geographically diverse recent Homo sapiens as comparative samples.

Keywords: aging
bony labyrinth
development
morphology
variation
Advisor: Viola, T Bence
Silcox, Mary T
An Institutional Ethnography of the Social Relations that Shape Reproductive Health Care Experiences for Women with Female Genital Mutilation/Cutting/Circumcision (FGC) in Toronto, Ontario, Canada

In recent social science research, it has been reported that women with female genital mutilation/cutting/circumcision (FGC) often experience stigmatization during reproductive health care. However, there has not been investigation into how these experiences come to take place. To address this gap in knowledge, the social relations that shape the reproductive health care experiences of women with FGC were investigated using Institutional Ethnography. Qualitative interviews were conducted with eight women with FGC, seven obstetrician/ gynecologists, and two general practitioners. Interviews revealed a set of social relations that organized women with FGC’s experiences of feeling “different” during care, which included anti-FGM discourse, organization of obstetric/gynecological work, and legislation. Immigrant women with FGC learned they were “different” in Canada from anti-FGM discourse in public conversations that opposed FGC. Women worked to mitigate this stigmatization before entering the clinic by engaging in “emotional health work”. This work carried over into the appointment itself and was shaped by the organization of doctors’ work, which was surgically focused. Finally, aspects of the Canadian legal and health care systems disproportionately disadvantaged women with FGC since the Criminal Code of Canada (Bill C-27) guarantees women their rights, but limits such rights to what is “normal” in the west through the dictation of surgeries to which women have access. This dissertation highlights how the ruling discursive knowledge of the “normal” reproductive body holds women’s bodies up against western ideals. These ideals have a normalizing function that shaped women with FGC’s reproductive health care experiences, as they learned how “normality” was inaccessible to them. Women also viewed their racialization as overlooked within medical training and by health care personnel. Racialization has not often been explicitly discussed in the broader FGC literature. It is imperative to actively make space for the perspectives of Black women with FGC in strategies that work toward their protection and to also modify the focus in FGC research and advocacy from gendered discrimination instead onto intersectional stigmatization. By better addressing the intersectional stigmatization to which women with FGC are exposed, they may not have to work so hard to navigate reproductive health care.

Keywords: female genital cutting
female genital mutilation
health research
institutional ethnography
qualitative research
Advisor: Einstein, Gillian
Grace, Daniel
Troubling Intersections: Physical Intimate Partner Violence Against Women in Bangladesh

In the underbelly of beautiful Bangladesh lies the widespread practice of male intimate partner physical violence (MIPPV) against women. Although women’s different socio-demographic risk factors for MIPPV are known, whether their intersecting individual-, community-, and cross-level social locations shape their MIPPV experiences across Bangladeshi communities have not been examined. Therefore, applying Crenshaw’s intersectionality theory, the overarching objective of this dissertation was to make visible the currently married women’s different intersectional social locations that shape their experiences of MIPPV in Bangladesh. McCall’s intercategorical intersectionality approach guided this research. Study participants comprised 14,557 (Studies 1 and 2) and 15,421 currently married women (Study 3) across 911 communities from the 2015 Bangladesh Violence Against Women Survey dataset. Two-level logistic regression models were used to predict women’s MIPPV experiences in the past year and estimate the predicted probabilities at women’s each intersectional location. These probabilities were compared to generate different configurations of inequalities. Study 1 findings indicated that younger age, lower educated and higher educated, poor women compared to older, higher educated and higher educated, nonpoor women had 13.57% (95% CI, 9.25, 17.89) and 12.02% (95% CI, 6.87, 17.17) higher probabilities of experiencing MIPPV. Study 2 found that women living in higher-earning-participation, higher-educated communities had higher probabilities of experiencing MIPPV than those in lower-earning-participation, higher-educated communities (29.90%, 95% CI 25.66 to 34.15 vs. 23.85%, 95% CI 22.40 to 25.30). While our specific hypotheses regarding differences between disadvantaged and advantaged communities were not supported, Study 3 found significant within community differences: younger, poor compared to older, nonpoor women had significantly higher MIPPV probabilities (the minimum difference=12.7%, 95% CI, 2.8, 22.6) in all communities. Similar trend was observed between younger, lower educated compared to older, higher educated women in all except poor communities. Thus, using intersectionality theory made visible Bangladeshi women’s troubling intersections of experiencing MIPPV. Future research might examine the structures and processes that put women at these precarious locations to ameliorate their socio-economic-educational inequalities and reduce MIPPV in all communities. This intersectionality theory-oriented research might advance scholarship on MIPPV in Bangladesh and quantitative intersectionality globally.

Keywords: Bangladesh
Communities
Cross-sectional survey research
Domestic violence
Intercategorical intersectionality
Intersectionality theory
Advisor: Einstein, Gillian
Hip Replacement Head-Neck Taper Connection Tribocorrosion Reduction by Head Material, Head Size and Taper Geometric Optimization

Modular femoral head hip replacement components connect to the femoral stem via matching tapers. Metals commonly used to manufacture femoral heads and stems rely on a passive oxide layer to resist corrosion. Under cyclic loading (i.e. gait) relative micromotion between the head and stem causes wear, removal of the oxide layer and subsequent corrosion by a process called tribocorrosion. Metallic debris released by tribocorrosion may result in adverse local tissue reactions called trunnionosis and may require revision surgery.The objective of this research was to investigate factors affecting head-neck taper tribocorrosion, including head size, material and taper geometry. A systematic review of prosthetic design, manufacturing and surgical technique factors related to taper connection tribocorrosion was performed. The review included 91 studies investigating 35 unique factors, of which only 7 had adequate evidence to support a recommendation. In particular, a gap in evidence related to taper connection design was identified. It was found that poor study design resulted in inconclusive or contradictory evidence for the majority of factors. A second review was performed of taper tribocorrosion in-vitro test methods to improve study design and increase clinical translation of results. A deficiency in current in-vitro test methods was identified where samples are only cyclically axially compressed. Frictional torques due to joint movement that may be larger with larger femoral heads are excluded. Therefore, a novel instrumented hip simulator was developed to measure corrosion related electrical activity during simulated gait. The test apparatus was employed to investigate susceptibility to corrosion of different head sizes (28 vs 36mm cobalt-chrome femoral heads), materials (cobalt-chrome, ceramic and oxidized zirconium) and taper geometry (angle, diameter, length and surface finish). The study of taper geometry followed design of experiments methodology. Twenty-five uniquely designed test samples with a range of taper angles, diameters, lengths and surface finishes were custom manufactured and tested. It was found that large diameter cobalt-chrome femoral heads are most susceptible to corrosion, oxidized zirconium exhibits similar corrosion resistance to ceramic, and that thicker, shorter tapers with either low roughness and high angle, or high roughness and low angle, are least susceptible to short term corrosion.

Keywords: corrosion
hip
orthopedics
taper
tribocorrosion
Advisor: Schemitsch, Emil H
Whyne, Cari M
Combining Laser Spectroscopy and Mass Spectrometry for Structural Analysis of Biologically Relevant Molecules in the Gas Phase

The combination of laser spectroscopy with electrospray ionization (ESI) mass spectrometry has enabled conformational analysis of gaseous ions that retain some solution-phase characteristics. Mixtures of thermodynamically favoured gas-phase conformers and kinetically trapped conformers from solution may be probed simultaneously to reveal distinct photophysical properties. This body of work exploits the kinetic trapping of biologically relevant molecules to elucidate structural properties intrinsic (i.e., without solvent interactions) to systems including fluorescent sensors and DNA-drug complexes. Chapters 2 and 3 explore the trapping of multiple protomers of two fluorophores: a DNA minor groove binder and a ratiometric fluorogenic probe. The presence of multiple protomers was supported by fluorescence, photodissociation and quantum mechanical calculations. A previously unreported protomer of the DNA minor groove binder was uncovered while excitation-dependent and vibronically resolved fluorescence emission facilitated spectral assignments for the fluorogenic probe. Chapter 4 describes a collaborative effort to understand the origin of fluorescence emission enhancement for an amyloid-sensing dye by altering the local environment through macrocycle encapsulation. A hybrid computational method was used to predict gas-phase structures of the host-guest complex, with the most stable complex showing favourable electrostatic interactions that could attenuate access to non-radiative relaxation pathways. Lastly, Chapter 5 details the extension of gas-phase Förster Resonance Energy Transfer (FRET) towards detecting conformational changes in DNA duplexes induced by the binding of small molecule drugs. Changes in FRET response were detected with the incremental addition of single drug molecules to the duplex, highlighting the advantage of measuring fluorescence from mass-selected complex ions. The work in this thesis develops the utility of optical spectroscopy performed on mass-selected ions with key results showing that distinguishable deactivation pathways result from different protonation sites or non-covalent interactions and that gas-phase FRET can detect conformational effects of individual drug binding events on DNA.

Keywords: density functional theory
DNA
fluorescence
mass spectrometry
noncovalent interactions
spectroscopy
Advisor: Jockusch, Rebecca A