VictorJuiz/thesis huggingface dataset:
Evaluation of Strategies for Managing Anemia and Transfusion in Cardiac Surgery and Risk Factors for Cardiovascular Health

Patients with high cardiovascular risk may develop coronary artery disease requiring surgical intervention. The primary focus of this thesis was to evaluate strategies for reducing the potential risks associated with anemia in cardiac surgical patients. A secondary focus of this thesis was to explore the potential cardiovascular risks associated with cannabis in young adults. The first study was a subset analysis of the Transfusion Thresholds in Cardiac Surgery (TRICS-III) trial evaluating transfusion thresholds in patients with acute myocardial infarction on long-term cardiovascular outcomes, and a synthesis of the results with all available evidence through a systematic review and meta-analysis. We identified that liberal transfusion strategies may reduce the risk for long-term major adverse cardiovascular events. The second study was a subgroup analysis of the TRICS-III trial evaluating transfusion thresholds in patients with diabetes undergoing cardiac surgery. Despite patients with diabetes having increased cardiovascular risk, restrictive transfusion did not increase the risk for clinical outcomes and was more effective at reducing transfusion. The third study was a translational study of the TRICS-III trial evaluating the role of plasma methemoglobin as a marker for anemia-induced tissue hypoxia. Reductions in hemoglobin were associated with increases in methemoglobin, and elevated post-surgical methemoglobin was associated with an increased risk for neurological outcomes. The fourth study was a cross-sectional analysis of the nationally representative Behavioral Risk Factor Surveillance System survey to evaluate the association between recent cannabis use and myocardial infarction in young adults. Recent cannabis use was associated with a 2-fold increase in the risk for myocardial infarction. This risk was elevated in more frequent users of cannabis, and was sustained across all methods of consumption. We demonstrated that there may be differences in the susceptibility of anemia and tolerance to transfusion in specific subgroups of patients with high cardiovascular risk undergoing cardiac surgery, and incorporation of a biological marker of anemic stress may better inform clinical decision making for personalizing transfusion therapy for improving postoperative clinical outcomes and reducing unnecessary exposure to banked blood. Additionally, insights from our cross-sectional study may inform individual decision making regarding an underappreciated cardiovascular risk associated with cannabis use.

Keywords: Anemia
Cardiac Surgery
Cardiovascular Disease
Transfusion
Advisor: Mazer, C. David
Improving Precision of Vancomycin Dosing in Neonatal Sepsis based on Clinical Outcome Evaluation and Population Pharmacokinetics

Background: Neonatal sepsis is commonly treated with vancomycin in the neonatal intensive care unit (NICU). Vancomycin dosing remains a challenge in neonates due to significant pharmacokinetic variability and unclear vancomycin target range.Objectives: This research aims to determine vancomycin target range associated with clinical outcomes and develop a better dosing strategy using population pharmacokinetics (popPK) to maximize probability to reach study-derived target range in neonates. Methods: A systematic review was conducted to summarize vancomycin popPK models in neonatal and paediatric patients. A retrospective cohort study included NICU patients receiving intravenous vancomycin. The associations between vancomycin trough concentrations and persistent/recurrent infections and mortality or acute kidney injury were assessed using logistic regression and classification and regression tree (CART) analyses. A popPK model was derived and validated using nonlinear mixed effects modelling. The predictive performance of the derived popPK model was compared against published popPK models. Monte Carlo simulations (MCS) were performed to derive optimal dosing regimens. Results: A one-compartment model incorporating weight, postmenstrual age (PMA), and serum creatinine (SCR) best described the observed data from 655 vancomycin courses in 448 neonates with highest accuracy and precision compared to other published models. A strong association between time to reach target range and composite outcomes was demonstrated (p=0.005). A vancomycin trough concentration >10 mg/L was associated with lower odds of persistent/recurrent infections (adjusted odds ratio: 0.3, 95% confidence interval (CI): 0.09-0.86, p=0.023) and >15 mg/L was associated with increased risk of acute kidney injury (adjusted hazard ratio of 2.94, 95% CI: 1.10-7.90, p=0.003). CART-derived area under the concentration-time curve over 24 hours (AUC24h) of 420-650 mg*h/L appeared to be associated with lowest risk of persistent/recurrent infections or mortality (p=0.025). MCS-derived vancomycin doses achieved >90% target attainment for trough target range of 10-15 mg/L in majority of PMA and SCR categories (78%). Conclusion: A vancomycin trough target range of 10-15 mg/L was associated with most optimal outcomes in treating neonatal sepsis, which supports using vancomycin trough concentrations for therapeutic drug monitoring in neonates. A vancomycin dosing guideline using loading dose was derived to increase probability of target attainment and time at target in neonates.

Keywords: neonatal intensive care unit
neonates
population pharmacokinetics
therapeutic drug monitoring
vancomycin
Advisor: Seto, Winnie
Walker, Scott
Investigating WDR12 as a Therapeutic Target in Breast Cancer

Breast cancer is the most diagnosed and lethal cancer globally in women. Presently, there is a need for novel targets for the development of improved therapeutics. Data mining through genetic screens suggests that the ribosome biogenesis protein WDR12 is essential for breast cancer cell proliferation. In this study, we characterize the effects of WDR12 knockdown in a panel of breast cancer cells. We show that WDR12 knockdown induces ribosomal RNA (rRNA) processing defects resulting in strong growth inhibition in all breast cancer cells tested, however only a subset of lines displayed short-term cell cycle defects. To further understand the cellular consequences of WDR12 suppression, we investigated the global proteomic landscape and found that WDR12 knockdown results in a perturbation of translational and ribosome biogenesis-related networks. Furthermore, we performed RNA-sequencing to assess the global transcriptional changes upon WDR12 knockdown and found dysregulation of the endoplasmic reticulum (ER) stress response pathway. Finally, we characterized the effect of long-term WDR12 suppression and found that growth inhibition was in part due to cellular senescence. Our results demonstrate that WDR12 is implicated in breast cancer cell growth and senescence, and its suppression may represent a viable therapeutic target for breast cancer.

Keywords: breast cancer
drug target
ribosome biogenesis
senescence
WD40 repeat
WDR12
Advisor: Al-awar, Rima
Investigating RNA-binding Protein Dependencies in Hematopoietic and Acute Myeloid Leukemic Stem Cells

Hematopoiesis is sustained through a delicate balance of hematopoietic stem cell (HSC) self-renewal versus differentiation. Leukemic stem cells (LSCs) arise from mutations in hematopoietic stem or progenitor cells and are both seeds of initiation as well as drivers of progression and relapse in acute myeloid leukemia (AML). Targeting LSCs represents a key therapeutic goal in AML, but is challenged by their seemingly overlapping features with HSCs. Therefore, understanding the unique molecular circuitries that regulate HSCs versus LSCs is crucial to the development of LSC-targeted therapies in AML. Emerging evidence demonstrating the importance of post-transcriptional regulation in stem cells and solid tumors highlights the critical need for further efforts to understand these mechanisms in healthy and malignant HSC contexts. The work presented in this thesis aims to uncover key RNA-binding protein (RBP) dependencies in HSC and LSC in order to gain insights into vulnerabilities that can be harnessed for therapeutic targeting. In the second chapter, an in vivo CRISPR-mediated dropout screen of RBPs whose expression is enriched in LSCs uncovered 32 hit RBPs essential for leukemic propagation and/or LSC self-renewal, From this, we identified ELAVL1 as one of the top hits and demonstrate that its genetic and pharmacological inhibition impairs human primary AML LSCs, engraftment and promotes myeloid maturation while relatively sparing healthy HSCs. An integrative multi-omics approach reveals mitochondrial metabolism to be a key axis through which ELAVL1 enacts its functional phenotypes in AML with the mitochondrial protein, TOMM34 being a key effector of ELAVL1. In the third chapter, an oncofetal RBP, IGF2BP2 was identified in a BioID screen as an interactor of the HSC pro-self-renewal RBP, MSI2. Functional studies in fetal and adult mouse BM demonstrate that IGF2BP2 knockout does not impair hematopoietic engraftment. However, IGF2BP2 knockdown in human primary AML shows a trend toward decreased leukemic burden, suggesting that IGF2BP2 may have a selective functional role in AML. Altogether, our findings demonstrate the importance of interrogating the post-transcriptional level of regulation in LSCs as exemplified by the characterization of ELAVL1 as a potentially LSC-specific post-transcriptional dependency in AML.

Advisor: Hope, Kristin J
Meeting in the Middle: Teacher-Facilitation of Play and Math Learning in Contemporary Kindergarten

Early math ability is a powerful predictor of future academic learning and opportunity (Duncan et al., 2007). To teach early math skills, many kindergarten programs world-wide endorse (Tafa, 2008), or mandate, play-based pedagogy (Ontario Ministry of Education, 2016), yet all play is not equal when it comes to math learning. Experimental evidence shows that a specific type of teacher-facilitated play, called guided play, leads to greater math learning gains than traditional approaches like direct instruction or free play (Fisher et al., 2013; Skene et al., 2022), however, classroom-based research shows that guided play is uncommon in practice (Wickstrom et al., 2019). Further work is needed to understand how teachers are successfully translating theory into practice by optimizing the middle ground of guided play to support early math learning.This study used qualitative inquiry and thematic analysis to respond to this central challenge. It began by collecting survey data to understand kindergarten educators’ perspectives regarding play, math, and the integration of play and math. Participants who described guiding play to support math were purposefully selected for follow up interviews. Results identified three key findings. First, the majority of educators described more indirect approaches to play and math learning in kindergarten, where children learn math through opportunities for free play without adult intervention. Conversely, only a minority of educators described more direct, or teacher-facilitated, approaches to math learning in kindergarten through various approaches to play and direct instruction. Second, educators who described these teacher-facilitated approaches also described evolving their conceptualizations of play and math learning into a singular and unified construct, that young children learn math through play. Third, this evolved perspective helped educators to then implement various approaches to guided play in practice. Implications of these findings point to a larger conversation about the need to move away from child-led approaches to early math learning and towards teacher-facilitated approaches instead. Importantly, this discussion will identify the key factors that educators leveraged to help them successfully transition towards teacher-facilitated approaches to math and will discuss what can be done to support more educators in also successfully making this transition.

Keywords: kindergarten
mathematics
play
Advisor: Pyle, Angela
Elucidating the Role of Lipid Binding Domains in V-ATPase a-subunits

V-ATPases are H+ pumps essential for housekeeping functions such as acidifying Golgi, lysosomes, and endosomes. V-ATPases on the plasma membrane (PM) of osteoclasts pump acid onto the surface of bone to demineralize bone, while V-ATPases on the PM of tumour cells acidify the extracellular space required for metastasis. A drug design towards inhibiting V-ATPase activity to prevent bone loss or metastasis must develop a strategy for targeting only V-ATPases on the PM of tumour cells or osteoclasts without affecting V-ATPases involved in housekeeping roles. In mammalian cells, the V-ATPase a subunit has four isoforms, a1-4, that are responsible for targeting V-ATPases to specific cellular locations. Human mutations in the four isoforms have been linked to different diseases. Among the four isoforms, a2 is found in the Golgi membrane while a3 and a4 are primarily expressed on the PM of osteoclast, and kidney cells, respectively. In invasive cancer, both a3 and a4 at the PM of tumour cells are required for tissue invasion and metastasis. Protein primary structures reveal a putative phosphoinositide (PIP) binding domains, containing a highly conserved basic motifs within all a isoforms. Using site-directed mutagenesis, I showed that the basic motifs to affect PIPs interaction and that disruption of the interaction impaired membrane targeting of the N-terminal domains of both a2 and a4 isoforms. In addition, altered levels of membrane PIPs mislocalized both proteins. Mutations in a1, a2, a3 and a4 are associated with epileptic encephalopathy, cutis laxa, osteopetrosis and renal tubular acidosis (dRTA), respectively. To understand the role of a subunit-PIPs interaction in human diseases, disease-causing mutations occurring within the putative binding domains, specifically: a2.K237_V238del (cutis laxa), and a4.K237del (dRTA) demonstrated defective PIP binding in vitro and impaired membrane retention/targeting in HEK293 cells. This data suggests that the a2-PI(4)P interaction is required for Golgi retention/targeting, and a4¬-PI(4,5)P2 interaction is required plasma membrane retention/targeting. This work enhances our understanding of a subunit functional domains, and informs potential targeted therapeutic treatment for metastatic cancer and bone loss pathologies.

Keywords: membrane protein
phosphoinositides
V-ATPase
Advisor: Manolson, Morris F
STEM Discourses and Distinction in An Elite School: Leadership through Relationships to Knowledge

STEM (Science, Technology, Engineering and Mathematics) has become an influential discourse in many educational contexts. Despite varied conceptualizations and practices of STEM and STEM education, main goals of these discourses have largely been to support skilled STEM workforce to compete in the global economies. Although there is a plethora of publication regarding STEM education, a still underexplored context for STEM education is elite private schools. The rationale for examining STEM education discourses in elite private schools stems from these schools’ roles in perpetuating the status quo and securing privilege to dominant social groups. They do so by supporting their students to cultivate recognizable forms of capital, a sense of distinction, and entitlement to their privilege. As such, they allow their students to envision leadership roles. Hence, examining how STEM education is conceptualized and practised in these schools can provide understanding of how elite identifications might be facilitated through available STEM discourses and related meanings of excellence and distinction. This is particularly significant when acknowledging that STEM fields tend to have and produce their own status hierarchy. Through critical discourse analysis, this research examines STEM discourses that are available in an elite independent, co-educational, secondary, day school in Ontario, Canada, and how educators in this school conceptualize distinction in and through STEM (education). Using semi-structured interviews with teachers/administrators and document analysis of the school’s website and viewbook, this research further theorizes how these constructs might contribute to elite identifications. This research shows that, in contrast to the narrative of skilled STEM workforce, in this elite school there is an overarching discourse of leadership that defines what distinction in STEM means and what tends to be embraced, rejected and/or recontextualized regarding dominant STEM discourses. Such a leadership discourse subsumes other discourses of impact, intellectual distinction, competitive achievements and active participation. These discourses and related conceptualizations and practices can support students to develop particular “relationship[s] to knowledge” (Bourdieu, 2004) or, more specifically, particular harmonised relationships to STEM knowledge as thinkers, experts and risk-takers, allowing students as such to envision and assume leadership roles and to validate their high status/elite positions.

Keywords: Bourdieu
Canada
Elite Schools
Leadership
Relationship to Knowledge
STEM
Advisor: Bencze, J. Lawrence
The Unacknowledged Ones: An Investigation of The Resistance of LGBTQI+ Syrians

The ongoing tribulations in Syria have catapulted the number of displaced refugees to devastating levels. The trauma experienced by Syrian refugees extends onward from Syria; Syrian Canadians, regardless of their citizenship status, face a host of isolating experiences such as discrimination, racism, Islamophobia. Lesbian, gay, bisexual, transgender, queer, and intersex (LGBTQI+). Syrians are particularly susceptible to these injustices. LGBTQI+ Syrians face discrimination from multiple sources, including homophobia from their cultural groups, and racism, Islamophobia, and homophobia from Western cultures. This can contribute to the development of psychological difficulties, and appreciably compromise their integration into social networks. The purpose of this study was to investigate how the lived experiences of discrimination and oppression impacted the lives of the eleven LGBTQI+ Syrians that were interviewed as participants in this research, and the types of resistance and resilience-based coping strategies that they utilized to promote successful integration of their multiple identities while settling into Canadian society. This study employed a qualitative approach and was informed by minority stress theory while operating within an intersectional framework. Additionally, the study used a community-based, narrative approach that explored the tribulations and resistance strategies of LGBTQI+ Syrians concerning their intersecting identities. The main finding of this dissertation revealed that there is ongoing discrimination which left the participants feeling inferior and led to complications in integrating their identities within a Syrian and Canadian context. Results indicated three significant themes regarding coping strategies that participants utilized in response to experiences of discrimination, humour, therapy, and social support. This dissertation added empirically supported culturally responsive practice insights, specifically tailored culturally responsive training and community resources, which are expected to improve the design and delivery of interventions that aimed to promote psychosocial wellbeing and positive experiences of immigrating to Canada for LGBTQI+ Syrians.

Keywords: LGBTQI+
Refugee
Resistance
Syrian
Advisor: Gillis, Roy
Peptide-based Inhibitors of Bacterial Small Multidrug Resistance Proteins

Antibiotic resistance is a global crisis that first appeared in 1940, shortly after the introduction of penicillin. With the introduction of each new antibiotic, bacteria compensated with mechanisms to avoid their lethal effects. As an alternative approach to conventional antibiotics, this thesis explores a novel, rational drug design to inhibit a resistance mechanism of antibiotic-resistant bacteria. One resistance mechanism involves membrane-embedded multidrug efflux pumps that can effectively extrude an array of substrates, including common antibiotics, dyes, and biocides. Among these pumps are the small multidrug resistance (SMR) membrane transport proteins that consist of four transmembrane (TM) helices, which homodimerize in an anti-parallel fashion through a GG7 motif in TM4. To disable this pump, we synthesized a series of TM4 peptides that contain this dimerization motif designed to disrupt the dimer interaction and reduce substrate efflux. The peptides contain two terminal tags: a C-terminal tri-lysine tag to direct the peptides toward the negatively-charged bacterial membrane, and an uncharged N-terminal sarcosine (N-methyl-glycine) tag to promote membrane insertion. A series of these TM peptides were designed to target various SMRs, and as the GG7 dimerization motif was highly conserved across bacterial species, the peptides were tested for interspecies inhibitory activity. We found that peptides designed to target the P. aeruginosa SMR (PAsmr) were shown to competitively disrupt PAsmr-mediated efflux and re-sensitize bacteria to previously sublethal doses of the commonly-used hospital disinfectant benzalkonium chloride. A range of inhibition was induced across peptides, with the inhibitor peptide for PAsmr displaying the best broad-spectrum activity. To then elucidate the biophysical details of the peptide-membrane interactions, we used circular dichroism and fluorescence spectroscopy, which confirmed that these peptides were inserted and assumed a helical conformation in membrane environments. Interestingly, differential scanning calorimetry showed that peptide insertion into liposomes caused lipid reorganization, yet dye-based in vivo and in vitro assays found that the peptides displayed minimal non-specific peptide-induced disruption of the bacterial membrane per se. As such, the efflux inhibitors designed herein show promise not only for improved treatment of bacterial infections, but more generally, may provide a successful platform to target and disrupt other membrane-embedded protein-protein interactions.

Keywords: Antibiotic Drug Resistance
Bacterial Multidrug Resistance
Efflux Pump Inhibitors
Membrane Protein-Protein Interactions
Membrane-Active Peptides
Advisor: Deber, Charles M.