VictorJuiz/thesis huggingface dataset:
Customized Approaches for Inhibition and Degradation of Drug Targets
Keywords: crosstalk
degradation
drug discovery
epigenetics
histone modifiers
inhibition

Diseases are often caused by increase or decrease of specific proteins, and changes in the level of their activities in cell. Many cancers have already been directly or indirectly linked to such changes, for example. This necessitates development of therapeutics for diseases caused by such imbalances and dysregulations. Therefore, the dysregulated proteins are attractive drug targets, and small molecules are needed to modulate their function or antagonize their interactions with partner proteins. However, some protein targets may not be druggable, and finding small molecule modulators of their function may not be practical. Alternative approach would be to selectively target these proteins for degradation. This approach utilizes protein degradation pathway to specifically ubiquitinate the protein of interest by E3 ligases and mark it for degradation. My research takes advantage of all available options for modulating the level of activities of drug targets. Major step in the discovery of small molecule modulators of drug targets is to characterize their function and develop high throughput methods for screening. In the first chapter of my thesis, I focused on better understanding of the mechanism of function of protein arginine methyltransferase (PRMT) 1 in nucleosome setting by investigating its crosstalk with other methyltransferases. This study resulted in discovery of the activating effect of monomethylation of H4K20 on nucleosome by SETD8 on H4R3 methylation by PRMT1. In the second chapter, I focused on discovery of ligands for DDB1 Cul4-associated factor 1 (DCAF1) to employ the protein degradation approach. This project resulted in discovery of a potent antagonist of DCAF1 with a Kd value of 38 nM, a great step in the development for a chemical probe or PROTAC. Utilizing the two different approaches in targeting proteins of interest, will result in new opportunities that can facilitate early-stage drug discovery.
Informal Caregiving: Health System Cost Implications and Caregiver Outcomes
Keywords: Caregiving experience
Family caregiving
formal and informal care
Healthcare expenditure
Healthcare utilization

Care provided by unpaid caregivers, is often seen as a lower cost substitute to care provided by health care providers (formal care), and hence the prevailing assumption is that caregivers’ contributions reduce healthcare costs. One unintended consequence of caregiving is a deterioration in caregiver’s health which could a) impact caregivers’ ability to provide care affecting care-recipients’ use of formal healthcare services; and b) result in a potential increase in healthcare utilization for caregivers themselves. Changes in healthcare resource use due to caregiving health consequences are direct costs to the healthcare system which have been largely omitted in healthcare policy and research. The overarching objective of this thesis is to provide a more accurate estimation of costs and consequences associated with caregiving. This is done by investigating patterns of: 1) healthcare use among caregivers; 2) healthcare use among care-recipients due to the consequences of caregiving; and 3) developing and validating a comprehensive tool that could facilitate routine measurement of caregiving and systematic inclusion of caregiving consequences in the policy making process. The first study was a difference-in-differences cohort study examining the impact of caregiving on caregivers’ use of healthcare services, before and after caregiving in comparison to non-caregivers using administrative databases. Results showed that adjusted total healthcare costs for caregivers were 10% lower than non-caregivers two years into caregiving. The second study was a longitudinal study examining the impact of caregiver distress on care-recipient’s use of healthcare services using administrative databases. The study found that caregiver distress was associated with a 4% increase in care-recipient’s total healthcare costs every six months. The third study reported on the development and validation of a caregiving survey. The survey was co-designed with caregivers providing a simultaneous measurement of caregivers’ health, experience of care, and costs. The analysis of the survey revealed four scales relating to care burden, care partner, caregiver assessment, and care integration. This thesis used novel data and methods to estimate the cost and consequences of caregiving and identifies issues that should be considered in healthcare policy making and in the design and evaluation of healthcare services.
Contextualizing the Crisis in the Hospital Discharge Process for People Experiencing Homelessness in Toronto, Canada: “Danger and Opportunity”
Keywords: context
critical realism
discharge planning
discharge process
homelessness
qualitative

Canadian scholarship shows higher rates of hospital readmission among homeless than housed populations, signaling that their health needs are not being met post-discharge. The discharge process is meant to ensure patients’ care is transitioned to the community and is recognized by communities and homelessness researchers as a critical point of transition; yet little research has examined this process from acute physical care services. This exploratory qualitative study aimed to characterize the hospital discharge process for people experiencing homelessness when discharged from general medicine in Toronto, Canada. Informed by critical realism, it explains how and why discharging homeless patients remains a challenge. Semi-structured in-depth interviews were held with 16 hospital workers involved in the discharge process from three urban hospitals, six shelter workers who receive discharged patients, and 11 key informants with expertise in homelessness and healthcare. Results broadly characterize the process, situating inadequate discharges as a consequence of the failure of multiple systems on which the discharge process relies: barriers to publicly-funded systems, and silos and gaps between these systems. Further findings shed light on contextual influences of two features of the discharge process. First, finding an appropriate discharge destination was challenged by historical and contemporary social and economic contexts that triggered the adoption of efficiency and accountability measures in hospitals, and eligibility and exclusion criteria in shelters. Second, within the legal context of health information protection in Ontario, knowledge sharing between hospitals and shelters was complicated by the concept of circle of care that excludes shelter workers from the discharge process. Certain geographic and organizational contexts have activated the development of institutional- and individual-level relationships between some hospitals and shelters or their workers, which improved knowledge sharing. Despite the agency exhibited by our participants, the discharge process was marred by uneven power dynamics between hospitals and shelters and a service gap where neither hospitals nor shelters are responsible for the wellbeing of homeless patients post-discharge. Future research should centre the voices of people experiencing homelessness who go through the discharge process and adopt an intersectional analysis to better understand how the discharge process is shaped by patients’ intersecting social locations.
Observing and Describing the Sigmoidal Growth of Bone Anchorage from Endosseous Healing with Empirical Models
Keywords: Bone
Empirical Modeling
Implants

The concept of endosseous healing creating a secondary biologic stability is firmly established in the dental literature, but mathematical growth curves have not been used to describe the resultant increase in bone anchorage (BA). This work investigates the hypothesis that the effect of implant surface topography on BA can be quantified using the appropriate empirical model and that increases in BA follow a sigmoidal growth curve with features that are consistent with the three general phases of endosseous healing: the lag phase with osteoconduction, the growth phase with de novo bone formation, and the plateau phase with remodeling. BA of rectangular implants placed in rat femora were tested in both shear and tension. Initial anchorage measurements taken at 5-days occurred after the lag phase, but growth and plateau phases were apparent in the data and could be measured using the asymptotic model. Testing method was found to significantly affect the peak BA and the inclusion of nanotopography on a microtopographically complex surface significantly decreased the required healing time. The effect of nanotopography was found to be greater than the effect of surface chemistry or hydrophilicity. Cylindrical and threaded implants were tested in torsion after being placed in rat tibiae for up to 6 months. By taking BA measurements at 3-days after placement the lag phase could be observed, enabling the fitting of sigmoidal functions with the logistic function producing the best fit. This allowed for the description of the peak anchorage, inflection point, and healing time. By differentiating between the phases of endosseous healing it was found that implant topography had a significant effect on de novo bone formation but not remodeling. This work has shown the three phases of increasing BA, related the increase of BA to bone formation, and found that curve fitting is an effective means of comparing different implant designs with respect to BA achieved through endosseous healing.
Identifying Host-adaptive Genomic Signatures in the Pseudomonas syringae Species Complex
Keywords: Comparative genomics
Genome-Wide Association Studies
Host adaptation
Machine learning
Pseudomonas syringae

Pseudomonas syringae is a diverse bacterial species complex capable of causing disease on various crop and wild plant species. Despite the relatively high number of affected crops, an understanding of the genetic basis allowing P. syringae to promote disease on many of these hosts is lacking. My goal was to identify genomic signatures from P. syringae genomes associated with adaptation to distinct types of hosts. I hypothesized that such signatures were overrepresented in pathogens from a given host, and that they could be extracted when compared to genome data from non-pathogens. Using statistical approaches such as GWAS and machine learning, I identified five plasmid-borne type III secreted effectors (T3SEs) and 32 other plasmid-borne genes strongly associated with isolation from diseased coffee plants. We then showed that isolates lacking this plasmid exhibit reduced growth on coffee leaves, suggesting that these genes play an important role on coffee colonization by P. syringae. Furthermore, I employed machine learning techniques to investigate if we could use genomic data to predict P. syringae virulence on bean and found that our model could predict virulence with high accuracy (mean absolute error = 0.05). I functionally validated the model by predicting virulence for 16 strains and found that 15 (94%) had virulence levels within the bounds of estimated predictions, demonstrating the power of machine learning for predicting host-specific adaptation. Finally, I also identified specific T3SE gain and loss events potentially associated with bean adaptation and showed that the loss of the HopAZ1 T3SE contributed to this process. Its presence reduced the growth of the strong kidney bean pathogen P. syringae pathovar phaseolicola 1448A on bean. Altogether, my thesis shows that pathogen genomes contain a written history of past evolutionary events associated with adaptation to specific hosts. Such signatures can be unraveled by applying statistical approaches to next-generation sequencing data.
Historical Thinking in Ontario Secondary Schools: A Multiple Case Study
Keywords: Historical Thinking
Historical Thinking Concepts
History Education
History Teaching

In recent decades, history and education scholars in the Western world have argued for a constructivist approach to disciplinary thinking in history, known as historical thinking. This generated a large body of scholarship and many curriculum revisions. In Canada, these included the articulation of six historical thinking concepts designed to operationalize historical thinking for the classroom. Four of these concepts were embedded into the 2013 secondary school history curriculum in Ontario, the context of this present study. Yet, there has been little classroom-based empirical research exploring how teachers implement and enact historical thinking, generally, and historical thinking concepts, specifically. The present study asks: How do Ontario secondary school history teachers, who conceptually and practically embrace historical thinking as their approach to teaching history, understand and implement the Ontario history curriculum? Multiple-case study methodology was used, with the participation of four history teachers. Data for each case was generated by a survey, three interviews, two think-aloud activities, five classroom observations, document analysis of lesson plans, student and teaching resources, and assessments. The results revealed teachers’ different interpretations and expressions of the Ontario history curriculum. Two pedagogical profiles emerged. In one, teachers understood historical thinking concepts as skills for developing students’ critical thinking, as a transferable generic skill. Historical thinking was a means to this end. In the other profile, teachers used historical thinking concepts as critical inquiry lenses for creating new knowledge about history; they used historical thinking to help students understand history as a process of interpreting humanity and society over time. Historical thinking was its own end. These results support other studies in suggesting that there is no singular pedagogical approach for delivering a secondary school curricula. The particular contribution of this study, however, is in its detailed descriptions and analysis of how and why teachers negotiate between curriculum imperatives and their own teaching philosophy, and how they adapt their knowledge and understanding of historical thinking to do so. This study concludes by exploring the implications of this research for curriculum implementation, for teaching practice, for teacher education (both pre-service and in-service), for curriculum development, and further classroom-based research.
Linking Polar Bear Physiology and Ecology via Models of Their Energetics
Keywords: climate change
energetics
modelling
parasites
polar bears

Polar bears require a sea ice platform to access and capture energy-rich marine prey. Climate warming is lengthening summer ice-free periods, forcing polar bears to survive increasingly longer periods of food deprivation while also leaving less time to accumulate body energy stores through on-ice periods. Dynamic energy budget (DEB) models have been used to estimate physiological and demographic impacts of sea ice loss for polar bears, accurately reflecting declines in body condition, reproduction and survival already observed in several subpopulations. To date, data limitations have restricted assessments to the effects of increased summer ice-free periods on the reproduction and survival of adult bears. My thesis increases our understanding of polar bear energetics by developing and refining models for estimating the energy polar bears have stored in lipid and protein reserves, developing new methods for collecting polar bear energetics data, and by exploring how polar bears acquire energy-draining parasites. In Chapter 2, I used data from dissected polar bears to develop a body composition model that separately estimates protein and lipid energy storage, expanding the applicability of the polar bear DEB framework to conditions where the molecular composition of energy storage changes rapidly (i.e., feeding). In Chapter 3, I developed and tested a method for morphometric data collection from captive polar bears using crate training. Sequential straight line body length measurements of captive bears showed no difference in precision compared to those collected from wild polar bears, opening new avenues for collecting physiological data necessary for further DEB development. In Chapter 4, I applied energy budget and demographic arguments to establish marine prey muscle tissue as the most likely transmission pathway of the parasite Trichinella nativa to polar bears. Understanding how polar bears acquire parasites facilitates understanding how changes in diet might affect parasite load, and thus, polar bear energetics. My thesis highlights the power of implementing novel methodologies while concurrently repurposing existing data and rethinking traditional collections to better understand difficult-to-observe processes like energy acquisition or disease transmission. As human-driven environmental change continues to push ecosystems beyond regularly observed extremes, methods enabling predictions of unobservable phenomena using measurable variables are invaluable.
The Transgenerational Effects of a Dpaminergic Drug on the Behaviour and Morphology of the Trinidadian guppy (Poecilia reticulata)
Keywords: Dopamine
Epigenetics
Guppy
Paternal effects
Ritalin
Transgenerational effects

Maternal effects are ubiquitous, but paternal effects, the nongenetic influence of fathers on their offspring, were traditionally thought to be limited to animal species with paternal care/investment, however, there is now evidence that fathers can influence their offspring via nongenetic factors (interactions with females, modifications to sperm/ejaculate). There is also limited evidence that both maternal and paternal effects can span several generations, i.e. they can be transgenerational, but it is not yet clear if this phenomenon is generalizable across taxa. For my dissertation, I asked if there were parental and transgenerational effects of a dopaminergic drug (the psychostimulant methylphenidate hydrochloride (MPH), known as Ritalin or Concerta) on Trinidadian guppies. I selected MPH because it is highly prescribed for the treatment of Attention-deficit/hyperactivity disorder and, given its pharmacology, it was predicted that it could cause transgenerational effects; despite this, the paternal and transgenerational effects of MPH were unknown. I found that MPH treatment had significant effects on the behaviour of first-generation males, and the morphology of first-generation males and females. I also found that some of these effects persisted across generations. First, MPH treatment directly affected male mating behaviours, with downstream effects on the behaviour of offspring; there was evidence that paternal effects were mediated by females for the offspring of control fathers, but, not for the offspring of MPH-treated fathers, suggesting nongenetic modifications to sperm as a potential mechanism. I also describe transgenerational effects of MPH in later generations and observed that behavioural effects of MPH were transmitted through the paternal, but not maternal, line to male and female great-grandoffspring—a generation that was not directly exposed to MPH. For morphological traits (body size and male colouration), I observed that both maternal and paternal treatment affected some offspring and grandoffspring morphological traits, highlighting the importance of exploring maternal and paternal effects in tandem. Taken together, this research is the first to demonstrate that MPH can cause transgenerational effects, which highlights the need to consider parental and transgenerational effects in studies of human health and the responses of natural populations to anthropogenic effects (e.g. exposure to pollutants, climate change).
Identification of Androgen-regulated Genes in a Breast Carcinoma Cell Line, BT474, using Transcriptomic and Proteomic Techniques
Keywords: Androgen Receptor
Breast Cancer
Proteomics
RNA Sequencing

Breast cancer (BCa) is the second most common cancer worldwide and the most prevalent cancer in women. The majority of BCa cases are positive for the estrogen receptor (ER+, 80%), and progesterone receptor (PR+, 65%), whereas some express human epidermal growth factor receptor 2 (HER2+, 20%). The androgen receptor (AR) is also found to be expressed in 77% of patients with invasive BCa and is now considered a promising biomarker and therapeutic target for BCa. However, the biological significance of androgens (A) and the AR in BCa remains unclear. Thus, in this study, the BT474 cell line was used as cell line model because it is an ER+PR+AR+ BCa cell line with high response to androgen treatment. The main purpose of this work was to investigate the effect of androgens in this cell line at the transcriptomic and proteomic level. The first step was to perform a pilot study using the androgenic hormones (dihydrotestosterone and norgestrel) to identify the expression of androgen-related molecules, using RNA sequencing and stable isotope labelling by amino acids in cell culture (SILAC)-based proteomics. As a second step, the effects of dihydrotestosterone and progesterone hormone were examined in a more precise way to identify potential androgen-regulated genes and molecular pathways that are involved in BCa pathology, using the same techniques. Thirtly, validation of candidate mRNAs and proteins was perfomed using qRT-PCR and parallel reaction monitoring (PRM)-based proteomics, respectively. Lastly, verification of the expression of selected androgen-regulated genes was assessed in other BCa cell lines. The high expression of kallikrein 3 (KLK3), also known as prostate specific antigen (PSA), under androgen stimulation, was used as a positive control for all experiments. Several known and unknown androgen-regulated genes were identified. Pathway analysis revealed that androgen stimulation changed the abundance of proteins involved in lipid metabolism, cell cycle, and estrogen-dependent processes known to be associated with BCa progression. The validated results from these orthogonal techniques contribute to the overall knowledge of AR’s role and significance in BCa. Furthermore, new androgen-regulated genes identified through this work may be considered for further investigation as biomarkers or target molecules for personalized treatments.