VictorJuiz/thesis huggingface dataset:
Towards Characterization of a Nematode Stress Reporter Suppressing Streptomyces Extract for Anthelmintic Use

Parasitic worms, commonly termed helminths, infect >20% of humans, livestock, and agricultural crops worldwide. Helminths exhibiting resistance to most anthelmintic classes are emerging and new drugs are needed to lessen the burden on the global economy and public health. Here, I probed a library of potentially novel natural products (NPs) towards identifying bioactive compounds against stress response pathways in helminths using the model nematode Caenorhabditis elegans. NPs account for >50% of FDA-approved therapeutics, with the bacterial genus Streptomyces producing >50% of the most important microbial NPs. In total, I screened 970 Streptomyces extracts and found 82 that suppressed stress response reporters in C. elegans. I focused on one extract that suppressed the infection stress reporter NLP-29. Unfortunately, this bioactivity was challenging to reproduce. I present my screening, biochemical purification, and target characterization efforts, emphasize implemented controls along the project pipeline, and propose additional measures for a more stringent future pipeline.

Advisor: Roy, Peter
Nodwell, Justin
The Introduction of Learner-centred Pedagogy in Northwest China: a Critique

Learner-centred pedagogy did not originate within a Chinese educational framework. The implementation of this borrowed policy therefore poses difficulties for Chinese educators on cultural, systematic, and practical levels. A review will be undertaken of the scholarly understanding of the practice of policy borrowing and lending, with the goal of better understanding the reasons and significance of the adoption of learner-centred pedagogy in China. I review the development of learner-centred pedagogy, and my understanding of it. With a reliance on my experience as a scholar, teacher, and student of the Chinese education system, the difficulties of integrating learner-centred pedagogy into the China will be examined and analyzed. In conclusion some thoughts are presented on how the principals of learner-centred pedagogy might be expressed in Chinese classrooms, in a manner more sensitive to context, and more harmonious with the existing culture, and needs of Chinese teachers and learners.

Keywords: China
Culture
Learner-centred pedagogy
Policy borrowing and lending
Advisor: Cooper, Karyn
Dissecting the Factors Involved in mRNA Trafficking to Germ Granules

Small RNA pathways have emerged as key regulators of gene expression, and across animals small RNA pathway components localize to perinuclear sites of mRNA regulation termed germ granules. In the C. elegans germline, several small RNA pathways localize to germ granules and target unique subsets of the transcriptome. An important question that arises is: how do transcripts get sorted into specific small RNA pathways as they enter germ granules? To begin to address this broad question of transcript sorting, in this study I established a system to track transcripts of interest in their export and subsequent germ granule localization. I will discuss data derived from this pipeline in interrogating the role of a panel of mRNA processing/export, germ granule, nuclear pore and small RNA pathway factors that may contribute to the proper export and cytoplasmic localization of the target of a single small RNA pathway, the CSR-1 pathway.

Advisor: Claycomb, Julie M
The Direct and Indirect Effects of Syntactic Awareness on French Reading Comprehension in French Immersion Students

This study investigated the direct and indirect effects of syntactic awareness on reading comprehension among sequential bilingual and trilingual students in French Immersion programs. We furthermore explored the mediational effects of word reading and vocabulary in both within-language models and cross-language models through structural equation modelling (SEM). Sixty-eight Grade two children (40 female, M age in months = 94.59, SD = 7 months) were administered an experimental syntactic awareness task in both English and French. They were furthermore administered a battery of reading-related measures. Results showed that English was a stronger predictor of French reading comprehension than French syntactic awareness due to the students’ oral language exposure in English. French word reading was shown to have a strong mediational effect in all models, while vocabulary had weak-moderate effects. This study confirms that syntactic awareness performance is intrinsically tied to age and development in bilingual children.

Keywords: French Immersion
Language transfer
Oral language
Psycholinguistics
Reading comprehension
Syntactic awareness
Advisor: Chen, Xi
Theorizing Feminist Struggle in Post-War Iraq

The 2003 imperialist occupation of Iraq brought out the worst in the society, unleashing Islamist religious extremism, ethnic division, and misogyny, causing atrocities on women such as enslavement, trafficking and misogynist legislation. This research is based on personal experience of founding the Organization of Women’s Freedom in Iraq, a secular feminist organization to confront patriarchy and capitalism. The research begins with an analysis of the forced socio-political changes and proceeds to investigate the problematic of extreme patriarchal violence against women and demonstrates the ways in which feminists of the organization resisted and challenged patriarchy through establishing a network of women’s shelters. This research is a Marxist feminist analysis of systemic patriarchal violence, concluding a theoretic framework of its concepts, power relations, and social structures; thus, informing the articulation of an organizational feminist platform to guide the struggles of Iraqi women to dismantle patriarchy and capitalism within a revolutionary movement.

Keywords: feminism
Iraq
marxism
OWFI
US occupation
women
Advisor: Mojab, Shahrzad
Implementation of Critical Care Response Teams in Ontario. Impact on the Outcomes of Surgical Patients

Critical care response teams (CCRTs) are thought to improve patients’ outcomes by attending to patient clinical deterioration earlier. Failure to rescue is defined as the risk of death among patients who had a surgical complication. CCRTs were implemented in the province of Ontario in 2006. The aim of this study was to 1) evaluate, in surgical adult patients in Ontario who develop a complication, if CCRTs decreases mortality rates (decrease in FTR) by accounting to secular trends and 2) if this decrease in FTR is different according to the type of surgical procedure. A comparison of the risk of FTR before and after the implementation of CCRTs was performed between centers that implemented CCRTs and those that did not. A difference-in-difference analysis was performed to estimate the association between the implementation of CCRTs and FTR. A total of 810,279 surgical patients were included in the study, of whom 148,882 developed a surgical complication and comprised the study population. Among all surgical patients the risk ratio for FTR was 0.99 (0.89-1.09). Among patients undergoing an orthopedic intervention, the risk ratio was 0.84 (0.75-0.95). While implementation of CCRTs did not reduce the risk of FTR among all surgical patients in Ontario, patients who had orthopedic surgery may appeared to benefit most.

Keywords: Critical Care Response Team
Failure to Rescue
Implementation
Advisor: Urbach, David
“It’s Just Safer When I Don’t Enter”: Examining Barriers to Trans Inclusion in Binary-gendered Locker Rooms and Restrooms

This thesis explores the experiences of trans individuals within binary-gendered locker rooms and restrooms. Using a semi-structured interview method, in this study I garnered stories and reflections from 14 trans interviewees to explore how they experience these spaces. This study is initiated in response to the work of Fusco et al. (2015) and Cavanagh (2010) identifying locker rooms and restrooms as gateway spaces to trans inclusion. I argue that difficulty accessing these spaces results in exclusion from sport and the public sphere. Employing an intersectional analysis (Crenshaw, 1989), I theorize how these spaces act as crucial gateways to trans involvement in physical activity and public space. To conclude, I draw upon interviewee reflections to outline a repertoire of interventions, such as trans-positive membership policies and visual pedagogies, for making locker rooms and restrooms safer and more trans-inclusive.

Keywords: binary-gender
gender
gender-segregate
sexuality
transgender
transsexual
Advisor: Fusco, Caroline A
From the Ground Up: Herbaceous Community Diversity and Management in Coffee Agroforestry Systems

The herbaceous community (HC) is an understudied yet critical aspect of tropical agroecosystems. I measured the diversity and perceptions of the HC within organic coffee systems in the Central Valley of Costa Rica. The HC was taxonomically and functionally diverse; comprised of 39 species from 20 taxonomic groups. Farms below the regional mean size and those with canopy openness of 20-30% had higher HC functional diversity. Farmers perceived tall species with low SLA and LNC, but high height and LDMC to be undesirable, due to slow decomposition rates and management limitations. Farmers’ cognitive map complexity was positively related to HC functional richness, and negatively related to functional evenness and functional dissimilarity. All farmers placed higher emphasis on soil health and organic matter than coffee yield, which may be indicative of their role as land stewards. Workshops are needed to disseminate HC management information to optimize labour and ecosystem functioning.

Keywords: agroecology
Costa Rica
functional traits
herbaceous communities
organic management
weeds
Advisor: Isaac, Marney E
Suppressing α-Synuclein Expression and the Knockdown’s Effect on α-Synuclein’s Prion-like Propagation

Parkinson’s disease and related synucleinopathies are neurodegenerative disorders characterized by misfolded and aggregated α-synuclein (α-syn). It is hypothesized that α-syn’s propagation is prion-like, meaning misfolded α-syn serves as a structural template for additional α-syn misfolding. Decreasing α-syn levels has therapeutic potential. However, the blood-brain barrier (BBB) presents a significant challenge to targeting pathology in the central nervous system. In the first aim, focused ultrasound-mediated BBB disruption facilitated non-invasive delivery of shRNA targeting the α-syn gene. α-Syn knockdown was confirmed in multiple distal brain regions of mice expressing human wildtype α-syn. In the second aim, the therapeutic benefit of α-syn knockdown was tested on a seeded synucleinopathy model. Here, mice injected with shRNA targeting α-syn had delayed pathology onset. Attenuation of pathology progression in this model corresponded with α-syn knockdown of 20-35%. These data suggest that α-syn knockdown has therapeutic potential in synucleinopathies, and that it can be achieved non-invasively.

Keywords: blood brain barrier
focused ultrasound
Parkinson's Disease
protein propagation
shRNA
α-synuclein
Advisor: Tandon, Anurag
A Systematic Review of the Localities of Food Purchasing and Consumption Behaviors

In the past decade, researchers have increasingly explored the environmental determinants of food behaviors to support population dietary health. Recently, numerous papers have begun to integrate actual places of food behaviors, with a notable focus o¬n the concept of activity spaces. In this study, we presented a systematic review of research using activity spaces to conceptualize the food environment. Using the PRISMA systematic review framework, a standardized search query to find research that examined the localities of food-related behaviors since 1995 was submitted. A total of 17 papers were determined to be eligible for inclusion. We synthesized these various findings to better understand the influential factors of the location of food purchasing and consumption behaviors, and particular attention was paid to a range of population subgroups (e.g., adults, adolescents). Finally, gaps in this literature were reviewed, and future research directions were suggested.

Keywords: Activity Space
Food behavior
Food environment
Food Location
Literature Review
Advisor: Widener, Michael
Dentin Substrate Modification with Chitosan-Hydroxyapatite Precursor Nanocomplexes

The purpose of the study was to develop and characterize Chitosan-Hydroxyapatite precursor (C-HA) nanocomplexes and to evaluate the effect of dentin conditioning with C-HA nanocomplexes on (1) tricalcium silicate sealer (TCS) penetration, (2) interfacial remineralization and (3) dentin mechanical property. In Phase-I, physico-chemical/bioactivity characterization of C-HA nanocomplexes was done along with assessment of ultimate tensile strength (UTS) of dentin. In Phase-II and III, tubular penetration of TCS and chemical characterization after conditioning of dentin was evaluated using fluorescent imaging and time-of-flight secondary ion mass spectrometry respectively. The results showed polyanionic, hydrophilic and bioactive nature of C-HA nanocomplexes along with increased TCS penetration and UTS of conditioned dentin. Conditioned dentin was modified with formation of ion-rich layer constituting of abundant phosphates, calcium, calcium-phosphates and chitosan fragments at the TCS-dentin interface and subsurface. The study highlighted the potential role of C-HA nanocomplexes in enhancing TCS penetration, interfacial remineralization and UTS of dentin.

Keywords: chitosan
dentin
interface
nanocomplexes
sealer-dentin interface
time-of-flight secondary ion mass spectrometry
Advisor: Kishen, Anil
An Assessment of Opioid Prescribing Behaviors in Ontario Family Physicians before and after Participation in ECHO Chronic Pain/Opioid Stewardship

Canada is in the middle of an opioid crisis. The Ontario Ministry of Health and Long-Term Care funded a demonstration project of the first replication of Project ECHO in Canada to tackle the opioid crisis. ECHO Ontario Chronic Pain / Opioid Stewardship started in June 2014. Participants attending ECHO acquire knowledge related to chronic pain management with or without opioids. This study aims to assess opioid prescribing behaviours among family physicians who attended ECHO compared to those who did not. We conducted an observational study with two control groups: a matched cohort and a random sample of 3,000 primary care physicians in Ontario using the Narcotics Monitoring System. We found that none of the groups reduced the number or proportion of patients on opioids. Secondary outcomes showed a reduction in high-dose opioid prescriptions in the ECHO group, but not in the control groups during the same comparable periods.

Keywords: chronic pain
ECHO
Extension for community healthcare outcomes
pain
tele health
tele medicine
Advisor: Furlan, Andrea D.
The Effect of Electronic Health Records On Undergraduate and Postgraduate Medical Education: A Scoping Review

Background: There is limited educational research on how EHRs impact medical education (MedEd). The purpose of our scoping review was to systematically examine the literature to help map and analyze the role of EHRs in MedEd. Methods: Five databases were searched, and after screening 9186 citations, 82 articles were included in the final review for a quantitative and thematic analysis. Results: Most articles were from the United States (85.4 %) and were descriptive (67.1%), with lack of longitudinal and theory-guided educational research. Residents spend substantial amounts of time using EHRs, with effects on workflow, documentation and communication. For medical students, main concerns included access to EHRs, with curricular development still lacking definition and standardization of EHR-related competencies and learning outcomes. Conclusion: There is a lack of research related to EHRs effect on MedEd. Collaboration between medical educators, health informaticians, clinicians and learners is needed to help optimize EHRs that facilitate student and resident learning.

Keywords: Curriculum
EHRs
Electronic Health Records
Medical Education
medical student and residency education
Medicine
Advisor: Inman, Robert D.
Optimization of a Trachea Bioreactor Design and Cell Seeding Parameters for the Re-epithelialization of Tracheal Scaffolds: a CFD Approach

Successful re-epithelialization of de-epithelialized tracheal scaffolds remains a challenge for tracheal graft success. Currently, the lack of understanding of the bioreactor hydrodynamic environment, and its relation to cell seeding outcomes, serve as major obstacles to obtaining viable tracheal grafts. In this work, we used computational fluid dynamics to (a) re-design the fluid delivery system of a trachea bioreactor to promote a spatially uniform hydrodynamic environment, and (b) optimize the perfusion cell seeding protocol to promote a spatially uniform cell deposition. Results showed that the proposed design change achieves these design goals. Lagrangian particle-tracking simulations showed that low rotation rates provide more uniform circumferential and longitudinal patterns of cell deposition, while higher rotation rates only improve circumferential uniformity but bias cell deposition proximally. Validation experiments with BEAS-2B cells confirm that the model accurately predicts cell deposition but not cell attachment, suggesting the need for including biologically accurate cell-cell and cell-scaffold interaction mechanisms in the simulations.

Keywords: Bioreactor
Cell Seeding
Computational Fluid Dynamics
Optimization
Re-epithelialization
Trachea Regeneration
Advisor: Amon, Cristina
Live Migration of FPGA Applications

With the recent and growing trend of Field Programmable Gate Arrays (FPGAs) being deployed into the data centers, cloud computing service providers are finding it difficult to manage these devices efficiently because traditional server management concepts and techniques are not yet available for FPGAs. In this thesis, we explore how to bring one of these management techniques, live migration, to FPGAs. We develop a system using partial reconfiguration, bitstream readback and memory pre-copying to live migrate a running hardware application from one physical FPGA to another physical FPGA. Our system is transparent and does not need to modify the hardware application, allowing for hardware designed with RTL and/or HLS to be migrated. Our approach can migrate hardware applications that use off-chip memory and that are network connected. We demonstrate this by live migrating a hardware Memcached server.

Keywords: Cloud
Data Center
FPGA
Migration
Reconfigurable
Virtualization
Advisor: Chow, Paul
The Effect of Electrical Stimulation on Endogenous Neural Stem and Progenitor Cell Behavior

Electrical stimulation to the central nervous system, such as deep brain stimulation, is a well-established neurosurgical technique used to treat a variety of neurological disorders. Despite its use as a promising therapy, the effects of electrical stimulation on different neural cells have not been fully explored. We examined the effects of electrical stimulation on the behavior of neural stem and progenitor cells (neural precursor cells; NPCs) found in the periventricular niche of the adult forebrain. We demonstrate that in vitro stimulation of primary periventricular cells at 250mv/mm gives more neural precursors. In vivo, an expansion in stem cells was concomitant with an increase in progenitor cell proliferation in vivo. The increase in the NPC pool can be accounted for by increasing the amount of symmetric divisions the stem cells undergo. These findings provide insight into the effects electrical stimulation on NPCs and its potential use in regenerative medicine strategies.

Keywords: Deep Brain Stimulation
Electrical stimulation
Neural stem cells
Stem cell activation
Advisor: Morshead, Cindi
Popovic, Milos
Elucidating the Gene Regulatory Network of the Sonic Hedgehog Subgroup of Medulloblastoma

Sonic Hedgehog subgroup medulloblastoma (SHH MB) is classified by the molecular signature of overactive Hedgehog (Hh) signaling pathway. GLI2, the major transcriptional activator of Hh pathway, is often amplified or overexpressed in SHH MB. My project examines two molecular components of Hh signaling pathway in SHH MB. The first part focuses on SUFU, a key regulator of GLI2. SUFU mutations are commonly found in SHH MB patients, however the molecular actions of SUFU are poorly characterized. Through CRISPR/Cas9-mediated knockout of SUFU, I unveiled that SUFU is required for stabilization of GLI2 in human SHH MB. The second part focuses on a candidate GLI2 partner, OLIG2. My results suggested that OLIG2 has a tumor-promoting role in SHH MB, and it possesses the ability to transcriptionally repress as well as activate GLI2 target genes. Together, my study allowed the elucidation of the molecular actions of human SUFU, and unveiled a novel player, OLIG2, in SHH MB.

Keywords: Hedgehog signaling
medulloblastoma
Advisor: Hui, Chi-chung
Understanding Undergraduate Food Behaviours: A Spatiotemporal and Socioeconomic Analysis

Food behaviours and food insecurity are complex topics, but there is minimal research on the food behaviours of post-secondary students, a population at higher risk of food insecurity. To understand the financial and temporal constraints faced by this population, this study uses a mixed-method approach. Ten semi-structured interviews were conducted, and an online survey was administered to 743 undergraduate students at the University of Toronto. The results of the analyses indicate students who live with their families’ face fewer barriers to accessing food, and students are more likely to report a healthy diet when they prioritize healthful food consumption. The findings demonstrate a need for more research on undergraduate student nutrition and lifestyle in relation to temporal and financial constraints. Such work will help universities and public health researchers gain a better understanding of how students purchase, prepare, and consume food, and ultimately contribute to student success and well-being.

Keywords: Financial constraints
Food Access
Food behaviours
Student health
Student Life
Temporal constraints
Advisor: Widener, Michael J
Comparing the Compensatory Responses to Floral Damage by Herbivores and Heatwaves in the Oilseed Crop Camelina sativa

Tolerance is thought to evolve as a generalized response to different types of damage experienced in the plant’s lifetime. Flexible flowering schedules and the production of ‘spare’ late-produced flowers, which is widely observed, can be a very general mechanism used by plants to tolerate a variety of environmental insults. I have conducted two experiments to investigate how damage-induced shifts in flowering schedules in Camelina sativa contribute to tolerance of heatwaves and floral herbivory. We found that while heat damaged plants initiated compensatory responses through additional flower and branch production, reduced fertilization and increased seed abortion led to lower total yield than unheated plants. Floral herbivory did not result in compensatory growth, but rather a shift in resource allocation to remaining flowers, resulting in tolerance. Camelina sativa responds differently to heatwaves and herbivory because the extent of damage to plant tissues is greater during heat stress than floral herbivory.

Advisor: Weis, Arthur E