VictorJuiz/thesis huggingface dataset:
The influence of assessor training on scoring and feedback: A qualitative study of assessor perceptions

Assessor training is essential for defensible assessments of physician performance. This study explored the perceived influence of training and assessment tools on assessors’ conduct of assessments. Using a constructivist grounded theory approach, we interviewed 13 assessors about the effects of training and scoring tools on their conduct of assessments. Participants reported that training taught them about the potential variability of assessor judgement and prompted more reflective scoring. Using the new scoring tools reportedly led participants to sample performance data differently, choose ratings in accordance with the scoring tools, and provide more detailed feedback to assessed physicians. Participants did not perceive training or the tools to substantially affect their numeric ratings, but noted an increased confidence in scoring. Participants involved in developing the tools reported more pronounced effects of training and the tools. These findings support the continued study of assessor training programs as a method of enhancing assessor consistency.

Keywords: Assessment
Assessors
Advisor: Brydges, Ryan
Synthesis and Characterization of Small Molecule Dysregulators of the Bacterial ClpP Protease

Caseinolytic protease P (ClpP) is a protease highly conserved in bacteria and eukaryotes. With an ATPase partner, it functions to maintain protein homeostasis and regulated elimination of folded proteins. Without its ATPase partner, bacterial ClpP can only degrade small peptides. Recently, Activators of Self-Compartmentalizing Proteases (ACPs) were discovered, using a high-throughput screen, that activate the protease in the absence of its ATPase partner. Co-crystal structures with E. coli ClpP showed ACPs bind in two configurations. Improving on initial hits and to completely fill the binding pocket, 16 new phosphine oxide-based compounds (ACP6) were synthesized and investigated for their ability to enhance the ClpP peptidase activity. Several of the ACP6 analogs showed increased activity against E. coli ClpP compared to the initial ACPs. This work showed that a new class of compounds can also activate bacterial ClpP and can be pursued as chemical leads for the development of antibiotics.

Keywords: ACP
Caseinolytic protease P
ClpP
E. coli
N. meningitidis
Phosphorous
Advisor: Houry, Walid A.
Batey, Robert A.
SPORADIC: An Anytime Architecture for Intermittent Computing

Energy-harvesting is an emerging computing paradigm that allows systems to run solely off energy harvested from their environment. However, these systems are subject to frequent and unpredictable power outages. Ensuring forward progress under such circumstances is crucial. Energy-harvesting applications are typically amenable to approximation. We propose SPORADIC, a set of anytime approximation techniques: Subword pipelining, Subword vectorization and Skim points. Subword pipelining and Subword vectorization decompose data words so that they can be processed as subwords, sequentially from most to least significant. Skim points fundamentally decouple the checkpoint location from the recovery location upon a power outage. SPORADIC transforms the processing on energy-harvesting devices from all-or-nothing to as-is computing. We find that under frequent power outages, SPORADIC yields speedups of 2.16× and 3.02× on non-volatile and checkpoint-based volatile processors, while still producing high-quality outputs.

Keywords: Approximate Computing
Energy Harvesting
Intermittent Computing
Advisor: Enright Jerger, Natalie
Characterization of the Microbial Community in a Sequentially Fed Anaerobic Digester Treating Solid Organic Waste

A lab-scale solid phase anaerobic digester of novel design that treats organics waste was operated at for 88-weeks at the University of Toronto. Characterizing the microbial community inside the digester enables fundamental understanding of the system performance and operational limits. The microbial community was characterized through amplicon sequencing and correlated with operating parameters such as, biogas production rate. Clostridium spp. and organisms from Candidate Division WS6 were the two most dominant bacterial phylotypes and Methanobacterium and Methanoculleus were the two most dominant archaeal phylotypes. A direct relationship between the population of Clostridium spp., proportion of food waste, and biogas production rate was found while Candidate Division WS6 showed better adaptability to fibre rich substrate conditions. Shortened hydraulic retention time of leachate affected the microbial community. Shifts in dominant hydrogenotrophic methanogen spices were observed when HRT was decreased. Clostridium spp. were largely responsible for the enhanced “synergistic” biogas production from fibers.

Keywords: Anaerobic Digestion
Candidate Division WS6
Clostridium butyricum
Microbial Community
Organic waste
Advisor: Edwards, Elizabeth A
Investigating the Effects of Automated Vehicle Driving Operations on Road Emissions and Traffic Performance

Automated vehicles (AV) will inevitably have an impact on the movement of people and goods. Assessing the effects of AVs on land use, congestion and the environment have become of great interest to researchers. This study explores the effects of AVs and vehicle electrification on greenhouse gas emissions using traffic microsimulation and emissions modeling. The driving behaviour parameters of a traffic simulation package, most relevant to AVs, are tested within the ranges deemed to be representative of potential AV operations. The effects of AVs are evaluated under both uninterrupted and interrupted traffic flow operating environments, as well as under high and low traffic demand. The main findings indicate that automated vehicles can bring positive changes in terms of emission and traffic flow performance. The significance of the impacts is more evident when AVs are tuned to more aggressive driving settings and especially under high traffic conditions in uninterrupted flow operations.

Keywords: Automated vehicles (AV)
Driving behaviour
Emission modelling
Greenhouse gas (GHG) emissions
Traffic microsimulation
Traffic operations
Advisor: Hatzopoulou, Marianne
Roorda, Matthew J.
The Physician Trainee Environment and its Associated Effects on Trainees and their Patients

Introduction: The physician trainee’s work and educational environment impacts patient care and trainee learning and is understudied. Methods: A cross-sectional survey of trainees at a paediatric hospital evaluated learning, patient care, and adverse trainee events (crashes, needlestick injury, inappropriate personal comments, assaults or threats). Results: Completed surveys described 132 trainee months and 101 duty periods; 49 (37 %) respondents reported an adverse trainee events. Learning was rated median (IQR) of 6 (5-7) on a 10-point scale. Patient care was rated 4 or more in a 5-point scale by 93%. Multivariable analyses found staff supervision and attendance at education sessions independently associated with increased learning. Trainee adverse events were associated with seniority and working fewer nights. Conclusion: Preliminary distribution shows questions are understood, a modest distribution of safety responses, and few positive relationships, in this single center pilot. Future iterations in multiple centers can evaluate these questions further.

Keywords: Patient care
Physician trainee environment
Survey
Trainee learning
Trainee wellbeing
Advisor: Parshuram, Chris
Indoor Environmental Quality in Social Housing: review, thermal comfort and odour control

In this work, I explored the indoor environmental quality (IEQ) in social housing, and also discussed the indoor pollution associated with the operation of sources of scents that may be common in these units. I found that public housing residents may be disproportionally exposed to fine particulate matter (PM2.5), nitrogen dioxide (NO2), and pesticides. I also found that poor thermal comfort conditions are prevalent in social housing, mostly due to excess heat. Lastly, I found that incense and ultrasonic oil diffusers, which are commonly used to produce pleasant scents indoors, generate considerable amounts of PM2.5. Considering the negative health effects associated with poor IEQ conditions, my results suggest that minimizing sources of pollution and improving comfort conditions should be prioritized in any retrofits planned in social housing developments, as similar improvements have been found to be effective in improving occupant health and reducing exposure to pollutants.

Keywords: Indoor Air Quality
Social Housing
Thermal Comfort
Advisor: Siegel, Jeffrey
A Qualitative Investigation of the Mental Health Needs of Syrian Refugees and Immigrants

The mental health of Syrian refugees has become extremely important for refugee and mental health scholars worldwide. A scoping review of 14 publications was conducted to synthesize current findings on this issue, which displayed a gap in understanding Syrian coping strategies and well-being. A qualitative investigation was done to explore the mental health perceptions and related resources of Syrians that migrated to Canada both before and after the war. Thirty semi-structured interviews were conducted with Syrian immigrants, 15 non-refugees and 15 refugees. The purpose was to investigate perspectives on mental health, resilience, and desired or received services. Study findings showed refugees’ mental health was affected by traumatic events and their resettlement process. Non-refugees expressed feelings of sadness because their homeland has been destroyed. All participants sourced social support as extremely helpful in their lives and was preferred over professional help. These findings can help develop appropriate mental health resources.

Keywords: immigrants
mental health
psychological
refugees
social support
Syrian
Advisor: Kidd, Sean
Laboratory and Analytical Study of Shattering Jelly Roll Smelt

During kraft chemical recovery, smelt created in a recovery boiler is shattered into droplets before falling into a dissolving tank. Although a rare occurrence, highly viscous smelt is created when the smelt temperature is close to the smelt freezing temperature, so-called jelly roll smelt. The viscosity of jelly roll smelt is estimated as between 10^4 to 10^5 cP. In this research, a laboratory study was conducted and an analytical model was developed to study the shattering of such highly viscous smelt. The study shows that an increasing viscosity undermines the shattering effectiveness by delaying the complete breakup of the liquid stream, and creating large droplets. The analytical model is based on the physics of co-axial atomization, and is shown to fit the lab scale droplet size distribution very well. Given the shattering conditions, the model appears able to estimate the droplet size distribution and maximum shatterable viscosity.

Keywords: Jelly Roll Smelt
Pulp and Paper
Recovery Boiler
Smelt Shattering
Viscous Liquid Atomization
Advisor: Bussmann, Markus
Tran, Honghi
Caffeinated FPGAs: FPGA Framework for Training and Inference of Convolutional Neural Networks With Reduced Precision Floating-Point Arithmetic

This thesis presents a framework for performing training and inference of Convolutional Neural Networks (CNNs) with reduced precision floating-point arithmetic. This work aims to provide a means for FPGA and machine learning researchers to use the customizability of FPGAs to explore the precision requirements of training CNNs with an open-source framework. This is accomplished through the creation of a High-Level Synthesis library with a Custom Precision Floating-Point data type that is configurable in both exponent and mantissa widths, with several standard operators and rounding modes supported. With this library a FPGA CNN Training Engine (FCTE) has been created along with a FPGA CNN framework FPGA Caffe, which is built on Caffe. FCTE has a peak performance of approximately 350 GFLOPs, and has been used to show that a mantissa width of 5 and exponent width of 6 is sufficient for training several models targeting the MNIST and CIFAR-10 datasets.

Keywords: Convolutional Neural Network
FPGA
Inference
Low Precision
Training
Advisor: Chow, Paul
Analysis of Automated Fare Collection Data from Montevideo, Uruguay for Planning Purposes

Automated Fare Collection (AFC) and smartcard systems have been rapidly adopted by transit systems all over the world. The datasets produced by these systems are extensive and can be analyzed for planning purposes and system evaluation. This thesis analyzes the AFC data from the bus transit system in Montevideo, Uruguay and proposes methods to reconstruct itineraries, identify the alighting locations of transactions, and understand travel behaviour of smartcard users. The methods used successfully build itineraries for 97% of bus runs, identify 87.7% of alighting locations, and recreate 67.5% of complete trip chains of smartcard users. The complete trip chain data is then used to pair smartcards with individuals from the Montevideo travel survey. Only 10 to 15% of individuals from the survey could be paired with smartcards. These findings have important implications for incorporating AFC datasets in transportation planning and evaluating transit systems.

Keywords: AFC: Automated Fare Collection
Public Transit
Smartcard
Advisor: Miller, Eric J
lncRNA-GATA2: The Functional Role of Long Noncoding RNA GATA2 in the Vascular Endothelium

Long noncoding RNAs (lncRNA) are new, important players in gene regulation. We examined the role of lncRNA-GATA2: a novel, abundant, cytoplasmic, endothelial cell (EC)-enriched lncRNA divergently transcribed from the GATA2 transcription factor (TF). Interestingly, four of the six GATA TFs loci harbor a divergent lncRNA (GATA2, 3, 5 and 6). We investigated whether lncRNA-GATA2 regulates EC phenotype and if this involves a relationship with GATA2. Loss-of-function studies demonstrated that lncRNA-GATA2 regulates 1374 EC genes. Several are EC-enriched, including ESM1, NOTCH4, vWF, and ANGPT2. lncRNA-GATA2 also controlled EC response to hypoxia through contrasting regulation of HIF1a and HIF2a. With respect to GATA2, lncRNA-GATA2 represses GATA2 protein. Importantly, we demonstrate lncRNA-GATA2 in GATA-family cross-talk and controlling the cell-specific GATA program, as lncRNA-GATA2 regulated the GATA TFs and associated lncRNAs. lncRNA-GATA2 regulates the EC phenotype in a context-dependent manner, through the regulation of enriched genes important for EC biology and the GATA family.

Keywords: Cell Identity
Endothelial
GATA2
Gene Regulation
Hypoxia
Long Noncoding RNA
Advisor: Marsden, Philip A
Priority Setting in Pediatric Preventive Care Research

Objectives: To identify unanswered research questions in pediatric preventive care that are most important to parents and clinicians and to assess differences in priorities between the two groups. Methods: Unanswered research questions were collected from parents of children aged 0-5 years and clinicians via an online questionnaire using a James Lind Alliance-developed methodology. Similar submissions were combined and ranked. Parents and clinicians selected the 10 most important unanswered research questions at a consensus workshop. The categories of questions from parents and clinicians were compared. Results: 1046 submissions were combined into 79 indicative questions. The top 10 unanswered research questions related to mental health, parental stress, physical activity, obesity, childhood development, behaviour management and screen time. Parents were more likely to ask questions about screen time and environmental toxins. Conclusions: The top 10 most important unanswered research questions in pediatric preventive care from the perspective of parents and clinicians were identified.

Keywords: Health research
James Lind Alliance
Pediatrics
Preventive Care
Priority setting
Research priorities
Advisor: Laupacis, Andreas
Hundred Farad-scale Supercapacitor with Monolithic Biochar Electrodes – a Feasibility Study

Supercapacitors are high power density electrochemical storage devices that are hindered from widespread adoption by prohibitive material costs, low energy densities for practical applications, and poor scalability. This thesis seeks to solve all three issues by using large-scale monolithic maple-derived biochar as an effective electrode material. Biomass-derived carbon monoliths are pyrolyzed at 800oC and treated with 0.5M nitric acid at room temperature. Two electrode pairs, measuring ~5mm x 5mm x 5mm and ~23mm x 13mm x 10mm respectively, orders of magnitude thicker than typical supercapacitor electrodes, are tested using a suite of electrochemical techniques in 4M KOH electrolyte. Additional testing is done on large electrodes in 1M and 6M KOH, as well as in 1M TEA-TFB organic electrolyte. Capacitive performance of 107 F or 38.2 F/g is observed in the large monolithic electrodes, along with an exceptional energy density of 9.12 Wh/kg.

Keywords: Biochar
Large-scale
Maple-derived Biochar
Monolithic
Supercapacitors
Advisor: Jia, Charles Q
The Role of Deep Level States in the Optical and Electronic Properties of ZnSe Nanowires

II-VI semiconductor nanostructures are excellent candidates for next-generation optoelectronic devices, including tunable emitters. ZnSe nanowires can be fabricated easily, and show promise in blue emission applications. However, their practicality is limited by deep level defect states that inhibit their performance. The primary objective of this thesis is to relate the defect structure to the optical and electronic properties of ZnSe nanowires. To this end, a heat treatment procedure to improve the microstructure was identified, and measurements were performed before and after the treatment. Using low temperature photoluminescence spectroscopy, the dominant recombination mechanisms were related to the total defect concentration. The carrier concentration and electron mobility were determined by electron transport measurements on single nanowire transistors. The measured experimental data was used to construct a model describing the type, energies, and ionized fractions of relevant defects, and develop an understanding of how ZnSe nanowires can be tailored for optoelectronic applications.

Keywords: defects
microstructure
nanowires
optoelectronics
Advisor: Ruda, Harry E
Food Literacy Education: A Philosophical Perspective

In this thesis, I will argue through a critical democratic education lens for the inclusion of philosophical perspectives in a comprehensive food literacy education program in Ontario high schools. Food is a democratic issue of philosophical concern, requiring critical educational attention. I maintain that if we do not properly deal with food issues in schools we fail to fulfill the democratic social reconstruction aims of education. Utilizing a critical democratic dialogue framework, I combine the work of Laura Pinto and Heesoon Bai, whose approaches to collective communication promote social justice and critical democratic education. To conclude, I offer two concrete pedagogical applications of this framework to high school classrooms. This paper supports initiatives already underway to expand the teaching of food literacy in Ontario high schools, but is significant because of its focus on critical democratic education, and my strong insistence on the inclusion of philosophical perspectives and teachings.

Keywords: Critical Democratic Dialogue
Critical Democratic Education
Food Literacy Education
Philosophical Dialogue
Philosophy Education
Secondary Education
Advisor: Portelli, John P
Short-Term and Long-Term Performance of Glass Fibre Reinforced Polymer (GFRP) Bent Bars

Corrosion-resistant Glass Fibre Reinforced Polymer (GFRP) bars have been growing in popularity as an alternative to steel reinforcement. Newly developed GFRP bent bars were tested in this study, in which strength reduction of the bends in relation to the straight portion was investigated, as well as the long-term behaviour under sustained load. Two test methods were used to determine the instantaneous strength, consisting of 24 stirrups in the standardized testing procedure, and 10 bent bars in the shape of a “J” in a modified direct tension pullout test. The bend strengths ranged from 35% to 55% of the straight portion. Additionally, sustained load levels were applied to eight stirrups to determine the load level the bars could sustain for a 100-year service life. This stress was extrapolated from a logarithmic creep equation developed from regression analysis of the experimental results and found to be 50% of the ultimate short-term capacity.

Keywords: Bend
Creep
Fibre
GFRP
Stirrups
Sustained
Advisor: Sheikh, Shamim A
The Liberal Arts Curriculum in China’s Christian Universities and Its Relevance to China’s Universities Today

This thesis considers the historical background, the development, and the characteristics of China’s Christian universities, with a special focus on their curriculum design. Through the lens of postmodern theory, the thesis explores the concept and essence of liberal arts education as reflected in the curriculum of the Christian universities through a qualitative methodology, focusing on the analysis of historical archival material. The purpose is to find insights for today’s trend towards reviving liberal arts education in China’s elite universities as a way of countering the influence of utilitarianism and neo-liberalism in an era of economic globalization.

Keywords: Christian universities
higher education reform
Liberal arts education
whole person education
Advisor: Hayhoe, Ruth
Detecting Signals of Coevolution within Immune Response Pathways in the African-American Ancestral Population

The natural variation of human populations was shaped by mechanisms of evolutionary selection as our species began their worldwide migration thousands of years ago. Candidate gene and genome-wide association studies have revealed evidence for ancestry-specific positive selection, yet we lack insights regarding the broader biological context of population-driven selection. In this thesis, I describe my efforts to explore how interactions within biological pathways might impact evolution, using a comparative population-based analysis of pathway enrichment and inter-chromosomal allelic association. I compared genetic data from individuals of European-American and African-American ancestry, and identified enrichment for several biological processes, with prominent signals of genetic coevolution in two immune-associated pathways among African-Americans exclusively. Substantiated by considerable experimental-based literature, these findings suggest an effect of population variation on pathway-level selection, in which a global comparative analysis would further the ultimate goal of precision medicine.

Keywords: Evolution
Genetic interactions
Pathway analysis
Population genetics
Advisor: Boone, Charles
Bader, Gary
Topological Origins of Bound States in the Continuum for Systems with Conical Intersections

Bound states in the continuum (BSCs) were reported in a linear vibronic coupling model with a conical intersection [Cederbaum et al. Phys. Rev. Lett. 2003, 90, 013001]. It was also found that these states are destroyed within the Born-Oppenheimer approximation. We investigate whether a nontrivial topological or geometric phase associated with the conical intersection is responsible for BSCs. To address this question we explore modifications of the original 2D two-state linear vibronic coupling model supporting BSCs. These modifications either add geometric phase effects after the Born-Oppenheimer approximation or remove the geometric phase within a two-state problem. Using the stabilization graph technique we have shown that the geometric phase is crucial for emergence of BSCs.

Keywords: Born-Oppenheimer
bound states in the continuum
conical intersection
geometric phase
resonance states
stabilization method
Advisor: Izmaylov, Artur F