VictorJuiz/thesis huggingface dataset:
Pertussis Vaccine Effectiveness and Waning Immunity

A resurgence of pertussis cases among immunized and unimmunized individuals raised questions about vaccine effectiveness and waning immunity. We performed a test-negative case-control study, utilizing Ontario administrative and laboratory data. We used crude and adjusted multivariable logistic regression models to estimate odds ratios (ORs) comparing the odds of cases being vaccinated against that of controls. Vaccine effectiveness was calculated as (1-OR)x100. There were 5,867 individuals available for analysis (486 test-positive cases and 5,381 test-negative controls). Vaccine effectiveness was 80% (95%CI, 71%-86%), 84% (95%CI, 77%-89%), 62% (95%CI, 42%-75%), and 41% (95%CI, 0-66%) at 15-364 days, 1-3 years, 4-7 years, and ≥8 years since last immunization, respectively. The odds of developing pertussis increased 27% (95%CI, 20%-34%) per year from last immunization. Acellular, compared to whole cell, vaccine priming was associated with a two-fold increased risk of pertussis. These results have important policy implications for optimizing pertussis control and to spur vaccine development.

Keywords: Immunity
Pertussis
Vaccine effectiveness
Advisor: Stukel, Therese A
Kwong, Jeffrey C
Atypical Neural Synchronization during a Socially Relevant Inhibitory Control Task in Children with Autism Spectrum Disorder

Impairments in inhibitory control may underlie and exacerbate the core symptoms of autism spectrum disorder (ASD), particularly restricted and repetitive behaviours. Current models suggest that ASD can be characterized by atypical patterns of neural synchronization among distributed brain regions. Using magnetoencephalography (MEG), we investigated patterns of inter-regional phase synchronization in children with and without ASD during an emotional go/no-go task that tested inhibitory control in the presence of happy and angry faces. We observed reduced theta band synchronization in children with ASD in happy face trials which involved regions that are important for inhibitory control: the right inferior frontal gyrus, right orbitofrontal cortex, and right inferior parietal lobule. This study provides new insight into the biological basis of inhibitory control in social contexts in children with ASD.

Keywords: autism spectrum disorder
emotional face processing
inhibitory control
magnetoencephalography
theta band synchronization
Advisor: Doesburg, Sam M
Taylor, Margot J
A Retrospective Study of Stainless Steel Crowns as a Posterior Permanent Tooth Restoration

Purpose: This retrospective cohort study assessed the long-term clinical and radiographic outcomes of the stainless steel crown (SSC) as a posterior permanent tooth restoration. Methods: Study included 271 patients registered at Mount Sinai Hospitalâ s Dentistry Clinic for Persons with Special Needs. A total of 2621 posterior restorations were documented: 766 SSCs, 1651 amalgams, and 204 composite resins. Radiographic analysis of SSCs included 127 bitewing, and 118 periapical films. Results: Ten year survival rate for new SSC and amalgam restorations was 79.2% and 63.5%, respectively. Ninety-one SSC failures included loose/lost SSCs (24) and chronic periodontal disease (25). Ninety-three percent of alveolar bone loss measurements from mesial and distal sites were

Keywords: Extracoronal
Permanent
Prefabricated
SSC
Stainless Steel Crown
Survival
Advisor: Andrews, Paul
Azarpazhooh, Amir
Characterizing the Structure and Function of the Cytoplasmic Domains of Ptch1

The Hedgehog (Hh)-pathway is a critical signalling cascade that determines cell fate and is required for embryonic and postnatal development. A central component of this molecular-genetic pathway is the receptor for the Hh-ligands, Patched-1 (Ptch1), a 12-pass, transmembrane glycoprotein that is essential for Hh-signalling. Despite its essential role in Hh-signalling, it is still unclear how Ptch1 mediates canonical Hh-signalling through Smo, though intracellular regions of Ptch1 have been suggested to be involved. We show that the deletion of the cytoplasmic â middle loopâ (ML) domain (a.a. 584-734) generates a Ptch1 mutant that, despite binding to ligand, constitutively suppresses Hh-signaling and increases the length of primary cilia. The constitutive activity due to deletion of this region is reversed, by further deletion of the cytoplasmic C-terminal domain (CTD) (a.a. 1162-1432). We show that the intracellular ML and CTD of Ptch1 are dispensable for canonical Hh-signalling.

Keywords: Hedgehog
Hh-signalling
Ptch1
Advisor: Hamel, Paul A
Exploring the Relationship between Motor and Frontoparietal Brain Networks in Upper Limb Motor Outcome Post-stroke

Background: A network-approach may help understand how extensive neural changes arise from localized damage. Given that motor and frontoparietal networks are implicated in motor learning, these networks may also be implicated in motor re-learning post-stroke. This thesis studies the relationship between motor and frontoparietal networks and movement post-stroke. Methods: Twenty-seven chronic stroke participants underwent behavioural assessments and magnetic resonance imaging. The resting state connectivity (rs-connectivity) within (intra-network) and between (inter-network) motor and frontoparietal networks were correlated with behavioural scores. Results: Intra-network: i) Participants with higher rs-connectivity between the primary motor cortex and supplementary motor area have less hand impairment and greater motor function; ii) Participants with higher rs-connectivity between the dorsolateral prefrontal cortex and mid-ventrolateral prefrontal cortex have less hand impairment. Inter-network: participants with higher rs-connectivity between the motor and frontoparietal networks have greater motor function. Conclusion: Connectivity of motor and frontoparietal networks may be a biomarker of movement post-stroke.

Keywords: chronic stroke
frontoparietal
motor
network
resting state fMRI
task-switching
Advisor: Chen, Joyce L
Dawson, Deirdre R
Discontinuation Patterns of Substances of Abuse in Pregnancy in a Cohort of Women Seeking Addiction and Parenting Support: A Mixed Methods Study

Background: Substance use during pregnancy is a major public health concern, stemming from potential physical and psychosocial harms to both the mother and child. Objective: It was my aim to characterize substance use patterns throughout pregnancy and explore the reasons that women attribute to these patterns of use. Methods: A mixed methods approach was used to investigate a group of women that attend(ed) Breaking the Cycle (BTC). BTC is a â one-stopâ comprehensive service available to pregnant or parenting women who have substance use issues. Results: Through a chart review (N=470), I found that the greatest number of women used tobacco and cannabis for the duration of pregnancy (N=231 and N=101, respectively), while the proportion of women continuing opioid use was comparably high (61.8%). The results from the two focus groups highlighted the importance of self-efficacy and quality relationships for women who are trying to make positive changes to their substance use during pregnancy.

Keywords: Addiction
Mixed Methods
Pregnancy
Social Work
Substance abuse
Women's Health
Advisor: Ito, Shinya
Study of Phosphorus Behaviour in Levitated Silicon-iron Droplets

While the treatment of relatively inexpensive ferrosilicon alloys is a potential refining route in order to generate solar grade silicon, phosphorus is one of the more difficult impurities to remove by conventional processing. In this project, electromagnetic levitation was used to investigate the dephosphorization of ferrosilicon alloy droplets exposed to H2-Ar gas mixtures under various experimental conditions including, refining time, temperature (1450째C-1720째C), H2-Ar gas concentrations and flow rate, iron alloying content, and initial phosphorus concentration. Reaction rates increased with higher refining times, temperatures, and H2 gas concentrations. With unknown parameters associated with the kinetics of gas phase reactions, the approach involved comparison of apparent activation energies derived for the chemical reaction and gas diffusion steps of the dephosphorization process. The phosphorus removal rate is thought to be controlled by the interfacial reaction step; further work is required to confirm this conclusion.

Keywords: Engineering
Kinetics
Metallurgy
Solar Grade Silicon
Thermodynamics
Advisor: McLean, Alexander
Automatic Power Quality Monitoring with Recurrent Neural Network

The electric power grid constantly experiences disturbances that hinder efficiency and reliability of the grid. This thesis is concerned with the development of automatic power quality monitoring system that classifies power quality disturbances based on the voltage waveform. The classification process involves generating training data, extracting features, and classifying the data at every time step with a neural network. The feature extraction is implemented based on short-time Fourier transform, wavelet transform, and S transform, and we present comparisons of their performance for this application. The extracted features are used as the inputs for the neural network, and the outputs are classes that the waveform belongs to. We introduce recurrent neural network as the classifier for the first time in this application. The recurrent neural network has the ability to memorize information in a time sequence data by passing information through its hidden units. We show that recurrent neural network achieves better performance than conventional feedforward neural network.

Advisor: Kundur, Deepa
Surveying the Human Genome for Genetic Markers Associated with the Mutator Phenotype and Chromosomal Instability

Cancer is a genetic disease that develops as a result of the acquisition of stable somatic mutations. Many cancers are believed to acquire mutations at significantly increased rates, a state commonly referred to as the "mutator phenotype". In this study, I utilize whole genome sequencing data available from the ICGC Pancreatic Cancer Sequencing Initiative (PCSI) and PanCancer Analysis of Whole Genomes (PCAWG) projects to identify genes that may be associated with chromosomal instability or mutator phenotypes. I have found two novel candidate genes (XIRP2 and STARD9) that appear to increase the accumulation of double-stranded breaks in pancreatic cancer. Additionally, 15 candidate genes are identified across the PanCancer data set that increase the rate of accumulation of simple somatic mutations. Finally, I have also developed a novel non-parametric method for cancer driver discovery through the identification of mutations distributed uniformly across samples relative to differing background mutation rates.

Advisor: Stein, Lincoln
EFL Learners' Perceptions of (In)formality: Address Forms in Interaction with Other (In)formal Register Markers

Perception and production of stylistic variation is an important aspect of sociolinguistic and pragmatic competence. Whereas most research has focused on the production of (in)formal variants by native speakers, this study compares perceptions of formality by English-dominant (ED) speakers and advanced English-as-a-foreign-language (EFL) learners measured on a 5-point Likert scale for 20 examples of e-mail workplace communications in which (in)formal greetings, address forms, and vocabulary are variously combined as three register markers. Participants also reported how certain they felt about their formality ratings on a 4-point Likert scale, and identified features that they considered significant in their perceptions of formality. Statistically significant differences between the two participant groups emerged in 11 of the formality and 12 of the certainty ratings. A trend which needs to be substantiated by further research was observed suggesting that the EFL learners found address forms more and vocabulary less salient than the ED speakers.

Keywords: EFL learners
formality
perception
pragmatic competence
sociolinguistic competence
stylistic variation
Advisor: Kerekes, Julie
Intergenerational Transmission of Values on Parenting and Education

This project provides a detailed portrait of the intergenerational transmission of values on parenting and education. The parenting process is commonly observed between the parent and child, but it is also influenced by the parentâ s relationship with his or her parents, and the individualâ s surrounding environment, culture, and history. In order to understand the intricate nature of human relationships, I used a rare collection of archival data from the first Canadian Mental Hygiene (Canadian Mental Health Agency) movement in the 1920s. I studied one normative family through the archival data and conducted my own series of interviews with a member of this family. Using multiple methods, I analyzed three generations and coded the data by emergent themes. The results indicate that each generation fosters distinct parenting practices and highlight the complexity of human adaptation and relationships, and the need to study human development within a relational developmental systems framework.

Keywords: Adaptation
Case Study
Education
Life-Span
Parenting
Values
Advisor: Volpe, Richard
Pelletier, Janette
Use of Need for Closure Scale to Predict and Affect Individual Tendency for Design Fixation

Not all individuals may be equally susceptible to design fixation. I sought to identify characteristics that could predict and affect individual tendency for design fixation, and explored the use of Kruglanski’s Need for Closure Scale for this purpose. The Need for Closure Scale is an individual/dispositional difference variable, as well as an environmental variable that can be manipulated in the laboratory. I devised two experiments that involved developing concepts for which an example solution was provided. The first experiment investigated whether correlations exist between participants’ score on the Need for Closure Scale and the degree of fixation in concepts elicited. A pilot experiment and second experiment investigated whether environmentally-induced Need for Closure could be used to change participants’ likelihood to fixate. Significant results were found in the first and second experiments, supporting that Need for Closure can be used to predict and affect individual tendency for design fixation.

Keywords: Design Fixation
Fixation
Need for Closure
Advisor: Shu, Li
Identification of CD Marker Expression and Neutrophil Surface Marker Changes in Health and Disease using High-throughput Screening Flow Cytometry

Neutrophil hyperactivation can contribute to tissue damage in inflammatory diseases. Although many cell-surface proteins are known to be expressed on neutrophils there is no comprehensive study of the surface-markers that can be used to phenotype neutrophils. Neutrophils subpopulations isolated (blood and oral rinses) from healthy and chronic-periodontitis patients were screened against a panel of 374 known Cluster of Differentiation (CD) antibodies to identify cell-surface markers specific to neutrophils. This screen identified CD11b+, CD16b+, and CD66c+ as markers that are always expressed on neutrophils. Cell-sorting with an antibody against CD11b/CD16b/CD66c allowed for the enrichment of mature neutrophils, yielding populations of up to 99%, confirming the validity of these markers when isolating neutrophils. These findings provide a simple method for isolating neutrophils from humans, and thereby establish a validated method that allows for the accurate identification of neutrophils. This knowledge will be crucial for identifying neutrophil subtypes associated with neutrophil-mediated inflammatory diseases.

Keywords: high throughput flow cytometry
neutrophils
Periodontal Disease
Advisor: Glogauer, Michael
A Microfluidic Device for Producing Controlled Collisions Between Two Soft Particles

We report the design and operating characteristics of a computer-controlled microfluidic device for the confinement and manipulation of two particles in a viscous fluid undergoing a two-dimensional extensional flow. Using this device, two particles are trapped at two stagnation points in a circular slot having three alternating fluid inlets and outlets which are connected to a pressure-controlled liquid reservoir. By employing a control algorithm based on theoretical flow pattern and model predictive control, two particles can be steered to arbitrary target positions within the slot by adjusting the fluid flow rates into and out of the slot. Thus, two soft particles can be trapped indefinitely at two different points, and be manipulated along arbitrary, independent trajectories in the slot. This device is suitable for investigation of coalescence between drops, and adhesion between vesicles by achieving collisions between two particles at precise contacting forces and glancing angles.

Keywords: Hele-Shaw flow
Hydrodynamic trap
Model Predictive Control
Advisor: Ramchandran, Arun
Atomistic Investigation of the Structural, Transport, and Mechanical Properties of Cu-Zr Metallic Glasses

The unique set of mechanical and magnetic properties possessed by metallic glasses has attracted a lot of recent scientific and technological interest. The development of new metallic glass alloys with improved manufacturability, enhanced properties and higher ductility relies on the fundamental understanding of the interconnections between their atomic structure, glass forming ability (GFA), transport properties, and elastic and plastic deformation mechanisms. This thesis is focused on finding these atomic structure-property relationships in Cu-Zr BMGs using molecular dynamics simulations. In the first study described herein, molecular dynamics simulations of the rapid solidification process over the Cu-Zr compositional domain were conducted to explore inter-dependencies of atomic transport and fragility, elasticity and structural ordering, and GFA. The second study investigated the atomic origins of serration events, which is the characteristic plastic deformation behaviour in BMGs. The combined results of this work suggest that GFA and ductility of metallic glasses could be compositionally tuned.

Keywords: Amorphous metals
atomistic modeling and simulaitons
Bulk metallic glasses
computational material science
glass forming ability
mechanical properties and plastic deformation
Advisor: Singh, Chandra V.
Environmental Attitudes and Election Issues

Research examining the ways in which attitudes towards policy issues may affect or be affected by election outcomes has yet to explore the increasingly relevant area of environmental policy. Over two studies, linear regression and multi-level modeling is used to create predictive models of voting behavior and attitude change over time, with data from the 2015 Canadian national election. The present research engaged 226,892 participants who visited a political website before the election (Study 1) and 81 participants in a longitudinal study that preceded and followed the election (Study 2). These studies show that although attitudes towards national protection may determine the level of environmental voting at the individual level, attitudes towards social issues do so at the regional level. Furthermore, proenvironmental attitudes seem to increase following the election of a relatively proenvironmental candidate, but only for individuals who voted proenvironmentally, following a pattern of cognitive dissonance for proenvironmental concerns.

Keywords: Election
Environmental Attitudes
Environmentalism
Politics
Psychology
Voting
Advisor: Page-Gould, Elizabeth
The Effects of Varenicline on Neurocognitive Function in Non-smokers with Schizophrenia

Background: Effective treatments for neurocognitive deficiencies among schizophrenia patients remain an unmet need. The nicotinic partial-agonist varenicline, approved for smoking cessation, has been shown to enhance neurocognition in schizophrenia, but its effects in non-smokers are unknown. Methods: This study was a randomized, double-blind, placebo-controlled, cross-over design assessing effects of 3 different varenicline doses (0, 1, and 2mg/day) in non-smokers with schizophrenia (n=15) and non-psychiatric controls (n=15) on neurocognitive performance. Primary outcome assessed working memory, while secondary outcomes assessed other neurocognitive domains. Results: Overall patients appeared to perform better on 1mg/day dose across visuospatial working-memory, verbal memory and executive function, while controls appeared to perform better on 2mg/day dose on these domains. Across time in the 2mg/day dose, patients demonstrated increased inattentiveness, whereas controls had greater executive function, attention, and decision-making performance. Varenicline was generally well-tolerated in both groups. Conclusions: Varenicline may treat neurocognitive dysfunction in schizophrenia patients in a non-linear dose-related fashion.

Keywords: nAChRs
Neurocognition
Non-smokers
Schizophrenia
Varenicline
Visuospatial Working Memory
Advisor: George, Tony P
An Inter-center Comparison of Dental Arch Relationships, Craniofacial Form, and Nasolabial Aesthetics in Patients with Complete Unilateral Cleft Lip and Palate Treated with Different Pre-surgical Infant Protocols

The purpose of this study was to compare the dental arch relationships nasolabial esthetics, and craniofacial form of mixed dentition patients with complete unilateral CLP originally treated with distinct infant orthopedic (IO) approaches (Latham, modified McNeil, nasoalveolar molding (NAM), and no IO). A total of 138 study models, 180 photographs and 124 cephalograms were assembled from existing records at five different North American cleft centers. Six trained, calibrated judges blindly rated dental arch relationships using the Goslon yardstick, and the nasolabial esthetics using the method of Asher-McDade. The radiographs were analyzed using hard and soft tissue landmarks on Dolphin Imaging software. The most favorable occlusal relationships and skeletal relationships were achieved at the center using no IO (p

Keywords: Cleft
Advisor: Daskalogiannakis, John
Using Human Factors Engineering to Improve Surgical Safety: An Observational Study of System Factors Affecting Risk and Resilience during General Laparoscopic Surgery

Laparoscopic surgery is a uniquely complex sociotechnical work system wherein surgical successes prevail despite pervasive safety threats. Characterizing intraoperative factors that thus support system resilience in addition to those that threaten patient safety is critical for optimizing surgical safety overall. In this exploratory observational study, 19 video-recordings of complex general laparoscopic surgical procedures were analyzed using a qualitative systems-based approach to identify and categorize intraoperative human factors with the potential to impact patient safety. A total of 1083 relevant observations were made over 39.8 hours of operative time, enabling the identification of 80 distinct safety threats and 68 resilience supports within the surgical system. Safety threats associated with the physical environment, tasks, organization, and equipment were prevalent, while supports for resilience were predominantly attributed to clinician behaviours. To optimize safety in the specific system observed, immediate system-level interventions to address recurring equipment malfunctions and intrusive intraoperative noise are recommended, as is the prioritization and reinforcement of resilience-supporting communication patterns.

Keywords: Human factors
Human factors engineering
Laparoscopic surgery
Patient safety
Resilience
Advisor: Grantcharov, Teodor