VictorJuiz/thesis huggingface dataset:
Social Inclusion and Oral Health in Elderly Canadian Population

Introduction: The distribution of age groups in Canada has significantly changed over time, with seniors making up an ever-growing segment of the Canadian population. Given this, factors like social inclusion—measured as social participation and social support—has been recognized to play a critical role in people’s health, specifically as people age. Also recognized is the importance of oral health to healthy aging. This study thus aims to examine and explore the association between social inclusion and self-reported oral health (SROH) in the elderly Canadian population age 65 years and above. Methods: Binary and multivariate logistic regression was used to assess the association between social inclusion and SROH. Results: Our study showed that low levels of social support and a low frequency of social participation increased the odds of reporting fair and poor oral health. Conclusion: This study revealed a negative association between social inclusion and SROH.

Keywords: Canadians
Elderly group
Oral health
Social inclusion
Social participation
Social support
Advisor: Quiñonez, Carlos R
Stressful Experiences, Emotion Regulation, and Nonsuicidal Self-Injury Among University Students

Nonsuicidal self-injury (NSSI) is a widespread mental health concern among students in university (Swannell et al., 2014). Stressful experiences in university may lead to increased risk for NSSI by undermining an individual’s ability to cope with distress. However, longitudinal examinations of the link between stressful experiences in university and NSSI, and the mechanism driving the association, are lacking. The current study investigated the process through which stressful experiences may heighten risk for NSSI in a sample of 1132 undergraduate students (70% female, mage = 19.11). Participants reported on daily stressors in university, difficulties in emotion regulation, and NSSI each year for three consecutive years. Path analysis revealed a significant indirect effect from stressful experiences to NSSI through emotion regulation. This association was bidirectional; greater frequency of NSSI predicted increased risk for stressful experiences through emotion regulation. Theoretical and practical implications are discussed.

Keywords: Emerging Adulthood
Emotion Regulation
Nonsuicidal Self-Injury
Stressful Experiences
University Students
Advisor: Hamza, Chloe A
Functional Analysis of Neutrophil Cytosolic Factor 4 (NCF4) in the pathogenesis of Pediatric Inflammatory Bowel Disease

Genetic variants in NADPH oxidase are known to increase susceptibility of Very Early Onset Inflammatory Bowel Disease (VEOIBD). NADPH oxidase generates superoxide anions for bactericidal activity in phagocytes. Defects in NADPH oxidase lead to Crohn’s disease (CD) and Chronic Granulomatous Disease (CGD) like phenotypes, characterized by defective respiratory burst and inefficient pathogen clearance. This study evaluates the functional consequences of an autosomal recessive nonsense variant in NCF4 in the onset of pediatric IBD. It truncates p40phox (p40phox (W239X)), a subunit of the NADPH oxidase. It is reported that p40phox (W239X) loses its interaction with its known binding partner p67phox in NADPH oxidase and mislocalizes to early endosomes; instead of the cytoplasm. Impaired intracellular oxidative burst and reduced bactericidal activity were observed in macrophages stably expressing p40phox (W239X). It is proposed that p40phox (W239X) does not interact with NADPH oxidase causing its functional impairment and prompting the onset of pediatric IBD.

Advisor: Muise, Aleixo M
Biophysical Characterization and Evolutionary Analysis of the Presynaptic Voltage-gated calcium (Cav2) Channel in Trichoplax adhaerens

Trichoplax adhaerens is a primitive metazoan with six cell types that lacks a nervous system and synapses. One cell type, dubbed gland cells, line the periphery of its flat disc- shaped body and resemble neurons by expressing membrane apposed secretory vesicles and proteins required for regulated neuronal exocytosis including a presynaptic Cav2 calcium channel homologue. Trichoplax is a motile behaving animal that can integrate sensory information with cell activity, where it will pause its ciliary locomotion upon detecting algae under its body, then locally secrete hydrolytic enzymes to lyse and consume the algae by external digestion. In this project, a molecular characterization of the cloned Trichoplax Cav2 channel, with a focus on its biophysical and pharmacological properties will be examined. My work will provide insights into the evolution of the nervous system, where pre-synaptic calcium channels are essential for translating electrical signals into regulated secretion of neurotransmitters and neuropeptides.

Advisor: Senatore, Adriano
Multiscale Response of soft matter and their fiber reinforced composites for shock damping applications

Highly Adaptive properties of soft matter has made a topic of great interest in many fields of research. Some of which include mechanical, microfluidics, biomedical applications, and other applications. However, little is known about the multiscale dynamic mechanical response of these soft matter and their fiber reinforced composite structures. More specifically, little is known about the effects of multiscale structures and their effects on the dynamic mechanical response of these composite structures. In addition, the nonlinear and dissipative viscoelastic behavior of soft matter and its fiber reinforced composite structures makes it challenging for researchers and scientists to develop structures with a desired dynamic mechanical response. This is specifically true for researchers working in development of structures with improved shock damping response. Therefore this thesis will focus on developing and characterizing the multiscale dynamic mechanical response of novel soft matter and their fiber reinforced composites for improved shock damping response.

Keywords: Fiber Reinforced
Multiscale
PDMS
Polydimethylsiloxane
Soft Matter
Advisor: Naguib, Hani E
Fracturing the Prairies: An examination of small-scale, high-frequency energy development and cumulative effects management

Hydraulic fracturing is an innovative technology that has allowed for the exploitation of previously unextractable resources. The province of Saskatchewan has embraced this technology, allowing for its deployment in high-frequency with little regulation. Hydraulic fracturing is associated with many negative environmental, and human health effects, and its frequency can lead to cumulative impacts far greater than that of a single well-site. Further, the area in which Saskatchewan is employing hydraulic fracturing is an endangered landscape, inhabited by 38 federally-listed species at risk. This thesis examines the Saskatchewan case study and performs a comparative analysis of other sub-national Canadian jurisdictions’ regulatory approaches towards the technology. The analysis presents regional management frameworks as a ‘best practice’ and suggests the lack of public opposition as a reason Saskatchewan has taken a minimalist regulatory approach. Further, this thesis identifies adoptable frameworks and highlights how such a framework would benefit Saskatchewan without hindering the economy.

Keywords: Cumulative effects
Environmental management
Hydraulic fracturing
Saskatchewan
Advisor: Olive, Andrea
Neural Precursor Cell Galvanotaxis is Conserved Across Age and is Modulated by Resting Membrane Potential

Neural stem and progenitors cells, together termed “neural precursor cells” (NPCs), line the subependyma of the mammalian brain. NPCs are multipotent and undergo a proliferative and migratory response in development as well as in response to injury, making them an attractive target for cell replacement therapeutics. NPCs respond to electric fields with increased migratory directedness and speed. This thesis focuses on characterizing the differences in galvanotactic migration over age. We have discovered that NPC galvanotaxis showed conserved migratory patterns in the presence or absence of niche factors over age. We demonstrate that resting membrane potential modulations, using the hyperpolarizing drug Diazoxide, induced increased migration. Moreover, NPC niche derived factors found within conditioned media is able to modify the NPC galvanotactic response. Our preliminary studies have identified IGF-1 as a potential modulator of membrane potential and NPC galvanotaxis. This work will inform the efficacy of neural repair strategies across age.

Keywords: Aging Conditioned Media
Diazoxide
Galvanotaxis
Neural Stem Cell
Resting Membrane Potential
Stem Cell Niche
Advisor: Morshead, Cindi M
The Impact of Pre-transplant Dialysis Duration on Kidney Transplant Recipient Survival: An Instrumental Variable Approach

Background: Dialysis prior to kidney transplantation may have a detrimental effect on post-transplant outcomes. Methods: A retrospective cohort study was conducted in all deceased-donor kidney transplants performed in Ontario, Canada from April 1, 2002 to March 31, 2013. Patient blood type was chosen as an instrumental variable and a two-stage modelling procedure was conducted. Result: Among 4,728 patients, the risk of death increased non-linearly with dialysis time and was more prominent during the earlier years. Each dialysis year prior to 3 (3.05) years was associated with a 42% increase in the relative hazard of death. The relative hazard fell to 5% per additional dialysis year thereafter. Conclusions: Longer dialysis time leads to a non-linear increase in mortality risk after kidney transplantation. These findings highlight the urgency to develop strategies to shorten waiting times and optimize the management of wait-listed patients.

Keywords: dialysis
instrumental variable
kidney
kidney transplantation
post-transplant outcome
waiting time
Advisor: Coyte, Peter C
Thermal Design and Control for Stratospheric Balloon-borne Telescopes

Balloon-borne experiments present unique thermal design challenges. Radiation and conduction are the predominant heat transfer mechanisms, with convection effects being difficult to characterize at an altitude of 35-40 km. This greatly constrains the thermal design options and makes predicting flight thermal behaviour difficult. SuperBIT aims to study weak gravitational lensing using a 0.5 m modified Dall-Kirkham visible-to-near-UV telescope capable of achieving 0.02” stability. To achieve the theoretical resolution of 0.25”, mirror deformation gradients must be less than 15 nm and the thermal environment must be stable on hour-long time scales. The 2018 test flight served to collect data for post-flight characterization and to test the newly-developed heater control process. The post-flight characterization algorithm developed allows for parameter optimization, such as physical properties or applied heat loads, based on the temperature profile. An overview of the in-flight heater control performance, and extensive simulation results for the parameter-optimization-based thermal design are presented here.

Keywords: balloon
optimization
stratosphere
telescope
thermal
weak lensing
Advisor: Damaren, Christopher J
Zee, Robert
Manipulating Phenotypic Plasticity to Improve Population Establishment of a Classical Biological Control Agent (the Psyllid, Aphalara itadori Shinji) for Invasive Knotweeds

The psyllid Aphalara itadori was approved for release as a biocontrol agent for invasive knotweeds (Fallopia sp.) in Canada, but has had limited success establishing in the field. Establishing biocontrol agent populations in the field is a common problem and one unexplored possibility in improving establishment is the manipulation of an agent’s phenotype prior to release. We developed a series of laboratory bioassays to assess the psyllid’s fecundity and offspring fitness in response to host plants of varying quality. Results show an increase in fitness measures that appear unrelated to the host plant quality and more closely determined by temperature or humidity. This suggests phenotypic plastic responses in A. itadori populations are less sensitive to changes in their host and more sensitive to environmental variables. Determining which environmental factors drive changes in these fitness variables and rearing A. itadori in these conditions prior to release may improve population establishment.

Keywords: Aphalara itadori
Biocontrol
Japanese knotweed
Phenotypic plasticity
Advisor: Smith, Sandy M
Bourchier, Robert
Adsorption, Desorption, and Biodegradation of Benzotriazole in Bioretention Cells

Benzotriazole, a common anti-corrosion additive in vehicle fluids and antifreeze liquids, is frequently detected in urban stormwater runoff with highest concentrations in colder seasons. Bioretention cells are capable of reducing stormwater contamination; however little is known about the fate of polar trace organic compounds such as benzotriazole in these urban green infrastructures. This work investigated the adsorption, desorption, and biodegradation potential of benzotriazole in bioretention cells. Comparison of two bioretention substrates, engineered soil and hardwood mulch, showed higher adsorption for the soil than the mulch. Benzotriazole adsorbs predominantly to organic matter, and polar functional groups in the soil organic matter may have a higher affinity for benzotriazole than the lignin in the mulch organic matter. Cold-climate environmental factors such as low temperatures and road salt concentrations yielded increased benzotriazole adsorption. The biodegradation study was inconclusive and further research is needed to understand the potential for benzotriazole degradation in bioretention cells.

Keywords: Adsorption
Benzotriazole
Biodegradation
Bioretention cell
Desorption
Advisor: Passeport, Elodie
DISTINCT NEUTROPHIL RESPONSES TO ORAL COMMENSAL AND PATHOGENIC BIOFILMS

Periodontal disease, one of the most prevalent inflammatory conditions affecting millions of people each year, is initiated by microbial dysbiosis. The accumulation of bacteria in the gingival sulcus results in the recruitment of host immune cells, mostly neutrophils and, when excessive, can trigger a chronic inflammatory response leading to periodontitis. Neutrophils make up 50-70% of the white blood cells and are the first line of defense against bacterial biofilm forming around the teeth. Using flow cytometry, we have characterized neutrophil responses to several significant oral commensal and pathogenic bacteria by assaying the changes in neutrophil surface expressions of specific clusters of differentiation (CD) markers, induction of ROS production and NETosis. In this study, we are able to show that certain commensal bacteria activate neutrophils more than pathogenic bacteria thus providing better insight into the etiology of periodontal disease.

Advisor: Glogauer, Michael
PAIN-RELIEF ALTERNATIVE FOR SHOULDER SURGERY (PASS TRIAL): The Novel Anterior Suprascapular Nerve Block vs. Conventional Interscalene Brachial Plexus Block for Pain-Relief Following Arthroscopic Shoulder Surgery: A Multi-centre Randomized, Patient and Assessor Blinded, Non-inferiority Trial

Introduction Interscalene nerve block (ISB) is the pain relief standard for shoulder surgery. But ISB is invasive and associated with complications. Suprascapular nerve block (SSNB) may be an alternative; but evidence of comparative efficacy is sparse. We examine whether SSNB is non-inferior to ISB for pain after shoulder surgery. Methods 140 shoulder surgery patients were enrolled into this multi-centre non-inferiority trial. Patients were randomized to ISB or SSNB. Pain at 6 hours (Numerical Rating Scale, NRS) was designated as primary outcome. A difference of -1.3 units was set as non-inferiority margin. Results The mean difference (90% confidence interval) in pain for the (ISB-SSNB) comparison was -0.40 (-1.10, 0.30), less than the non-inferiority margin (P=0.016), suggesting non-inferiority of SSNB for pain at six hours. Conclusion SSNB is an effective alternative to ISB for pain after shoulder surgery. SSNB can be considered for patients at high risk for complications with ISB.

Advisor: Laupacis, Andreas
Beyond the traditional simulation design for evaluating type 1 error: from ‘theoretical’ to ‘empirical’ null

When evaluating a new statistical test, it’s important to check the type 1 error (T1E) control, often achieved by the `theoretical' design S0. In whole-genome association analyses, people scan through large numbers of genes (Gs) for the ones associated with an outcome(Y). Y comes from an unknown alternative and is not associated with the majority of Gs, This reality can be represented by two `empirical’ designs, where S1.1 simulates Y from G then evaluates its association with independently generated Gnew; while S1.2 evaluates the association between permutated Yperm and G. Using scale tests, location tests with single and multiple Gs as examples, we show that not all designs are equal. For certain statistics, T1E inflation can only be revealed under 1empirical’ designs and doesn’t diminish as sample size increases. This important observation calls for new practices for methods evaluation and interpretation of T1E control.

Keywords: Interaction
Simulation
Type 1 error
Variance heterogeneity
Whole-genome association study
Advisor: Sun, Lei
A Pseudomonas putida IclR-Type Transcriptional Regulator is Involved in Rhizosphere Related Interactions

Pseudomonas putida KT2440 is a ubiquitous plant growth promoting rhizobacteria that is known for its ability to degrade a wide range of aromatic hydrocarbons. Its genome has been fully sequenced, but despite extensive investigation into its metabolic capabilities, many of its genes remain uncharacterized. In this thesis, I will evaluate one of its uncharacterized IclR type transcriptional regulators (PP_2609). Based on previous research, I hypothesized that PP_2609 regulated the expression of the pp_2605-08 gene cluster and the genes in this cluster have related functions. Additionally, these genes are likely involved in rhizosphere related interactions. By using RT-PCRs, EMSAs, β-galactosidase assays, it was demonstrated that PP_2609 specifically binds to a promoter of the pp_2605-08 operon and suppresses its expression in a concentration-dependent manner. PP_2609 also binds the promoter with a greater affinity in the presence of A. thaliana root exudate, an interaction that enhances PP_2609’s repressive effect.

Keywords: IclR
PGPR
Pseudomonas putida KT2440
rhizosphere interaction
soil bacteria
transcriptional regulators
Advisor: Christendat, Dinesh
Grit, Coping, and Math Anxiety: Examining the Pathways Through Which Devotion to Long-Term Goals May Promote Student Well-Being

This study sought to determine the extent of the relationship between grit and academic coping in upper elementary school children, and whether proactive coping accounts for lower self-reported school-related internalizing symptoms in grittier students. The sample included 56 children and adolescents in Grades 4 through 6. In agreement with predictions, students who reported higher levels of grit also reported greater strategizing and commitment in response to academic challenges, strategies classified as proactive independent coping approaches. This relationship between grit and coping was mediated by affiliated increases in self-efficacy for self-regulated learning and autonomous academic motivation. Analyses also showed evidence of a significant negative indirect effect of grit on math anxiety through proactive independent coping, indicating that grittier students reported greater proactive coping which in turn was associated with lower math anxiety. Given its relationship with adaptive coping and reduced academic emotional stress, grit may constitute a factor promoting student resilience.

Keywords: Academic Motivation
Coping
Grit
Math Anxiety
Self-Efficacy for Self-Regulated Learning
Advisor: Martinussen, Rhonda
Exploring the Role of Perception in Language Learning: A Plurilingual and Ecological Perspective on Students’ Perceptions of French-English Proximity

This study explores adult students’ subjective perceptions of the proximity between French and English. Through a plurilingual, ecological perspective (Piccardo, 2017; van Lier, 2004a) and the theory of affordances (Gibson, 1979/1986; Rietveld Kiverstein, 2014), perception of language proximity is conceptualized as a dynamic construct that can either facilitate or hinder learning. This study implements four methods (drawing task, language background questionnaire, cognate recognition task and semi-structured interview) to analyze participants’ perceptions of French-English similarities at three levels of analysis (cognate characteristics, patterns within groups and individual perceptions). The findings suggest that participants who viewed cognates as facilitative for their language learning had greater metalinguistic awareness and recognized more French-English cognates. Conversely, participants who perceived cognates as detrimental to their learning tended to demonstrate a lack of metalinguistic awareness and recognized very few French-English cognates. The study highlights the importance of fostering close perceptions of language proximity in language learning.

Keywords: ecological perspective
French language learning
metalinguistic awareness
plurilingualism
student perceptions
theory of affordances
Advisor: Piccardo, Enrica
An Integrative DNA Sequencing Panel To Assess Mismatch Repair Deficiency

Detecting mismatch repair (MMR) deficiency requires serial testing of both germline and tumour DNA using several assays to determine the underlying mechanism of MMR gene disruption. We have created an integrated targeted panel (MultiMMR) that tests for multiple sources of genome variation from a single aliquot of tumour or normal DNA. We have profiled 11 genes related to MMR deficiency or hereditary cancer syndromes on 82 individuals. For each sample, we performed hybrid capture of a single DNA sequencing library constructed using methylated adapters for parallel bisulfite and conventional sequence analysis. MultiMMR recapitulated clinical testing in 22/24 cases and was able to explain the mechanism of MMR loss in an additional 28 patients. This study has shown the utility of integrated mutation, copy number, and methylation profiling to detect hereditary and somatic causes of MMR deficiency. MultiMMR amalgamates the current step-wise and complex clinical testing workflow into a single assay.

Keywords: genetics
lynch syndrome
multigene panel
Advisor: Pugh, Trevor J
Differential Experiences of Climate Change: Local Knowledge and Perspectives of Severe Flooding in the Peruvian Amazon

In the context of rapid climate change, the frequency and magnitude of environmental hazards in Amazonia are continually increasing. This study seeks to understand the lived realities of environmental hazards in the Peruvian Amazon, and in particular flooding, and how experiences are shaped by differential positionalities. The study draws upon data from the Peruvian Amazon Rural Livelihoods and Poverty Project community survey (n=919) and household survey (n=3,941), as well as interview (n=24) and survey (n=25) data collected during fieldwork in Éxito, a riverine village in the Department of Ucayali, Peru. The research findings indicate that flooding experience is highly determined by intersecting lines of difference at the individual, household and village levels; that fishing occupies several related yet contested roles within the village; and that given the positive and negative implications identified of four key flood types, we need to reconsider how we define environmental hazard in the Amazonian context.

Keywords: Amazonia
Differential Vulnerability
Environmental Hazards
Flood Variability
Peruvian Amazon
Rural Livelihoods
Advisor: Abizaid, Christian
Isakson, S. Ryan