VictorJuiz/thesis huggingface dataset:
The Role of the Gut Microbiome in Modulating the Pathogenesis of Kawasaki Disease

The gut microbiome consists of trillions of microorganisms in constant interaction with the body. There is increasing evidence that these microbes have immunomodulatory effects and an important role in the pathogenesis of disease and autoimmunity. Kawasaki Disease (KD) is an inflammatory condition with a predilection for the coronary arteries. In this study, a murine model of KD using Lactobacillus casei cell wall extract (LCWE) was used to assess the effects of the microbiome in the pathogenesis of KD. We found marked changes in the microbiome between two animal facilities which correlated with disease susceptibility. Furthermore, depletion of the microbiome in susceptible mice was able to reduce disease incidence, while the transfer of cecal samples from susceptible to less susceptible mice was able to increase disease incidence. This project demonstrates an important role of the microbiome in modulating the development of coronary inflammation in a murine model of KD.

Keywords: Gut Microbiome
Kawasaki Disease
LCWE
SFB
Advisor: Yeung, SM Rae
Sustained Effect of Ex Vivo Lung Perfusion on Nitric Oxide Metabolite levels in Lung Tissue after Transplantation

Limited availability of donor lungs results in high mortality of patients waiting for lung transplantation. Modern techniques such as ex vivo lung perfusion (EVLP) or interleukin-10 (IL-10) gene therapy expand the donor pool and may improve the quality of donor organs and outcomes following lung transplantation remain inferior compared to other organ transplantations. Alterations in metabolic pathways, such as L-arginine/nitric oxide (NO) metabolism can contribute to post-transplantation organ dysfunction. We investigated the L-arginine/NO metabolism in pig models of lung transplantation. We found significant differences in the L-arginine/NO metabolism in lungs from brain death compared to non-brain death donors after prolonged hypothermic preservation. Moreover, we found that EVLP decreased NO metabolite concentrations in lung, a sustained effect after transplantation that was unaffected by IL-10 gene therapy during EVLP. In conclusion, donation circumstances and preservation methods may alter the L-arginine/NO metabolism in transplanted lungs, which may contribute to clinical outcomes after transplantation.

Keywords: IL-10
L-arginine
Lung transplantation
Nitric oxide
Advisor: Grasemann, Dr. Hartmut
A Reach Control Approach to Bumpless Transfer of Robotic Manipulators

This thesis focuses on the modelling, control design, and simulations for executing a robotic manipulation task to approach and maintain contact with a solid environment. The task involves a transition between position and force control, which may result in bouncing. This thesis shows that the bumpless transfer problem (achieving no bouncing) can be formulated and solved using the reach control problem (RCP), a methodology that emphasizes the control of transient behaviour. To that end, analysis of a given force control scheme leads to the formulation of logic control specifications (a tool used in RCP designs), and a polytopic state space that restricts the manipulator states to trajectories that achieve bumpless transfer. Then, a hybrid controller is developed which consists of so-called reach controllers, a given force controller, and a switching logic. Finally, the proposed methodology is simulated for the Special Purpose Dextrous Manipulator, which executes the task without bouncing.

Keywords: Bumpless Transfer
Force Control
Hybrid Systems
Reach Control Problem
Robotic Manipulator
Advisor: Broucke, E Mireille
Behaviour and Analysis of Steel Fibre-reinforced Concrete under Reversed Cyclic Loading

It is well known that the monotonic behaviour of reinforced concrete can be improved with the addition of steel fibres. However, test data on the influence of steel fibres on reinforced concrete's cyclic behaviour are scarce. Ten large-scale panels were tested with the objective of obtaining data useful for developing constitutive relationships for the reversed cyclic behaviour of steel fibre-reinforced concrete (SFRC). The parameters of study included the fibre volume fraction, fibre diameter, and loading protocol. Mechanical properties of the concrete used were also determined through uniaxial tension tests and bending tests. Test results showed that SFRC was effective in resisting damage from the cycling of load, and the panels' reversed cyclic envelope curves closely matched their monotonic backbone curves. Analyses of the panels and other member-level specimens using VecTor2, a nonlinear finite element program, showed that the reversed cyclic behaviour of SFRC can be adequately represented with currently available constitutive models.

Keywords: ductility
panel tests
reinforcement
shear
steel fibre
strength
Advisor: Vecchio, J Frank
An Investigation into the Feasibility of Utilizing Fluidic Shear Stresses to Functionally Organize Conducting Airway Epithelium

There are currently no reliable clinical treatments for reconstructing large segments of injured trachea. Recent implants have suboptimal mucociliary clearance in the trachea due to improper organization of the airway epithelium. Organization of the airway epithelium determines ciliary beat direction and coordination for proper mucociliary clearance. Fluidic shear stresses have been shown to influence ciliary organization and short-term airflow shear stresses have been shown to affect ciliary function. An in vitro fluidic flow system is developed for inducing long-term airflow shear stresses on airway epithelium to influence epithelial organization. Validation of the system is determined by measuring cell viability and mature epithelial cell markers. The system is utilized to investigate the organizational effects of long-term airflow shear stresses on maturing cells. From the experiments, airflow shear stresses are unable to override existing organizing cues. The goal of this study is to provide valuable information on strategies to generate functional epithelium.

Keywords: Airflow
Airway Epithelium
Mechanobiology
Shear Stress
Tissue Engineering
Advisor: McGuigan, P. Alison
The Effect of Interstitial Pressure on Tumour Stiffness

This work investigates the dependence of the stiffness of a solid tumour on its interstitial pressure. Supersonic shear imaging, a type of ultrasound elastography, was used for measurements of shear modulus. Experiments on

Keywords: angiogenesis inhibitors
cancer
elasticity
interstitial pressure
kidney
ultrasound
Advisor: Burns, Peter
Characterizing the Role of L3MBTL3 in Megakaryopoiesis Using Cell and Chemical Biology Approaches

The histone code regulates a number of processes including transcription, DNA replication, and DNA repair. L3MBTL3 is a putative histone code reader that possesses methyl-lysine binding MBT domains. This study commences with the cellular characterization of UNC1215, the first potent and selective chemical probe targeting a methyl-lysine reader domain, the MBT domains of L3MBTL3. Once established as a potent, selective, and cell-active chemical probe, UNC1215 was used to study the biological function of L3MBTL3. L3MBTL3 was shown to bind histone H3 and to associate with the repressive BHC complex in HEK293 cells and in the erythroid leukemia K562 cell line. Possibly via its association with this complex, L3MBTL3 impairs megakaryopoiesis in a manner dependent on its MBT domains. Additionally, L3MBTL3 may promote erythroid development. In summary, this study utilized cell and chemical biology approaches to obtain insights into the mechanistic function of L3MBTL3, and uncover a role in repressing megakaryopoiesis.

Keywords: Chemical probe
Epigenetics
Histones
L3MBTL3
Megakaryopoiesis
UNC1215
Advisor: Arrowsmith, H Cheryl
MicroRNA-17 Targets JAK1 and STAT3 to Inhibit Osteoblast Differentiation

MicroRNA-17 (miR-17) was hypothesized to target janus kinase 1 (JAK1) and signal transducer and activator of transcription 3 (STAT3) to inhibit osteogenesis in pre-osteoblast cells. Mouse calvarial cells (MC3T3-E1) stably overexpressing miR-17 were found to produce significantly lower levels of mature osteoblast markers through qRT-PCR and staining. JAK1 and STAT3 proteins were found to be directly targeted by miR-17 through Western Blot and Luciferase Reporter Assay analysis. Stable knockdown of JAK1 and STAT3 mRNA using shRNA rendered MC3T3-E1 cells with impaired differentiation capacity. Rescue of miR-17 levels to baseline in cells overexpressing miR-17 leads to restored JAK1 and STAT3 mRNA levels, and restores differentiation potential. Therefore, it appears that miR-17 is exhibiting an inhibitory effect on osteogenesis in pre-osteoblast cells by down-regulating JAK1 and STAT3 protein levels. Further study into this regulation may elucidate novel therapeutic opportunities for the management of osteoporosis and bone metastasis.

Keywords: bone formation
JAK-STAT
microRNA
Osteoblast Differentiation
Osteogenesis
osteoporosis
Advisor: Yang, Burton
Baseline Testing and Beyond: A Comprehensive Concussion Assessment Pilot Study

Increased recognition of sport related concussion show that improved assessment methods are needed. Current assessment methods lack objectivity and sensitivity, limiting their efficacy. This study aimed to collect pilot data to evaluate physiological measures (heart rate variability, grip strength and blood pressure) before and after concussion. Routinely used concussion assessment measures of concussion symptoms, cognition, balance, mood, activity and sleep were included to examine the influence of concussion on these parameters. Measures were assessed in Varsity athletes pre and post-concussion. Results from this pilot study indicate that several frequency domain measures of HRV displayed decreased values day 1 post injury compared to baseline. Our findings suggest that HRV may have the potential to be used as an objective measure to indicate concussion. Cognitive and balance scores demonstrated inconsistent patterns when compared to baseline. Mental activity in the acute phase may contribute to prolonged recovery and would benefit from further study.

Keywords: Assessment
Concussion
Heart Rate Variability
Advisor: Keightley, Michelle
The Effect of Ginseng (The Genus Panax) on Glycemic and Vascular Health

The objective was to conduct a systematic review and meta-analysis of RCTs to assess ginseng's effect on glycemic control and further undertake a RCT to explore the therapeutic potential of the economically-grown, non-steamed Korean ginseng variety, Korean white ginseng (KWG). The meta-analysis of 16-trials (n=770) showed that ginseng significantly improved fasting blood glucose relative to control (P=0.03), with no effect on other glycemic parameters. The RCT in 25-subjects with type-2-diabetes revealed that acute administrations of 1g, 3g, and 6gKWG were safe, but did not improve postprandial glycemia and blood pressure measures relative to control. Nevertheless, 3gKWG demonstrated significant improvements in augmentation index compared to control (P=0.04). Overall, the meta-analysis results indicate that ginseng may serve as an adjunct to conventional diabetes therapy. The clinical findings further suggest that KWG may possess promising vascular benefits, offering a potential cost-effective natural health alternative. However, these results are preliminary and warrant long-term exploration.

Keywords: Diabetes
Ginseng
Korean White Ginseng
Meta-analysis
Randomized Controlled Trial
The Genus Panax
Advisor: Vuksan, V Vladimir
Bundling Spatially Correlated Prefetches for Improved Main Memory Row Buffer Locality

Row buffer locality is a consequence of programs' inherent spatial locality that the memory system can easily exploit for significant performance gains and power savings. However, as the number of cores on a chip increases, request streams become interleaved more frequently and row buffer locality is lost. Prefetching can help mitigate this effect, but more spatial locality remains to be recovered. In this thesis we propose Prefetch Bundling, a scheme which tags spatially correlated prefetches with information to allow the memory controller to prevent prefetches from becoming interleaved. We evaluate this scheme with a simple scheduling policy and show that it improves the row hit rate by 11%. Unfortunately, the simplicity of the scheduling policy does not translate these row hits to improved performance or power savings. However, future work may build on this framework and develop more balanced policies that leverage the row locality of Prefetch Bundling.

Keywords: DRAM
memory controller
prefetching
row buffer locality
scheduling
Advisor: Moshovos, Andreas
Experimental and Numerical Investigation of Structure and Extinction Limits of Biofuels in Laminar Counterflow Diffusion Flames

Extinction of laminar counterflow diffusion flames were investigated at atmospheric pressures as a function of nitrogen dilution through experiment and two-dimensional axisymmetric full domain numerical analysis. An opposed-jet burner with two flow configurations was used in experiments and an advanced, state-of-the-art, high-fidelity, solution algorithm was used to obtain the numerical results. A comprehensive investigation of flame extinction process was conducted. Nozzle velocity flow distributions and burner geometry were found to influence global extinction strain rate significantly, whereas effects of radiative heat loss and gravity were minimal. The local strain rate at extinction was shown to be a fundamental property of the fuel. Chemical kinetic mechanisms best suited for extinction limit calculations were also identified.Using these insights, gaseous biofuels and ethanol extinction were studied. The numerical prediction of gaseous biofuels agreed well with experimental results. However, over-predictions were observed for ethanol, likely caused by limitations of available chemical kinetic mechanisms.

Keywords: Ethanol combustion
Flame extinction
Laminar counterflow diffusion flames
Numerical combustion modelling
Strain rate
Syngas combustion
Advisor: Gulder, L Omer
No Association between Periodontitis and Obesity in a Nationally Representative Sample of Canadian Adults

Objective: To study the relationship between obesity and periodontitis in Canadian adults. Materials and methods: Data were obtained from the 2007/09 Canadian Health Measures Survey. The sample included dentate individuals aged 20-79 who participated in both the anthropometric examination, including body mass index and waist circumference (WC), and the periodontal examination, consisting of probing depths and attachment loss (n=2795). Univariate, bivariate, and logistic regression analyses were conducted. Results: Approximately 15% of the weighted sample had periodontitis, 35% were overweight and 20% were obese, while 33% had WC above normal cut-off points. A higher prevalence of periodontitis was demonstrated in obese participants, as compared to those who were not obese; however, this difference was not statistically significant. Age, cultural/racial origin, smoking, sex and having no dental insurance were significantly associated with the presence of periodontitis. Conclusion: This study found no statistically significant association between periodontitis and obesity in Canadian adults.

Advisor: Quiñonez, Carlos
Beta-blocker Use and Morbidity from Chronic Lung Disease in Patients Undertaking Pulmonary Rehabilitation

Cardiovascular diseases are common in patients with chronic lung diseases. Beta-blockers reduce their morbidity, but are underutilized because of concerns over pulmonary side effects. In this retrospective cohort study, we evaluated the association of beta-blocker use with survival in elderly patients enrolled in pulmonary rehabilitation between 1996-2008. Patient characteristics were abstracted from hospital charts and linked to administrative health databases. Primary outcome was time to death or first hospitalization. Matching on propensity score was used to account for potential confounding. No significant increase was seen in the hazard of death or hospitalization in beta-blocker users. In patients with obstructive lung disease, survival was non-significantly longer among beta-blocker users. Residual imbalance in important confounders remained despite repeated refinement of the propensity-score.Survival to death or hospitalization was not significantly associated with beta-blocker use. Beta-blockers should not be withheld from patients with lung disease who have clinical indications for them.

Keywords: beta-blockers
clinical epidemiology
lung diseases
propensity score
Advisor: Stanbrook, B Matthew
Identification of Genes and Pathways Linking Cancer Metabolism to Cell Surface Dynamics through Protein N-glycosylation

N-glycosylation is a co-translational modification that covalently attaches oligosaccharide to and regulates proper folding, trafficking, and surface residency of secreted proteins. MGAT5 encodes a glycosyltransferase that synthesizes β1,6GlcNAc-branched N-glycans in medial Golgi. MGAT5 is frequently up-regulated in and associated with the progression of multiple types of human carcinomas. In order to identify Mgat5 interacting genes and signaling pathways, immortalized mouse embryonic fibroblast (MEF) cell lines that are Mgat5 wild-type and null were established on p53 null genetic background. Pooled lentiviral shRNA drop-out screens revealed that mTOR pathway was essential in the wild-type MEFs, whereas signaling dependency shifts to RAS-MEK-ERK pathway was observed in the null cells. Metabolite profiling of the MEFs and human cell lines with MGAT5 knock-down showed drastic changes in tricarboxylic acid cycle metabolites and amino acids upon MGAT5 disruption. Together, these approaches permitted a global survey of genetic and metabolic changes that occur when MGAT5 is disturbed.

Keywords: Cell Signaling
Metabolism
Mgat5
N-glycosylation
Pooled Lentiviral shRNA Drop-out Screen
Advisor: Dennis, W James
Uncovering Middle School's Teachers' Perceptions about Learning: A Reflective Practice Approach

Teachers' beliefs and perceptions play a significant role in how teachers experience learning and strongly influence what they will, or will not do in their classrooms. This study seeks to understand how teachers learn by using reflective practice to interpret teachers' collective experiences. Interpreting teachers' perceptions will result in new ways of understanding the types of learning experiences and professional development programs that best support their needs. A phenomenological approach was utilized in order to interpret the collective experiences of nine middle school teachers. Data collection included focus group dialogues, semi-structured interviews and reflective journals. Findings revealed that teachers desire the need to be in charge of their own learning; critical reflection and inquiry are significant for learning to take place and that teachers learn while sharing and exchanging best practices with each other and within supportive environments.

Keywords: learning
professional development
reflective practice
teacher beliefs
teacher perceptions
Advisor: Kooy, Mary
Application of Parametric Hazard Analysis with Time-dependent Covariables to Analyze Durability of Right Ventricle-to-pulmonary Artery Conduits Implanted in Infants and Young Children with Congenital Heart Disease

Background: Interpretation of survival analyses is difficult if time-dependent procedures affecting the outcome are not fully accounted for. This thesis describes a unique modification of parametric hazard analysis incorporating therapeutic events as time-dependent covariables, and demonstrates this method's application to generate clinically relevant models used to inform management decisions.Methods: From a cohort of young recipients of vascular conduits, a parametric hazard model of conduit durability was created. Each child's longitudinal record was divided into segments representing unique states. Risk factors for earlier conduit replacement were generated by multivariable regression. The parametric equation was solved to create prediction plots.Results: The predictive model included time-dependent and time-independent covariables. Prediction plots illustrate conduit durability based upon different clinical scenarios.Conclusion: Addition of time-varying covariables into parametric hazard analysis controls for time-dependent risk factors unaccounted for by conventional methods, and may increase the accuracy of predictive model estimates.

Keywords: congenital heart disease
parametric hazard analysis
pulmonary conduit
statistics
survival analysis
Advisor: Caldarone, A Christopher
Synthesis of Superhydrophobic Nanocomposite Coatings using Electrodeposition

The focus of the current research is to produce a metal matrix composite material that possesses a superhydrophobic surface using electrodeposition. The objective is to create a multifunctional coating that is able to provide high strength as well as high water repellency using nanocrystalline nickel and polytetrafluoroethylene (PTFE) particles. The co-deposition process was first studied. It was determined that the amount of PTFE co-deposited is highly dependent on the concentration of PTFE particles in the electroplating bath. The wetting angle of the surface greatly increased when the PTFE content increases. Next the electroplating procedure of pure nickel is altered to produce a nanocrystalline material, resulting in a large increase in the hardness of the nickel coatings. The two techniques are combined to produce a nanocrystalline Nickel-PTFE composite. Under optimum conditions, the composite coating displayed a highly water repellent surface and improved mechanical properties.

Keywords: Composite
Electrodeposition
Nanocrystalline Nickel
PTFE
Superhydrophobic
Advisor: Erb, Uwe
Searching Out Loud Together: Reflections from a Faculty Learning Circle

This qualitative study explored the experiences and reflections of nine part-time and newly hired College educators who agreed to participate in the development of a Faculty Learning Circle. A collective case study methodology was used to explore the emergent themes, responses and experiences of the participants who engaged with the FLC over the course of a year. Data was obtained by audio-recording the FLC sessions, participant reflections, as well as a group exit interview. The findings indicated that the FLC was an effective vehicle for sustained and meaningful informal professional development. The FLC allowed participants to explore their professional identities, garner peer support within a collegial community, and numerous opportunities to collaborate for professional learning that had benefits both within and outside the classroom. As a result, this thesis offers insights for both faculty and College administrators into the advantages of a collaborative, peer-led approach to professional development.

Keywords: College educators
faculty learning circles
professional development
professional learning
Advisor: Kooy, Mary
Schooling for Colonization and White Supremacy: Failures of Multicultural Inclusivity

Discourses around the exclusions of racialized and Indigenous students from schooling often follow familiar scripts of deficiency that perpetuate white supremacist and colonial logics. Policy-driven attempts to address inequities in schooling have not led to transformative change. Instead, through the institutionalization of multiculturalism and 'inclusivity', the school site legitimizes the colonial state through depoliticizing Indigeneity and 'difference'. This thesis focuses on the Toronto District School Board (TDSB) as a site to analyze how white supremacy and colonization are legitimized and reproduced through schooling and the actions of white people. I employ Critical Discourse Analysis and anti-racist and anti-colonial theory to engage with Ontario Ministry of Education and TDSB policy and curriculum documents. This thesis considers ways to reconceptualize the purpose of schooling to dismantle the white supremacist and colonial status quo.

Keywords: Anti-colonial
Anti-racism
Curriculum
Schooling
Whiteness
Advisor: Dei, S George