VictorJuiz/thesis huggingface dataset:
Genetic Variation in Innate Immunity, Diet and Biomarkers of the Metabolic Syndrome

Chronic low-grade inflammation is associated the Metabolic Syndrome (MetS) and may contribute to its development. A diet high in saturated fat (SFA) has been associated with increased inflammation and development of the MetS. SFAs have been shown to elicit pro-inflammatory signaling through proteins of innate immunity, TLR4 and Nods 1 and 2. We determined whether common polymorphisms in the genes of these proteins could modify the association between fat intake and biomarkers of the MetS. Fat intake was measured using a food frequency questionnaire and genotyping was completed using real-time PCR. The TLR4 Asp299Gly (rs4986790) polymorphism was associated with decreased insulin sensitivity while an intronic polymorphism (rs5030728) modified the association between dietary SFA and HDL-cholesterol. The Nod1 Glu266Lys polymorphism modified the association between dietary SFA and HOMA-IR. These results suggest a role for innate immunity in mediating some of the effects of dietary SFAs on factors associated with the MetS.

Keywords: Genetics
Toll-like receptor 4
Nucleotide binding oligomerization domain 1 and 2
dietary fat
metabolic syndrome
Advisor: El-Sohemy, Ahmed
The Development of an Animal Model of Complicated Atherosclerosis for Non-invasive Imaging

The goal of this thesis was to produce an animal model that develops atherosclerotic plaque featuring plaque neovascularization leading to intraplaque hemorrhage and is suitable for noninvasive imaging studies. Several strategies were tested for their effectiveness in producing such plaques in the rabbit aorta, including: a high cholesterol diet, vascular endothelial growth factor injections, therapeutic contrast ultrasound, and balloon catheter injury. It was found that a combination of the high cholesterol diet and balloon injury was able to achieve plaque neovascularization in a manner dependent on circulating plasma cholesterol levels. In addition, a contrast-enhanced magnetic resonance imaging technique implemented in the animal model was able to detect plaque neovascularization and monitor its change over time in a single group of animals. In conclusion, an animal model was created where plaque neovascularization occurs in a predictable fashion and can be studied with non-invasive magnetic resonance imaging.

Keywords: Animal model
Atherosclerosis
Vessel wall disease
Medical imaging
Magnetic resonance imaging
Neovascularization
Advisor: Moody, Alan
Oxidative Stress and Risk of Cardiovascular Disease Associated with Low- and High-monounsaturated Fat Portfolio Diets

The objective was to assess the effect of a high-monounsaturated fat (MUFA) dietary portfolio of cholesterol-lowering foods on oxidative stress and cardiovascular risk. Twenty-four hyperlipidemic subjects followed a very low-saturated-fat therapeutic control diet for 4 weeks after which they were randomized to receive the dietary portfolio, consisting of soy protein (20g/1000kcal), viscous fibre (10.3g/1000kcal), plant sterols (2-3g) and almonds (21.5g/1000kcal), in combination with high- or low-MUFA (25.9% and 12.9% MUFA, respectively) for the next 4 weeks, where MUFA replaced 13.0% of dietary carbohydrate. On high-MUFA, there were significantly greater increases in HDL-C and apoA1 and significantly greater reductions in total:high-density lipoprotein cholesterol (total:HDL-C) ratio and high-sensitivity C-reactive protein (hs-CRP) compared to the low-MUFA dietary portfolio. In all diets there were significant increases in protein thiols and reductions in conjugated dienes and thiobarbituric acid reactive substances (TBARS) measured in the LDL-fraction, however no difference between the high- and low-MUFA diets.

Keywords: oxidative stress
cholesterol
Advisor: Jenkins, David J. A.
Synthesis and Application of Polymer Stabilized Lanthanide Fluoride Nanoparticles

A new class of polymer coated lanthanide fluoride nanoparticle aggregates (NPAs) was developed as potential MRI contrast agents. The NPA synthesis has been perfected to control the size distribution and optimize relaxivities. Polyacrylic acid was used as a stabilizing polymer, and was conjugated to folic acid to improve targeting to SK-BR-3 breast cancer cells. Terbium was incorporated in the synthesis to study the passive and active targeting properties of NPAs. Through a series of microscopy experiments, a significant difference in uptake between NPAs with and without targeting moieties occurs after 48 hours of incubation. The relaxivity of the optimized nanoparticles was measured to be 56 s-1(mg/ml)-1 using a 1.5 T scanner, which may be compared to that of the commercially available Gd3+-DTPA [R1 = 7 s-1(mg/ml)-1]. Abdominal perfusion studies in rats also demonstrated that the NPAs provide better contrast of the vasculature than Gd3+-DTPA does at the same mass concentration.

Keywords: lanthanide fluoride nanoparticle aggregates
folic acid
magnetic resonance imaging
contrast agents
targeted imaging
Advisor: Prosser, Robert Scott
The Role of FKBP5 in Influenza Virus Infection

FK506 binding protein 5 (FKBP5) is a peptidyl propyl cis-trans isomerase that has been shown to interact with cellular immune pathways such as calcineurin and NF-κB. During an influenza infection, FKBP5 is up-regulated at the lung in an in vivo ferret infection model, yet the effect of FKBP5 on influenza replication and immune response is not understood. An in vitro model of human alveolar epithelial cell line A549 was established to study the cause and the function of FKBP5 up-regulation during an influenza infection. In this in vitro model, FKBP5 was not up-regulated by influenza replication, but instead it was up-regulated when A549 cells were treated with glucocorticoid. FKBP5 up-regulation did not have any effect on rate of influenza replication. However, FKBP5 up-regulation mediated the suppressive effect of glucocorticoid on pro-inflammatory cytokine production, since FKBP5 knock-down by siRNA increased cytokine production in the presence of glucocorticoid. Overall, the results suggested that the up-regulation of FKBP5 is a physiological response of lung cells to the increase of glucocorticoid during influenza infections, which facilitates the suppressive effect of glucocorticoid on pro-inflammatory cytokine production.

Keywords: FKBP5
Influenza
Glucocorticoid
Advisor: Kelvin, David J.
Examining the Wrongs Against the Present African Women: An Enquiry on Black Women’s Roles and Contributions from Antiquity - A Black African Male Scholarly Comparative Perspective

The thesis examined the roles and contributions of Black women during the African ancient civilization by analyzing the lives, roles and contributions of Queen Hatshepsut and Nefertiti as case studies and interrogates how Black women positioned themselves as political, military and spiritual leaders during the age of antiquity. The argument is that African women were more involved as leaders in the affairs of their communities as compared to the contemporary times. By using African centered paradigms, Afrocentricity and juxtaposing robust anti-colonial and Black feminist thoughts, the thesis investigates and recreates systematic narratives of the past roles of African women at the very height of African civilization, discussed the changes in sex-gender roles and explained why contemporary women continue to experience difficulties in assessing position of leadership and resources. The study reproduces measured facts to confront the blurred roles and contributions of African women and situates it at the centre of education.

Keywords: African Women
Queen Hatshepsut
Afrocentricity
African Spirituality
African centered paradigms
Queen Nefertiti
Egypt
Black feminist
African civilization
Anti-Colonial
Meroë
Anti-Racist Theory
Colonialism
Africanist Historiography
Africa
Ancient civilization
African Feminist Thoughts
Neo-Colonialism annd Post-colonialisms
Myths and Mythology
Culture
Black
Women Empowerment
Indigeneity
African Cullture and Tradition
European colonization
indigenous order
Eurocentric education
Housewification and domestication of African women
Advisor: Wane, Njoki
Farmers' Markets and their Practices Concerning Income, Privilege and Race: A Case Study of the Wychwood Artscape Barns in Toronto

The popularity of Farmers’ markets is on the rise; in Canada there are 425 farmers’ markets, with over 130 in Ontario alone (Feagan, Morris, & Krug, 2004). Farmers’ markets provide high quality, local produce and are often considered an environmentally sustainable food practice (Taxel, 2003; King 2008). United States studies have scrutinized farmers’ markets as exclusionary white spaces that are not equitably accessible, but similar Canadian studies are rare. A case study at the Wychwood Artscape Barns, located in an economically and culturally diverse neighbourhood, in Toronto Ontario has been conducted. Demographics surveys of patrons were compared with existing demographic data; interviews were conducted to discover who shops at the market and for what reasons; results were analyzed using whiteness theory. Results were consistent with U.S. studies – Wychwood Farmers’ Market patrons were white, high income,individuals with university educations; these individuals shop at the market disproportionally to the demographic data.

Keywords: whiteness
farmers' markets
sustainability
equity
Advisor: Eichler, Margrit
Psychological Functioning Following Violence: An Examination of Posttraumatic Growth, Distress, and Hope among Interpersonal Violence Survivors

Trauma research has been predominantly focused on the study of the negative psychological sequelae of traumatic experience. Recently, however, increased empirical attention has been paid to the potential for positive changes, or posttraumatic growth, derived from survivors’ struggle with trauma. There is evidence accumulating in support of this phenomenon following various types of traumatic events. Using an online, cross-sectional design, the present study examined posttraumatic growth among 143 survivors of interpersonal violence. Furthermore, the relationship between posttraumatic growth and the severity of psychological distress symptoms, as well as between growth and hope was explored. Results indicated that the severity of depressive symptoms was negatively related to growth, while the severity of posttraumatic stress disorder symptoms and hope were found to positively predict growth. Associations between posttraumatic growth and demographic and interpersonal violence characteristics did not emerge. The potential implications of these findings and directions for future research are discussed.

Keywords: Trauma
Interpersonal violence
Psychological functioning
Posttraumatic growth
Distress
Posttraumatic stress disorder
Depression
Hope
Advisor: Stermac, Lana
Spatial Patterns of Zooplankton and Water Currents Near the Confluence of Two Major Fetches in Lake Opeongo,Ontario

This study combines Optical Plankton Counter data on zooplankton abundance and Acoustic Doppler Current Profiler data on water currents to test hypotheses about spatial zooplankton distributions near a major point of land affecting local wind and water current patterns. Data were collected by repeatedly sampling a 2 km linear transect in the South Arm of Lake Opeongo, Ontario, Canada during July, 2008. Moving Split Window techniques were used to identify breakpoints in both zooplankton biomass concentration and a measure of water turbulence, and confirmed an effect of the topographic feature on local zooplankton distributions. Using additional data collected in 2001 and 2003, zooplankton abundance distributions were also tested under three wind speed ranges predicted from physical principles to correspond to varying stability of the water column. Significant differences were found in the variability and patch sizes of the distributions, indicating the importance of wind speeds on zooplankton patchiness.

Keywords: Zooplankton
Spatial patterns
Water currents
Lake Opeongo
Moving Split Window
Advisor: Gary, Sprules
Japan's Colonized Other: A Case Study of the Media Representations on the Deportation of a Filipino Family

This research investigates Japanese society's gaze towards those former colonized subjects, who now reside in Japan as foreign residents. More specifically, it explores the representations, in two leading Japanese newspapers and a popular internet discussion board, of a Filipino family facing deportation in 2009. Using Foucault's archaeology of knowledge as the main analytical framework, it examines emergent and silenced discourses in each media. While the newspapers generally reported in favour of the family, they often unintentionally constructed the child as innocent, and the parents as illegal. The internet discussion board tended to depict the family as criminals. By silencing the colonial history between the Philippines and Japan, both media outlets have failed to address the continuing neo-colonial relationships between the two nations. In conclusion, the various implications of this research on the strategies advocating citizenship rights of irregular residents are examined, by applying anti-oppressive education frameworks to the research findings.

Keywords: Japan
media representation
Filipinos
irregular residents
advocacy
archaeology of knowledge
Advisor: Coloma, Roland Sintos
Kathy, Bickmore
The Buddhalakshana

The physical representation of the Buddha (Siddhartha Gautama) is characterized by some thirty-two uncommon attributes that are described in the Lalitavistara as the marks of a great man. The origin of these attributes, whether they are actual physical observations, of symbolic origin or a combination is unclear. In various art forms depicting the Buddha, he is usually shown with some but not all of these attributes. We have examined the origin of these physical attributes, by considering what is known of similarly described physical variations in humans (both congenital and acquired) and by examining the Sanskrit medical texts, such as the Sushruta-Samhita and the Charaka-Samhita, for descriptions of these and similar attributes. It is plausible that the observation of most of these thirty-two uncommon physical attributes might well have been accumulated over centuries as a result of contact by observers with various afflicted persons. It is kept in mind that the Buddha is described as physically well endowed and healthy, while the occurrence of the physical attributes themselves are sought in disorders. The concept of the physical marks of a great man, having been formulated in an earlier period, is applied to the image of the Buddha himself.

Keywords: Sanskrit
Buddhism
Advisor: Sandahl, Stella
Coaxial Cable Equalization Techniques at 50-110 Gbps

Next generation communication systems are reaching 110Gbps rates. At these frequencies, the skin effect and dielectric loss of copper cables cause inter-symbol interference (ISI) and frequency dependent loss, severely limiting the channel bandwidth. In this thesis, different methods for alleviating ISI are explored. The design of the critical blocks of an adaptive channel equalizer with up to two times oversampling are presented. The circuits were fabricated in a 0.13μm SiGe BiCMOS technology. The linear, adaptive equalizer operates up to 70Gbps and its measured S-parameters exhibit a single-ended peak gain of 12.2dB at 52GHz, allowing for 31dB of peaking between DC and 52GHz. Equalization is demonstrated experimentally at 59Gbps for a cable loss of 17.9dB. These results make it the fastest receive equalizer published to date. A retiming flip-flop operating between 72 and 118 GHz, the highest reported in silicon, is also designed and characterized, showing less than 500-fs jitter.

Keywords: Equalizer
ICs
SiGe BiCMOS
Retimer
Variable gain amplifier
high-speed ICs
Gbps
jitter
Advisor: Voinigescu, Sorin
Influence of Length of Time to Diagnosis and Treatment on the Survival of Children with Acute Lymphoblastic Leukemia and Hodgkin Disease: A Population-based Study

Introduction: Objectives were to describe time intervals between presentation to a tertiary care center, diagnosis and treatment in pediatric acute lymphoblastic leukemia (ALL) and Hodgkin disease (HD), and measure their impact on overall survival (OS) and event-free survival (EFS). Methods: Children in POGONIS (Pediatric Oncology group of Ontario Networked Information System) with ALL or HD from 1997-2007 were eligible. Time intervals were dichotomized at clinically defined cut-points. OS and EFS were examined with univariate and multivariable Cox proportional hazards (CPH) models. Results: In ALL, in multivariable analysis, those with treatment > 3 days after diagnosis had inferior OS (adjHR=2.49; 95%CI 1.4-4.43;p=0.002), and inferior EFS (adjHR=1.73; 95%CI 1.01-2.96;p=0.047). In HD, in multivariable analysis, those with treatment > 7 days after diagnosis had superior EFS (adjHR=0.37; 95%CI 0.18-0.77;p=0.008). Conclusions: Time to treatment is associated with survival in ALL and HD. Future research will further delineate the relationship between time to treatment and outcome.

Keywords: Pediatrics
Oncology
Advisor: Sung, Lillian
To, Teresa
Perioperative Process Improvement using Discrete Event Simulation

A discrete event simulation was applied to model the perioperative process in the general surgery service at Toronto General Hospital, aiming at reducing the number of surgical cancellations and improving the perioperative process. This model includes emergency case interruptions with two types of emergency cases with different levels of urgency, and takes into account the availability of three types of post-surgical beds: medical surgical intensive care unit, step-down unit and ward beds in decision making level. The effect of three types of scenarios on the number of surgical cancellations was explored: 1) applying effective scheduling rules based on the utilization of post-surgical beds, 2) sequencing the surgical operations based on the length of surgeries and the variance of surgery durations, 3) increasing the number of post-surgical beds.

Keywords: simulation
perioperative process
Advisor: Aleman, Dionne
The Trimentoring Program: A study of a Unique Mentoring Program to Engage Students

This research project explores the Tri-mentoring Program’s impact on enhancing the student experience, specifically for the new emerging population of racialized and first generation undergraduate students in a Canadian urban university. The study examines how the TMP model attempts to address these students’ unique challenges by creating a holistic student experience, that acknowledges and addresses their lived experiences; encourages them to retain their racial/cultural identities (and values) and external community commitments and beliefs; and facilitates them becoming more empowered and engaged on campus. This research also contributes to the production of knowledge in the area of student engagement. This study introduces and validates the voices and lived experiences of racialized students into the literature, which will be valuable in the future development of new models of student engagement where power is shared and indigenous knowledge and epistemologies are valued- leading to a more engaged and successful student experience.

Keywords: post secondary education
Race and first generation students
Advisor: Olson, Paul
The Production of a Potential Feedstock for Biodiesel using Water and Isopropyl Alcohol to Extract Yellow Mustard Oil

The aim of this project was to produce a potential feedstock for biodiesel by developing a process to extract oil from yellow mustard seeds using aqueous and isopropyl alcohol extraction. The aqueous extraction of yellow mustard flour was performed at pH 11 using 4:1 water to flour ratio and constant stirring at room temperature for 30min, with a second washing stage. Oil was separated as oil-in-water emulsion with 37% oil recovery from the flour. The oil in the emulsion was then extracted with isopropyl alcohol. Single and multiple stage extractions were evaluated and the optimal conditions were four-stage extraction at 2:1 IPA:Oil weight ratio, with 96.3% oil recovery from the emulsion. A preliminary evaluation of the final solution of isopropyl alcohol, water and yellow mustard oil concluded that it is indeed a potential feedstock for biodiesel, however it needs to be further processed to meet optimal conditions for transesterification.

Keywords: Biodiesel
Feedstock
Yellow Mustard Oil
Extraction
Isopropyl Alcohol
Water
Emulsion
Advisor: Diosady, Levente L.
Identification of a Carboxysomal γ-Carbonic Anhydrase in the Mesophilic Cyanobacterium Anabaena sp. PCC7120

Analysis of the genome of Anabaena sp. PCC7120 reveals that it lacks the gene, ccaA, which encodes the bonafide carboxysomal, β-class carbonic anhydrase (CA) CcaA. However, the carboxysome enriched fraction of Anabaena PCC7120 exhibits CA activity. Bioinformatic analysis reveals that the N-terminal region of the carboxysome protein CcmM has high sequence and structural similarity to the γ-class CA of Methanosarcina thermophila. Recombinantly expressed CcmM is found to be inactive in in-vitro CA assays. E. coli cell extracts containing an overexpressed form of CcmM comprised of the N-terminal 209 amino acids (CcmM209) are also inactive. However, CcmM209 displays CA activity after incubation with the thiol oxidizing agent diamide or when bound to an affinity matrix. It appears that CcmM is indeed a functional γ-CA which is active under oxidizing condition. It is hypothesized that the C-terminal RbcS like domain in CcmM may regulate activity by allowing CcmM activation only when sequestered within the carboxysome.

Keywords: Cyanobacteria
Carbonic anhydrase
Anabaena PCC7120
CcmM
Carboxysome
Carbon dioxide concentrating mechanism
Advisor: Espie, George
Psychological Debriefing of Workplace Trauma: A Case Study of the Toronto Transit Commission (TTC)

Mental stress resulting from a traumatic event in the workplace has a noteworthy impact on employees. Psychological debriefing is offered to TTC employees as a means of immediate trauma support, however, the usefulness of the intervention is unknown. This thesis explores the debriefing intervention using a mixed methods approach. TTC employees who have experienced a traumatic event were recruited. Post Traumatic Stress Disorder (PTSD) symptom development and time lost from work were compared between debriefed and not debriefed employees. In addition, purposively selected employees were qualitatively interviewed. The quantitative analysis showed no significant differences in PTSD symptomatology or lost time from work between the groups. Despite these results, however, employees who were debriefed had an overall positive perception of the intervention. Further exploration in this area of study would be beneficial to not only the TTC, but to all workplaces at high risk of exposure to traumatic events.

Keywords: psychological
debriefing
workplace
trauma
PTSD
lost time
Advisor: Links, Paul
The Effect of Helicobacter pylori on Innate Immunity

The innate immune system is important in both acute and chronic infection. In this thesis, I investigated the effect of H. pylori infection on 1) DCs, key orchestrators of the immune system, and 2) autophagy, recently identified as an important component of innate immunity. I determined that H. pylori activates the STAT3 pathway in DCs, increasing DC maturation and inducing production of IL-10, IL-12p40 and TNF-α, without IL-12p70. This cytokine profile may favour an immunoregulatory response, promoting persistent H. pylori infection. In addition I determined that H. pylori’s VacA toxin induced autophagy, ROS production and Parkin aggregation which has been implicated in mediating autophagy in response to mitochondrial damage. Thus H. pylori alters these key effectors of innate immunity which may play a role in promoting its chronic infection and disease.

Keywords: H. pylori
Immunity
STAT3
Dendritic Cell
Autophagy
VacA
ROS
Parkin
Advisor: Jones, Nicola L.