VictorJuiz/thesis huggingface dataset:
Risk Factors for High-risk, Oncogenic Human Papillomavirus (HPV) anal Infection in HIV-positive and HIV-negative Men who have Sex with Men (MSM)

Background: Most anal cancers are caused by high-risk (HR)-HPV, occurring at much higher rates in MSM. There is little evidence on specific risk factors for HR-HPV in this population. Objective: To determine sexual and behavioural risk factors for HR-HPV anal canal infection. Methods: Cross-sectional study recruiting a clinic-based MSM sample. Participants completed a questionnaire, and had HPV/STI testing. Multivariable logistic regression was performed to assess HR-HPV risk factors. Results: 442 MSM were recruited: 267 HR-HPV-positive, 162 HR-HPV-negative. Multivariable analyses revealed risk factors associated with HR-HPV infection: HIV status (OR: 1.86, 95% CI 1.20-2.89); current smoking status (OR: 2.24, 95% CI 1.33-3.79); and >50 lifetime sexual partners (OR: 2.37, 95% CI 1.05-5.35). Conclusions: This study highlights important risk factors for HR-HPV anal infection. On a background of limited evidence for HPV screening modalities, this information may shed light on novel ways to risk stratify MSM to further anal cancer screening interventions.

Keywords: Anal cancer screening
Human immunodeficiency virus
Human papillomavirus
Men who have sex with men
Sexually transmitted infections
Advisor: Loutfy, Mona R
Tropospheric Ozone Variations over North America

The spatial and temporal variations in tropospheric ozone over North America from the 1970s to 2000s are studied using the newly developed Trajectory-mapped Ozonesonde dataset for the Stratosphere and Troposphere (TOST) and the ozonesonde data. The variations in the lower, middle, and upper troposphere are examined in long-term, by decade and season. Throughout the decades, the highest ozone concentrations generally appeared over central mid-latitudes of North America in the lower and middle troposphere, while in the upper troposphere, high concentrations appeared over the Arctic. The overall ozone trends in the four decades averaged over the North America are positive, increasing with altitude. TOST is compared with the ozonesonde data at selected stations and both datasets correlate closely, stronger in high latitudes. TOST is resolved in latitude, longitude, and altitude so new insights gained from this study on the variations of tropopsheric ozone in these dimensions are particularly valuable.

Keywords: Ozone
Ozonesonde
TOST
Trends
Troposphere
Variations
Advisor: Liu, Jane J
The Privacy/Security Tradeoff for Multiple Secure Sketch Biometric Authentication Systems

When designing multiple biometric authentication systems, there is tension between minimizing privacy leakage and maximizing security. This work studies the tradeoff between the two measures for jointly designed "secure sketch" systems. Secure sketch is a biometric system architecture where, as with error-correcting codes, a system is characterized by a parity-check matrix over a finite field. Single systems have been widely researched, but little is known about the privacy and security of joint designs, when leakage of one system can compromise the security of the others. This work introduces worst-case measures of privacy leakage and security for sets of systems and studies the tradeoff between them: First by studying the algebraic structure of the problem, then through a continuous relaxation of the problem (in a restricted case) and performing optimizations. An analytic expression for the tradeoff in that restricted case is proposed which aligns with simulation results.

Keywords: Biometrics
Coding Theory
Information Theory
Optimization
Privacy
Security
Advisor: Draper, Stark C
Measuring Changes in Membrane Structure and Rhodopsin levels in Drosophila Melanogaster Retinas using THG Microscopy

Third harmonic generation (THG) microscopy is a valuable imaging modality that can be used to reveal structural information in a biological system without staining. THG signal is observed at an interface between refractive indices and is augmented in the presence of conjugated carbon chains. I sought to determine whether THG microscopy could serve as a platform for developmental studies. I used the eye of Drosophila melanogaster as a model for its well-known anatomy and availability of genetic tools. In the first series of observations THG microscopy was shown to be an effective tool for monitoring photoreceptor development. In the second series of experiments, using dietary restrictions or genetic alleles, THG microscopy detected rhabdomere degeneration and reduced rhodopsin expression earlier than fluorescence microscopy. In conclusion, THG microscopy presents itself as a new technique to detect retinal degeneration. Further development of this technology could aid in early detection of human retinal degeneration.

Keywords: Drosophila
Pupal Development
Retina
Rhodopsin
THG microscopy
Advisor: Stewart, Bryan
Barzda, Virginijus
Open for Reporting: An Exploration of Open Data and Journalism in Canada

This thesis describes how open data and journalism have intersected within the Canadian context in a push for openness and transparency in government collected and produced data. Through a series of semi-structured interviews with Toronto-based data journalists, this thesis investigates how journalists use open data within the news production process, view themselves as open data advocates within the larger open data movement, and use data-driven journalism in an attempt to increase digital literacy and civic engagement within local communities. It will evaluate the challenges that journalists face in gathering government data through open data programs, and highlight the potential social and political pitfalls for the open data movement within Canada. The thesis concludes with policy recommendations to increase access to government held information and to promote the role of data journalism in a civic building capacity.

Keywords: data journalism
data literacy
journalism
open data
open data movement
Open government
Advisor: Shade, Leslie R
Automated Serial Sampling in Hummingbirds Obviates Laborious Ecological Studies of Behaviourally Induced Rises in Departure Stores

I examined the feasibility of automating the collection of free-ranging hummingbird mass data facilitated by low-cost, low-power radio frequency identification (RFID) technology. Wild hummingbirds were captured, subcutaneously implanted with passive integrated transponder (PIT) tags, and released. Detection of tagged hummingbirds perched on balances at feeder stations outfitted with RFID readers initiated the recording of masses at regular intervals, continuing for as long as the birds remained. Mass data showed consistent trends at multiple temporal scales: the individual feeder visit, single days, and whole seasons. Using these data, I modelled changes in foraging behaviour during the morning, mid-day and evening, and examined rates of overnight mass change to determine how wild hummingbirds achieve premigratory fattening. Premigratory hummingbirds increased the duration of visits and thus total time spent at the feeders during the mid-day only and exhibited greater use of overnight torpor, as evidenced by a reduced rate of overnight mass loss.

Keywords: Energetics
Foraging behaviour
Hummingbirds
Radio Frequency Identification (RFID)
Seasonal migration
Torpor
Advisor: Welch, Kenneth C.
Characterizing the Expression and Localization of Drug Transporters and Metabolic Enzymes in the testes of Uninfected and HIV-1 Infected, Treated Subjects – Potential Contribution to an HIV-1 Sanctuary

Previous studies have reported that HIV-1 is capable of both acute and persistent infection in the testes. The naturally restrictive environment in the testes, due in part to the expression of drug transporters at the blood-testes-barrier (BTB), could limit antiretroviral (ARV) penetration into this tissue and contribute to the formation of a viral sanctuary. Therefore, we conducted a comprehensive characterization of gene and protein expression and localization of major drug transporters and metabolic enzymes relevant to ARV therapy in testicular tissue isolated from both uninfected and HIV-1 infected, treated individuals. We also quantified drug concentration levels in testicular tissue versus plasma to gain additional insight on ARV drug penetration into the testes. Overall, our findings indicate that the testes express many key drug transporters and metabolic enzymes relevant to ARV therapy, which could limit the penetration of certain ARV compounds, and contribute to persistent HIV-1 infection and formation of a viral sanctuary site.

Keywords: Drug Metabolism
Drug Transporters
HIV
Sanctuary Site
Testes
Advisor: Bendayan, Reina
Role of the Human Globus Pallidus in Tremorgenesis

The GPi is a nucleus that serves as an output of the basal ganglia; a collection of nuclei which function in selecting movements to be executed. Tremor is defined as an unintentional, rhythmic, sinusoidal contraction of body parts. Currently, no scientific consensus has been reached as to where in the brain tremor arises. Using microelectrode recordings in human patients with and without tremor, we discovered a sub-population of cells that are capable of being induced into a brief theta oscillation following microstimulation. However, we found that theta burst stimulation was incapable of inducing visible tremor when microstimulating in the GPi, Vim, or STN. We also found preliminary evidence that this theta oscillation is capable of producing an LTP-like response within the GPi. We believe that this work adds strength to the “pallidocentric” view of tremor initiation which holds that the GPi is responsible for the onset of tremor.

Keywords: Globus Pallidus Internus
Microelectrode Recordings
Movement Disorders
Parkinson's Disease
Theta Oscillations
Tremor
Advisor: Hutchison, William D
A Scalable Heterogeneous Dataflow Architecture For Big Data Analytics Using FPGAs

Due to rapidly expanding data size, there is increasing need for scalable, high-performance, and low-energy frameworks for large-scale data computation. In this thesis, we build a dataflow architecture that harnesses FPGA resources within a distributed analytics platform creating a heterogeneous data analytics framework. This approach leverages the scalability of existing distributed processing environments and provides easy access to custom hardware accelerators for large-scale data analysis. We prototype our framework within the Apache Spark analytics tool running on a CPU-FPGA heterogeneous cluster. As a specific application case study, we have chosen the MapReduce paradigm to implement a multi-purpose, scalable, and customizable RTL accelerator inside the FPGA, capable of incorporating custom High-Level Synthesis (HLS) MapReduce kernels. We demonstrate how a typical MapReduce application can be simply adapted to our distributed framework while retaining the scalability of the Spark platform.

Keywords: Apache Spark
Big Data
Distributed Architecture
FPGA
MapReduce
Advisor: Chow, Paul
Functional Characterization of the HopF Family of Type III Effectors in Arabidopsis thaliana

Pseudomonas syringae is a Gram-negative bacterial phytopathogen that causes disease in economically important crops. An essential virulence strategy of P. syringae involves injecting type III secretion effectors (T3SEs) into host cells to inhibit immune signaling. Advances in genomic sequencing have lead to an increase in the available number of sequences of plant bacterial pathogens, which has lead to identification of divergent homologs of known T3SEs. The HopF family of T3SE contains over 40 diverse family members. In order to explore the functional diversification of HopF family, this thesis undertakes the functional characterization of HopF T3SE in Arabidopsis thaliana. Functional analysis revealed multiple members with novel immune responses in Arabidopsis. A reverse genetics approach was used to identify the mechanism underlying the novel immune responses triggered by HopF family of T3SE. The Arabidopsis R protein X was required for recognition of a novel member of the HopF family.

Keywords: Arabidopsis thaliana
Effector triggered immunity
HopF
Plant Immunity
P. syringae
Advisor: Desveaux, Darrell
Videoconference-delivered Physical Activity Peer Support Programs for Adults with Spinal Cord Injury: A Receptivity Survey and Pilot-test

Videoconference-based physical activity support (VPAS) is a novel method for overcoming time and space barriers to receiving peer support among persons with spinal cord injury (SCI). This thesis examines the receptivity towards VPAS (Study 1) and the feasibility, acceptability and usefulness of a VPAS pilot program (Study 2) in a sample of adults with SCI. An online questionnaire assessing needs, preferences and barriers towards VPAS was administered to 30 LTPA intenders and actors with SCI (Study 1). Nine of the survey respondents took part in the VPAS program; consisting of four, weekly 60-minute group Skype® sessions (Study 2). The majority of survey respondents (60%) expressed interest in the four-week VPAS program. PA level and age characterized videoconference participation and family and work commitment barriers, respectively. Overall, the pilot program demonstrated a modest level of feasibility; and high acceptability and usefulness. Taken together, group-based videoconferencing holds promise for delivering PA-enhancing interventions.

Keywords: group-mediated cognitive–behavioural training
physical activity interventions
pilot-testing
receptivity
spinal cord injury
videoconference
Advisor: Arbour-Nicitopoulos, Kelly P
Isolation and Characterization of the Corazonin Receptor and Possible Physiological Roles of Corazonin in the Kissing Bug, Rhodnius prolixus

Neuropeptides control many physiological and endocrinological processes in animals, acting as neuroactive chemicals within the central and peripheral nervous systems. Corazonin (CRZ) is one such neuropeptide that has a variety of physiological roles associated with control of heartbeat, ecdysis behaviour initiation, and cuticle colouration. These physiological effects are mediated by the CRZ receptor (CRZR) which is a G protein-coupled receptor. In order to understand the role of the CRZ-signalling pathway in Rhodnius prolixus, the cDNA sequence encoding the Rhopr-CRZR has been isolated and cloned. The specificity of the Rhopr-CRZR was examined using CHOK1-aeq cells. Spatial expression pattern using quantitative PCR revealed receptor expression in the central nervous system, dorsal vessel, abdominal dorsal epidermis, and prothoracic glands. Receptor knockdown using dsRNA showed that CRZ maintains a higher heartbeat frequency in intact insects. Preliminary results using the knockdown have yet to show any effect on ecdysis or cuticle colouration.

Keywords: G protein-coupled receptor
Insect
Neuropeptide
Advisor: Orchard, Ian
Lange, Angela
Cost-effectiveness Analysis of Hepatocellular Carcinoma Surveillance in Patients with Hepatitis C Related Cirrhosis after Sustained Virological Response

Hepatitis-C virus related cirrhosis is associated with hepatocellular carcinoma (HCC). Antiviral therapy resulting in a sustained virological response (SVR) substantially decreases the risk for HCC. Surveillance for HCC in cirrhosis patients has been shown to be cost-effective; whether it remains so post-SVR is unknown. A Markov model was developed to evaluate the cost-effectiveness of biannual ultrasound surveillance versus no surveillance for HCC in post-SVR patients from the healthcare-payer perspective. Parameter values were obtained from the literature and expert opinion. Primary outcomes were quality-adjusted life-years (QALYs) and costs, both discounted at 5%, and the incremental cost-effectiveness ratio (ICER). Surveillance, with 0.5% annual HCC incidence, provided an additional 0.0705 QALYs leading to an ICER of $204,301/QALY. Sensitivity analyses identified HCC incidence and transition to symptomatic disease in the unscreened population as the main drivers of the analysis. With current estimates of HCC incidence post-SVR, ultrasound surveillance is unlikely to be cost-effective.

Keywords: Cirrhosis
Cos-effectiveness
Hepatitis C
Hepatocellular Carcinoma
Surveillance
Sustained Virological Response
Advisor: Feld, Jordan J
Assessment of Postural Deviations Associated Errors in the Analysis of Kinematics Using Inertial and Magnetic Sensors and a Correction Technique Proposal

The MVN BIOMECH Awinda system has been used to analyze motion kinematics beyond laboratory conditions. However, it has a limitation in the rehabilitation field since it relies on a predefined posture to calibrate the sensors: the “N-Pose”, which is impossible to attain for some patient populations. The aims of this thesis are to assess the postural deviation error in gait kinematics measured with this system as well as two proposed correction approaches: the orientation correction (OC) and planar angle correction (PAC). After analyzing the crouch gait of four able-bodied participants it was found that the postural deviation error can be considered as a constant shift in kinematic values and that it can be corrected with both approaches. Digital images are explored as a means to capture the true body posture attained during the calibration.

Keywords: Assessment
Error
Gait
IMMU
Kinematics
Postural deviation
Advisor: Andrysek, Jan
The Effect of Oat and Barley β-glucan on LDL-C and Emerging Clinical Lipid Targets for Cardiovascular Disease

Background: β-glucan is a viscous soluble fibre recognized for its cholesterol lowering benefits. Objective: To synthesize available data on the effects of β-glucan from oats and barley on LDL-C and emerging clinical lipid targets, non-HDL-C and apoB. Methods: A systematic review and meta-analysis was conducted of randomized controlled trials investigating the intake of all doses of oat or barley β-glucan on LDL-C, non-HDL-C or apoB. Data were pooled using the generic inverse variance method with random effects model and expressed as mean differences with 95% confidence intervals. Results: Pooled analyses demonstrated a significant reduction of LDL-C and non-HDL-C when 3.8 or 7.0 g/day of β-glucan from oats or barley was consumed for 4 or 7 weeks, respectively. ApoB was reduced when 3.6 g/day of oat β-glucan was consumed for 6 weeks. Conclusion: Inclusion of oats or barley may improve blood cholesterol and apolipoprotein levels for the risk reduction of CVD.

Keywords: Barley
Beta-Glucan
Blood Cholesterol
Cardiovascular Disease
Oats
Soluble FIbres
Advisor: Ho, Hoang VT
Modeling the Effect of Repeated Sub-concussive Impacts in Soccer Players Using The Virtual Brain

Repeated sub-concussive impacts (blows transmitting force to head, but not causing overt concussion symptoms) have been linked to negative outcomes later in life, such as chronic traumatic encephalopathy. However, the effects of sub-concussive impacts in the short-term are only beginning to be explored. The present study analyzed post-season structural (T1, DTI), and functional (fMRI) data collected from a group of university-aged soccer players and non-collision sport controls. Whole-brain functional connectivity was higher in soccer players relative to controls, while structural connectivity did not differ between groups. Additionally, The Virtual Brain (TVB), a whole-brain simulator of functional brain dynamics, was validated in this population by producing functional connectivity matrices that correlated with empirical data. Together, results indicated that repeated sub-concussive impacts may affect functional connectivity in the short-term, and that TVB could be a valuable tool in future studies of this population.

Keywords: brain connectivity
brain networks
computational modeling
Repetitive sub-concussive impacts
The Virtual Brain
whole-brain model
Advisor: McIntosh, Anthony R
Redesigning an Outpatient Pharmacy Workflow Using Generic Simulation Modelling to Maximize a Renovation Opportunity

The renovation plans of the outpatient pharmacy at Princess Margaret Cancer Centre presented an opportunity to apply discrete event simulation (DES) to help decision makers estimate the resource and space required for the pharmacy to support prescription volume growth over a ten-year horizon. There is an extensive literature on renovating existing pharmacy workspaces, but research on future capacity planning of pharmacy workspaces is sparse. The trend of increasing spending on prescription drugs underscores the importance of researching capacity planning of outpatient pharmacies. The goal of this study was to develop a generic simulation model that could be reused to plan the future capacity of any outpatient pharmacy. The generic DES was applied to two different pharmacies to explore different workflow configurations and assess the impact of introducing automation. Recommendations were provided to each pharmacy management team on the number of workstations and space required to achieve the target patient wait time.

Keywords: Generic simulation
Health care
Pharmacy redesign
Advisor: Carter, Michael W
Role of Urban Transportation Through the Lens of Homeless Individuals: A Case Study of the City of Toronto

Mobility has the potential to improve the quality of life for vulnerable population segments, including provision of opportunities for homeless individuals to break free from the cycle of poverty. Our research seeks to focus analysis on the travel behaviour of homeless individuals in the City of Toronto. The research relies on a specially designed interview instrument, which embodies both revealed preference and stated adaptation questions. The results of 159 face-to-face interviews with homeless individuals in Toronto identify the intricacies of homeless individuals’ travel decisions. We find that both travel time and cost influence street people’s mobility, and their potential to engage in employment and social activities. We find that subsidies can improve homeless individuals’ transport-related social exclusion and freedom of choice in their mode selection. Consequently, the relationship between transport-related social exclusion and homelessness is complex as the role of transportation heavily depends on one’s personal experiences.

Keywords: homelessness
public transit
social exclusion
transport policy
Advisor: Nurul Habib, Khandker
Emissions and Properties of Bio-oil and Natural Gas Co-combustion in a Pilot Stabilised Swirl Burner

Fast pyrolysis oil, or bio-oil, has been investigated to replace traditional fossil fuels in industrial burners. However, flame stability is a challenge due to its high water content. In order to address its instability, bio-oil was co-fired with natural gas in a lab scale 10kW swirl burner at energy ratios from 0% bio-oil to 80% bio-oil. To evaluate the combustion, flame shape, exhaust and particulate emissions, temperatures, as well as infrared emission were monitored. As the bio-oil energy fraction increased, NO emissions increased due to the nitrogen content of bio-oil. CO and particulate emissions increased likely due to carbonaceous residue exiting the combustion zone. Unburnt Hydrocarbon (UHC) emissions increased rapidly as combustion became poor at 60-80% bio-oil energy. The temperature and infrared output decreased with more bio-oil energy. The natural gas proved to be effective at anchoring the bio-oil flame to the nozzle, decreasing instances of extinction or blowout.

Keywords: biofuel
biomass
bio-oil
combustion
lime kiln
natural gas
Advisor: Thomson, Murray J
Tran, Honghi N