VictorJuiz/thesis huggingface dataset:
The Impact of Alternative Oxidase on Nitrogen Stress in Nicotiana tabacum

The alternative oxidase (AOX) is a stress response protein that is thought to safely dissipate excess reductant that accumulates when certain plant species are supplied with low concentrations of nitrate, or high concentrations of ammonium. To investigate whether AOX has an impact on these "nitrogen stress" scenarios wild-type Nicotiana tabacum, in addition to AOX knockdown and overexpression lines, were grown hydroponically in varying concentrations of nitrate or ammonium. Using gas exchange and chlorophyll a fluorescence, in addition to qRT-PCR and western blotting, we demonstrate that AOX was imposing photosystem stoichiometry adjustments in plants grown in low nitrate. All plant lines displayed symptoms of ammonium toxicity when grown in high ammonium; however, AOX expression was significantly positively correlated with photosynthetic capacity in later parts of the day. These results demonstrate that AOX is an important component of the nitrogen stress response in plants and could even be beneficial under extreme nitrogen stress conditions.

Keywords: Abiotic Stress
Alternative Oxidase
Ammonium Toxicity
Nitrogen
Photosynthesis
Respiration
Advisor: Vanlerberghe, Greg C
Investigating the Role of a Natural RecA Mutation on BCG-Russia Vaccine Properties

The Bacille Calmette-GuĂŠrin (BCG) vaccine is the only vaccine for tuberculosis (TB) control. Although effective in preventing disseminated forms of TB in children, its efficacy in preventing pulmonary TB in adults is highly variable. BCG-Russia, one of the most widely used substrains to produce the vaccine, is a natural RecA mutant. Whether the presence of functional RecA affects the virulence and efficacy of BCG-Russia remain unknown. Here I show that a recombinant BCG-Russia expressing functional RecA, rBCG-RecA, is more attenuated than its parental counterpart in SCID mice and this difference is due to slower growth within the animals. I also demonstrate that rBCG-RecA confers equivalent protection against M. tb challenge as the parental strain in guinea pigs with similar bacterial burden in the organs. Taken together, the presence of RecA in BCG-Russia allows for a safer yet equally protective vaccine. This work provides new insight to future TB vaccine design.

Keywords: BCG
BCG-Russia
RecA
Advisor: Liu, Jun
Resistance and Binding Profile of Cabozantinib, a ROS1 Inhibitor and Design of Peptidomimetic Inhibitors of STAT5 Protein

Genes encoding for tyrosine kinases that undergo rearrangement at chromosomal breakpoints have been associated with constitutively activated transcript products. Repressor of silencing 1 (ROS1) tyrosine kinase fusions have been shown to drive cellular proliferation and survival signaling pathways in numerous human cancers. First generation kinase inhibitors of ROS1 suffer from acquired resistance due to a point mutation in the ROS1 kinase domain. This work looks to determine the structural features of cabozantinib, a potent inhibitor of both wildtype and mutant ROS1. Inhibitor binding to the ROS1 kinase domain and specific scaffold contributions with synthesized analogues will be covered. Additionally, a peptidomimetic strategy was employed to design inhibitors of the SH2 domain of the signal transducer and activator of transcription 5 (STAT5) protein, a transcription factor constitutively phosphorylated in hematological malignancies and inflammatory diseases. Native receptor peptide sequences that interact with the STAT5 SH2 domain were used for the initial library.

Advisor: Gunning, Patrick T
Alternate Stable States in Coupled Fishery-aquaculture Systems

Stagnating capture fisheries production has led to rapid aquaculture development due to an increasing shortfall of wild fish in meeting demand. Farmed fish can negatively ecologically affect nearby wild fish and they can interact economically by supplying similar products to the market, but general theory on how these interactions affect fishery-aquaculture population dynamics and system resilience is lacking. I develop simple theoretical models integrating the ecology, economics, and management of capture fisheries and aquaculture and demonstrate that alternate stable states and hysteresis of equilibrium population abundances can exist, indicating decreased system resilience. Abrupt transitions from a capture fishery-dominated state to an aquaculture-dominated state with few or no wild fish can occur that are difficult to reverse. Empirical patterns of salmonid capture fisheries and aquaculture production data are examined considering the developed theory, which may apply to other systems with wild and domesticated species that are coupled ecologically and economically.

Keywords: alternate stable states
aquaculture
coupled human and natural systems
fisheries
salmon
theoretical modeling
Advisor: Krkosek, Martin
Molnar, Peter
Characterizing Genes Associated with Social Interactions in Drosophila melanogaster

Social behaviour is seen among a variety of organisms. Drosophila melanogaster engages in many social behaviours including courtship and mating. The fly has also exhibited the ability to alter the rhythmic timing of its behaviours based on the social composition of the group. The rhythmic timing of behaviours in Drosophila is regulated by the endogenous biological clock. There are many crucial components of the circadian clock, which work together to help regulate behavioural rhythms. Some of these components, such as clock genes, can thereby be used to examine the status of the clock. The aim of this work is to characterize the role that the CG42343 locus plays in directing social interactions. We demonstrate that the CG42343 locus plays a role in regulating social interactions through changes in expression levels of clock genes, and that this phenomenon is likely mediated through chemosensory signalling.

Keywords: Drosophila melanogaster
fruit fly
genetics
microbiology
Advisor: Levine, Joel D
Why do only Some Women Develop Postmenopausal Osteoporosis?

Although all women experience postmenopausal bone loss, only 25-30% will develop postmenopausal osteoporosis, therefore another mechanism must be working with estrogen deficiency to cause this disease. Our proposed mechanism outlines the accumulation of advanced glycation endproducts (AGEs) as the driving force behind bone loss through intracellular signaling after ligation to the receptor for advanced glycation endproducts (RAGE). The study employed a high-fructose diet to initiate production of AGEs and investigated the effects on bone loss and RAGE expression after ovariectomy. This study investigated changes in bone quality and oxidative damage due to diet and surgeries as well as levels of soluble and bone collagen bound AGEs. It also worked to evaluate RAGE expression in serum and osteoclasts. Results show there was no production of AGEs, and bone quality and oxidative damage were affected by ovariectomy only. Soluble RAGE expression was increased due to ovariectomy alone, however cell-bound RAGE was unchanged.

Keywords: advanced glycation endproducts
osteoclasts
oxidative stress
postmenopausal osteoporosis
receptor for advanced glycation endproducts
Advisor: Grynpas, Marc D
Willett, Thomas L
Quantifying Variation in Discrete Force-time Characteristics during the Sprint Start: Considerations for Monitoring Training Adaptations

Biomechanical quantities during the sprint start have been correlated with race time. “Typical” training variation in these quantities must be understood to interpret changes. Purposes were to: (1) describe variation; and (2) compare variation between-session. Using force plate-instrumented starting blocks, foot-block interactive forces were measured from four starts in two training sessions (n=10). Pre-tension (PT), reaction time (RT), block time (BT), rate of force development (RFD), peak force (PF), impulse, time of force application (TFA), time to peak (TTP), peak force offset (PFTO), and force ‘off’ offset (FOTO) were derived trial-by-trial. Variable-specific coefficients of variation (CoVs) were calculated within-session, and compared between-session. PT, BT, RFD and TTP exhibited within-session CoVs ≤ 10%. TTP CoVs were significantly different (p

Keywords: biomechanics
block start
human movement
sprint start
training
variability
Advisor: Beach, Tyson A C
Recolonization Trends of Fish Communities Following the Restoration of a Great Lakes Coastal Wetland

The Great Lakes coastal wetlands are in decline due to various anthropogenic factors including invasive species. An invasion by Phragmites australis in Long Point Crown Marsh, Lake Erie, reduced the amount of open-water habitat for wildlife. Dredging occurred to restore the environment and create more open water. I studied the recolonization trends of fish communities by examining changes in species richness, population density, and community composition, 2012-2014, in four created and two reference ponds. Then, I examined how water chemistry and vegetation influenced the fish communities using variance partitioning and redundancy analysis. Fishes colonized the created ponds immediately after dredging, but ponds showed variation in population density and community composition indicating that created ponds may not be functioning similar to the reference ponds. Water chemistry and vegetation accounted for very little variation in the communities indicating that other factors are influencing the fish communities.

Keywords: Aquatic Ecology
Conservation of Fishes
Wetland Restoration
Advisor: Mandrak, Nicholas E
Reid, Scott M
Prevalence of Heavy Prenatal Alcohol Exposure in Uganda via Analysis of Fatty Acid Ethyl Esters in Meconium

Fetal alcohol spectrum disorder (FASD) manifests as a continuum of permanent birth defects and neurodevelopmental impairments that originate from maternal alcohol use during pregnancy. The number of recognized FASD cases in parts of Sub-Saharan Africa is growing, which is a cause for concern. Prenatal alcohol exposure was examined via regional hospital population-based collection of meconium, and analysis of the fatty acid ethyl esters (FAEEs) contained within. Meconium samples were collected from five hundred ten neonates over a two-month period at Mbarara Regional Referral Hospital. Each meconium sample was accompanied by a maternal questionnaire. The prevalence of prenatal alcohol exposure using the maternal questionnaire was 16.1% (81 of 510). The overall prevalence of prenatal alcohol exposure via FAEE-meconium analysis in this population was 1.6% (8 of 510). This is the first population-based study of an entire local neonatal population examining fetal alcohol exposure via meconium-FAEE analysis conducted in Uganda.

Keywords: fatty acid ethyl esters
fetal alcohol spectrum disorder
meconium
prenatal alcohol exposure
prevalence
Advisor: Ito, Shinya
Early Adoption of Aliskiren in Ontario: Prescribers’ Characteristics and Patients’ Outcomes

Little is known about the patterns of adoption of new antihypertensive drugs. The objectives of this study are: 1) examining trends of aliskiren prescribing in Ontario, 2) determining physicians' characteristics associated with aliskiren prescribing, and 3) comparing morbidity and mortality outcomes, and prescription drug costs, among patients treated by early versus late and non-adopters of aliskiren. We hypothesize that early adopters are largely represent by primary care providers, and patients treated by those physicians will have worse outcomes and higher prescription costs than patients treated by late or non-adopters. We examined a population-based cohort using linked administrative databases. Results showed primary care providers were earlier and heavier prescribers of aliskiren. Patients treated by early adopters incurred higher prescription costs. However, no difference in mortality and morbidity outcomes was observed between patients treated by early vs. late or non-adopters, suggesting that early adopters provided quality of care similar to other physicians.

Keywords: adoption
aliskiren
antihypertensive
early
new
prescribers
Advisor: Lee, Douglas
Three-dimensional High Dynamic Range For Wearable Sousveillance Technologies

This thesis presents high dynamic range (HDR) algorithms, for three camera types, used on wearable sousveillance technologies (wearable technologies where there are cameras observing the world around the user). The camera types, for which the HDR algorithms are presented here, are, colour cameras; structured-light depth sensing cameras (such as Microsoft's Kinect); and time-of-flight depth sensing cameras (such as SoftKinetic's DS325). For colour cameras, CPU and GPGPU accelerated HDR algorithms are presented. The GPGPU algorithms achieved real-time processing speeds. For the structured-light depth sensing cameras, an HDR technique is proposed that helps recover lost depth information in parts of the scene. And for the time-of-flight depth sensing cameras, an HDR algorithm is proposed, which increases the overall depth sensing range and reduces the noise in the measured depth values. For the depth sensing cameras, the application of focus is user input, via hand gestures, for augmented reality glasses.

Keywords: Depth Cameras
HDR
High Dynamic Range
Real-time
Sousveillance
Wearables
Advisor: Mann, Steve
Analysis and Interpretation of In Situ Rock Bolt Pull Tests in Hard Rock Mines

Rock bolts are the principal reinforcement element of many underground support systems. This thesis investigates and characterizes the behaviour and performance of rock bolts as measured by a pull test. A database composed of 985 pull tests from six mines in the Sudbury Basin was assembled. Procedures and apparatuses used to conduct these tests were compared to ASTM's standards and ISRM's suggested methods. The results from the pull tests were used to compare the behaviour of reinforcement elements with theoretical models and to quantify performance metrics and their distributions. The influence of bolt, installation and rock mass parameters on the performance of certain rock bolts was investigated, and distributions of expected behaviour were constructed. These may be used in the design of hard rock underground excavations using methodologies that incorporate both the load capacity and displacement behaviour of rock bolts.

Keywords: Pull test
Rock bolt
Underground reinforcement
Underground support
Advisor: Hadjigeorgiou, John
Policy Analysis and Evaluation of National Clinician-reported Practices for the Diagnosis of Autism Spectrum Disorder

Timely autism spectrum disorder (ASD) diagnosis is critical to access early intervention. The objectives of this thesis were to 1) conduct a systematic review of ASD diagnosis guidance documents; 2) conduct a policy scan of Canadian and UK policies for ASD diagnosis; 3) describe Canadian ASD diagnostic practices through a national survey of paediatricians; and 4) identify determinants of wait times for ASD diagnosis. The systematic review and policy scan showed varying recommendations for ASD diagnosis. The 91 survey respondents described divergent ASD diagnostic assessment practices. Duration of the assessment was a determinant of wait time for the first visit of the assessment and total wait time. The mean adjusted wait time from referral to communication of the diagnosis was 254 days (95% confidence interval 214, 302). ASD diagnostic guidance and practices vary widely. Efficient assessment practices are a key element of reducing wait times and facilitating access to intervention.

Keywords: Autism spectrum disorder
Health service delivery
Policy analysis
Advisor: Ungar, Wendy
Sweet GLUTs: Quantitative Analysis of Glucose Transporter and Fructolytic Enzyme Transcript Densities in Ruby-throated Hummingbirds (Archilochus colubris)

Hummingbirds are able to fuel energetically expensive hovering flight entirely with recently ingested glucose or fructose. In other animals, several steps in the pathway of flux of sugars from the gut to muscle are rate-limiting, such as transport into muscle and subsequent phosphorylation. I examined relative expression of facilitative sugar transporters and enzymes of fructolysis in various ruby-throated hummingbird (Archilochus colubris) tissues via quantitative polymerase chain reaction. I hypothesized that the expression of these proteins would be upregulated in hummingbird flight muscle compared to other vertebrates. I found that hummingbird pectoralis displays the highest expression of certain sugar transporter transcripts among vertebrates. I also demonstrated that relative transcript densities of fructolytic enzymes are minimal in hummingbird muscle, suggesting that fructolysis is not a pathway used to rapidly metabolize fructose in these muscles.

Keywords: fructolysis
glucose transporter
hummingbird
metabolism
Q-PCR
sugar
Advisor: Welch, Kenneth C
The Role of Telomere Maintenance in Adult Mammalian Acute Central Nervous System Injury and Retinal Ganglion Cell Apoptosis

Telomeres are DNA-protein complexes that cap eukaryotic chromosome ends. They have dynamic secondary structures that interact with networks of telomere-associated proteins, protecting genomic integrity and maintaining proliferative success of cells. When telomeres are destabilized, chromosome ends are misrecognized as DNA double-stranded breaks eliciting DNA damage responses that lead to cellular apoptosis. There is sparse evidence that telomere destabilization plays a role in the pathology of central nervous system (CNS) insults. This study examines this possibility during the acute injury-induced degeneration and apoptosis of retinal ganglion cells (RGCs). By administering or knocking-down key telomere-associated proteins, this work demonstrates that TERT expression promotes RGC survival while Telomerase activity has no role, that TCAB1, TRF1, Ku70, and EST1A play important roles in RGC survival while TRF2 and DNA PKcs do not, and that, overall, telomere maintenance cannot be eliminated as a contributing factor in RGC degeneration and apoptosis within the acutely injured CNS.

Keywords: Apoptosis
Central Nervous System
Neuron
Retinal Ganglion Cell
Telomere
Telomere-Associated Protein
Advisor: Koeberle, Paulo
Agur, Anne
Structural and Biochemical Characterization of UDP-glucose: Glycoprotein Glucosyltransferase

Endoplasmic reticulum quality control is a crucial process in eukaryotic cells to ensure glycoprotein folding. It utilizes N-glycan modification as an indicator of glycoprotein folding status. Monoglucosylated glycoproteins are recognized by calnexin and calreticulin that recruit ERp57 to assist folding. The glycoproteins are released from calnexin and calreticulin upon removal of the glucose residue by glucosidase II. UDP-glucose: glycoprotein glucosyltransferase (UGGT) recognizes incompletely folded glycoprotein and adds a glucose residue to the glycoprotein. Addition of the glucose residue leads to re-association of the glycoprotein with calnexin and calreticulin for further folding. In this study, we focus on characterizing UGGT and its substrate interaction. We expressed Fabs against UGGT as a tool for crystallization. The binding of Fabs to UGGT was assayed by the surface plasmon resonance technique. We also assayed UGGT activity using a radioactive UDP-Glc-based assay. The results provided a basis for understanding UGGT and its substrate interaction.

Keywords: endoplasmic reticulum quality control
mammalian expression
phage display Fabs
radioactive assay
surface plasmon resonance
UDP-glucose: glycoprotein glucosyltransferase
Advisor: Rini, James M
Cost-utility Analysis of Oral Antiseptic Chlorhexidine in decreasing Ventilator-associated Pneumonia in Intensive Care Units

Purpose: To evaluate the cost-utility of chlorhexidine (CHX) mouthrinse (0.12-2%) as compared to placebo/usual care in preventing ventilator-associated pneumonia (VAP), among ventilated intensive care unit (ICU) patients. Methods: A cost-utility (and its sensitivity) analyses were performed using a state transition model. We assumed a daily cycle, lifetime horizon, third party payer perspective, 2015 Canadian Dollars adjusted costs, and a 5% discounted benefits. We performed a meta-analysis to obtain CHX effectiveness in preventing VAP and associated survival. Results: Use of CHX was associated with 0.008 life-years, 0.005 Quality-adjusted life-years (QALYs) lived, and a cost savings of $804.53/patient. Sensitivity analyses showed that an increased mortality risk or reduced effectiveness associated with CHX, or reduced number of prolonged ICU days results in reduced life-years lived and QALYs. Conclusions: CHX oral antiseptic in ICU for preventing VAP as compared to the care without CHX resulted in comparable health outcome, yet it was cost saving.

Keywords: Chlorhexidine
Cost-utility
Intensive care unit
Oral antiseptic
Ventilated associated pneumonia
Advisor: Azarpazhooh, Amir
A Framework for FPGA-based Acceleration of Neural Network Inference with Limited Numerical Precision via High-level Synthesis with Streaming Functionality

Deep neural networks (DNN) are achieving state-of-the-art performance in many artificial intelligence tasks, such as computer vision and speech recognition. Due to the high computational requirements of DNN, there is an increasing need to design custom hardware for accelerating the DNN computation with a low power budget. This thesis proposes an FPGA-based acceleration solution for DNN inference, realized on a SoC device where software controls the execution and off-loads compute-intensive operations to the hardware accelerator. To minimize the hardware cost, limited precision data representations are investigated for DNN computations, and incorporated in the accelerator design. Streaming functionality is added to the LegUp high-level synthesis tool, allowing the hardware accelerator to be designed entirely in C-language and synthesized to pipelined hardware. The accelerator solution is not tied to a particular DNN architecture; rather, it is configurable in software, permitting the acceleration for a range of DNN architectures proposed in recent literatures.

Keywords: Embedded System
FPGA
High-level synthesis
LegUp
Neural Networks
Streaming Hardware
Advisor: Anderson, Jason H
Information Theoretic Privacy in Smart Metering Systems Using Rechargeable Batteries

In modern electricity grids, smart meters are deployed in households to communicate fine-grained timeseries power usage data from a user's household to the utility provider. The correlation of the power usage with a user's private activities leaves open the possibility of inference attacks. One possible solution to this privacy problem is to partially obscure the load profile by using a rechargeable battery. The charging and discharging of the battery has the effect of distorting the household's load profile. This thesis studies the optimal privacy preserving charging policies under a mutual information privacy metric. We provide some methods to compute the private information leakage rate and a Markov Decision Process reformulation of the problem. For the case of i.i.d. power demand statistics, we provide an explicit characterization of the optimal information leakage rate and charging policy.

Advisor: Khisti, Ashish