VictorJuiz/thesis huggingface dataset:
Investigating the Role of LRR-VIII-2 Receptor-like Kinase genes in Intra- and Inter-species Pollinations in Arabidopsis thaliana.

Successful fertilization in flowering plants requires tightly controlled pollen-pistil interactions to promote compatible pollen and prevent interspecies hybridizations. In Arabidopsis, previous research has mainly focused on the later stages of compatible pollen tube growth and ovular reception in the pistil and the pre-zygotic interspecies barriers acting at this stage. Previously, we identified a group of Leucine-Rich Repeat (LRR) VIII-2 Receptor-Like Kinase (RLK) genes that function in the female reproductive tract to support compatible pollen. Here, I have shown that wildtype compatible pollen tubes deposit smaller callose plugs when growing through LRR-VIII-2 RLK mutant pistils from two different higher-order mutants. LRR-VIII-2 RLK mutants were also impaired in establishing an interspecies barrier against Capsella rubella pollen tubes. The stigma-specific expression of one member, RKF1, in the LRR-VIII-2 RLK septuple mutant was sufficient to rescue these mutant phenotypes. Thus, my research further defined the functions of these LRR-VIII-2 RLKs in supporting the earlier stages of compatible pollen-pistil interactions and blocking interspecies pollen.

Keywords: Arabidopsis thaliana
Compatible Pollination
Interspecies Pollination
Malectin
Pollination
Receptor-Like Kinases
Advisor: Goring, Daphne R
Short-term Effects of Elevated Levels of Glucocorticoids on Lipolysis in Differentiated Murine White Adipocytes

Adipose tissue (AT) is a dynamic organ that can change its morphology in response to environmental cues. Expansion or compression in the size of AT depends on the balance between lipogenesis (biosynthesis and storage of triglycerides) and lipolysis (hydrolysis of triglycerides) which can be affected by steroid hormones such as glucocorticoids (GCs). GCs can work through binding to the glucocorticoid receptor (GR-mediated effects) or exert non-GR mediated effects, which are currently understudied in AT. The purpose of this thesis was to expand the knowledge about GR and non-GR mediated effects of GCs on lipolysis in AT, with a primary focus on elucidating the mechanism behind the non-GR mediated effects of GCs on white adipose tissue (WAT) lipolysis. In this study, 3T3-L1 cells were used as a model of WAT and it was evident that elevated GC levels could decrease lipolysis in short durations, through effects that were independent of GR and gene transcription.

Advisor: Beaudry, Jacqueline
Distinguishing between Adsorption and Biodegradation of MIB and Geosmin in Operational Granular Activated Carbon (GAC) Filters

Water treatment facilities commonly use granular activated carbon (GAC) filters to remove taste and odour (T&O) compounds, such as geosmin and 2-methylisoborneol (MIB). However, filter exhaustion is challenging to predict due to the seasonal nature of T&O events. Thus, a tool is needed to qualify performance. Therefore, the φ parameter of the pore surface diffusion model (PSDM) was calculated from parallel minicolumn data to determine filter performance. Here, the biodegradative and adsorptive φ were measured using parallel biologically active and suppressed minicolumns, thus, distinguishing their relative contribution to the removal rate. When evaluated near GAC full-scale empty bed contact times, the average removal efficiency of MIB and geosmin were 53 ± 30% and 80 ± 14%, respectively. Additionally, based on principal component analysis, the full-scale conditions at the time of GAC collection significantly impact φ.

Keywords: Adsorption
Biodegradation
Drinking water treatment
Granular activated carbon
Advisor: Hofmann, Ronald
Ascending Aortic Geometry and its Association with Type A Aortic Dissection and Biomechanical Properties of Aortic Tissue

Current diameter-based guidelines are ineffective in identifying aortic aneurysms at risk to dissect. Aortic length has recently been proposed to better predict risk of dissection; however, the data evaluating length as a metric to predict dissection is limited and how it adds to long-standing diameter thresholds is unclear. In this thesis, ascending aortic geometry (i.e., diameter and length) and its association with normal, aneurysmal, and dissected aortic states were examined. Furthermore, mechanical properties of aortic tissue (i.e., energy loss, modulus of elasticity, and delamination strength) were also examined to determine the association between aortic geometry and mechanical risk of aortic failure. After adjusting for covariates associated with aortic length, patients who had dissection exhibited disproportionately longer aortas than normal or aneurysmal states. However, aortic length did not correlate with mechanical properties of aortic tissue associated with mechanical failure. Additional research is needed before length-based thresholds can be considered.

Advisor: Simmons, Craig
Chung, Jennifer
Limiting S-Palmitoylation of Pro-Inflammatory Signals by Inhibiting Fatty Acid Synthase

S-palmitoylation is the addition of an acyl-CoA to a cysteine residue of a protein via a thioester bond. The attachment of this hydrophobic moiety can impact the protein targeting, trafficking and protein function, and is often observed in the immune-regulatory system, including being required for NOD1/2 signal transduction and the MyD88-dependent TLR4 pathway. Dampening of S-palmitoylation in the immune system via inhibition of FASN-mediated de novo lipogenesis has been shown in vitro, however holds little translational use due to dangerous toxicity of these inhibitors. Here, I investigate the potential of new FASN-inhibiting TVB compounds to decrease inflammatory signalling. TVB-3166 decreased intracellular palmitoyl-CoA and reduced translocation of NOD1/2 to the PM in epithelial cells and was able to reduce NF-kB transcriptional activity and IL-1β and IL-6 secretion from macrophages. Thus, we believe TVB compounds, upon further investigation, could provide a therapeutically viable approach to modulating severe inflammation as seen in sepsis.

Keywords: Fatty Acid Synthesis
IBD
Inflammation
Palmitoylation
Palmitoyltransferase
TVB
Advisor: Fairn, Greg D
Lee, Warren
Experimental Study of Laterally Offset RHS X-Connections in Branch Axial Tension

In all predominant design guides for truss-type welded Rectangular Hollow Section (RHS) connections, the branch and chord member axes are assumed to lie in the same plane. To investigate the effect of laterally offset branch members on the strength and behaviour of welded RHS connections, 14 full-scale experiments (five full-width matched, four stepped, and five laterally offset) have been performed on cold-formed RHSto-RHS X-connections with quasi-static branch axial tension loading. A recent recommendation made for extending the validity range of full-width connection failure models to high-strength steel is re-evaluated, and resistance factors are proposed for design. Recommendations for the design of laterally offset connections subject to branch axial tension are also evaluated and resistance factors are proposed for design.

Keywords: Hollow structural sections
Laterally Offset RHS X-Connections
Rectangular hollow sections
Steel structures
Truss connections
Welded joints
Advisor: Packer, Jeffrey A
Black Speculative Fiction as a Pathway to Collective Responsibility

Introduced by critical race scholar, Kimberlé Crenshaw in 1991, “intersectionality” has become a term used to untangle multiple identities such as race, ability, and gender to better understand “how systems of power work within and beyond identity claims alone" (Schalk, 2018, p. 8). This thesis investigates the social expectations that fall in an unbalanced way onto Black communities to be overly responsible for service, especially related to the pursuit of justice and liberation. Informed by a Black feminist disability framework (Bailey & Mobley, 2019), I explore how speculative fiction can disrupt these expectations. I turn to Rivers Solomon’s (2019) novella, The Deep, to gain insight on similar, but fictionalized accounts of the underseen impacts that effect the body and the mind. I further inquire what it might mean to introspect through sense, memory and feeling as a method to redistribute the responsibility to be of service as a collective responsibility.

Keywords: Black Feminism
Disability Studies
Identity
Indigenous Feminism
Social Justice
Specualtive Fiction
Advisor: Titchkosky, Tanya TT
Experimental Warming of Flower Temperatures and Influence on Pollinator Visitation

Climate change and the urban heat island effect are warming temperatures in cities, putting pollinators at risk as they increasingly experience temperatures close to or above their thermal tolerance range. I evaluated patterns in flower visitation in relation to temperature and hypothesized that an increase in floral temperature will result in decreased visitation. Using an in-situ temperature manipulation experiment, I experimentally heated flowers of three pollinator-dependent plant species in spring, summer, and late summer. Between paired plots of heated and control (i.e., unheated) plants, I recorded 617 plant visitations and painted 96 bees for a mark-recapture experiment. Pollinator visitation declined on heated flowers during the peak of summer when the temperature is hottest. Additionally, the number of blooms per plot increased pollinator visitation in all seasons. Knowledge gaps in our understanding of influences on microclimatic temperature and how this applies to quantifying temperature in field experiments are discussed.

Keywords: Bogert Effect
Climate Change
Plant-pollinator interaction
Urban Heat Island Effect
Wild Bees
Advisor: MacIvor, Scott
Quantifying Lower Limb Sagittal Plane Alignment Based on 3D Scans: Method Validation and Implementation to Compare Conventional and Digital AFO Shape Capture Processes

Lower limb alignment is a key aspect of ankle foot orthosis design which needs to be addressed in the development of digital technology workflows. The goal of this work was to develop a practical and accurate method to measure the sagittal plane ankle angle from 3D scans and investigate alignment differences achieved in conventional and digital shape capture processes. The sagittal plane ankle angle was measured by three orthotists using a digital goniometry tool and through an alignment algorithm. The digital goniometry tool was found to be a reliable method for measuring the sagittal plane ankle angle, and the algorithm produced measurements equivalent to the orthotists’ measures. Alignment differences were found between the digital and conventional shape capture processes ranging from 8° of dorsiflexion to 11° of plantarflexion. This work has highlighted the need for further investigation into a digital design process to enable the correction of the lower limb alignment.

Advisor: Andrysek, Jan
Targeting the TIGIT/CD226/CD96 Signaling Axis using the IgV Domain of PVR

PVR (poliovirus receptor) functions as a ligand that signals through TIGIT and CD96 to induce suppression of T-cell and NK-cell responses and binds to CD226, resulting in a co-stimulatory signal. PVR and its immune-cell receptors have been implicated in several diseases including cancer and autoimmune disorders. Therefore, my thesis focused on engineering a soluble version of the PVR extracellular domain that could serve to modulate immune responses responsible for such diseases. We developed vdPVR-Fc by fusing the murine IgV binding region of PVR to the Fc-domain of human IgG1. vdPVR-Fc bound to recombinant forms of its receptors TIGIT, CD96 and CD226 with similar low nanomolar affinities. Additionally, vdPVR-Fc could suppress murine T-cell activity ex-vivo. Importantly, vdPVR-Fc suppressed inflammatory responses in-vivo by reducing disease severity in murine models of psoriasis and colitis. Collectively, these results demonstrate that the minimal IgV domain of PVR is sufficient to dampen T-cell mediated immune responses.

Keywords: Cancer
Immunotherapy
Inflammation
Advisor: Gariepy, Jean
Pooling Donations in Human Milk Banks using Machine Learning and Optimization

Human milk is considered the ideal nutrition for preterm infants. Donor milk is collected, processed and distributed by milk banks. The macronutrient content of donor milk is critical to infant development but varies substantially between donations. To reduce this variance, milk banks pool multiple donations together to create a product. Approximately half of all North American milk banks do not have the resources to measure the macronutrient content of donations, which means pooling is done heuristically. For these milk banks, an approach is needed to optimize pooling decisions. We propose a data-driven framework combining machine learning and optimization, to predict macronutrient content of donations, then optimally combine them in pools. We rigorously simulate milk bank operations to evaluate our framework then conduct a year-long trial implementation comparing between our model to current practice. Pools created by our approach met macronutrient targets more often, demonstrating the value of a predict-optimize approach.

Keywords: Healthcare
Human Milk Banking
Machine Learning
Neonatal nutrition
Optimization
Predict-then-Optimize
Advisor: Chan, Timothy CY
Linking Peripheral Blood Biomarkers with Neuroinflammation in the Brains of Alzheimer’s Disease and Amnestic Mild Cognitive Impairment Patients

To evaluate brain inflammation - translocator protein (TSPO) can be used as a target in positron emission tomography (PET) imaging. In Alzheimer’s Disease (AD) patients, TSPO is elevated compared to both healthy volunteers (HVs) and subjects with amnestic Mild Cognitive Impairment (aMCI). Peripheral biomarkers, such as cytokines (CKs) and fatty acids (FAs), are also indicative of inflammation. To understand whether peripheral biomarkers are predictive of brain TSPO, a secondary exploratory analysis of two previously acquired TSPO imaging studies was conducted in a HAB subsample of AD, aMCI and aged-matched HVs, as no data were acquired for MABs in the aMCI cohort rendering their inclusion impossible. Serum IL-6 and IL-10 were found to be elevated in AD compared to the aMCI and HVs. A limited number of exploratory associations were observed between region-specific TSPO and FAs in aMCI, and between Aβ42 and TSPO signal in AD.

Advisor: Mizrahi, Romina
McPherson, Peter
Investigating the Fate of Bio-based Plastics in Anaerobic Digestion

The anaerobic digestibility of three bio-based after-market plastics used for food packaging applications was evaluated. These plastic samples were tested in a lab-scale solid-state digester, called Daisy, that was operated for 26 weeks. Daisy comprises 6 sequentially fed leach beds (~10 kg each) fed with a mixture of fibres and food waste, with each leach bed having a residence time of 6 weeks. The mass loss of polyhydroxyalkanoate straws, bamboo-fibre coffee cups, and polylactic acid clamshell containers was evaluated as a measure of anaerobic biodegradability. The PHA straws exhibited a mass loss of 55 % ± 17, the bamboo-fibre cups had a mass loss of 54% ± 15, and the PLA clamshell containers had no measurable mass loss. Scanning electron microscopy was conducted on samples of each bioplastic before and after digestion. These images revealed the formation of a biofilm and potentially the presence of methanogens on all bioplastic types.

Keywords: anaerobic digestion
bioplastics
food packaging
Advisor: Edwards, Elizabeth A
Non-Invasive Tendon Release for Contractures using Magnetic Resonance-Guided Focused Ultrasound: Feasibility, Monitoring and Assessment

Contracture is the permanent tightening of muscle or tendon causing pain, deformity, and a restricted range of motion. Patients with contracture often undergo surgical tendon lengthening to improve their range of motion. This thesis investigated focused ultrasound (FUS) as a non-invasive treatment option for tendon lengthening. Porcine Achilles tendons were successfully released in vivo using a hybrid therapy of FUS cavitation and ablation, resulting in improvements in the range of motion of the ankle. Ex vivo experiments determined that passive cavitation detection can monitor inertial cavitation in tendon in real time, with sensitivity to histotripsy parameters. Finally, the effect of FUS on longitudinal tendon stiffness was quantified using ultrafast shear wave elastography. Results indicate that treating tendons with FUS causes a significant decrease in shear wave speed, and consequently in tendon stiffness. The thesis concludes with recommendations for future studies to advance the understanding of FUS tendon lengthening.

Keywords: contracture
focused ultrasound
magnetic resonance imaging
non-invasive therapy
Advisor: Drake, James M
Self-Regulated Learning, Self-Assessment of Writing, and Writing Abilities at the Microstructure and the Macrostructure Level: The Effects of Gender and Diagnosis of Attention Deficit Hyperactivity Disorder

Students with ADHD struggle with most aspects of writing (Graham et al., 2016). Furthermore, girls outperform boys on both reading and writing tasks (Reilly et al., 2018). This study investigated the relationship between self-regulated learning and writing ability at the microstructure and macrostructure level, and determine how this relationship is moderated by gender or diagnosis of ADHD. Results showed that ADHD students compared to non-ADHD had lower scores on both levels of writing. In addition, female students had higher scores on the two levels of writing than male students. Finally, no significant interactions were found between SRL and ADHD diagnosis. However, gender moderated the relationship between SRL and microstructure writing: Female students with high SRL scores were more likely to have high microstructure writing scores. These results underline the complexity of the writing process and emphasize the role of gender and diagnosis in students’ writing ability at different levels.

Keywords: ADHD
automated writing evaluation
gender
self-regulated learning
writing ability
writing self-assessment
Advisor: Jang, Eunice Eunhee
Considering the Observational Approach in a Probabilistic Setting

The observational approach is utilised when the prediction of geotechnical behaviour is challenging. The main principle of the observational approach is reviewing the design during construction after discovering that it is inadequate. Design modification decisions must be appropriately justified to prevent over-reliance on the engineer’s judgement. This could be achievable by predicting the effects of any potential design modifications in advance. This thesis investigates the observational approach from a probabilistic perspective in evaluating design options. For this purpose, a probabilistic convergence-confinement model is established for a tunnel design scenario that requires modification. In addition, a probabilistic traffic light system which quantifies the risks associated with each observation is developed. It is concluded that the suggested procedure can help assess support design options for various ground conditions.

Advisor: Harrison, John
Geology and Origin of a Coastal Placer Chromite Deposit, Port au Port Bay, Western Newfoundland, Canada

Detrital chromite (Cr) is currently accumulating in the modern wave-influenced and gravel-dominated shoreface environment of eastern Port au Port Bay, western Newfoundland. Chromite concentrations of up to 7485 ppm occur in modern cross-bedded shallow marine gravel and pebbly sand facies derived from a large late- and early postglacial fan delta complex undergoing rapid marine erosion. The fan delta fills a broad coastal embayment and was constructed during an early postglacial phase of rapid crustal rebound and low relative sea level that lasted until about 9,500 ybp. Since coastal outcrops of the fan delta have undergone rapid erosion and sediments in response to ongoing postglacial sea level rise outpacing the rate of crustal recovery, chromite-bearing sediment is being re-transported and reworked southwards by shore parallel currents resulting in much higher concentrations within a nearshore chromite placer deposit, some 8 km long and 2 km wide.

Keywords: chromite
coastal evolution
glacial sedimentology
placer deposits
sedimentary facies
Advisor: Eyles, Nick
Microwave-Assisted Methane Pyrolysis in a Fluidized Bed Reactor for CO2-free Hydrogen and Solid Carbon Production

Hydrogen has the potential to decarbonize energy systems if it can become simpler to distribute and cleaner to produce. Methane pyrolysis can produce hydrogen without direct CO2 emissions with modest energy inputs. Microwaves are an efficient method of adding the required energy for this endothermic reaction. This thesis investigates a novel method of low-GHG hydrogen production via methane pyrolysis using microwaves and carbon particles in a fluidized bed reactor. Activated carbon particles in the fluidized bed absorb microwave energy and create a hot medium (>1200℃) in contact with flowing methane. As a result, methane decomposes into hydrogen and solid carbon causing carbon catalyst deactivation with over 90% methane conversion rate and hydrogen selectivity. The produced carbon possesses an autocatalytic effect thus bypassing the need for catalyst regeneration or replacement. This modular pyrolysis system can be built anywhere with access to natural gas and electricity, enabling distributed and localized hydrogen production.

Keywords: Clean Hydrogen
Distributed Hydrogen
Fluidized Bed
Hydrogen Production
Methane Pyrolysis
Microwave-driven Pyrolysis
Advisor: Thomson, Murray
Long-term Carbon Accumulation in a Cedar (Thuja occidentalis) Swamp in the Lake Simcoe Watershed, Southern Ontario, Canada

Cedar swamps stand out amongst forested wetlands as containing high soil carbon stocks; however, factors determining rate of peat accumulation remain unclear due to uncertain carbon turnover rates across spatial and temporal gradients. To address this, this thesis first analyses Ontario peatland and forest inventory data to compare peat properties among forested wetlands, showing significant regional differences, with northern swamps being more acidic and containing lower peat bulk densities compared to southern swamps. Secondly, we analyse a series of cores in a mineral-rich cedar swamp in southern Ontario, showing that peat development and long-term carbon accumulation vary with water table depth. While rates of carbon accumulation in the cedar swamp were slower (5.7 g m-2 yr-1) than non-forested peatlands, carbon stocks were significant (60.3 kg m-2) and basal radiocarbon ages suggest decamillennial development of these wetlands, showing their significance as carbon pools and their vulnerability to peat-degrading disturbances.

Keywords: Carbon accumulation
Forested wetland
Long term accumulation
Paleoecology
Peat
Swamp
Advisor: Finkelstein, Sarah A