VictorJuiz/thesis huggingface dataset:
Investigating the Role of BRASSIKIN1 (BKN1) in the Compatible Pollen-stigma Interactions in Arabidopsis Species

The basal compatible pollen response pathway in the stigma is initiated upon recognition of compatible pollen. A previous attempt to identify candidate genes in this signal transduction pathway led to the discovery of two tandemly-linked genes that encode pseudokinases, BRASSIKIN1 (BKN1) and BKN2. Interestingly, Arabidopsis thaliana Col-0 is predicted to encode a truncated BKN1, but A. thaliana Hh-0 and Arabidopsis lyrata BKN1 genes encode full length proteins. The A. thaliana bkn2 mutant in the Col-0 accession showed a mild pollen hydration defect when wild-type pollen was placed on the mutant stigmas, and the bkn1-bkn2 double mutant did not show additional defects. To further understand the role of BKN1 in the compatible pollen pathway, BKN1 cDNAs from A. lyrata and A. thaliana Hh-0 were used to complement the bkn1-3 bkn2-5 mutant. Additionally, BKN1 deletions were generated in the A. thaliana Hh-0 accession with the CRISPR/Cas9 system. Results show that BKN1 complementation restored the minor pollen hydration defects when wild-type pollen was placed on stigmas from the complementation lines, and no significant fertility defect was seen in A. thaliana Hh-0 bkn1 mutants, both results suggesting the functional redundancy between BKN1 and BKN2.

Advisor: Goring, Daphne
Inclusion et Langue Française : Stratégies Linguistiques des Membres du Personnel Responsables des Groupes LGBTQ+

Cette étude explore les stratégies linguistiques utilisées par le personnel enseignant responsable des groupes LGBTQ+ dans des écoles de langue française en Ontario en demandant : « Quelles stratégies linguistiques le personnel enseignant responsable des groupes LGBTQ+ utilise-t-il en fonction de son rôle d’appui à la communauté LGBTQ+ dans l’école ? » et « Quelles sont les possibilités et les contraintes à l’utilisation de stratégies linguistiques inclusives de la communauté LGBTQ+ dans le contexte discursif des écoles de langue française de l’Ontario? ». Les données sont recueillies à l’aide d’une analyse de documents et de six entretiens semi-structurés avec des membres du personnel enseignant responsable de groupes LGBTQ+ dans des écoles de langue française en Ontario. L’étude révèle deux catégories de stratégies linguistiques, soit discursives et grammaticales, qui sont analysées selon cadres de la littératie queer de miller (2015) et des moments sécuritaires, positifs et queering de Goldstein et al. (2007).

Keywords: français inclusif
français neutre
groupe LGBTQ
inclusion LGBTQ
milieu minoritaire
personnel enseignant
Advisor: Farmer, Diane
A Cardiac Microtissue Platform With Integrated On-chip Stiffness Measurement Capabilities

In vitro cardiac fibrosis models that monitor fibrotic markers have been developed to better understand fibrotic progression in humans. However, these platforms lack the ability to non-invasively monitor change in tissue stiffness, a hallmark of fibrosis. This motivated the development of a microtissue platform capable of non-invasive tissue stiffness measurement. Tissue stiffness on the platform was determined by force readouts through deflection of a PDMS rod and tissue strain achieved by noncontact magnetic stretching. As proof of concept, no difference was found in on-chip and tensile test measurements of rubber band stiffness. Tissue stiffness measurements on-chip failed due to reliability issues with the platform. However, when manually stretched, tissue stiffness determined on-chip was not different from that measured by atomic force microscopy. Full realization of this platform will result in fibrotic microtissue stiffness tracking throughout an experiment, leading to a better understanding of cardiac fibrosis progression.

Advisor: Simmons, Craig
The Effects of Early-life Inflammation on Seizure Development and Memory in Neurofibromatosis Type 1

Neurofibromatosis type 1 (NF1), a neurocutaneous disorder, can cause various neurological manifestations including learning impairments and epilepsy. Experimental early-life immune activation can promote later-life seizure susceptibility and neurocognitive impairments and can lead to spontaneous seizures in certain neurodevelopmental disorders, but the effect in NF1 is not known. We hypothesized early-life immune activation by systemic lipopolysaccharide (LPS) would further exacerbate the increased seizure susceptibility and cognitive impairments previously described in Nf1+/- mice. We found that systemic LPS induced a comparable acute cytokine response in post-natal day 10 Nf1+/- and WT mice. In adulthood, spontaneous seizures were only found in LPS-challenged Nf1+/- mice, while early-life LPS had similar effects on seizure susceptibility in both genotypes and did not affect spatial learning and memory. Our findings suggest second-hit environmental events, such as early-life immune activation, may be required for epileptogenesis in the Nf1+/- mouse and may be a risk-factor for NF1-associated epilepsy

Keywords: Early-life
Epilepsy
Immune activation
Lipopolysaccharide
Memory
Neurofibromatosis type 1
Advisor: Reid, Aylin Y
The Impact of Ongoing Coparenting Conflict on Female Domestic Violence Survivors and their Parenting of Very Young Children

There are inconsistent results from studies on how maternal parenting is affected by experiencing domestic violence (DV) and most research does not consider ongoing DV or even ongoing conflict. In a sample of 42 mothers of children aged 2 months to 77 months, mostly DV survivors, the relationship between previous week conflict in the coparenting relationship and maternal parenting capacity was assessed, as well as whether maternal trauma symptoms mediated this relationship. Analyses found an indirect, but not direct, relationship between ongoing conflict and self-reported maternal parenting capacity, specifically parenting related stress and parenting self-efficacy, through maternal trauma symptoms. The results suggest ongoing conflict may be important to consider in research examining the maternal parenting of DV survivors and that the focus on improving mothers’ mental health and parenting may be misplaced if there is still ongoing conflict.

Keywords: domestic violence
intimate partner violence
mothering
parenting
post-traumatic stress
trauma
Advisor: Scott, Katreena
Higher Intensity Exercise Increases Protein Turnover and Daily Protein Requirements of Male Endurance Athletes During Recovery

Purpose: Examine the effect of exercise intensity of prolonged running exercise on whole-body protein metabolism and protein requirements during recovery. Methods: Seven male endurance athletes completed two randomized exercise trials (20-km run) at LOW (~55% V ̇O2peak), or HIGH (~72% V ̇O2peak), intensity. Participants consumed 0.6g·kg-1 CHO pre-exercise. During the 8 h post-exercise, participants consumed 8.6g·kg-1·d-1 CHO and hourly meals providing 0.93g ·kg-1·d-1 protein, enriched with indicator AA [13C] phenylalanine. Breath and urine samples were collected to determine whole-body phenylalanine flux (PheRa), oxidation (PheOx), protein synthesis (PS), breakdown (PB) and net balance (NB). Results: The rate of CHO oxidation during exercise was 60% greater in HIGH vs LOW (P

Keywords: Dietary Protein
Exercise Intensity
Exercise Physiology
Protein Metabolism
Stable Isotope Tracers
Advisor: Moore, Daniel R
Investigation of Chromodomain Proteins, CEC-3 and CEC-6, in Maintenance of Germline Immortality

Germline immortality describes the ability of the germ cell lineage to be continuously passed down and, in C. elegans, is protected by proper regulation of histone modifications and small RNA pathways. Loss of two C. elegans chromodomain containing proteins that are able to recognize histone H3 Lysine(K) 9 (H3K9) and H3K27 methylation in vitro, CEC-3 and CEC-6, results in transgenerational progressive sterility. To understand how CEC-3 and CEC-6 protect germline immortality, I used several established phenotypic and transgenic reporter assays for gene silencing. I found roles of CEC-3 and CEC-6 in silencing of repetitive transgenes. I also identified roles in regulating nuclear RNA interference and the duration of inheritance of a germline directed RNA interference response. Together, my results suggest a role for chromodomain proteins in the small RNA and chromatin silencing pathways that protect germline immortality.

Advisor: Saltzman, Arneet L
Free-stream Turbulence Effects on Laminar Separation Bubbles at Low Reynolds Numbers

This thesis investigates the behaviour of a laminar separation bubble (LSB) on a low Reynolds number airfoil, at various free-stream turbulence intensities. The experiments were conducted in a wind tunnel for Reynolds numbers 1.0 × 10^5 – 2.0 × 10^5, at angles of attack 4◦ – 15◦, over free-stream turbulence intensities 0.05% – 1.1%. Particle image velocimetry and oil film interferometry were used to measure skin friction, separation and reattachment points, displacement thickness, and flow transition. The experimental results indicate that increasing turbulence intensity reduces the overall LSB effect, by reducing its length and height. The length reduction is driven by the reattachment point moving upstream, due to an earlier transition to turbulence, and the separation point moving downstream, due to additional upstream mixing. The height reduction results in decreasing skin friction magnitudes within the LSB and is the result of a decrease in the wall-normal velocity fluctuations, indicating more 3-D turbulent structures.

Keywords: Experimental aerodynamics
Free-stream turbulence
Laminar separation bubble
low Reynolds number
Oil film interferometry
Particle Image Velocimetry
Advisor: Lavoie, Philippe
Role of Stem Cell Antigen-1 in Vessel Remodeling

Vessel remodeling underlies several vascular diseases and involves the expansion and differentiation of stem cell antigen-1 (Sca-1)-expressing progenitor cells into vascular smooth muscle cells and related myofibroblast-like cells. Although used to identify progenitor cells, the functional role of Sca-1 has not been examined in vascular remodeling. Here, we first identified the dynamics of Sca-1 expression in a wire injury model of vessel remodeling. To determine the requirement for Sca-1, mice deficient in Sca-1 (Sca1KO) and wild-type controls underwent carotid wire injury. Sca1KO displayed more intimal and adventitial remodeling post-injury. At 8d, non-leukocyte proliferation was increased throughout the vessel, and confined to the adventitia at 14d post-injury. Minimal differences in endothelial- and smooth muscle cells were observed, but fibroblasts and leukocytes were significantly increased, suggesting disinhibited pro-fibrotic and pro-inflammatory responses to injury. Our findings suggest that Sca-1 expression protects against vessel remodeling by suppressing fibrotic and inflammatory responses to injury.

Keywords: Progenitor Cells
Restenosis
Stem Cell Antigen-1
Vascular Biology
Vessel Remodeling
Advisor: Husain, Mansoor
Dismantling Dominant Discourse Surrounding Complex Death with Indigenous Youth Experience

Suicide is commonly described as an urgent health concern and tragedy afflicting Indigenous communities in Canada. This work aimed to develop more contextual understandings of complex death, specifically Indigenous youth deaths by suicide that considered social, economic, historical, ecological, and political factors. This work centered the voices of an often-overlooked demographic, urban-based Indigenous youth, and utilized qualitative methodology that included thematic analysis of archival interview data conducted with Indigenous youth wellness facilitators in British Columbia, Canada. Thematic analysis identified multiple socio-political, historical, and colonial factors that contribute to Indigenous youth challenges with suicidality, and mental health. Furthermore, Indigenous youth in the study conceptualized wellbeing in a manner that resisted psychocentrism and described creative, institutional, and structural interventions that are key to promoting a livable life. Critical implications of this work are discussed, particularly, regarding the roles of the psy-disciplines (psychology and psychiatry) in preventing Indigenous youth suicide in Canada.

Keywords: Canada
Indigenous Youth
Life Promotion
Mental Health
Suicide
Advisor: Ansloos, Jeffrey
Tuck , Eve
'Sharing My Truth": An Arts-informed, Secondary Analysis on the Psycho-social and Educational Experiences of Youth and Young Adults with Cystic Fibrosis

Among the multitude of literature unravelling the biomedical paradigm of chronic illnesses in youth and young adults, there is a lack of knowledge surrounding this population’s personal narratives, specifically through the use of visual storytelling. Storytelling is an unparalleled method for creating a bridge between different life phases. Specifically, young individuals with chronic conditions need platforms to share the truths of living with a life-altering condition. The purpose of this arts-informed secondary analysis is to explore and understand the psycho-social and educational experiences of youth and young people with Cystic Fibrosis (CF), using verbal narratives and self-created storybooks. Participants shared experiences of increased levels of negative mental health, limited social relationships, increased levels of CF stigma, adequate support from elementary and high school educators, and negative barriers in post-secondary educational settings. This new knowledge can lead to the development of interventions to assist this population in navigating through these systems.

Keywords: Arts-Based Research
Chronic Illness
Cystic Fibrosis
Developmental Psychology
Education
Psycho-Social Well-Being
Advisor: Volpe, Richard
Magnetic Particles for Sample Preparation in Microfluidic Paper-based Analytical Devices

This work investigates the of using iron oxide particles in a paper substrate to develop a sample preparation method for a microfluidic paper-based analytical device. The compatibility of three particles (2800 nm, 400 nm and 30 nm diameter) in Whatman Grade 1 paper was evaluated based on their colloidal stability and magnetic susceptibility. The particles were conjugated to horseradish peroxidase to produce a colourimetric signal for tracking in paper. Particle batch variation was evaluated through quality assurance testing to determine the impact on the selected bioconjugation scheme. Results indicated that less colloidally stable particles, due to their larger size or particle-particle interactions, adsorbed to paper, thereby preventing their magnetic field manipulation. The smaller nanoparticles had improved stability, but lower magnetic susceptibility, which reduced their magnetic manipulation. Lastly, the challenges in working with paper were discussed with regards to data collection and analysis (i.e. smartphone versus desktop scanner).

Keywords: Iron Oxide particles
Magnetic particles
Non-specific adsorption
POC
Sample preparation
µPAD
Advisor: Krull, Ulrich J
Unsupervised Multivariate Time Series Anomaly Detection via Transformer-based models and Time Series Encoding

This thesis has investigated the anomaly detection problem on multivariate time series. In particular, we have studied two different directions: the point-based approach and the range-based approach. For the point-based approach, one novel Transformer-based model: Transformer Conditional Variational Autoencoder (T-CVAE) has been designed and compared with state-of-the-art multivariate time series anomaly detection baselines. Through exhaustive experiments on three open-source datasets, our model T-CVAE has outperformed all baseline models in terms of the F1 score. On the other hand, for the range-based approach, we have developed and implemented two time series encoding techniques: Outer product Matrix (OM) and Gramian Angular Field Matrix (GAFM). We have compared the two methods with the existing Gram Matrix approach in the literature. Based on empirical experiment results, we have found that GAFM time series encoding performs best among the three in terms of the F1 measurement.

Keywords: Anomaly Detection
Machine Learning
Multivariate Time Series
Advisor: Plataniotis, Konstantinos N.
Lawryshyn, Yuri A.
Multiplexing Quantum and Classical Channels for a Commercial Quantum Key Distribution System

Wavelength-division multiplexing of quantum and classical channels is a necessary requirement for the integration of commercial quantum key distribution (QKD) systems with existing fibre infrastructure since it drastically reduces the cost of implementation. However, due to the high power of the classical signals in relation to the quantum signal, multiplexing poses a significant technical challenge for QKD systems: the production of optical noise. This thesis will present the first experimental realization of QKD performed using a commercial system with multiplexed quantum and classical communication channels. Using the ID3200 Clavis3 commercial QKD system, key generation was performed under a variety of conditions to generate system-level data which was used to construct and verify mathematical models of the key generation process. Once verified, the models were optimized via exhaustive search to obtain optimal system parameter values such that a maximal secret key rate was achieved for each set of experimental conditions.

Keywords: Coherent One-Way Protocol
Optimization
Quantum Key Distribution
Wavelength-Division Multiplexing
Advisor: Qian, Li
Lo, Hoi-Kwong
Magnetogenetic Stimulation of Human Embryonic Stem Cell-derived Cardiomyocytes and Smooth Muscle Cells

Spatiotemporal stimulation of bioengineered channels offers a powerful tool for modulating cellular activity. Recently, a chimeric ion channel termed “Magneto” has been postulated to function as a genetically encoded magnetoreceptor. Here we tested the hypothesis that overexpression of Magneto could be used to remotely stimulate Magneto expressing cells by the application of a magnetic field. Using CRISPR/Cas9-mediated gene editing, we created a transgenic human embryonic stem cell (hESC) line that stably expressed Magneto. Next, we differentiated Magneto+ hESCs into cardiomyocytes and smooth muscle cells and evaluated the protein expression and subcellular localization of Magneto by immunoblotting and immunofluorescence. To test the channel’s magnetoreceptor function, we employed in vitro calcium imaging of Magneto+ hESC-derived smooth muscle cells in response to various magnetic fields. We found that magnetic stimulation did not elicit calcium transients in Magneto+ cells, while the parasympathomimetic drug carbachol did elicit cellular depolarization when used as a positive control.

Keywords: hESC-CMs
hESC-SMCs
Human embryonic stem cells
Magneto
Magnetogenetics
Remote cellular control
Advisor: Laflamme, Michael A
Deep Hierarchical Reinforcement Learning

The biological paradigm of learning by trial and error has motivated tremendous success in the field of Machine Learning. While Reinforcement Learning (RL) rests behind a myriad of breakthroughs, its practical application to real-world scenarios remains an open question. This thesis addresses the three challenges of restricted scalability, reduced robustness and limited practical viability through the lens of hierarchies serving as abstractions of composite behavior. Novel evolutionary RL methods present an evolving hierarchy which provisions scalability among members of its population. Novel energy based RL schemes, on the other hand, minimize surprise utilizing low energy configurations among members of the multi agent hierarchy. The framework of energy-based surprise minimization steers practical application of hierarchical RL to the setting of trade execution. The end result of this study is a hierarchical scheme demonstrating trade patterns analogous to humans with this thesis serving as a motivation for application of RL to practical problems.

Keywords: Energy
Hierarchies
Mutation
Reinforcement Learning
Trade
Advisor: Lawryshyn, Yuri
Plataniotis, Konstantinos
Geology and Geochemistry of the Newly-discovered VOLPA Seafloor Massive Sulfide Deposit, Niua Volcanic Arc Complex, Tonga, SW Pacific

The VOLPA hydrothermal vent field is a newly-discovered seafloor massive sulfide deposit located on the Niua volcanic complex, on the Tonga-Kermadec arc. Mapping of Niua reveals a unique morphology dominated by volcanic fissures, indicating influences from extensional tectonics. Hydrothermal fluids are mainly focused along crater wall structures. Average metal concentrations are 2.7 wt% Cu, 12 wt% Zn, 2.9 wt% Pb 7.2 ppm Au and 422 ppm Ag. Three distinct types of chimneys are identified based on mineralogy and geochemistry: chalcopyrite-rich chimneys with >10 wt% Cu; sphalerite-rich chimneys with >5 wt% Zn, and zoned chalcopyrite-sphalerite chimneys with

Keywords: Seafloor massive sulfides
Advisor: Anderson, Melissa O
The Effect of the Positon of Consonantal Elements in Words on Second Language Spelling Among Grade Two English Language Learners with Different Home Backgrounds

This study investigated the role of development, phoneme position and first language (L1) typology on second language (L2) spelling in grade two English Language Learners (ELLs) coming from two typologically different home languages: alphabetic (Portuguese and Spanish, N=83) and logographic (Chinese, N=81). The participants completed real and pseudoword spelling, word reading and various cognitive tasks. Common to both groups was the observation that (1) consonantal elements in the onset position were spelled more accurately than in the coda position; and (2) singletons were spelled most accurately but they struggled with consonant clusters and digraphs. Furthermore, L1 typology, dual-route model of spelling and home literacy practices jointly explained how the logographic group made more errors on consonantal elements absent in their L1 when spelling pseudowords, but spelled real words more accurately compared to the alphabetic group. Educational and clinical implications of assessing ELLs’ spelling skills in early grades are discussed.

Advisor: Geva, Esther
Investigating a Role of the Lateral Entorhinal Cortex in Temporal Duration Memory: Contextual Discrimination of Temporal Sequences

The lateral entorhinal cortex (LEC) is proposed to be a site of origin of a timing signal that is transmitted to the hippocampus for the generation of episodic time. However, the LEC’s role in temporal duration memory remains elusive. The present study investigated effects of LEC inactivation on retrieval and acquisition of temporal duration memory. Rats were trained on a novel temporal duration task to discriminate event sequences comprising cues of differing durations. Rats learned to press a lever for food reward upon hearing one auditory sequence and another lever for reward for a second sequence. Pharmacogenetic inactivation of the LEC post-acquisition left memory expression intact on tests of recognition memory. In a subsequent experiment, inactivation of the LEC prior to daily training revealed behavioural differences in early acquisition that diminished with time. These data implicate the LEC in early encoding, but likely not retrieval, of temporal duration memories.

Advisor: Ito, Rutsuko
Lee, Andy CH