VictorJuiz/thesis huggingface dataset:
Global Retrieval of the Maximum Carboxylation Rate (Vcmax) of Plant Leaves by Solar-induced Chlorophyll Fluorescence from TROPOMI

The maximum carboxylation rate (Vcmax) is a significant parameter in photosynthesis simulation. However, global Vcmax25 (Vcmax normalized to 25°C) datasets are limited in its spatial and temporal coverages. In this thesis, a global Vcmax25 dataset is retrieved with a daily temporal and a 0.1° × 0.1° spatial resolution from March 7th, 2018 to October 31st, 2018. The Vcmax25 dataset is derived in following two steps: 1) Retrieval of TROPOMI sun-induced fluorescence (SIF) dataset to study the relationship between SIF and gross primary productivity (GPP) at the canopy level; 2) Retrieval of Vcmax25 using a data assimilation system from GPP estimates of sunlit leaves in the canopy, which are estimated from the TROPOMI SIF dataset and a process-based ecosystem model (BEPS), respectively. The derived Vcmax25 dataset shows agreements with existing Vcmax25 datasets, literature Vcmax25 values, and local phenology information globally, indicating that the new Vcmax25 dataset is reliable.

Keywords: global climate change
maximum carboxylation rate
photosynthetic capacity
sun-induced chlorophyll fluorescence
Vcmax
Advisor: Chen, Jing M.
Offloading and Resource Allocation in Mobile Edge Computing with Multiple Computing Access Points

In this thesis, we analyze three-tier mobile offloading networks consisting of multiple mobile devices, each with a single task to be processed, multiple computing access points for possible task offloading, and a remote cloud server as an additional possible offloading site. Our objective is to produce offloading and resource allocation decisions that minimize the system cost, while achieving stability under the assumption of selfish users. We first consider a centralized optimization approach under a strictly defined objective function, using semidefinite relaxation to develop a heuristic solution that performs nearly optimally under simulation. We then use that solution as an initial starting point to computing the Nash equilibrium, exploiting the potential game property of that particular system. We then develop a solution method to compute the optimal correlated equilibrium, which is applicable under a wider range of system models and also meets the necessary stability requirements while minimizing the system cost.

Advisor: Liang, Ben
Heteroepitaxy in the Sub-monolayer Regime: Ag on Si(001) and CuPc on Cu(111)

The structure and properties of atoms and molecules at coverages of one monolayer or less often differ from their bulk behaviour. Scanning tunneling microscopy and density functional theory were employed to investigate 1) Ag atoms on the Si(001) surface and 2) CuPc molecules on the Cu(111) surface. A combination of experimental results and theoretical modelling provides evidence that previous models of the (2×2)-Ag reconstruction are incorrect and that Ag tetramers provide a more complete explanation of the 1 ML (2×2)-Ag covered Si(001) surface. Sub-monolayer deposition of CuPc molecules were found to polymerize into molecular clusters after annealing through a dehydrogenation reaction. When the size of these molecular clusters are sufficiently small cluster motion is observed. The behaviour of larger clusters is explained by Cu(111) surface defects acting as pinning points that hinder cluster motion by creating energetic barriers.

Keywords: CuPc
density functional theory
scanning tunneling microscopy
Si(001)
surface science
Advisor: Nogami, Jun
Singh, Chandra Veer
The Effects of Functional Electrical Stimulation and Visual Feedback Balance Training on Standing Balance Performance in Individuals with Incomplete Spinal Cord Injury: A Case Series

Damage to the spinal cord produces sensorimotor impairments below the level of injury leading to significant balance deficiencies. Individuals with an incomplete spinal cord injury (iSCI) are highly susceptible to falls during periods of walking or standing. Balance training interventions provide an opportunity to decrease the risk of falling and increase the level of independence and mobility for individuals with iSCI. Our objective was to evaluate the effectiveness and meaningfulness of a therapeutic tool for standing balance that combined functional electrical stimulation with visual feedback balance training (FES+VFBT). Five adults with iSCI completed a total of 12 FES+VFBT sessions. Balance abilities were assessed pre- and post- training using clinical and biomechanical assessments. Two semi-structured interviews were completed by each participant following the end of the training program. FES+VFBT showed potential as an intervention for standing balance as it effectively improved standing balance abilities post-training and proved meaningful to the participants.

Keywords: balance training
functional electrical stimulation
neurorehabilitation
spinal cord injury
visual feedback
Advisor: Musselman, Kristin E
The Gendered Experiences of Men with Traumatic Brain Injury (TBI): A Qualitative Study

Research shows that gendered constructs influence traumatic brain injury (TBI) recovery and should be incorporated into clinical interventions. To inform the future development of such interventions, this study explored the experiences of men with TBI through a gendered lens. Specifically, it aimed to (1) analyze their gendered perceptions and behaviours in relation to TBI recovery, and (2) understand how they viewed gendered constructs within their lives. Semi-structured interviews were conducted with men of all TBI phases and severities. A qualitative thematic analysis approach was used to interpret interview data, guided by the concept of hegemonic masculinity. Three key themes were discerned from the interviews of 22 men: performativity of masculinity in treatment and recovery, masculinity in motivations for return to work and activities, and men’s explicit versus implicit understanding and discussion of gender. These findings can be translated into patient-driven therapy strategies and gender-specific materials for men with TBI.

Keywords: Gender
Masculinity
Qualitative research
Rehabilitation
Traumatic brain injury
Advisor: Colantonio, Angela
Effect of Ionizing Irradiation on Mechanical Properties and Translucency of Monolithic Zirconia

Objectives: To evaluate the effect ionizing irradiation therapy (RT) on mechanical properties and translucency of monolithic zirconia. Methods: High translucency (HT) and low translucency (LT) yttria-stabilized zirconia (Y-PSZ) were used to prepare 60 bar-shaped fully sintered specimens (14×4×1.5mm) of each material and allocated in four groups (n=30): Control or irradiated (70 Grays single dose). Specimens were evaluated for flexural strength (FS) (n=10), fatigue limits (FLs) at 100,000 cycles (n=15), and translucency parameter (TP)(n=5). Data of FS and TP were analyzed by one-way Analysis of Variance (ANOVA) and Tukey HSD. FLs data was analyzed using Dixon and Mood method. Results: RT affected FS (p

Keywords: Dental ceramics
Fatigue resistance
Flexural strength
Radiotherapy
Y-TZP
Advisor: De Souza, Grace M
Computational Study on Spatially Distributed Sequential Stimulation for Fatigue Resistant Neuromuscular Electrical Stimulation

Functional electrical stimulation (FES) is used to artificially induce muscle contractions in paralyzed limbs in individuals with stroke and spinal cord injury, however, the efficacy of FES is hindered by the rapid fatiguing of the targeted muscle. A unique stimulation method, called spatially distributed sequential stimulation (SDSS), has been shown clinically to reduce fatiguing during FES, but further improvement is needed. The purpose of this thesis project was to gain a better understanding of SDSS-induced neural activation in the lower leg using a computational approach. We developed a realistic finite element model of the lower leg to investigate SDSS, by solving the electric field generated by SDSS and predicting neural activation. We found that SDSS can reduce muscle fatigue during FES by allowing for 25, 45, and 10% of activated lower motor neurons (LMNs) to only be activated at 10, 20, or 30 Hz, respectively.

Keywords: Finite Element Model
Functional Electrical Stimulation
Neuromodulation
Spatially Distributed Sequential Stimulation
Tibialis Anterior
Advisor: Yoo, Paul B
Masani, Kei
The Efficacy of Cannabidiol in Mitigating Delta-9-Tetrahydrocannabinol-induced Harms: A Systematic Review

Introduction: Delta-9-tetrahydrocannabinol (THC) produces acute and chronic psychological, cognitive, and physiological effects, and increases the risk for dependence in certain individuals. Cannabidiol (CBD), in contrast, displays anxiolytic, neuroprotective and anti-inflammatory properties when administered alone. Methods: A systematic review of human randomized controlled trials (n=19) was conducted to determine whether chemovars that include CBD are more protective over the THC-only aforementioned effects. Results: THC+CBD chemovars may mitigate anxiety, symptoms of psychosis and certain cognitive impairments provoked by THC-dominant chemovars, particularly when administered orally. Abuse liability and physiological parameters appear to be unaltered by THC+CBD chemovars compared to THC, although THC+CBD may exert greater protective properties among infrequent users. Discussion: Findings from this review indicate that the effects of THC+CBD cannabis may be protective for psychological and certain cognitive outcomes, certain individuals, and perhaps at certain ratios of THC:CBD. Future research should design longitudinal investigations exploring the effects of differing doses and ratios of THC:CBD based on current frequency of use.

Keywords: cannabidiol
cannabis
CBD
cognitive
psychological
THC
Advisor: Rueda, Sergio
Using A Body-part Compatibility Paradigm as an Index of Tool-embodiment

Previous research, using the body-part compatibility (BPC) task, has revealed that tool embodiment might emerge through both real and virtual interactions. The purpose of the present study was to investigate the validity of using a BPC task to measure tool-embodiment that typically only emerges from active tool-engagement. Participants completed a BPC task in which they responded with either a foot or hand press to targets presented on an image of a model holding a rake. Targets were presented on the model’s foot, hand, and the rake. This response time (RT) task was performed before and after one of two interventions. Participants in the first group made reaching movements to targets presented on static images of the virtual tool-use task. Participants in the control group completed math problems. Overall, the study indicates that, perhaps, a BPC task is not a valid paradigm to assess tool-embodiment for active tool-use.

Keywords: Body Schema
Body-Part Compatibility
Tool-Embodiment
Advisor: Welsh, Timothy
Serum Undercarboxylated Osteocalcin is Associated with Verbal Learning in Adults with Type 2 Diabetes

Objective: Type 2 diabetes mellitus (T2DM) has been found to be associated with an increased risk for cognitive decline, including verbal learning. Serum undercarboxylated osteocalcin (unOC) has been found to be lower in patients with T2DM. This study explores the association between unOC and verbal learning in people with T2DM. Methods: The California Verbal Learning Test, 2nd Ed. (CVLT-II) was administered consecutively to patients with T2DM entering an exercise and education-based rehabilitation program. Serum unOC concentrations were measured from fasting blood samples using sandwich ELISA. Correlations with unOC were tested using linear regression models adjusting for age and gender. Results: Among 30 adult participants with T2DM (n=30, age 63.3±8.9, 60% female, duration of diabetes 8.2±8.6 years, HbA1c 7.64±0.01%), serum unOC was associated with CVLT-II learning (Trials 1-5) (=0.423, p=0.019), after controlling for age and gender. Conclusions: Serum unOC concentrations were associated with verbal learning in these relatively healthy adults with T2DM.

Advisor: Swardfager, Walter
Oh, Paul I
Administrative Intelligence: Exploring Balanced Human-AI Decision-making Relationships in Canadian Administrative Contexts

One of the many promising potentials of artificial intelligence (AI) is its ability to improve public decision-making. But, until there is enough confidence for AI systems to act independently, humans will still play a prominent role in making decisions. However, these human-AI decision-making relationships create a new dynamic that, if not properly structured, can end up working against the principles and goals of administrative law. This thesis will focus on the human element in human-AI decision-making relationships and how these dynamics can be structured to promote the goals and principles of public decision-making. From the perspective of Canadian administrative law, the focus of this thesis will be a qualitative case study on three prominent AI decision-making systems – COMPAS, iBorderCtrl, and PredPol – that are already implemented in jurisdictions with analogous administrative law requirements.

Keywords: Administrative Law
Artificial Intelligence
Canada
Cognitive Biases
Due Process
Opacity
Advisor: Ratto, Matt
Choo, Chun Wei
Metal Carboxylate Salts as an Avenue to Protecting Group Free Peptide Couplings

Peptide coupling has had a long history, beginning its story in 1882 using the silver salt of glycine, continuing to solid phase peptide synthesis and the introduction of protecting groups. However protecting groups create a lot of needless waste. This thesis explores potential work in the area regarding the use of metal carboxylates as means to get around the need for these groups, as well as taking things further to do more than a single coupling couplings in one pot in solution phase chemistry. Despite variable success throughout, making a one-pot tripeptide in good yield and low epimerization was indeed achieved, with the help of these metal carboxylates and ONp esters.

Keywords: Amides
Amino acids
Green Chemistry
Metal carboxylates
Peptides
Protecting Group free
Advisor: Batey, Robert A
Patterning of Cerebellar Inhibitory Interneurons by the Clustered Protocadherins

Precise wiring of brain circuitries requires coordinated interactions of neurons with their environment for regulations of their cell numbers, distributions, and connectivity patterns, and selection of synaptic partners. The molecular cues and recognition molecules that orchestrate these interactions are not well understood. Here, I provide evidence that the gamma clustered Protocadherins (Pcdhγs) are essential for regulating cerebellar molecular layer interneuron (MLI) survival and neurite arborization. By conditionally deleting the Pcdhγs prior to or after MLI integration, I demonstrate differential roles for the Pcdhγs in regulating MLI survival and neurite branching. Early developmental loss of Pcdhγs results in reduced survival of MLIs, in addition to profound alterations to their neurite patterning. In contrast, late deletion of Pcdhγs did not affect MLI numbers, but led to similar reductions in dendritic and axonal arborization. Taken together, these results demonstrate that the Pcdhγs are required for interneuron survival and neurite arborization during two windows of development.

Keywords: Cerebellum
Interneuron
Protocadherin
Advisor: Lefebvre, Julie
Cooperate-and-Radiate Co-Evolution Between Ants and Plants

Mutualisms can be considered â key innovationsâ that spur lineage diversification in one partner, but no study has evaluated whether mutualism accelerates diversification in both lineages. Recent literature suggests that angiosperms that attract ant mutualists for defense or seed dispersal have higher diversification rates than non-ant associated lineages. We ask whether the reciprocal is true: does the ecological interaction between ants and angiosperms also accelerate diversification in ants? In other words, do ants and plants cooperate-and-radiate? Using a novel text-mining approach, we assembled trait data for ant taxa that interact with plants by nesting in domatia or feeding on extrafloral nectar, food bodies, or elaiosomes. We investigated patterns of trait evolution and lineage diversification using phylogenetic comparative methods on species- and genus-level ant phylogenies. When combining data on all ant-plant mutualism types, we found that mutualistic ants have elevated diversification rates compared to non-mutualistic ants, suggesting that ants and plants cooperate-and-radiate.

Keywords: angiosperm
ant
diversification
mutualism
phylogeny
Advisor: Frederickson, Megan
Development of an Animal Phenotype of Gambling Disorder: Chronic Reward Uncertainty Induces a Gambling Disorder-like State of Sensitization and Dysfunctional Decision-Making

Gambling Disorder (GD) is a behavioural addiction whose etiology is uncertain. Thus, it is unclear whether repeated exposure to uncertainty may induce a GD-like phenotype (indicated by dopamine (DA) sensitization and risky decision-making). Therefore, rats were trained to nose-poke on a Fixed/Variable Ratio (FR/VR) schedule of reinforcement to activate a conditioned stimulus (CS) that predicted saccharin 50/100% of time (CS50/100%). Following 66 sessions, the VR+CS100% and VR+CS50% rats demonstrated a locomotor sensitization (index of DA sensitization) to a d-amphetamine (AMPH) challenge, while only the VR+CS50% group showed impaired decision-making on the rat gambling task. To determine whether sensitization mediated impaired decision-making in the VR+CS50% group, effects of a sensitizing d-AMPH regimen on decision-making were assessed, and revealed a parallel pattern of impairment. Thus, repeated exposure to a VR schedule is implicated in a d-AMPH-like sensitization that interacted with the uncertain CS50% to mediate dysfunctional decision-making.

Keywords: amphetamine
decision-making
gambling
locomotor sensitization
preclinical
uncertainty
Advisor: Zack, Martin
Fletcher, Paul
Two-Colour Fluorescence Intermittency Spectroscopy: Shedding Light on Blinking in Nanocrystals

Even under continuous excitation, single semiconductor NCs `blink’—exhibiting periodic on/off photoluminescence switching on unusually long (milliseconds–seconds) timescales. This phenomenon hampers their performance as ensemble light-emitters, and particularly hinders their use in single-molecule fluorescence imaging. Here, we propose and implement a new two-colour fluorescence intermittency measurement to gain insight into the mechanistic causes of blinking. We use a home-built epifluorescence microscope to monitor the emission of individual nanocrystals under super-bandgap photoexcitation to avoid the obscuring effects of ensemble averaging. Then, we periodically expose the nanocrystals to sub-bandgap light, to preferentially provide additional energy to long-lived non-emissive (i.e. ‘trap’) states, shorten their duration and alter their emission statistics. Though temperature-dependent literature results anticipate that a light-induced modulation should be observable, no effect has yet been detected. We propose further experiments with greater sensitivity to further investigate the role of light-assisted modulation of blinking.

Keywords: Fluorescence Intermittency
Quantum Dot
Single Molecule
Spectroscopy
Advisor: Wilson, Mark WB
Examination of the Validity of Nutrient Profiling Models for Assessing the Nutritional Quality of Foods

Nutrient profiling (NP) is a method for evaluating the healthfulness of foods. Although many NP models exist, most have not been validated. This thesis aimed to examine various aspects of validity of four models developed by authoritative bodies. All four models demonstrated moderate content validity, which was assessed by examining the nutrients/components considered in the models. However, different models exhibited varying levels of construct or convergent validity with Ofcom, a previously validated model which served as the reference, in classifying over 15,000 Canadian pre-packaged foods from a branded, national database. Numerous incongruencies were identified for certain models, which highlights the importance of examining classifications across food categories, the level at which differences between models become apparent. The challenges associated with validating models are discussed. Overall, this thesis provides data that can inform regulators seeking to adapt existing NP models and validate them for use in country-specific applications for nutrition policies.

Keywords: nutrient profile
nutrient profiling
nutritional quality
nutrition policy
validation
validity
Advisor: L'AbbĂŠ, Mary R
Synthetic Strategies in Solid-Phase Peptide Synthesis: N-Terminus Modification

Solid-phase peptide synthesis (SPPS) is a technique used in the synthesis of peptides. SPPS is mainly used to synthesize linear peptides using natural Îą-amino acid precursors. In this thesis, different ways of modifying the N-terminus of polymer-supported peptides was investigated. The N-terminus was converted into urea and guanidine functionalities with the use of isocyanates equivalents. Alternatively, another method converted the N-terminus into isocyanates and carbodiimides, which then reacted with various amines. In addition, less common peptide coupling reagents, such as acyl chlorides and anhydrides, were examined with respect to polymer bound peptides. These reagents were then compared with more typical ones, such as HATU, on a variety of substrates.

Keywords: Carbodiimide
Coupling conditions
Isocyanate
N-terminus modification
Solid-phase peptide synthesis
Advisor: Batey, Robert A
Epigenetic Control of Mesenchymal-Epithelial Interactions Directs Gastrointestinal Development

Gastrointestinal development is orchestrated by expression of a complex network of transcription factors and signalling molecules. Epithelial-mesenchymal communication is highly regulated in gastrointestinal development, but the mechanistic underpinnings of this control are still unclear. My work investigated epigenetic regulation of mesenchymally derived developmental signals in gastrointestinal development. Ablation of the Polycomb Repressive Complex 2 in mice revealed its role in suppressing mesenchymal Wnt signaling, thereby regulating gastric epithelial fate and intestinal epithelial proliferation. Additionally, impairment of the MLL1-COMPASS-like complex caused a striking proximal shift in intestinal fate. Through these experiments, I have determined that chromatin modifications mediate the expression of key signaling ligands in mesenchymal cells, ultimately governing mesenchymal-epithelial crosstalk. As such, my work has uncovered a novel level of regulation required for proper gastrointestinal development: epigenetic control of mesenchymal-epithelial interactions.

Keywords: Chromatin Modifications
Developmental Biology
Epignetics
Gastrointestinal System
Intercellular Communication
Polycomb Repressive Complex 2
Advisor: Kim, Tae-Hee
Characterization of an NBEAL2-interacting partner

Platelets are small, abundant blood cells involved in many processes. Loss of function of Neurobeachin-like 2 (NBEAL2) is causative for Gray Platelet Syndrome (GPS), where patient platelets lack the crucial secretory α-granules. Thus, NBEAL2 is required for α-granule formation in platelet precursor megakaryocytes, but the functions and interaction partners of this protein are largely unknown. Here, I verified VAMP-associated protein A (VAPA) as an NBEAL2-binding protein. Co-immunoprecipitation (Co-IP) experiments confirmed the NBEAL2-VAPA interaction, which was mapped to at least five atypical FFAT motifs located within the PH-BEACH domain of NBEAL2. Structural modeling and docking simulations implicated one motif, termed ncFFAT*, however, Co-IP experiments with individual acidic residues in ncFFAT* (E2218K and D2224K) suggested that these residues are not uniquely involved. Immunofluorescence microscopy of human megakaryocytes and megakaryocytic cells suggested a partial interaction of NBEAL2 and VAPA. These studies suggest that NBEAL2-VAPA interactions may facilitate platelet α-granule formation.

Keywords: NBEAL2
Platelets
Îą-granules
Advisor: Kahr, Walter H.A.