VictorJuiz/thesis huggingface dataset:
Bioretention Cells under Cold Climate Conditions: The Effect of Freezing and Thawing on Water Infiltration and Nutrient Removal

Bioretention cells are widely used to reduce urban stormwater runoff, and improve water quality. However, their efficiency under cold climate is still poorly understood. The objective of this research is to understand the effect of freeze-thaw cycles on bioretention cell treatment and hydrological. In this study, soil column experiments were conducted with undisturbed soil cores collected from a bioretention site in Ajax, Ontario. A control column (at room temperature) and an experimental column were run. The experimental column underwent six freeze-thaw cycles consisting of 3 days at -10 Ë C followed by 2 days at 10 Ë C. Nitrate and phosphate concentrations were reduced by more than 95% in the drainage of both columns. Over the course of the experiments, the difference in drainage rates in the two columns increased slightly. The results of this research demonstrate that under cold climate conditions, bioretention cells can perform well for water infiltration and treatment.

Advisor: Passeport, Elodie
Exploring DNA Methylation in Tumour-adjacent Normal Prostate Tissue and Evaluating its Role as a Biomarker for PCa Detection

DNA methylation alterations as a result of field cancerization may be used as diagnostic biomarkers to improve Prostate Cancer (PCa) detection. To identify diagnostic biomarkers, we evaluated DNA methylation of KRTAP27-1, APC, HOXD3, CRIP3, KLK6 and RASSF1A in tumour, tumour-adjacent normal (TAN) and benign prostate tissue. DNA methylation of APC, RASSF1A and GSTP1 was detected in TAN tissue up to 8 mm from the tumour. KRTAP27-1 was discovered to be hypermethylated in TAN tissue using Global DNA methylation profiling. Overall methylation concordance of all genes between matched radical prostatectomy (RP) tumour and RP TAN or biopsy (Bx) TAN tissue was 81% and 66%, respectively. Hypermethylation of RASSF1A, KRTAP27-1 and HOXD3 in combination were most significantly associated with PCa (Benign vs. RP TAN: p = 5.87 x 10^-10, Benign vs. Bx TAN cases: p = 4.44 x 10^-8). My project demonstrates the benefit of using field cancerization biomarkers for PCa diagnosis.

Keywords: Biomarkers
Biopsy
Diagnosis
DNA Methylation
Field Cancerization
Prostate Cancer
Advisor: Bapat, Bharati
Game Design for Stroke Rehabilitation Robots: A Pilot Study Comparing Masked Versus Unmasked Game Designs

Appropriately-designed computer games can improve rehabilitation therapy outcomes by motivating stroke survivors to follow through with exercises. Supplementing conventional therapy with computer games and robotics enables patients to continue without therapists constantly present for repetitive parts of therapy. Studies have used “Basic” (framed as target exercise), “Unmasked” (simulating everyday activity), or “Masked” (fantasy activity) games, without addressing which design best maintains stroke survivors’ motivation and time on task. Three such games were developed for an upper limb robot and analyzed with gameplay measurements, questionnaires, and observations determining which game users preferred, played longer, and performed more repetitions. The “Masked” game had the greatest preference “votes” (5), time on task (24.2 ± 11.6 minutes), and motion repetitions (1191 ± 778), but also misses (180 ± 211) and standard deviations. We should individually tailor games, but continue developing “Masked” games, possibly blending game types. Future design and process recommendations were listed.

Keywords: Gamification
Masking
Motivation
Rehabilitation robotics
Stroke
Advisor: Mihailidis, Alex
Aerodynamic Shape Optimization of a Box-wing Regional Aircraft Based on the Reynolds-averaged Navier-Stokes Equations

The box wing is an unconventional aircraft configuration that has the potential to provide major savings in fuel consumption relative to the conventional cantilever wing. In order to further develop and evaluate this potential, high-fidelity aerodynamic shape optimization is applied to the aerodynamic design of a box wing and a cantilever wing, based on the Embraer E190 regional jet, with the latter serving as a performance baseline. The optimization framework consists of B-spline parameterization, free-form and axial deformation geometry control, an integrated mesh-movement scheme based on the theory of linear elasticity, a Newton-Krylov-Schur flow solver for the Reynolds-averaged Navier-Stokes equations, a gradient-based optimizer, and the discrete-adjoint method for gradient evaluation. Results indicate that a box-wing with a height-to-span ratio of 0.26 burns 7.61% less fuel at cruise than a conventional baseline of the same span and lift. Aerodynamic trends and trade-offs are investigated, and a weight sensitivity study is performed.

Keywords: Aerodynamic Shape Optimization
Box Wing
Computational Fluid Dynamics
High Fidelity
Sustainable Aviation
Unconventional Aircraft Configurations
Advisor: Zingg, David W
Bone Thermal Modelling for Magnetic Resonance Guided High Intensity Focused Ultrasound Therapy of Osteoid Osteoma with Human Clinical Data

Introduction: MR-guided high intensity focused ultrasound (MRgHIFU) is used to treat osteoid osteomas (OOs). However, there is uncertainty about inadvertent injury. This uncertainty can be addressed by MRgHIFU heat transfer simulation within bone. The research goal is to develop a simulator that can accurately and efficiently predict the temperature after the treatment sonication time. Methods: A simulator was developed with three main components: automatic bone segmentation, an acoustic model, and a heat transfer model. The simulated data was compared with the clinical MRgHIFU sonication data. Results: With automatic segmentation, the average maximum temperature difference after sonication, with the clinical data was 2.1Âą9.5 Â°C. The maximum simulation time was 119.5 seconds. Conclusions: The results revealed that the simulator could accurately and efficiently predict the maximum temperature after 20 second sonications. A robust MRgHIFU bone thermal simulation platform has the potential to significantly improve the safety and efficiency of MRgHIFU treatment.

Advisor: Drake, James
Aleman, Dionne
Microfluidic Investigations of CO2 and H2 Activation by Lewis Pairs

A microfluidic strategy has been used for the time- and labour-efficient evaluation of the relative efficiency and thermodynamic parameters of CO2 binding by three Lewis acid/base combinations, where efficiency is based on the amount of CO2 taken up per binding unit in solution. Neither tBu3P nor B(C6F5)3 were independently effective at CO2 capture, and the combination of the imidazolin-2-ylidenamino-substituted phosphine (NIiPr)3P and B(C6F5)3 was equally ineffective. Nonetheless, an archetypal frustrated Lewis pair (FLP) comprised of tBu3P and B(C6F5)3 was shown to bind CO2 more efficiently than either the FLP derived from 2,2,6,6-tetramethylpiperidine (TMP) and B(C6F5)3 or the highly basic phosphine (NIiPr)3P. Moreover, the proposed microfluidic platform was used to elucidate the thermodynamic parameters for these reactions. This microfluidic approach was also applied to obtain thermodynamic parameters for H2 activation by the FLP comprised of tBu3P and B(C6F5)3 with subsequent kinetic studies underway.

Keywords: Frustrated Lewis Pairs
Lewis Acids
Lewis Bases
microfluidics
microreactors
thermodynamics
Advisor: Stephan, Douglas W
Progress Towards the Total Synthesis of Depsipeptide Natural Products: Teixobactin and the Xentrivalpeptide Family

Depsipeptides (cyclic peptides containing one or more ester bond within the ring) are a class of natural products, many of which display biological activity, including antimicrobial and anticancer compounds. Depsipeptide synthesis via macrolactonization is often plagued with low yields or failure to cyclize, and has remained a challenge compared to lactamization. Despite this, macrolactonization of the seco-acid is still a preferred method due to facile synthesis of the linear precursors using solid-phase peptide synthesis (SPPS). The Batey group has recently published an efficient method of macrolactonization using lanthanide-(III) triflate salts alongside MNBA (Shiinaâ s reagent) for rings containing five amino acids. This method has been extended to include rings of various sizes. In particular, cyclizations of model systems towards the core of teixobactin, and the total synthesis of xentrivalpeptide A, Q and related analogues are reported.

Keywords: Chemistry
Depsipeptides
Organic
Synthesis
Teixobactin
Xentrivalpeptides
Advisor: Batey, Robert A
The influence of the presence of a dog or cat on perceptions of a psychotherapist

This experimental study examined the effects of companion animal presence on perceptions of an observed psychotherapist. One hundred thirty-three adults (72.2% female; Mage = 38.05 years) participated in an online study which used randomly assigned visual vignettes to elicit responses to a psychotherapist. The vignettes are described as the following: psychotherapist with a dog; with a cat; client touching dog; touching cat, and; no animal present. Respondents evaluated the therapist on various characteristics, and indicated willingness to self-disclose. Overall, participants rated the therapist as more friendly and likable when shown with an animal than without, but self-disclosure was not influenced by animal presence. There was no differential impact of animal type on the outcome measures. Implications for psychotherapy and methodological challenges of the study are discussed.

Keywords: animal-assisted interventions
human-animal interaction
psychotherapy
therapeutic relationship
Advisor: Schneider, Margaret
Stermac, Lana
Acoustic and Strobe-light Behavioural Barriers: Examining Behavioural and Movement Responses of Common Carp (Cyprinus carpio) at Laboratory and Mesocosm Scales

Acoustic and strobe-light behavioral barriers have been recognized as tools to limit the spread of Asian carps in the Great Lakes. Urgent research is needed to understand how these stimuli impact behaviour, and to evaluate barrier efficacy within realistic canal environments. In a laboratory study, Common Carp responses to stimuli were recorded with video trials (n=44). There were no differences in behavioural responses to acoustic, strobe-light, or combined stimuli. The stimulus period increased durations of carp movement, and the post-stimulus period had increases in movement duration and barrier passes. In a mesocosm study, Common Carp (n=6) and buffalo (n=3) were exposed to the same stimuli, and movement was analyzed using acoustic telemetry. Acoustic stimuli did not produce significant movement responses. Strobe lights (n=12) produced smaller utilization distributions, a decrease in relocations, and an increase in travel velocity near the stimuli (

Keywords: acoustic telemetry
Asian carp
behavioural barrier
invasive species
mesocosm
Advisor: Mandrak, Nicholas E
Math Discourse in a Grade 2 Knowledge Building Classroom

The goal of this study was to examine grade two Math Talk in geometry within a Knowledge Building community engaged in both face-to-face and computer-mediated discourse. Ontario Ministry of Education guidelines were used to identify grade two geometry concepts. Math vocabulary extracted from these guidelines was used, along with a content-based social network analysis tool, to explore the emergence of new domain-specific vocabulary in student discourse and to assess patterns of engagement surrounding use of those terms. A â Ways of Contributingâ analytic framework was used to assess the nature of both teacher and student contributions to face to face and online discourse. Findings suggest that students as early as grade 2 can engage productively in Knowledge Building Math Talk in both face-to-face and online contexts.

Keywords: Geometry
Knowledge Building
Math Talk
Online Discourse
Advisor: Scardamalia, Marlene
A Powered Wheelchair Parking Assistance Reasoning Co-pilot (PARC) System for Cognitively Impaired Older Adults

Intelligent Powered Wheelchairs (IPWC) can help maintain the independence of older adults with cognitive impairment who are unsafe powered wheelchair drivers. Docking at tables is a challenging task unaddressed by IPWCs. Following a requirements analysis, the Parking Assistance Reasoning Co-pilot (PARC) was designed to provide collision-free semi-autonomous docking assistance. Twenty adults docked a PWC with and without PARC under various conditions. PARCâ s docking success rate was 90.4%. Compared to the control group, PARC intervention reduced table collisions, had no effect on user satisfaction, other obstacle collisions, and perceived workload, but reduced other usability measures. A case study of two older adult powered wheelchair drivers yielded similar findings with contrasting acceptance and need of PARC between participants. In both studies, table collisions were frequent in control conditions. Skilled driers would benefit from PARCâ s table collision avoidance without navigation assistance. Further investigation into the determinants of IPWC acceptance and usability is recommended.

Keywords: Assistive Technology
Docking
Human-Robot Interaction
Intelligent Wheelchairs
Shared Control
Usability
Advisor: Mihailidis, Alex
Analysis and Design of Simple, Low Loss and Low Cost Reconfigurable Reflectarrays

With the growing of wireless technology, the need for lower-profile, electronically reconfigurable, highly-directive beam-steering antennas is increasing. This thesis proposes a simple low loss, low cost electronic beam-steering antenna architecture by combining a variety of concepts including the single bit phase shifter, sub-wavelength element spacing and delta-sigma modulation. The starting point in the design of reflectarray antennas is the derivation of the so-called S-curve, which maps changes in unit cell design parameters to the phase of the scattered field from the cell. Both numerical and analytical techniques for analyzing linear-polarized fixed and reconfigurable reflectarray unit cell with lumped element has been developed. A 16 Ă 16 element reflectarray prototype operating at 5.5 GHz is presented the low loss performance and a beam-steering range of -20 to +20 degrees with a single bit phase shifter.

Advisor: Hum, Sean V
Multi-network Analysis of Kindergarten Children's Interactions as a Foundation for Drosophila melanogaster Interaction Networks

Group structure is important for social animals like humans, where who we interact with can influence both our happiness, and our health. One of the ways we can examine a group’s organizational structure is through social network analysis. Traditionally, networks have only been extracted and examined for a single type of interaction between individuals (e.g. friendship, smoking, happiness). Yet we know that most animals, including humans, interact in multiple ways, and these different interactions and their targets may be related. Here, I take an unbiased multi-network approach to adapt existing methods into a protocol to investigate relationships between interaction types and their contributions to group structure. Application of this method to a dataset of kindergarten children’s interactions reveals non-trivial underlying patterns in children’s classroom social structures. Potential applications of this protocol to other social groups, particularly Drosophila, are discussed.

Keywords: Hierarchy
Kindergarten Children
Layered Networks
Social Behaviour
Social Structure
Advisor: Levine, Joel D
Characterizing Acquired Proteasome Inhibitor Resistance in Human Multiple Myeloma Cell Lines

Proteasome inhibitors (PIs) are a mainstay treatment for multiple myeloma (MM). Unfortunately, cure is rare. Here, we attempted to define mechanisms for PI resistance. Two PIresistant MM cell lines were serendipitously developed by blasticidin exposure. These cells had unfolded protein response profiles resembling their PI-sensitive parental cell lines. PI resistance was demonstrated to be due to Mycoplasma infection, which impeded drug inhibition of the proteasome target. Screening of patient samples however did not reveal mycoplasma infection in primary MM cells. Instead, gene expression analyses of primary MM suggested that epigenetic dysregulation (revealed by cancer testis antigen expression) correlates with clinical bortezomib resistance. We therefore screened small molecule epigenetic probes to identify regulators of PI response. While most had no effect on PI response, MM inhibition and bortezomib sensitization was observed with the pan-BET inhibition, JQ1, suggesting that additional evaluation of PIs in combination with BET (or BRD4) inhibitors is warranted.

Keywords: drug resistance
multiple myeloma
mycoplasma
proteasome inhibitor
Advisor: Tiedemann, Rodger
Differential Regulation of IgA+ B Cells in Vitro by Stromal Cells from Distinctive Anatomical Compartments

B cell development is regulated by stromal cells that form a supportive microenvironment. Bone marrow (BM), spleen (Sp), and the gut lamina propria (LP) constitute distinct anatomical compartments that support B cell differentiation. In order to examine the effect of stromal cells on IgA+ B cells, I developed an in vitro system to co-culture gut LP, BM, or Sp-derived stromal cells with B cell progenitors to characterize the signals to generate IgA+ B cells. In this study, I characterized optimal conditions for the in vitro generation of IgA+ B cells. I found that gut LP stromal cells promote IgA+ B cell accumulation through producing soluble stimulatory factors. In contrast, BM and Sp stromal cells impaired IgA+ B cell accumulation in vitro by inhibiting proliferation and differentiation of IgA+ B cells. These observations provide new insights into how stromal cells from different anatomical locations shape IgA+ B cell responses.

Keywords: B cells
gut
IgA cells
plasma cells
stromal cells
Advisor: Paige, Christopher J
Development and Characterization of a Microfluidic System to Model the Transendothelial Migration Mechanism of the Lyme Disease Pathogen Borrelia burgdorferi

Blood-borne bacteria like the Lyme disease pathogen Borrelia burgdorferi cause infection by migrating across the vascular endothelial barrier into target tissues. The mechanisms by which this occurs are poorly understood, largely because model systems inadequately mimic the in vivo environment or are too inefficient to dissect mechanisms. This unmet need is addressed in this thesis by the development of a microfluidic system and live cell imaging methods to model and study transendothelial migration of bacteria in vitro under physiologically relevant conditions. Real-time transmigration kinetics of B. burgdorferi across intact endothelium were obtained, for the first time, under static and flow conditions. Validation studies confirmed that B. burgdorferi transmigrate actively, with similar kinetics to conventional Transwell systems under static conditions. Additionally, physiological shear stress conditions appeared not to significantly alter transmigration kinetics. These data were uniquely obtainable with the microfluidic platform, supporting its utility for studying extravasation of blood-borne pathogens of worldwide significance.

Keywords: blood-borne bacteria
extravasation modeling
microfluidics
real time fluorescence microscopy
shear stress
transendothelial migration
Advisor: Simmons, Craig A
Moriarty, Tara J
Intravenous Delivery of a D1-D2 Interfering Peptide with Antidepressant-like Effects

Depressive disorders are common, debilitating diseases. Current treatments on the market are unsuccessful for many patients, have high rates of remission, and many side effects. After finding that the D1-D2 dopamine receptor complex is upregulated in post-mortem patients that suffered from major depressive disorder, our lab developed a peptide drug that interferes with this complex to serve as an antidepressant drug. Our lab has previously tested the efficacy of the D1-D2 interfering peptide through intracranial administration and intranasal administration. A major component of preclinical drug testing is finding the optimal method of administration. In this study, we find that the peptide has antidepressant- like effects compared to saline in rats in the forced swimming test at doses greater than 1.5nmol/g. These findings are an important step in the preclinical research of a peptide with antidepressant-like effects.

Keywords: Antidepressant
Depression
Dopamine
Peptide
Receptor interaction
Advisor: Liu, Fang
Spatial Patterns of Natural Resource Depletion among Rain Forest Communities in the Peruvian Amazon: The Role of Protected Areas and Indigenous Territories in the Conservation of Key Species

Human-induced environmental change is not a new phenomenon in biologically rich areas of western Amazonia. Rain forest communities have long modified their environments, pursuing a diverse portfolio of economic activities for subsistence and income generation. Globally, protected areas (PAs) are the chief conservation strategy. While the effectiveness of different PA models continues to be debated, recent research acknowledges the significance of extractive PAs and indigenous territories to the conservation of biodiversity in human-modified landscapes. Using community census data collected from rain forest communities in the data poor region of the Peruvian Amazon (N=919), spatial clustering and regression analyses are applied to evaluate the effect of proximity to extractive PAs and indigenous territories on relative availability of key species. Controlling for important environmental, market, and community characteristics, our research indicates that extractive PAs and indigenous territories have helped to preserve the availability of key species by certain measures that we isolate in the work.

Keywords: biodiversity
conservation
indigenous territories
Peruvian Amazon
protected areas
Advisor: Abizaid, Christian
The Effect of Congeners on Trait Evolution and Sexual Dimorphism in Lesser Antillean Anolis Lizards

The central goal of this work is to examine how species interactions affect trait evolution over macroevolutionary timescales. The Lesser Antilles offer a relatively closed system where the trait evolution of two closely related coexisting species can be compared to the trait evolution of solitary species. Competition as a selective force is predicted to affect a wide variety of characters. Trait divergence that increases interspecific resource partitioning can manifest in morphological, ecological, behavioural, or physiological differences. The present study is concerned with the evolution of body size, functional shape, and sexual dimorphism. Chapter 1 consists of several tests for character displacement on one and two-species islands, with the goal of evaluating the effect of congener presence on trait evolution. Chapter 2 tests the hypothesis that competition influences the degree of sexual dimorphism observed in Lesser Antillean anoles; this hypothesis is compared to an alternative explanation for the evolution of sexual dimorphism, Renschâ s rule.

Keywords: Anolis
Character displacement
Evolution
Macroevolution
Phylogenetics
Sexual dimorphism
Advisor: Mahler, Luke