VictorJuiz/thesis huggingface dataset:
Determination of Protein Needs Using Nitrogen Balance in Infants Immediately Post Cardiopulmonary Bypass Surgery

Background: The amount of parenteral protein to produce nitrogen balance in infants diagnosed with severe heart defects undergoing cardiopulmonary bypass surgery was investigated. Methods: Infants born at ≥36 weeks and ≤ 12 months of age were randomized to one of three parenteral protein intakes, the control group received 1.5 g/kg/d and intervention groups received either, 2.2 or 3.0 g/kg/d of protein, respectively. Timed 24 hour urine collections were obtained for three consecutive days following surgery. Total urinary nitrogen was measured through Kjeldahl analysis. Results: A significant difference was demonstrated between the lowest protein intake level of 1.5 g/kg/d and both 2.2 g/kg/d (p ≤ 0.03) and 3.0 g/kg/d (p ≤ 0.001), on study day 1. Nitrogen balance results were 4.0 ± 52.9 (1.5 g/kg/d), 97.0 ± 96.2 (2.2 g/kg/d) and 149.7 ± 90.9 (3.0 g/kg/d). Conclusion: Protein delivery of 1.5 g/kg/d was insufficient to produce nitrogen balance on post-operative day 1.

Keywords: nitrogen balance
infants
Advisor: Pencharz, Paul B.
Influences of Confluences on Reach Scale Morphology of Southern Ontario Stream Channels

Downstream adjustment in stream channel morphology is examined in the context of stream channel confluences. Stream channel confluences represent areas of point specific increases in discharge, flow energy and potential erosion in a river system which will in turn affect the post-confluence downstream morphology. Analysis of 12 confluence junctions from southern Ontario streams, constituting 36 channel reaches in total, show an internally consistent hydraulic geometry relationship but with specific controls on channel morphology related to boundary conditions. Predictions of mainstem morphologies is possible using tributary attributes but reach specific channel confinement and material type add significant influence.

Keywords: Stream Channel Morphology
Channel Confluences
Advisor: Desloges, Joseph R.
Proposed Strategies for Incident Information Flow, Organizational Learning, and Incident-driven Quality Improvement in Health Care

Every year, tens of thousands of patients in North America die from preventable errors. Incident learning can decrease this number, but is not currently reaching its full potential in health care. The goal of this research was to propose strategies to effectively report and learn from incidents to drive quality improvement. A detailed literature review, focus groups, in-depth interviews, and thematic analysis were used to identify potential process improvement strategies from aviation and nuclear power and assess these strategies for feasibility and desirability in health care. This work was guided by World Health Organization recommendations and Rasmussen’s risk management framework. An extensive list of strategies to address existing shortcomings was ultimately proposed for consideration in health care. These strategies can serve as guidelines to proactively improve incident learning processes. This should help create more effective systems and in turn, improve patient safety.

Keywords: incident reporting
incident learning
risk management
quality assurance
process improvement
Rasmussen
information flow
incident
organizational learning
quality improvement
patient safety
Rasmussen framework
preventable errors
focus group
in-depth interview
thematic analysis
health care
aviation
nuclear power
system design
closed-loop communication
Advisor: Easty, Anthony
Trbovich, Patricia
Role of Patched-1 Intracellular Domains in Canonical and Non-Canonical Hedgehog Signalling Events

Patched-1 (Ptch1) is the primary receptor for Hedgehog (Hh) ligands and mediates both canonical and non-canonical Hh signalling. Previously, our lab identified that mice possessing a Ptch1 C-terminal truncation display blocked mammary gland development at puberty that is overcome by overexpression of activated c-src. Testing the hypothesis that this involves a direct interaction between Ptch1 and c-src, we identified through co-immunoprecipitation that Ptch1 and c-src associate in an Hh-dependent manner, and that the Ptch1 C-terminus regulates activation of c-src in response to Hh ligand. Since the effects of Ptch1 intracellular domain deletions on canonical Hh signalling are ill-defined, we assayed this through luciferase reporter assays and qRT-PCR. Transient assays revealed that the Ptch1 middle intracellular loop is required for response to ligand, while qRT-PCR from primary cells showed that C-terminal truncation impairs canonical Ptch1 function. Together, this indicates that the intracellular domains of Ptch1 mediate distinct canonical and non-canonical functions.

Keywords: Hedgehog signalling
Molecular Biology
Advisor: Hamel, Paul A.
A Microsimulated Industrial and Occupation-based Labour Market Model for Use in the Integrated Land Use, Transportation, Environment (ILUTE) Modelling System

Urban microsimulators have been increasingly used to forecast land use, environmental and transportation conditions in cities and are a major tool for stakeholders to analyze the effects of urban policy. Although demographic and residential land use models have been well developed for the majority of these systems, labour market conditions and the forecasting of future jobs have at best been limited to high-level exogenous processes. This thesis aims to develop and implement a truly endogenous job supply and job matching model for use with the Integrated Land Use, Transportation, Environment (ILUTE) modelling system. Jobs within the system are tracked individually at both the occupational and industrial level, and matching occurs within an open market framework in an effort to simulate the true macroeconomic conditions of the real world.

Keywords: Labour Market
Microsimulation
ILUTE
Model
Advisor: Miller, Eric
Skilled Worker Selection and the Flawed Lawmaking Process

While Canadian immigration law has generally evolved incrementally, the law and policy around skilled immigrant selection has undergone generational shifts. The 1960s and 1970s saw the implementation of a human capital model, whereby immigrants were selected based on long-term adaptability to the labour market. This shift was accompanied by a broad national discussion on immigration. In the past decade, Canada has seen another generational shift away from the human capital model towards an employment-based model, where immigrants are chosen based on immediate employment prospects. The consequences of this shift are profound for our economy and society, but this change has not been accompanied by meaningful consultation or debate. Even more problematic has been the use of various lawmaking tools to limit debate and avoid judicial scrutiny. In contrasting recent changes and the accompanying lawmaking processes with the previous changes, this paper argues for a more comprehensive national conversation on immigration.

Keywords: Immigration
Advisor: Shachar, Ayelet
Developing and Validating Prognostic Scores for Patients with Acute Intracerebral Hemorrhage

Objective: To develop a score for hematoma expansion prediction, identify predictors of outcome, and validated existing prognostic scores in acute intracerebral hemorrhage (ICH). Methods: Data were obtained from a prospective multicenter ICH cohort. Patients were evaluated with computed tomography (CT) angiography, 24-hour CT, and 3-month outcome. Multivariable regression identified predictors of 24-hour expansion and 3-month outcome and a score was developed for expansion prediction. Existing scores were evaluated in the dataset. Results: The PREDICT Hematoma Expansion Score predicts 24-hour expansion based on number of spots, stroke severity, time from onset, and coagulopathy (c-statistic: 0.803). Prediction was improved over spot sign presence (p<0.001) and clinical variables alone (p=0.002). Existing scores for hematoma expansion and clinical outcome demonstrated reduced discrimination compared with the original reports. Conclusion: The PREDICT Hematoma Expansion Score may aid patient selection for future interventions aimed at reducing expansion however external validation is required. Existing scores demonstrated reduced discrimination.

Keywords: Stroke
Computer Tomography
Advisor: Laupacis, Andreas
Investigation of the Genetic Factors Associated with Attention/deficit Hyperactivity Disorder (ADHD), Reading Disability (RD) and Language Ability

Attention deficit/hyperactivity disorder (ADHD) frequently co-occurs with language disorders including reading disabilities (RD) and language impairment (LI). Results from recent genetic studies have implicated Cadherin 13 (CDH13) and Contactin Associated Protein-like 2 (CNTNAP2) as ADHD and LI candidate genes, respectively. Studies have also indicated genomic regions of overlap between ADHD and reading disability (RD), suggesting a shared genetic etiology for both disorders. In the present study, we conducted a family based association analysis to investigate whether CDH13 and CNTNAP2 genes are associated with ADHD, RD and language ability in ADHD and RD samples. Although we found several trends for associations between CDH13, CNTNAP2 and ADHD and language measures, none would remain significant following corrections for multiple tests. However, the study represents the first time CDH13 and CNTNAP2 have been studied for a relationship with language in ADHD/RD samples. Further studies employing larger sample sizes are necessary to confirm our findings.

Keywords: ADHD
RD
language
children
psychiatric
Advisor: Barr, Cathy
Phonon Properties in Superlattices

We use normal mode decomposition to obtain phonon properties from quasi-harmonic lattice dynamics calculations and classical molecular dynamics simulations in unstrained Lennard-Jones argon superlattices with perfect and mixed interfaces. Debye scaling of phonon lifetimes at low frequencies in both perfect and mixed superlattices and Rayleigh scaling for intermediate frequencies in mixed superlattices is observed. For short period mixed superlattices, lifetimes below the Ioffe-Regel limit are observed. The relaxation-time approximation of the Boltzmann transport equation is used to predict cross-plane and in-plane thermal conductivity. We find that using a dispersion relation which includes the secondary periodicity is required to predict thermal conductivity. The assumption of perturbative disorder, where Tamura elastic mass defect scattering theory can be applied, was found to be valid for predicting cross-plane thermal conductivities but not in-plane thermal conductivities in mixed superlattices.

Keywords: Phonons
Superlattices
Nanoscale Energy Transport
Molecular dynamics
Lattice dynamics
Advisor: Amon, Cristina
The Identification of Novel Proteins that Interact with the GLP-1 Receptor and Restrain its Activity

G-protein coupled receptors (GPCRs) have been shown to interact with an array of accessory proteins that modulate their function. I hypothesize that the GLP-1R, a B-class GPCR, similarly has interacting proteins that regulate its signaling. An unliganded human GLP-1R was screened using a membrane-based split ubiquitin yeast two-hybrid (MYTH) assay and a human fetal brain cDNA prey library to reveal 38 novel interactor proteins. These interactions were confirmed by co-immunoprecipitation and immunofluorescence. When co-expressed with the GLP-1R in cell lines, 15 interactors significantly attenuated GLP-1-induced cAMP accumulation. Interestingly, SiRNA-mediated knock down of three selected novel interactors, SLC15A4, APLP1 and AP2M1, significantly enhanced GLP-1-stimulated insulin secretion from the MIN6 beta cells. In conclusion, this present work generated a novel GLP-1R-protein interactome, identifying several interactors that suppress GLP-1R signaling; and the inhibition of these interactors may serve as a novel strategy to enhance GLP-1R activity.

Keywords: GLP-1 Receptor
Protein Interactions
Advisor: Wheeler, Michael
UnityFS: A File System for the Unity Block Store

A large number of personal cloud storage systems have emerged in recent years, such as Dropbox, iCloud, Google Drive etc. A common limitation of these system is that the users have to trust the cloud provider not to be malicious. Now we have a Unity block store, which can solve the problem and provide a secure and durable cloud-based block store. However, the base Unity system does not have the concept of file on top of its block device, thus the concurrent operations to different files can cause false sharing problem. In this thesis, we propose UnityFS, a file system built on top of the base Unity system. We design and implement the file system that maintains a mapping between files and a group of data blocks, such that the whole Unity system can support concurrent file operations to different files from multiple user devices in the personal cloud.

Keywords: Distributed File System
Cloud Computing
Computer Security
Advisor: Lie, David
Realtime HDR (High Dynamic Range) Image Processing For Digital Eye Glass Seeing Aid

The work of this thesis is motivated by the bene t of real-time HDR image processing which helps constructing better seeing aid devices for day-to-day uses. The seeing aids with HDR can achieve dynamic range greater than human eyes to capture visuals under various light conditions. Further, it helps range sensing devices to read the light codes better. This requires realtime HDR image processing running at 24 FPS. In this thesis, we demonstrate implementation of several HDR image compositing and tone mapping methods in CUDA to achieve realtime performance. In addition, a new tone mapping method termed PPEM is introduced as a novel tone mapping method by adjusting per pixel exposure. Finally, we apply relevant HDR methods to range sensing devices for robust reading.

Keywords: HDR
Digital Eye Glass
Advisor: Mann, Steve
Manufacturing of Dielectric Barrier Discharge Plasma Actuators for Degradation Resistance

The performance and broader application of dielectric barrier discharge (DBD) plasma actuators are restricted by the manufacturing methods currently employed. In the current work, two methodologies are proposed to build robust plasma actuators for active flow control; a protective silicone oil (PDMS) treatment for hand-cut and laid tape-based actuators and a microfabrication technique for glass-based devices. The microfabrication process, through which thin film electrodes are precisely deposited onto plasma-resistant glass substrates, is presented in detail. The resulting glass-based devices are characterized with respect to electrical properties and output for various operating conditions. The longevity of microfabricated devices is compared against silicone-treated and untreated hand-made devices of comparable geometries over 60 hours of continuous operation. Both tungsten and copper electrodes are considered for microfabricated devices. Human health effects are also considered in an electromagnetic field study of the area surrounding a live plasma actuator for various operating conditions.

Keywords: plasma actuator
degradation
Advisor: Lavoie, Philippe
Numerical and Experimental Crashworthiness Studies of Foam-filled Frusta

Thin-walled metallic components have been widely used as energy absorbers. One key drawback is the high initial crippling load, which typically results in passenger injuries. It is the objective of this study to introduce taper angle to thin-walled prisms, and to examine the crushing response of thin-walled frusta. Nonlinear finite element models of thin-walled frusta of different cross-sectional geometries were developed. Experimental investigations were conducted to validate these models. The effects of key design parameters on the energy absorption characteristics of frusta were explored. Comparison between thin-walled prisms and frusta show that taper angle helps to reduce the initial crippling load and increase the resistance to global buckling. To take advantage of the interaction effects, a novel multi-frusta configuration was developed and it was shown that the energy absorption efficiency is significantly increased. The results of this work are valuable for enhancing the crashworthiness performance of thin-walled metallic energy absorber.

Keywords: Crashworthiness
Frustum
Finite Element
Advisor: Meguid, Shaker A.
A Comparison of Heat Shock Protein Expression in Rat Skeletal Muscle After Lengthening or Shortening Contractions

The mechanism and subsequent patterns of Heat shock protein (Hsp) expression in skeletal muscle specific to contraction type was determined. Rat tibialis anterior (TA) muscle was forcibly lengthened (LC) or shortened (SC) in 5 sets of 20 repetitions before being removed at 2, 8, 24, 48, 72, or 168 hours and analyzed for muscle damage and Hsp25 and Hsp72 expression. Isometric peak torque was reduced to 63% and 33% (P<0.001) at 3-minutes after SC and LC, respectively. Muscle fibre damage appeared at 8h and beyond following LCs, but no damage was observed after SCs. Hsp25 content in LC muscle increased by 3.1±0.53 fold (P<0.01) at 48h and remained elevated. Hsp72 content increased by 3.8±0.66 fold at 24h and remained elevated. Neither Hsp25 nor Hsp72 content was elevated following SCs. Muscle damage associated with LCs results in a greater Hsp accumulation than SCs and 100 SCs do not result in increased Hsp content.

Keywords: Heat Shock Proteins
Muscle
Muscle Damage
Cell Stress
Advisor: Locke, Marius
The Case for Legal Personhood for Nonhuman Animals and the Elimination of their Status as Property in Canada

This article proposes that the legal relationship between humans and nonhuman animals in Canada must be redefined. It will be shown that the current Canadian legal system is based on the assumption of human superiority, which has resulted in the interests of nonhuman animals being given little to no legal consideration since at law they are merely property. This conceptualization of our relationship with nonhuman animals, and the resulting harm that it causes to them is in direct conflict with developments over the last century in science, ethics, and the laws, policies and jurisprudence of various countries. These developments support the argument that nonhuman animals are entitled to have their interests considered in law. This article proposes that the relationship in Canada be redefined to eliminate the property status of nonhuman animals, and that the new relationship should take the form of nonhuman animals being granted the status of legal persons.

Keywords: animal legal person
animals as property
animal law in Canada
Advisor: Green, Andrew
The Binding and Blinding Effects of Collective Ritual: Intergroup Biases and Processes

The aim of the present research was to show that collective rituals have the potential to promote not only ingroup favoritism but also outgroup discrimination. In two studies, I used a minimal group setup and had participants engage in a lab-created ritual over the course of seven days. Afterwards, participants came into the lab and performed the actions in their &lsquo;minimal&rsquo; group. In Study 1, I found that participants who performed the ad-hoc ritual distrusted outgroup members significantly more than did the control participants. Study 2 extended these findings by looking at ritual intensity as a factor of intergroup bias. Results showed, again, that participants in the two experimental conditions &ndash; elaborate and simple ritual &ndash; showed greater outgroup discrimination compared to the control, though the data showed no difference in biases between the two experimental conditions. I also found that tolerance to ambiguity moderated the effect of condition on intergroup bias.

Keywords: collective ritual
intergroup dynamics
Advisor: Inzlicht, Michael
Investigating the Folding Network of Calmodulin Using Fluorine NMR

Protein folding pathways can be extraordinarily complex. In this study, circular dichroism (CD) and 19F NMR are used to investigate the folding network of calmodulin, a calcium-binding protein, which is biosynthetically enriched with 3-fluorophenylalanine. In calmodulin’s calcium-loaded state, CD experiments identify the existence of a folding intermediate along a heat-denaturation pathway. In comparison to the native state, 19F NMR solvent isotope shifts reveal decreased accessibility of water to hydrophobic core, whereas O2 paramagnetic shifts show increased hydrophobicity of this folding intermediate. 15N-1H and methyl 13C-1H HSQC NMR spectra demonstrate that this folding intermediate retains a near-native tertiary structure, whose hydrophobic interior is highly dynamic. 19F NMR CPMG relaxation dispersion measurements suggest that this near-native intermediate state is transiently adopted below the temperature associated with its onset. The folding network also involves an unproductive off-pathway intermediate. In contrast, calmodulin’s calcium-free state exhibits a simpler folding process which lacks discernible intermediates.

Keywords: NMR
Fluorine
Protein Folding
Calmodulin
Advisor: Prosser, Robert Scott
Understanding a Methanogenic Benzene-degrading Culture using Metabolic Models Created from Metagenomic Sequences

Metabolic models were constructed from the metagenome of a methanogenic benzene-degrading community to understand the metabolite interactions among the key microbes in the culture. The metagenomic sequences were assembled, and it was found that assembling the short DNA fragments before they were combined with longer reads can contribute to the overall lengths of the resulting sequences. The metagenome was then taxonomically classified into the domain of archaea and bacteria, and domain-specific models were built. A mathematical framework to fill metabolic gaps at the community level was then developed and applied to the benzene-degrading community model to study how metabolic gaps can be filled by via interspecies metabolite transfer, and it suggested that among other metabolites, acetate, hydrogen, formate, coenzyme A and histidine produced by the bacteria population could potentially contribute to the growth of the methanogens. The computational framework demonstrated its ability to generate testable hypotheses about microbial interactions.

Keywords: modeling
metagenomics
Advisor: Mahadevan, Radhakrishnan
High-permittivity Hemispherical Lens for MIMO Applications with Closely-spaced Antennas

With the rapid adoption and development of new standards, Multiple-Input Multiple-Output (MIMO) technology is becoming a necessity in current wireless systems. One problem posed by using multiple antennas at a transmitter or receiver is the undesirable effect of signal correlation between closely-spaced radiating elements. This thesis presents the concept, design, and evaluation of a hemispherical lens antenna for use in MIMO systems. A high-permittivity dielectric material allows radiating elements to be placed in close proximity with reduced spatial correlation effects. An intermediate matching layer and a hemispherical lens design facilitate the preservation of the pattern characteristics in the transition between the dielectric and free-space. The antenna was simulated against benchmark antenna arrays in free-space and showed a 35%-70% improvement in channel capacity in multipath-rich environments, showing strength as a candidate for further development in MIMO applications.

Keywords: MIMO
Channel Capacity
Lens Antenna
Antennas
Advisor: Eleftheriades, George V.
Hum, Sean Victor