VictorJuiz/thesis huggingface dataset:
Understanding the Role of LRBA in Patients with Inflammatory Bowel Disease
Keywords: autophagy
ibd
inflammatory bowel disease
lc3
lrba
veoibd

Pathogenic mutations in LRBA is one of the genetic causes of very early-onset inflammatory bowel disease (IBD). A pediatric patient presented with immunodeficiency with chronic diarrhea and intraepithelial lymphocytosis features, which are highly suggestive of Autoimmune Enteropathy. We performed whole exome sequencing on the patient and identified a rare and damaging heterozygous nonsense mutation in LRBA (Lipopolysaccharide Response Beige-like Anchor). We confirmed LRBA deficiency in the patient by observing a loss of LRBA at the mRNA and protein level. The function of LRBA is poorly characterized; however, it has been speculated to have a regulatory role in autophagy and apoptosis. Furthermore, a BioID screen on LC3, an essential protein in the autophagy pathway, identified LRBA as one of the top interactors. We hypothesized that LRBA regulates autophagy through interaction with LC3, such that a loss of LRBA results in defective autophagy and increases cell death.
Metabolic Availability of Lysine in Cooked Sorghum in Healthy Adult Males using the Combined Indicator Amino Acid Oxidation and Slope Ratio Method
Keywords: cereal grains
indicator amino acid oxidation
metabolic availability
protein quality
sorghum

Metabolic Availability of Lysine in Cooked Sorghum in Healthy Adult Males Using the Combined Indicator Amino Acid Oxidation and Slope Ratio Method Alyssa Paoletti Master of Science The Department of Nutritional Sciences University of Toronto 2019 Abstract The metabolic availability (MA) of lysine was studied using the indicator amino acid oxidation (IAAO) method in 5 healthy adult men. Each subject participated in 8 experiments. Principles of slope-ratio were applied to evaluate the MA of lysine in sorghum by comparing the IAAO response to varying intakes of lysine in cooked sorghum relative to the IAAO response to free crystalline lysine. The IAAO response to complementing lysine from sorghum and lentils in a mixed meal format was also assessed. The MA of lysine from cooked sorghum was found to be 94%. Complementation with lentils resulted in a decline in oxidation reflecting increased protein synthesis. The findings demonstrate that most of the lysine in cooked sorghum is available for protein synthesis. A combination of sorghum and lentil in a 1: 1 ratio is recommended for individuals consuming a plant-based sorghum and lentil diet.
Moral Language Across the Political Spectrum
Keywords: moral foundations theory
morality
politics

Across two studies, we analyzed ideological differences in moral language use based on the moral categories posited by Moral Foundations Theory (MFT): fairness, harm, authority, purity, and ingroup loyalty. In Study 1 we used word counting to assess the moral language used on U.S. political talk shows, finding some support for MFT: Democrats used more language related to fairness and Republicans used more language related to authority. Republicans also used more language related to morality in general. No other differences were significant. In Study 2, we analyzed the Tweets of members of the 115th U.S. Congress, and found that Democrats used more moral language across all MFT categories than Republicans. A time series analysis revealed that these differences are larger after the 2016 Presidential election. These findings suggest that there are differences in moral language use across the political spectrum, and that these differences may be affected by political events.
A Radiopharmaceutical Kit to Prepare Unilamellar Porphysome Nanovesicles with Positron-emitting Radionuclide Copper-64 for Dual-modal Positron Emission Tomography and Fluorescence Imaging
Keywords: CGMP
Clinical Trial Application
Fluorescence Imaging
Nanovesicle
Positron Emission Tomography
Radiopharmaceutical

The Porphysome is a first-in-class, one-component nanomedicine self-assembled from porphyrin-phospholipid conjugates into nanoscale bilayered vesicles. Porphysomes have demonstrated unrivalled versatility and functionality for imaging advanced solid tumours with positron emission tomography (PET) and porphyrin fluorescence, motivating their further development in preparation for clinical phase 1 trials. To this end, a radiopharmaceutical kit to prepare positron-emitting Porphysomes with Copper-64 suitable for parenteral administration is manufactured in accordance with current good manufacturing practice regulations. Descriptions of the manufacturing process and process controls, active ingredient characteristics and specifications, analytical procedures and acceptance criteria are detailed in standard operating procedures. Positron-emitting Porphysomes are characterised in a preclinical model to ascertain their anatomical distribution and pharmacokinetic profile over a forty-eight hour period with two orthogonal modalities of quantification. Finally, modelling of the radiation dosimetry of positron-emitting Porphysomes in an adult male is performed with preclinical data to inform the design of early phase trials.
Identifying Causes of Delay in Interfacility Transports of Injured Patients Transported by Air Ambulance in Ontario
Keywords: Air ambulance
Delays
Injury
Interfacility transport
Prehospital care
Trauma

INTRODUCTION: The purpose of this thesis was to examine patient, paramedic, and institutional-related risk factors for delay and identify specific causes of delays in interfacility transfers by air ambulance. METHODS: Quantile regression was used to identify patient, paramedic and institutional risk factors for delay. Manual chart review to identify specific causes of delay during interfacility transport. RESULTS: Characteristics associated with shorter time intervals included nursing station as sending facility, rotor-wing aircraft and critical care paramedic crew. Patients requiring mechanical ventilation or transported from academic centres were all associated with prolonged times. A total of 458 causes of delay were identified. The most frequent delays included refuelling, waiting for land EMS escort, documentation, and delays for intubation, chest tube insertion and diagnostic imaging. CONCLUSION: Ventilator dependence, paramedic level of care, classification of sending facility and helipad availability are associated with delays to interfacility transport of injured patients.
Vision Based Human Pose Estimation for Gait Assessment of Older Adults with Dementia
Keywords: Computer Vision
Dementia
Gait Assessment
Human Pose Estimation

Falls are detrimental to older adults with dementia. While gait assessment is used as an indicator of falls risk, existing gait assessment methods are insufficient for use on the dementia population. Recent developments in computer vision have led to the availability of open source human pose estimation algorithms, which automatically estimate the joint locations of people in images. In this study, a pre-existing pose estimation model was experimentally evaluated on images of older adults with dementia walking. Gait features were extracted from recordings of gait bouts and significant associations of those gait features with clinical mobility assessment scores and future falls data were found. This showed that pose estimation models are able to accurately track joint locations in most collected videos and provided a preliminary validation of this approach for automated gait assessment based on gait and balance data which is collected frequently and unobtrusively.
Force Sensing and Force Feedback in Minimally Invasive Surgery
Keywords: Feedback
Force
Haptics
Headphones
Robotics
Surgery

Robotic surgery has begun to substitute both open surgery and laparoscopy. While there are many advantages to robotic devices such as the da Vinci Surgical System, there is a disconnection between hand and patient, resulting in a loss of haptics. There is an opportunity to re-establish the connection with the use of an external stimulus that can provide feedback, either through the visual, tactile, or auditory senses. The forces applied throughout the procedure can be measured and mapped to a change in colour, vibration, or sound, allowing the surgeon to have more awareness. Seven participants were given the task of completing a suturing task on a simulated phantom while either receiving no feedback, audio, visual, or combined feedback that represents the magnitude of their applied force. Trials involving feedback demonstrated reduced forces, suggesting more awareness and lower chances of post surgical complication for application to an actual operation.
The Identification of Novel Proteins of Interest in Pancreatic Islets and the Characterization of NIPAL1 as a Regulator of Secretion
Keywords: Diabetes
Glucagon
Insulin
Islet
Magnesium
Nipal1

Single-cell RNA-sequencing (scRNA-seq) has offered novel insight into individual islet cells. I hypothesize that investigation of scRNA-seq data will reveal previously uncharacterized genes related to islet function and secretion. Several recent datasets were explored in tandem with established databases. 915 candidates were investigated in silico; 28 of these progressed to transcriptional validation via qPCR; 4 progressed to translational validation via immunofluorescence studies. Through this process, magnesium influx transporter NIPAL1 was novelly identified in α-cells, Min6-K8 and α-TC6 cell lines. NIPAL1 shows partial Golgi co-localization and magnesium responsiveness. Neither overexpression nor knockdown affected Min6 insulin secretion under standard culture conditions. However, knockdown under hypo- and hypermagnesemic conditions disrupted basal secretion and decreased total insulin content. Overexpression increased total insulin content. These patterns were attributed to a magnesium-dependent increase in Min6 insulin secretion, which is regulated by NIPAL1. By extension, NIPAL1 may contribute to magnesium homeostasis important to α-cell secretion in islets.
Nutritional Status and Dialysis Modality: Effect on Folate Status 20 Years after the Institution of a National Folic Acid Fortification Program
Keywords: Dialysis
End-stage kidney disease
Folate
Folic Acid
Fortification

Canadian dialysis patients are supplemented with ≥1mg folic acid/day to prevent folate deficiency, which may not be appropriate post-fortification. Intake and blood concentrations of folate, B6 and B12 and their association with nutritional status (subjective global assessment [SGA]) and dialysis modality were evaluated in 70 subjects undergoing in-centre hemodialysis (IHD), peritoneal dialysis (PD) or home hemodialysis (HHD). Median total intakes for folate, B6, and B12 exceeded daily recommendations at 2050µg, 11.7mg, and 9.8µg, respectively. Mean folate (62.5nmol/L) and median B6 (121mg/L) concentrations were high, while B12 concentrations were within the normal range (532pmol/L). Significant differences were observed between HHD and the PD and IHD groups for median total intakes of folate, B6 and B12 (p
Net Zero Energy Potential and Parametric Analysis for Multiunit Residential Buildings in Toronto
Keywords: high-rise
multiunit residential buildings
MURB
net zero energy
sensitivity analysis
Toronto

This research studies how multiunit residential buildings (MURB) of varying heights can achieve a net zero energy balance in Toronto. A real 38-storey MURB was created in EnergyPlus and calibrated against an existing reference model in eQuest. A series of sensitivity analyses was then conducted in EnergyPlus to study the tradeoffs involved in the net zero MURB design, and the most impactful design parameters are identified. This research produces a deep physical understanding of how key design parameters interact, identifies design practices that should be prioritized in order to reach net zero, and determines the maximum number of floors allowed for a MURB to achieve net zero with various energy efficiency measures and photovoltaic configurations, all of which provide crucial information that will help the building sector to reduce its energy use, and in turn help Canada to transition to a low-carbon economy.
Advances in Pit Wall Mapping and Slope Assessment using Unmanned Aerial Vehicle Technology
Keywords: Blast optimization
Design compliance
Discrete Fracture Networks
Geotechnical data collection
Slope stability
Unmanned Aerial Vehicles

As mining in open pits progresses deeper, keeping slopes stable becomes more complex. Multi-bench scale instabilities can result in significant economic loss. To address this concern, systematic documentation and evaluation of the performance of benches in open pit mines is essential for pit slope assessment. This includes collecting structural and geomechanical data for rock mass characterization as well as information on the geometry and configuration of the benches. Advances in technology have made the use of unmanned aerial vehicles (UAV) for photogrammetry data collection more feasible. This thesis presents methodologies to integrate the UAV technology in open pit mine operations for collecting high quality data. The collected data was processed and useful information was extracted for design compliance audits, blast optimization studies, and slope stability analysis. This research aims to demonstrate the advantages and limitations of using this technology to collect and process field data.
Quantifying the Fracture Process using Surface Roughness Parameters
Keywords: fracture mechanics
surface roughness

When a crack tip passes through a material, it produces surfaces with characteristic undulating patterns, or roughness, that can reflect the mechanics of the fracture process. These surficial features can be quantitatively described using roughness parameters. Previous studies have attempted to link roughness with fracture mechanics parameters. However, they are derived from profilometric measurements of the surface that are subjectively obtained. This work proposes to apply surface (3D) roughness parameters to fracture surfaces through the surface roughness windowing (SRW) procedure. This procedure rescales roughness to a local perspective and assembles it into a form that allows for interpretation of the roughness of local features. Its application on indirect tensile fractures revealed fracture propagation paths and the local roughness variations. Roughness parameters and an estimated critical Mode I stress intensity factor (KIC) were positively correlated similar to correlations made in literature.
Influence of Grab Bar Orientation on Balance Recovery following a Perturbation during Bathtub Exits
Keywords: Balance control
Balance recovery
Centre of mass
Grab bars

Grab bars are recommended to assist bathing transfers; however, little evidence on their effectiveness for fall prevention exists. The objective was to explore how grab bar orientation impacts balance recovery during transfers (exit). A low horizontal grab bar, high horizontal grab bar, and vertical grab bar were evaluated. Ten younger adults reached to grasp the grab bar following perturbations (YA RTG) and the remaining younger and older adults used it proactively (YA HIP, OA HIP). Findings showed significantly high downward and resultant loads were applied on the low horizontal grab bar. There were no significant differences in loading between the high horizontal and vertical grab bar, other than in downward forces. Grasping condition, but not age, impacted loading and balance control. The YA HIP group applied significantly higher forces and displayed greater balance control than the YA RTG group. Findings can inform clinical recommendations and standard developments on grab bars.
Optimization of High-order Dense and Diagonal-norm Generalized Summation-by-parts Operators for Efficient Aerodynamic Computations
Keywords: computational fluid dynamics
numerical analysis
optimization
summation-by-parts

A general framework is developed for the symbolic construction and optimization of four primary classes of tensor-product generalized SBP (GSBP) operators. These classes encompass previously known dense and diagonal-norm GSBP operators, and extends the scope of previous work in optimizing SBP operators. Additionally, these operators are optimized in a multi-objective framework with objectives accounting for accuracy and spectral properties of the discretization. These novel operators are compared to previously optimized SBP operators and discontinuous Galerkin SBP methods for two linear test problems, where efficiency improvements are observed. Subsequently, novel non-tensor-product SBP operators are constructed on optimal cubature rules on quadrilateral elements. The non-tensor-product SBP operators use fewer nodes than equal degree tensorproduct operators. Additionally, these operators possess smaller derivative and quadrature error coefficients compared to tensor-product operators, with fewer nodes. Consequently, efficiency improvements over equal degree tensor-product SBP operators are observed for both the linear convection and the Euler equations
Generative Design Optimization of Thermal Management Systems for High Output Power Electronics
Keywords: CFD
Electric Vehicles
Genetic Algorithms
Optimization
Power Electronics
Thermal Modeling

Power electronic converters are becoming a critical part of the continuing electrification of transportation technology. With the increasing popularity of electric vehicles, high demands are being placed on the performance and reliability of these on-board modules. To meet these challenges, novel architectures and advanced design techniques are being utilized to address the growing issue of proper thermal management for compact power electronic devices. This thesis proposes a novel design methodology that utilizes genetic algorithms to optimize the liquid topologies of compact heat sinks for power electronic systems. By incorporating precise electrical design data into detailed thermal models, the optimization process accurately captures the heat spreading within these complex systems. The intelligence nature of this iterative program identifies ideal design characteristics to improve heat sink performance and generate optimized cooling structures, specifically tailored to target converter systems.
Deciphering the Interaction between Wood Components and Preservative Chemicals: A Comparison of Analytical Techniques
Keywords: characterization
FTIR
ITC
QCMD
ToF-SIMS
wood

The durability of preservative-treated wood is highly dependent on the interaction of wood components (cellulose, hemicellulose, lignin, and extractives) with preservative chemicals. Wood preservatives are generally comprised of metal ions, commonly copper, chromium, and arsenic, with iron as a pigment. This work establishes methods to quantify interactions between preservative chemicals and main wood components, to aid efforts in formulation development that extend the weathering performance of wood. Analytical methods for isothermal titration calorimetry (ITC) and quartz crystal microbalance with dissipation monitoring (QCMD) were developed. Iron was found to interact with organosolv softwood lignin and beechwood glucuronoxylan, whereas copper, arsenic, and chromium were found to interact with the glucuronoxylan only. Additionally, the impact of alkaline copper quaternary(ACQ)-type preservative treatment on the degradation of wood structures by UV-A light was studied using Fourier transform infrared spectroscopy (FTIR) and the distribution of copper ions visualized using time-of-flight secondary ion mass spectrometry (ToF-SIMS).
Corporate Sustainability Distinctions, Transitions and Perceptions: A Look to Canada’s Big Five Banks
Keywords: Canadian banking
corporate social responsibility
corporate sustainability
sustainability transitions

Corporate sustainability (CS) is becoming increasingly mistaken for or confused with corporate social responsibility (CSR). Literature in recent years has identified this muddied area and argues for further clarity. Clarifying this confusion and understanding the fundamentals of CS can help to ensure companies implement sustainable strategies that are beneficial for current and future generations, while also ensuring resiliency and long-term success. With the creation of a theoretical framework that sets CS and CSR apart, this research emphasizes the importance of sustainability within business and explores Canada’s Big Five banks as its case study. Through the analysis of 75 past and present reports (2002-2018), as well as interviews with employees of all five companies, the ways in which sustainability and social responsibility are perceived and implemented is investigated. Findings demonstrate clear shifts beyond CSR towards greater focus on CS within Big Five operations, allowing for lessons to be learned across sectors.
Distributed Trajectory Generation for Multiagent Systems
Keywords: Collision Avoidance
Model Predictive Control
Motion Planning
Multiagent Systems

Collision-free trajectory generation is a fundamental functionality of multiagent systems. As the number of agents increases, scalable algorithms are required to efficiently compute motion plans. In this thesis we developed a multiagent trajectory generation framework based on distributed model predictive control (DMPC). First, we introduced on-demand collision avoidance to solve the planning problem completely offline. We then extended the approach to online generation of the trajectories, and presented an event-triggered replanning strategy. The framework is validated through a wide variety of simulation tests and experiments with a swarm of up to 25 quadrotors flying in an indoor environment.
Characterizing BDNF Expression and Glial Cells in the Comorbidity between Chronic Pain and Depression
Keywords: Astrocyte
BDNF
Depression
Depression and Pain
Microglia
Neuropathic Pain

Acute pain is adaptive and important for survival, but lingering pain can transition to a maladaptive state and become chronic. Chronic pain affects many people, a high proportion of those being women, who also suffer from comorbid conditions such as depression. As such, it is important to understand and study the molecular mechanisms of chronic pain and associated depression, in both males and females, in order to create new treatments and pain management methods. This thesis used a mouse model of chronic neuropathic pain and measured depressive-like behaviours and brain changes in both male and female mice. Specifically, I characterized the changes in relative BDNF expression and activation of microglia and astrocytes in various pain and affect related brain regions. Results from this thesis may be useful in directing future functional studies to manipulate BDNF, microglia and/or astrocytes to elucidate their role in the comorbidity between chronic pain and depression.
Motivating Students in Online Courses: Designing for Dialogue and Social Presence
Keywords: Dialogue
Motivation
Online Learning
Social Presence

This thesis is based on a case study of a 2018 Masters Level Introductory Research Methods course taught online to 32 students. The purpose of the study was to determine what motivates students to engage in online learning environments. This exploratory mixed-methods study involved 14 students volunteering to complete a survey, and six of those students agreeing to a follow up interview. Both the survey and the interview asked students to comment on aspects of the social and built environment of the course, with specific attention paid to the role of video and text-based discussions in motivating student to engage in the course. Findings suggest that text-based forums, due to built design as well as lack of visual social cues, were less effective than video-based interactions in terms of creating social presence and the type of dialogue that led to increased student perceptions of learning.