VictorJuiz/thesis huggingface dataset:
Numerical Simulation of Complex Hydraulic Fracture Development by Coupling Geo-mechanical and Reservoir Simulator
Keywords: hydraulic fracturing
numerical simulation
reservoir simulation

Hydraulic fracturing is one of the standard techniques adopted by oil and gas industries to enhance production in unconditional reservoirs. Reservoir properties and treatment designs have a significant influence on the effectiveness of hydraulic fracturing treatments. Extensive studies on the mechanism of hydraulic fracturing have been conducted to optimize the hydraulic fracturing design. Recent advances in fracture diagnostic technology have brought new insights to the complex fracture geometry. Numerical simulation is an economical approach to investigate the generation of fracture geometry and its effect on post-treatment production enhancement. This work proposes a workflow to study the fracture complexity through coupling the geomechanical simulator Irazu and the reservoir simulator CMG. The geo-mechanical simulator is devised to simulate the hydraulic fracturing process employing the hybrid finite-discrete element method while the reservoir simulator CMG is used for the reservoir post-treatment production forecast.
A Model Reduction Framework with the Empirical Quadrature Procedure for High-dimensional Shape-parameterized Partial Differential Equations
Keywords: CFD
EQP
FFD
finite element method
model reduction
reduced basis

This thesis details a goal-oriented model reduction framework for parameterized nonlinear partial differential equations (PDEs), with an emphasis on shape-deformation problems with high-dimensional and non-affine parameter dependence. The framework builds on five technical ingredients: free-form deformation, which provides implicit geometry-independent shape deformations; reduced basis spaces, which provide rapidly convergent approximations of the parameterized solutions; the empirical quadrature procedure (EQP), which provides efficient hyper-reduction for nonlinear PDEs with non-affine parameter dependence; the dual-weighted residual (DWR) method, which provides a posteriori error estimation; and a greedy sampling method based on saturated parameter space assumptions, which provides efficient adaptive training in high-dimensional parameter spaces. This generalized framework enables automatic training of reduced order models that meets a user-prescribed error tolerance for a wide range of continuum mechanics problems. The versatility of this framework is demonstrated for many-query shape deformation problems in acoustics, aerodynamics, and hyperelasticity. The eventual application of this framework is to accelerate many-query problems such as shape optimization and uncertainty quantification.
Evaluating Model Uncertainty to Inform Offset Ratios for the Protection of Freshwater Fish Productivity in Canada
Keywords: Aquatic science
Fish
Fisheries
Modeling
Offsetting
Uncertainty analysis

Ecological models allow resource managers to evaluate human impacts on fish and their habitat. However, quantitative methods that incorporate and assess uncertainty in these models are rare. These models require fish life history information, which is often uncertain, and can thus lead to uncertain predictions and pose risks to either the environment or proponent. I utilized a multispecies size spectrum model to evaluate uncertainty surrounding estimates of three fish life history traits: (1) asymptotic weight; (2) the von Bertalanffy growth coefficient; and (3) weight at maturity. I then applied an existing framework for quantifying compensation ratios to achieve “no net loss” (NNL) in the context of a theoretical development project. The results of this study show that asymptotic size and forage fishes have the greatest influence on predictive uncertainty. I recommend that sampling effort be prioritized for these and demonstrate how to account for uncertainty in a precautionary management framework.
Associations between the Spatiotemporal Distribution of Kawasaki Disease and Environmental Factors: Discovering Clues into the Elusive Etiology of a Complex Disease
Keywords: Etiology
Kawasaki disease

Kawasaki disease is an acute vasculitis of childhood which may lead to coronary artery aneurysms, and is the most common cause of acquired heart disease in children in developed countries. The etiology remains unknown, but is currently felt to be the result of a dysregulation and hyper-stimulation of the inflammatory system occurring in genetically and developmentally susceptible individuals after exposure to one or more unidentified infectious or environmental trigger(s). The aim of this thesis was to determine how variations in the incidence of KD in Canada are spatiotemporally associated with the incidence of infections and atopic conditions, wind and weather components, pollution and aeroallergens. We established that immunomodulation may be influenced by pollution and habitual exposure to aeroallergens. We proposed that fungal and algal spores, viral gastrointestinal and bacterial lower respiratory tract infections may trigger KD. These findings add to the etiologic framework for KD.
Public Perception of the Scope of Practice of Oral Maxillofacial Surgeons in Ontario
Keywords: Oral Surgery
scope of practice

Purpose: Investigate and compare the General Public’s, General Dentists’ and Primary Care Physicians’ level of knowledge of the scope of practice of Oral and Maxillofacial Surgeons (OMS). Materials and Methods: A mail-out survey of the General Public, General Dentists and Primary Care Physicians in Ontario, Canada. Survey consisted of a screener along with 24 clinical scenarios. Responses between groups were compared to identify any significant differences between subjects with P value set at 0.05. Results: The majority of Dentists (100%) and Primary Care Physicians (95.5%) have heard of OMS, in contrast only 73.7% of the General Public (p
Teaching Electronic Medical Record (EMR) Data Discipline to Clinical Trainees: A Canadian Pilot Study
Keywords: data quality
electronic medical records
medical education

Evidence suggests that patients whose electronic medical records (EMR) are documented with high quality data obtain higher quality care. However, most clinicians do not routinely document with this data discipline, and to date how to instruct this has not been clear. In this study, the key components of such an educational session for Canadian family medicine trainees were determined, with a particular focus on improving trainee awareness of the importance of data discipline and their understanding of data consistency. We piloted our developed session in three academic teaching sites and found no statistically significant difference when comparing two instructional methods – exploratory case simulations versus didactic only. However, trainee performance in general was satisfactory, suggesting robust immediate learning regardless of teaching method. Trainees also confirmed a strong desire for education on data discipline. Going forward, the educational session can be improved, become embedded in curricula, and evaluated using real-world EMR data.
Assessing the Viability of Wideband Transmission of Pulse Width Encoded Data Over an Inductive Link for Wireless Neural Implants
Keywords: implant
neural
wireless

To date, there are no clinically available cortical neural implants which wirelessly transmit the full neural signal at an adequate data transfer rate while managing power dissipation limits. The current work addresses power consumption and data bitrate requirements using wideband transmission, omitting the use of a constant carrier wave, and short impulses to transmit pulse width modulation encoded data, transmitting more effective bits per cycle. An inductive link is used, reducing power consumption compared to radio frequency transmitters. 1 Msample/s transmission rate with 6 bits of resolution is demonstrated, providing proof-of-concept for a system that transmits the full neural signal outside the body. Such a system enables extracorporeal processing of the neural signal, potentially lending itself to applications such as brain-computer interfaces and diagnosis and treatment of neurological disorders. The intelligence of the system can be adjusted according to scientific advancements, without being limited to processing power onboard the implant.
Identifying the mRNA Targets of the RNA-binding Protein TIA-1 in Human Neurodevelopment
Keywords: neurodevelopment
RIP-seq
stem cells
TIA-1

TIA-1 is an RNA binding protein that is implicated in neurodevelopment. I conducted RIP-seq on lysates from three in vitro stages of neurodevelopment: human embryonic stem cells (hESCs), neural progenitor cells (NPCs), and cortical neurons, to identify TIA-1 targets during neurodevelopment. Despite minimal changes in TIA-1 expression or localization, TIA-1 binding efficiency decreases over neurodevelopment. RIP-seq identified 2365 TIA-1 targets in ESCs, 846 NPC targets, and 330 neuronal targets. ESCs targets included genes associated with neurodevelopment and autism, which were not bound in neurons. I validated TIA-1 binding to two mRNA targets critical to neurodevelopment, UBE3A and MECP2, using RIP qRT-PCR. These results provide insight into the network of TIA-1 targets during neurodevelopment and provide a first step towards defining the functional role of TIA-1 in neuronal differentiation. They suggest that TIA-1 regulates neurodevelopmentally relevant transcripts in early stages of development, but that this regulation decreases during neuronal differentiation.
Moisture Diffusion through Nanoporous Membrane and Protective Vents: Characterization and Modelling
Keywords: Gore-Tex
Moisture permeation
Moisture transmission
Nanofibrous membranes
Porous membranes

Porous membranes are widely used in various industries. Outdoor electronics that generate significant heating commonly use protective vents to allow free thermal expansion and contraction of air within their enclosure aimed to prevent pressurization. Fibrous membrane may be installed as a protective vent to stop contaminants and foreign particulate from entering the electronic enclosure. A challenge frequently encountered with these breathable vents is that moisture can easily permeate through them and diffuse into the electronic enclosure. If the internal relative humidity approaches saturation point, the risk of condensation intensifies. Formation of liquid water can potentially damage the electrical components or lead to a short-circuit. In this thesis, moisture transmission through a commonly used protective nanofibrous Gore-Tex vents was studied in various ambient conditions and a model was developed to estimate the internal relative humidity of a select electronic enclosure by calculating the moisture permeation rates in a transient environment.
An Integrative Analysis of the Effects of Neonicotinoid Pesticides on North American Hummingbirds
Keywords: dose-response
hummingbirds
imidacloprid
integrative biology
neonicotinoid pesticides

Neonicotinoids are neurotoxic systemic insecticides applied extensively worldwide. The impacts of neonicotinoid exposure on invertebrates are widely studied, however effects on essential vertebrate pollinators like hummingbirds have received little attention. My study into the effects of imidacloprid, a common neonicotinoid, on hummingbirds integrates lab-based and field-based assays with emphasis on cellular, systems, whole-organism, and behavioural levels. Within 2 h of exposure, hummingbirds exhibited a significant depression in energy expenditure (up to 25% +/- 11%). I did not observe effects on feeding behaviour, immune response, or cholinesterase activity in the lab, or stress hormone deposition in feathers collected in the field. I also determined that hummingbirds excrete imidacloprid quickly (elimination half-life of 2.1 h +/- 0.1 h) relative to other bird species. Hummingbirds exist on narrow energy margins, especially during migration and breeding seasons. Therefore, changes in their metabolism following exposures to imidacloprid observed herein could bear important energetic consequences.
Identifying Cases of Spinal Cord Injury/Disorder in an Ontario Primary Care Electronic Medical Record Database
Keywords: Case identification
EMR
Spinal cord injury

Currently, little health system information exists on the longitudinal course of spinal cord injury (SCI). The increasing availability of information from electronic medical records (EMR) offers an opportunity to fill this gap. An initial keyword search of all eligible records in a database of primary care EMR in Ontario, Canada, was conducted to identify possible cases of SCI. A random sample of possible cases was selected (n=803) and reviewed using a structured chart review process. 126 validated cases of SCI were identified and this reference standard cohort was used to develop and test potential algorithms. The optimal algorithm uses a combination of free-text keywords and ICD-9 codes, with a sensitivity of 70.6%, a positive predictive value of 89.9%, and an F-score of 79.1%. This cohort can be linked with administrative data to study longitudinally the health status and health care utilization of this population.
The Neurotrophic Actions of TCAP-1 in an Immortalized Neuronal Cell Line Under a Chronic-exposure Model
Keywords: Neurons
Neuroscience
Peptides
Signalling

Teneurin C-terminal associated peptide (TCAP) is a highly conserved ancestral bioactive peptide known to antagonize the cortical stress response. Recently, TCAP-1, along with its receptor, latrophilin, have shown to regulate energy metabolism in muscle cells, exhibited by increased glucose uptake, NADH turnover, and ATP production in vitro. Neurons, however, have historically failed to exhibit robust Ca2+ regulation upon acute TCAP-1 administration, challenging the notion of conserved intracellular signalling mechanisms across excitable cell types. Subsequently, I hypothesized that chronic TCAP-1 treatment would potentiate Ca2+-mediated outcomes, such as mitochondrial activation, morphological alterations, and glutamatergic signalling, in an exposure time-dependent manner. To test this, I examined the effect of a chronic TCAP-1 treatment in modulating neuroprotection, cytoskeletal dynamics, O2 consumption, and glutamate receptor expression in the N38 neuronal cell line. Taken together, findings indicate reversal of the ‘Warburg Effect’ via the differentiation of neurons upon chronic administration of TCAP-1.
Hardware Acceleration of Biophotonic Simulations
Keywords: Biophotonics
FPGA
HPC
Monte Carlo
OpenCL

The simulation of light propagation through tissue is important for medical applications like diffuse optical tomography (DOT), bioluminescence imaging (BLI) and photodynamic therapy (PDT). These applications involve solving an inverse problem, which works backwards from a light distribution to the parameters that caused it. These inverse problems have no general closed-form solution and therefore are approximated using iterative techniques. Increasing the accuracy of the approximation requires performing many light propagation simulations which is time-consuming and computationally intensive. We describe algorithmic techniques to improve the performance, accuracy and usability of the fastest software simulator for forward light propagation, FullMonteSW. Additionally, we explore two acceleration methods using a GPU and an FPGA. Our results show that the GPU and FPGA accelerator improve the performance by 4-13x and 4x, respectively, over the software baseline. We give insight for improving the performance and usability of the GPU- and FPGA-accelerated simulators for various medical applications.
Experimental Implementation of DC Microgrid with Energy Management System
Keywords: DC
Energy Management
Microgrid
Power Electronics
Renewable Energy
Solar

Due to the impacts of climate change, there is a need to reduce emissions from fossil fuel based electricity generation. DC microgrids are effective for integrating solar photovoltaics and battery energy storage together with local loads due to simple power conversion and control systems. This thesis focuses on a decentralized energy management strategy for a DC microgrid operating in islanded mode to ensure long-term health and protection of the battery energy storage systems. The energy management system utilizes variable-intercept droop characteristic adjustments to balance the state-of-charge of multiple storage elements, and a renewable source limiter to avoid overcharging batteries. The functionality of the energy management approach was validated through PSCAD/EMTDC simulations, and an experimental DC microgrid consisting of a PV source, two energy storage systems, and a DC load. The proposed decentralized energy management system achieved the intended objectives and proved its successful application to practical DC microgrids.
Hot, then Cold: Predicting Hypothesis Revision Strategies across Development with Rational Process Models
Keywords: Bayesian inference
belief revision
causal inference
causal learning
explore-exploit dilemma
process model

This research explores the hypothesis revision strategies of adults and children, and develops two computational models of Bayesian inference that predict distinct patterns of behaviour observed across development. Data were collected for adults (N = 90) and 4- to 6-year-old children (N = 119) on a causal inference task in which initial evidence supported a naively salient hypothesis, but was followed by evidence which violated this hypothesis. Consistent with prior work, adults showed an “exploitation-biased” strategy, performing better in a condition where the true rule governing the causal outcomes of the task was reachable through a process of iterative hypothesis revision than in a condition where reaching the true rule required abandoning a local optimum. Children, on the other hand, did not display this bias and performed equally in both conditions, perhaps due to a willingness to more broadly explore alternative hypotheses.
A Biomechanical Assessment of Stepping into and out of a Bathtub using a Temporary Rim-mounted Grab Bar
Keywords: Bathing
Bathing difficulty
Bathing safety
Grab bars
Rim-mounted grab bars
Temporary grab bars

Temporary rim-mounted grab bars are often recommended when installing a permanent grab bar is not feasible; however, their safety and effectiveness is unknown. This thesis explores the effect of using a rim-mounted grab bar for assistance as 10 older adults with bathing difficulty stepped into and out of the bathtub. Compared to the low and high rim- mounted grab bars, the vertical grab was safer and more effective at reducing task demands and preferred by participants. The high rim-mounted grab bar may reduce some task demands compared to low. Further research is required to investigate whether rim-mounted grab bars can withstand forces applied during use. Four participants refused to step into and out of the bathtub using only the wall. A summary of lower limb joint angles across all conditions provides insight into range of motion requirements to complete the task. Findings may inform clinical recommendations, grab bar design, and standards.
Determining the Role of Gαi3 in Ischemic Cardiac Injury
Keywords: Cardiac ischemia
Fibroblast
Gαi3
Macrophage

Gαi3¬ knockout was previously shown to reduce acute murine infarcts following ischemic injury. We assessed long-term effects of Gαi3 knockout on cardiac outcome by performing transthoracic echocardiography in Gαi3 wild-type and knockout mice at 1-, 2- and 4-week timepoints after permanent LAD-ligation. Additionally, we assessed region-specific cardiac fibroblast density and macrophage populations in Gαi3 wild-type and knockout mice at 5- and 28-day timepoints after injury. There were no significant effects of genotype on mouse cardiac function observed by echocardiography nor any effects of genotype on region-specific cardiac fibroblast density and cardiac macrophage populations after injury. Despite lack of statistical significance, Gαi3 knockout appeared to improve left-ventricular fractional shortening, anterior wall thinning cardiac fibroblast density in infarcts after injury. Prospective studies determining validity of these potential phenotypes should be conducted in larger mouse cohorts using transient LAD occlusion as Gαi3’s regulation of cardiac recovery was previously elucidated using an ischemia-reperfusion model.
Using Insect Communities from Window-pane Traps to Test the Sustainability of Forest Management in Northern Temperate Hardwood Forests
Keywords: DWD
Single-tree selection
Snag
Temperate
Vertical stratification

Conservation of biodiversity is an essential component of single-tree selection (STS) harvesting in Ontario’s hardwood forests. Here, I compare family-level insect communities (Coleoptera, Diptera, and Hymenoptera) between mature STS-managed and unmanaged stands. I also investigate the effects of trap placement on insect communities, including traps located in the lower-canopy and understory of sugar maple and eastern hemlocks and adjacent to early- and late-decay snags and downed woody debris (DWD). Finally, I explore insect community variation as a function of tree community composition and the quality and quantity of DWD and snags. In total, 57,434 insects were collected, and no overall statistical differences were observed between communities in differently managed stands. However, strong effects on insect community composition and larval trophic guilds were observed due to trap placement. I found little evidence that insect communities varied with habitat features, although abundances of several coleopteran and hymenopteran families varied with DWD quantity.
Design of Pressure Feedback Sensors for Miniaturized Intra-ventricular Neurosurgery Robotic Tools
Keywords: Concentric tube robots
Contact mechanics
Flexible pressure sensor
Haptic feedback
Microelectromechanical systems
Minimally invasive surgeries

Remote-controlled minimally invasive neuroendoscopic robotic surgical tools can be miniaturized to less than 2 mm-diameter range while maintaining their dexterity and force required to perform operations without open-skull surgeries. However, these platforms lack haptic information for surgeons, leading to possible loss of control over tissue. This thesis investigates two places on the surgical tool for integration of sensor systems: the bendable tube shaft of recently developed concentric tube robot, and the miniaturized magnetically driven forceps. For the tube shaft, a highly sensitive resistive based sensor is optimized, developed and wrapped around to provide force and location feedback while being adaptable to the tube’s changing curvatures during operation. For the microgipper, a microstrutured capacitive sensor design is proposed and optimized using computer simulations to measure normal and shear stresses. These sensors are then developed using microfabrication techniques before subjecting to bench-top and brain phantom tests for assessments of their performances.
Alveolar-Like Stem Cell-Derived Macrophages Protect Against RSV Induced Lung Damage
Keywords: alveolar like macrophage
alveolar macrophage
macrophage
respiratory syncytial virus
rsv
rsv therapeutic

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in young children and infants. There are no approved vaccines or effective antivirals. Alveolar macrophages are known to play an essential role in establishing and resolving the inflammatory response to infection. We have investigated the capacity for alveolar-like macrophages (ALM) generated from stem cells to protect against RSV infection and pathology. We initially established that ALMs are not productively infected by RSV, and co-incubations of ALMs and RSV led to a dose- and time-dependent reduction in viral titer. During in vivo studies, ALM groups were given an intra-tracheal instillation of ALMs prior to infection. Mice given ALMs prior to infection showed reduced weight loss, lower viral titers, and evidence of reduced lung inflammation and injury. These results suggest that ALMs currently being developed for lung disease therapies may be beneficial in protecting against RSV pathology.