VictorJuiz/thesis huggingface dataset:
Bacterial Stress Responses in Synthetic Biological Systems
Keywords: Biosensor
Stress Sensing
Synthetic Biology

Synthetic biology applies engineering principles to rationally design artificial biological systems, often constructed from combinations of naturally-occurring functional units found in a variety of organisms. For some real-world applications, it is important that these systems are designed to sense their environment, allowing for condition-dependent behaviour. Every organism has some form of stress response system enabling it to respond to a fluctuating environment; in Escherichia coil this includes the σ-factors, a protein family that initiates transcription. Preliminary work presented in this thesis is aimed to adapt select σS-controlled gene promoters to serve as stress sensors in synthetic biology. Results obtained in the probiotic E. coli Nissle 1917 strain demonstrate that several gene promoters displayed clear and significant up-regulation in promoter activation when exposed to additional varying concentrations of salts and acidic stress. Overall, this result provides an initial characterization for the adaptation of stress-responsive promoters as sensors.
Temporal and Spatial Variations of Tropospheric Ozone over the Arctic
Keywords: Arctic
Ozone
Spatial
Trend
Troposphere

This study aims to address the temporal and spatial variations of tropospheric ozone over the Arctic from the 1980s to 2010s, using ozonesonde data and the Trajectory-mapped Ozonesonde dataset for the Stratosphere and Troposphere (TOST) data. In the lower and middle troposphere, ozone abundances are the highest over Europe and over the Atlantic between 60-70°, while in the upper troposphere, ozone peaks over the Canadian Arctic. Seasonally, the regional means of ozone abundances in the lower and middle troposphere usually are at maximum in spring. During the four decades, the ozone trends over the Arctic troposphere are generally positive, and the fastest increase took place in the 1990s. By season, the increasing trends are larger in winter and spring than in summer and fall. This study offers new understanding of the tropospheric ozone variations in the entire Arctic from perspectives of spatial variations, seasonal variations, and long-term trends.
Stratify Colorectal Cancer Patients using Longitudinal QoL Measures and Explore Overall Survival
Keywords: Colorectal cancer patients overall survival
Genome wide association analysis
Growth mixture model
Longitudinal quality of life (QoL) measures
Stratify colorectal cancer patients

Colorectal cancer (CRC) is the third most common and deadly cancer worldwide. This study tends to have compressive exploration on the quality of life (QoL), the genetic variants, and overall survival (OS) performance for CRC patients. This is a placebo-controlled randomized trial with 750 CRC patients diagnosed with wild-type K-RAS CRC. Summary score of EOTRC C30 QoLs was calculated for each patient at different time points. Baseline summary score and change of QoLs were estimated for each individual based on longitudinal measurements by using growth mixture model (GMM). For each of the two treatment groups, patients were clustered into different subgroups by GMM. The clustered QoL subgroups show significantly different survival performance. Besides that, patients with higher baseline QoLs tend to have a better survival outcome. No genome wide significant genetic association has been identified. By studying the QoL clusters, we could help to predict CRC patients’ clinical outcomes.
Renal Consequences of Cadmium Exposure Among Pregnant Women in Dhaka, Bangladesh Receiving Placebo or Vitamin D Supplementation: An Observational Cohort Study Nested within a Randomized Controlled Trial
Keywords: Bangladesh
Cadmium
Pregnancy
Renal health
Toxic metals
Vitamin D

Bangladeshi women are exposed to the toxic metal cadmium (Cd) through consumption of contaminated foods, and exposure to tobacco products. At high levels of vitamin D supplementation, increasing gastrointestinal uptake of Cd may occur. Cd exposure could lead to renal dysfunction, especially during a sensitive period such as pregnancy. In a cohort of pregnant Bangladeshi women enrolled in a randomized placebo-controlled trial of vitamin D supplementation in Dhaka, we examined the effect of vitamin D supplementation on maternal blood and cord blood Cd concentrations and the association of Cd with renal biomarkers. There was no effect of vitamin D supplementation on maternal blood Cd concentrations at delivery; however, vitamin D supplementation increased the probability of detecting Cd in cord blood. Maternal blood Cd concentrations were not associated with markers of renal functioning. Further work is required to clarify the potential effect of vitamin D on maternal-fetal transfer of Cd.
The Sources of Microplastics in San Francisco Bay, California, USA
Keywords: Analytical chemistry
Aquatic ecology
Marine debris
Plastic pollution

Understanding the sources of microplastics to an ecosystem informs mitigation. Here, I determined the importance of specific sources of microplastics to San Francisco Bay – a heavily populated bay in California, USA. I quantified and characterized microplastics in surface waters of the bay and adjacent National Marine Sanctuaries (NMS). I also quantified and characterized microplastics in source waters: wastewater effluent and stormwater runoff. I compared the diversity of microplastics in source waters to surface water. My results suggest that stormwater runoff influenced microplastic concentrations in Central Bay and South Bay, while wastewater effluent influenced microplastics in North Bay and Lower South Bay. Our findings show that effective mitigation strategies may vary by location. Throughout this project, we came across difficulties identifying fibers using spectroscopic techniques and developed a method to circumvent barriers. The success of the method was confirmed and applied to samples from The Bay to demonstrate its applicability.
TXNIP and the GAPDH-Siah1 Signalling Pathway in Diabetic Nephropathy
Keywords: diabetic complications
diabetic nephropathy
thioredoxin-interacting protein
TXNIP

Thioredoxin-interacting protein (TXNIP) is markedly upregulated by high glucose (HG) and contributes to Diabetic Nephropathy (DN) development partly by inhibiting the endogenous antioxidant thioredoxin. We postulate that this contributes to the nitrosylation and oxidation of GAPDH, which has been found in neuronal cells to promote GAPDH-Siah1 binding and nuclear translocation, leading to apoptosis. The goal of this study was to determine if TXNIP regulates GAPDH-Siah1 signalling and if DN can be prevented by blocking this pathway. In vitro results show that HG caused significant nuclear localization of both GAPDH and Siah1 and upregulation of apoptotic markers in cultured wildtype mesangial cells (MCs), but not TXNIP-/- (KO) MCs. In vivo, deprenyl, an inhibitor of GAPDH-Siah1 binding, protected diabetic mice from developing various structural and functional markers of DN. These data suggest that the GAPDH-Siah1 pathway has a pathogenic role in DN and is downstream of TXNIP signalling.
Associations between Magnetic Resonance Imaging Detected Intraplaque Hemorrhage and Carotid Artery Atherosclerotic Plaque Components in Mild to Severe Stenotic Non-surgical Patients
Keywords: Atherosclerosis
Canadian Atherosclerosis Imaging Network
Carotid Artery
Intraplaque Hemorrhage
Multicontrast Magnetic Resonance Imaging
Volume

Stroke represents a major cause of death globally. One major cause of stroke is atherosclerosis, especially when developed in carotid arteries. Certain plaque components, such as intraplaque hemorrhage (IPH), lipid-rich necrotic core (LRNC), calcification, and high vessel wall (VW) volume are critical determinants for the stability of a plaque and can now be identified noninvasively with multicontrast magnetic resonance imaging (MRI). This thesis examined the feasibility of using a standardized multicontrast MRI protocol in a multicenter setting with only clinically available hardware and software and showed over 90% of patients had acceptable quality images to allow study of plaque components quantitatively. This thesis also examined the quantitative relationship of IPH with other plaque components. Specifically, the volume of IPH was significantly associated with volume of VW and LRNC but not calcification. Our results provided quantitative insights of IPH and may facilitate the planning of future multicenter endeavors studying carotid atherosclerosis.
Bidirectional and Multiple Reconfiguration of Discrete-event Systems
Keywords: Bidirectional
Discrete-Event Systems
Multiple
Nonblocking
Reconfiguration

Owing to the complexity and flexibility of modern industry, a system often has multiple operation modes and the reconfiguration mechanism is often required to be bidirectional. The unidirectional reconfiguration approach for discrete-event systems has been proved to effectively solve one-way reconfiguration problems modeled from real scenarios but fails to handle bidirectional reconfiguration problems. In this thesis, we study the fundamentals of bidirectional reconfiguration and multiple reconfiguration on discrete-event systems. Specifically, we introduce a bidirectional reconfiguration specification by analyzing states and events in each plant component and extend similar techniques to multiple reconfiguration in both monolithic and localized architectures. The proposed approaches are compatible with supervisory control theory, so the resulting supervisors can regulate both reconfiguration and normal behaviors of the system. Finally, the trigger requirement and guaranteed reachability are studied as notable issues in applications.
Control and Operation of a Utility Grid Connected DC Fast Charging Station
Keywords: Battery energy storage system
Electric vehicle
Fast charging
Short-circuit ratio
Supervisory control

This thesis investigates the impact and the performance of a grid-connected DC fast charging station (DCFCS) in a rural distribution system. The fast charging station consists of three DC fast chargers (DCFCs), each of which is rated at 800 V and 360 kW. The studies are conducted in time-domain using the off-line PLECS software. It is observed that, in the uncontrolled charging scenario, the lowest short-circuit ratios (SCRs) the charging station can operate in, without violating the system voltage drop constraint, are 7.1 under 2% unbalanced grid and 6.4 under balanced grid conditions. Subsequently, a curtailment scheme and a supervisory control strategy utilizing a battery energy storage system (BESS) are proposed to extend the DCFCS' operational SCR limit down to 4.0 in a 2% unbalanced grid. Both off-line and real-time simulation results verify that the BESS-enhanced DCFCS is able to operate under the extended grid SCR condition.
Scratching the Surface: Shear Dilation of Rock Joints Based on Quantified Surface Description
Keywords: dilation
in-elastic deformation
rock joint
rock mechanics
roughness
shear

In rock joints, the shear dilation deformation is heavily dependent on the details of the joint surfaces characterized by roughness. As a direct result of this deformation, the aperture of the joint changes, which in turn changes the transmissivity. Although dilation has been a recognized phenomenon, frequently seen in shear strength criteria, the deformation itself has been defined from its instantaneous inclination (dilation angle) by surface roughness parameters characterizing 2D profiles. This thesis aims to define the shear dilation deformation by relating roughness defined from 3D surfaces, stress, and displacements. The proposed dilation model is based on two 3D roughness parameters derived from digitized joint surfaces, and on results of twenty constant-normal-load direct shear tests conducted on natural rock joint replicas from bedding planes and tensile fractures, with another twenty supplementary direct shear tests performed on tensile fractured rocks. In the current study, only a subjective assessment of the effect of scale on roughness and the dilation deformation was made. The results and findings have been validated only in the range of joints surfaces and materials tested in the laboratory. Further investigations are needed to extend the applicability of the dilation model to field conditions.
Deep Radiomics Analytics Pipeline for Prognosis of Pancreatic Ductal Adenocarcinoma
Keywords: Pancreatic Cancer
PDAC
Radiomics
Transfer Learning

Pancreatic Ductal Adenocarcinoma (PDAC) is one of the most aggressive cancers with extremely poor prognosis. Radiomics has shown prognostic ability in multiple types of cancer including PDAC. However, the prognostic value of traditional radiomics pipelines, which are based on hand-crafted radiomic features alone, is limited due to high correlation among features and the multiple testing problem. Deep learning architectures, such as Convolutional Neural networks (CNNs) have been shown to outperform traditional feature-based approaches in computer vision tasks such as object detection. Nonetheless, they require large sample sizes for training which limits their application in medical imaging. As an alternative solution, CNN-based transfer learning has shown potential for achieving reasonable performance using datasets with small sample sizes. In this work, we developed a CNN-based deep radiomics pipeline based on transfer learning, which outperforms the traditional radiomics model in resectable PDAC prognostication.
Modeling and Design Optimization of Capacitive Touch Sensor Panels
Keywords: Capacitive Touch Sensor
Design Optimization
Human Computer Interaction

Nowadays, devices with capacitive touch sensors are more and more popular in our daily life. So far, engineers have mostly designed such sensors on a trial-and-error basis. This thesis introduces an efficient and systematic methodology for design, analysis, and optimization of capacitive Touch Sensor Panels (TSPs). It incorporates hybrid quasi-static/circuit simulations and applications of localization algorithms. An approach for optimizing electrode patterns of TSPs is also proposed. Pattern Search (PS) algorithm is applied to search for a TSP electrode pattern that provides high touch response and high localization accuracy. The optimized TSP has been validated by robust measurements using a Field Programmable Gate Array (FPGA) controller. Finally, results obtained from this optimized TSP have been compared with those of TSPs designed before. The end-to-end modeling tool developed in this thesis provides great insights for researchers in Human Computer Interaction (HCI) community.
Investigating Age-differences in Pattern Separation and Pattern Completion in a Cholinergic Framework
Keywords: Acetylcholine
Aging
Memory
Pattern Completion
Pattern Separation
Sustained Attention

Cholinergic function may mediate certain age-related changes in memory. Computational models predict that high cholinergic levels bias our internal states towards pattern separation processes and low levels toward pattern completion processes. Based on such predictions, I hypothesized that older adults, who often have reduced acetylcholine function compared to younger adults, would be impaired on tests of pattern separation compared to younger adults but not on tests of pattern completion. I also hypothesized these age-differences would be partially mediated by the integrity of their cholinergic system, which I will index using magnetic resonance imaging in my Ph.D., and currently index with sustained attention performance. In my preliminary sample, although older adults scored higher on the pattern completion index and lower on the pattern separation index than their younger counterparts, neither difference reached statistical significance. Eventually, I hope for my research to shed light on the variability of age-related memory changes.
The Role and Effects of CD200R Activation in Murine Models of Allergic Airways Inflammation
Keywords: Allergic Airways Inflammation
Aptamer
Asthma
CD200/CD200R
Eosinophilia
PEG.CCS13

The CD200/CD200R anti-inflammatory signalling pathway plays an important role in immune homeostasis and has been reported to be dysregulated in asthma, a chronic inflammatory airways disease. We hypothesized that activation of the CD200R will initiate an anti-inflammatory signalling cascade which will reduce features of asthma. We explored the role of the CD200/CD200R signalling pathway in the pathogenesis of an allergic airways inflammation model and evaluated the effects of CD200R activation with the agonist aptamer PEG.CCS13 on the features of asthma. Our results found the CD200/CD200R pathway imbalanced in a chronic model of allergic airways inflammation, suggesting it plays a role in the pathogenesis of the disease. We further found that activation of the receptor with PEG.CCS13 resulted in a reduction in features of asthma including eosinophilic inflammation, airway hyperresponsiveness and goblet cell hyperplasia. We concluded that activation of the CD200R is a promising therapeutic candidate for an asthma treatment.
Fine Position Estimation of the Myocardium using a UWB Radar for Magnetic Resonance Image Guided Cardiac Ablation
Keywords: Cardiac Ablation
GMM
MRI
Radar
Super Resolution
UWB

Heart surgeries, such as cardiac ablations, require an accurate estimate of the location of the myocardium in millimeters. This thesis develops the use of a UWB radar to track the position of the myocardium in real time. We construct a phantom to simulate the dielectric propagation path from the precordium to the myocardium which includes an obstacle to simulate the chest wall and a motion stage to simulate cardiac motion. We use an off-the-shelf radar operating with 6-10 GHz; however, this large bandwidth is still inadequate. Therefore, we utilize high sampling rates to interpolate, using the Gaussian transmitted signal, to obtain finer resolution. We test our approach by tracking the phantom position with a motion stage simulating sinusoidal and chirp movements. The results show that the radar can provide adequate resolution to track a myocardium phantom. We also successfully performed a preliminary verification on a human subject with ethics approval.
Mitigation of Classes of Attacks using a Probabilistic Discrete Event System Framework
Keywords: attack
control
cyber-security
discrete
mitigation
probability

Cyber-attack models and strategies for their mitigation have been studied recently in a deterministic discrete event system setting. The focus is on whether unsafe behaviour can be prevented using supervisory control. This thesis proposes the use of a probabilistic discrete event system (PDES) framework to incorporate a measure of the likelihood of unsafe behaviour in the attack model. The least unsafe (LU-)supervisor problem is introduced to minimize this unsafe likelihood measure and improve existing attack mitigation techniques. The LU-supervisor problem is reformulated as a Markov decision process (MDP) for analysis. The solution to the LU-supervisor problem is characterized under the assumption of full observability and an algorithm for its computation is developed. For partially observable systems, the LU-supervisor problem is shown to correspond to an infinite horizon partially observable MDP (POMDP) with a suitably chosen cost criterion. Lastly, the implementation of LU-supervisor is discussed and illustrative examples are presented.
Towards Robotic Cleft Palate Repair: Development and Characterization of a 3 mm Wrist for the da Vinci Surgical System
Keywords: cable guide channels
cleft palate
mechanical design
robotic surgery
robotic wrist
surgical instrument

Surgeons are interested in developing a robotic approach for cleft palate repair to improve outcomes and ergonomics for surgery in the infant oral cavity. However, the current instruments are too large for the workspace. The aim of this thesis was to develop a novel 2-degree-of freedom wrist with cable guide channels as a 3 mm diameter instrument for use with the da Vinci Surgical System. Specifically, a cam mechanism was built to solve the cable slack issue inherent to the novel wrist design. When evaluating motion accuracy, the mean error of moving in the same direction was found to be less than one degree, while the hysteresis resulted in an average error of 14 degrees when switching directions. Finally, proof of concept was demonstrated by using the instrument to suture silicone in a medicine cup, verifying that it is able to perform complex tasks and can apply sufficient forces, despite the hysteresis.
Exploring the Prevalence of Maltreatment amongst Canadian National Team Athletes
Keywords: Athletes
Canadian
Maltreatment
Prevalence

The purpose of this study was to assess the prevalence of maltreatment amongst National Team athletes in Canada. In total, 1001 male and female National Team athletes participated in this study, including 764 current athletes and 237 athletes who had retired in the last 10 years. Athletes completed an anonymous 127 item online survey consisting of questions on psychological, physical and sexual abuse, neglect, disclosure and reporting of instances of harm, and mental health outcomes. Athletes reported experiencing psychological harm most frequently, followed by neglect, sexual harm and physical harm. Harmful behaviours were enacted most frequently by coaches, followed by peers, high performance directors and sport administrators. The findings revealed significant and positive relationships between all forms of harm (psychological, physical, sexual and neglect) and the negative health outcomes of engaging in self-harming behaviours, disordered eating behaviours/eating disorders, and having suicidal thoughts. Finally, athletes provided recommendations for advancing safe sport.
Polarized Light Microscopy of Human Breast Cancer
Keywords: Breast Cancer
Collagen
Polarimetry
Stroma
Tumor Microenvironment

It has been shown that the stroma surrounding the tumour can play an important role in cancer behaviour and response to therapy. Polarimetry may be a suitable technique for this application because collagen, a fibrous component of stroma, is anisotropic and interacts strongly with polarized light. Polarimetry is also attractive because it is rapid, widefield, and non-ionizing. We proposed a novel and relatively simple methodology of polarized light microscopy to image thin, unstained histology slides using only crossed linear polarizers. The brightness of birefringent structures under crossed polarizers is dependent on the relative orientation of the structures and the polarizers. By imaging slides at various orientations, we can obtain retardance and fast axis orientation images, important measures of tissue biophysics. From images acquired, morphological features describing the density and alignment of the stroma within the tumour microenvironment are extracted to be used in a future breast cancer prognostication tool.
Re-evaluating the Other Accent Effect in Talker Recognition
Keywords: accented speech
language familiarity effect
phonology
speech perception
speech processing
talker recognition

Talkers are better recognized when they speak a language familiar to listeners than when they speak a language unfamiliar to listeners. This existence of this Language Familiarity Effect in talker recognition is uncontroversial. The Other Accent Effect (OAE), in contrast, is less well-established. Does a listener’s familiarity with a talker’s accent affect how well that talker is recognized? While some studies find an OAE, others do not. To resolve this apparent contradiction, we examined Canadian English listeners’ ability to recognize talkers in four conditions: a familiar language in the listeners’ own accent (Canadian English), a familiar language in another regional accent (Australian English), a familiar language in a non-native accent (Mandarin-accented English), and an unfamiliar language (Mandarin). We predict an OAE for the non-native but not for the regional accent, which is what we observe. We discuss how our findings bring us closer to resolving the OAE debate.