VictorJuiz/thesis huggingface dataset:
A Comparative Study of Regular- and High-fidelity Solvers for the Prediction of Aortic Hemodynamics
Keywords: Aorta Simulation
Aortic Hemodynamics
Computational Fluid Dynamics
Finite Element Methods
High-fidelity Solver

Computational Fluid Dynamics (CFD) simulations of cardiovascular systems are currently very time consuming. Simulation results significantly depend on the specific algorithms used and inappropriate choices of their settings may compromise accuracy. There is a clear need to understand the impact of algorithms and spatial/temporal resolutions on the accuracy of hemodynamics results. More efficient algorithms for cardiovascular flows in thoracic aorta are needed to allow incorporation of CFD simulations into the clinical decision cycle. In this thesis, we conducted a comparative study between regular-fidelity and high-fidelity CFD algorithms, in terms of performance and accuracy of predicted hemodynamic indices. The high-fidelity solver showed a superiority in detecting high-frequency flow patterns and, on par of accuracy, the high-fidelity solver was 150 times faster compared to the regular-fidelity solver. This thesis can also serve as a guideline to the selection of temporal and spatial resolutions to achieve accurate hemodynamic results for patient-specific aortic flow simulations.
Optical Measurement of Highly Reflective Surfaces
Keywords: 3D point cloud
Automated exposure selection
Image quality metric
Industrial metrology
Reflective surface measurement
Structured light (SL)

Measuring objects that have highly reflective surfaces with structured light (SL) is challenging. In traditional high dynamic range (HDR)-based technique, cumbersome exposure selection strategies are employed. This thesis proposes two novel SL-based methods to measure parts with highly reflective surfaces. First, an image enhancement-based method with only single exposure is developed. A new quantitative metric and a skip pyramid context aggregation network (SP-CAN) are proposed to select and enhance ingle-exposure images. Second, an automated exposure selection method is designed to improve the traditional HDR method. A new image quality metric is designed to evaluate captured images, based on which a multiple-exposures selection strategy is developed. Experimental results demonstrated that the first method can achieve 97.6% coverage rate and 0.040 mm measurement accuracy using only 0.6 second, while the second method can achieve a surface coverage rate of 97.4% and measurement accuracy 0.043 mm with only 3-4 exposures averagely (3.3 s).
Reconnecting with One's Lost Self: Experiencing the Emotion-focused Meditation Group Intervention
Keywords: Emotion-Focused Therapy
Grounded Theory
Group Therapy
LGBTQ
Mindfulness
Minority Stress

A qualitative approach was taken to explore the experiences of men who have sex with men (MSM) and who live with HIV (LWH) who participated in the Emotion-Focused Meditation (EFM) group intervention. EFM is an approach to meditation that combines key aspects of Emotion Focused Therapy with an open monitoring form of mindfulness known as Recollective Awareness. Archival audio recordings of group therapy sessions were transcribed and coded using a modified constructivist grounded theory approach to analysis. A core category of Reconnecting with One’s Lost Self: Experiencing the EFM Group Intervention emerged. A hierarchical model of reconnecting with one’s lost self was developed that subsumed all other categories. By extrapolating principles from this model, a theory of Reconnecting with One’s Lost Self was proposed which identifies factors that contribute to reconnecting with one’s lost self. Limitations of the current research are presented along with suggestions for further research.
Identification and Characterization of Bacterial Isolates that can Enhance Plant Immunity
Keywords: Arabidopsis
crop protection
induced resistance
PGPR
plant immunity
soil microbes

The ability of soil microorganisms to protect plants has been known for a century and their biotechnological use for crop protection has gained increasing attention. In this study, to identify bacterial strains that can protect crop plants and understand their mechanisms, two bacterial libraries were screened in Arabidopsis thaliana and/or Solanum lycopersicum (tomato) against Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst) DC3000. Through this project, a high-throughput imaging system was developed and in total, 19 bacteria were identified to mitigate disease symptoms. Some of these isolates exhibited direct anti-microbial activity, while other strains did not, suggesting that they induce immunity, termed induced systemic resistance (ISR). In addition, some of the strains showed plant growth promoting effects. Overall, I have established the high throughput method to identify plant immunity-inducing bacteria that can be used for further agricultural biotechnological research.
Remote Vital Signs Monitoring with Depth Cameras
Keywords: depth camera
heart rate
non-contact
remote
respiratory rate
vital signs

Remote monitoring of vital signs provides a low-cost, non-intrusive method of assessing an individual’s health. These systems have wide-ranging applications, including detection of patient deterioration in clinical settings and home monitoring of at-risk individuals. This thesis evaluates a novel remote vital signs monitoring system that integrates 3-D depth information and light intensity data to increase tolerance to subject motion. We use 3-D depth analysis and measurement of reflected light intensity due to blood volume variations to estimate heart rate and respiratory rate, two important vital signs. This method achieves a mean error of 1.7 beats per minute for heart rate and 0.05 breaths per minute for respiratory rate. Furthermore, techniques are also described to quantify the severity of motion artifacts, and methods of motion correction are applied to salvage physiological data from noisy signals. Future work will include examining additional data scenarios and improving analysis methods and motion tolerance.
(Re)Negotiating the Centre: A Qualitative Study Exploring the Black Community's Attitudes Towards Culturally Integrative African Healing Traditions and Western Psychotherapeutic Systems
Keywords: African Diaspora
African Healing Traditions
Critical Mental Health
Culturally Integrative Psychotherapy
Multicultural Psychotherapy
Western Counselling and Psychotherapy

The increased interest and use of holistic and traditional healing systems among diverse groups have inspired a demand for culturally integrative mental health treatments and research. This study used a postcolonial lens to explore how Canada’s African descendants might respond to a psychotherapeutic approach that culturally integrates African healing traditions (AHT) and Western systems. Ten participants were recruited for semi-structured interviews. The data were thematically analyzed using a grounded theory approach, and a mid-level theory was proposed. The findings indicated that the participants’ attitudes and experiences with AHT systems and Western psychotherapy influenced their attitudes and receptiveness towards interventions that aim to culturally integrate AHT and Western systems for psychotherapeutic purposes. Implications for clinical practice and theory were provided, along with recommendations for future research.
Regulation of Transporters in Human Placental Trophoblast Cell Lines
Keywords: ABC transporters
Inflammation
NF-kB
p38 MAPK
TH-17 cytokines

Pronounced inflammation or infection associated changes in the expression of many key placental transporters has been observed in human and rodent disease models, which are attributed to pro-inflammatory cytokines. Many infections and chronic inflammatory states are associated with activation of TH-17 and release of IL-17A and IL-23. However little is known about the impact of TH-17 associated cytokines on the expression of placental transporters. We observed a 50% decrease in the mRNA levels of BCRP and OATP2B1 in IL-23-/ IL-17-treated BeWo cells, while IL-17 reduced the mRNA levels of OATP2B1 and OAT4 by half in JAr cells. In BeWo cells, IL-17-/ IL-23-mediated downregulation of BCRP and OATP2B1 were attenuated by NF-kB and MAPK inhibitors. Similarly, IL-17-mediated downregulation of OATP2B1, but not OAT4, was attenuated with the NF-kB and MAPK inhibitors in JAr cells. These results suggest the placental transporter dysregulation caused by TH-17-associated cytokines is mediated through NF-kB pathway.
Docetaxel Loaded Nanobubbles for Ultrasound Triggered Antivascular Therapy and Localized Drug Delivery
Keywords: cancer
docetaxel
nanobubble
ultrasound

Docetaxel is a chemotherapeutic drug that plays an essential role in breast cancer therapy but exhibits suboptimal pharmacokinetic profiles with limited accumulation in tumours. In this thesis, ultrasound-stimulated, docetaxel-loaded nanobubbles are proposed to achieve localized drug delivery and induce antivascular therapy towards synergistic anti-tumour efficacy. Drug-loaded nanobubbles were synthesized via a precursor-lyophilization method. The drug loading capacity was found to increase with lipid concentration. DTX-NBs were formed with a mode diameter at ~230 nm, loaded with ~104 μg of docetaxel on ~1010 bubbles per ~0.4 μL of gas. Ultrasound cavitation facilitated the release of docetaxel and demonstrated comparable cytotoxicity to the commercial docetaxel formulation (i.e. Taxotere®) on mouse breast cancer cells. Ultrasound-stimulated nanobubbles were shown to induce acute blood flow reduction in the tumour center on Balb/c mice, indicating successful in vivo vascular shutdown due to nanobubble cavitation. These drug-loaded, ultrasound-responsive nanobubbles show high potential for increased anti-cancer efficacy.
Capturing Heightened Impulsivity In Adolescent Mice using A T-Maze Delay Discounting Task
Keywords: adolescence
delay discounting
dopamine
impulsivity
medial prefrontal cortex
ventral tegmental area

Delay discounting is a well-established measure of heightened impulsive decision-making during adolescence. The VTA and mPFC are implicated in delay discounting and undergo developmental alterations during adolescence. It remains elusive, however, as to whether the functional maturation of this circuit underlies age-dependent changes in delay discounting. In this study, we used a T-maze delay discounting task and found C57BLK6/J wildtype adolescent mice to exhibit steeper delay discounting than adults with a five second delay contingency. This difference in impulsivity was not driven by age-dependent abilities in cognitive and behavioural flexibility. To measure in vivo calcium signaling in dopaminergic VTA axons in the PL during delay discounting decision-making, we injected a Cre-dependent calcium sensor in TH-cre animals and saw no terminal viral expression after thirty days. Furthermore, TH-Cre adolescent animals exposed to deep anaesthetic ketamine did not exhibit heightened impulsivity compared to adult counterparts.
Investigating the Effects of Cranberry Proanthocyanidin and its Microbial Metabolites on the Human Intestinal MiRNome In Vitro
Keywords: cranberry
metabolites
microRNA
polyphenols
proanthocyanidin

The molecular basis underlying the known anti-inflammatory and anti-carcinogenic properties of cranberries is incompletely understood. The objectives of this project were to determine microRNA signatures of Caco-2BBe1 cells in response to a cranberry proanthocyanidin-enriched extract and two of its gut microbial metabolites, 3,4-dihydroxyphenylacetic acid and 3-(4- hydroxyphenyl)-propionic acid, evaluate if they were maintained in an inflammatory environment, and assess if the treatments mitigated inflammatory microRNA signatures. Each treatment generated a distinct microRNA signature, but the metabolites shared a “core” microRNA response. Treatment signatures were disrupted following IL-1β challenge, but the extract and 3,4- dihydroxyphenylacetic acid partially reversed microRNAs upregulated by IL-1β. Gene targets of microRNAs altered by the metabolites, but not the extract, were significantly enriched in many pathways relating to cell growth and development and pathways in cancer. Conclusively, the health effects of cranberry could be mediated via host microRNA and the gut microbiome may be indispensable to its bioactivity.
Progress Towards the De Novo Design of a Novel Protein Secondary Structure
Keywords: computational biology
de novo protein design
molecular dynamics
NMR
novel structure

Nature has sampled a very small fraction of the protein sequence space through evolutionary processes. The structures that these sequences adopt are relegated to permutations of just a few secondary structures. In fact, there are only two types of ‘regular’ secondary structures – the α-helix and β-sheet, although other types of non-regular secondary structures and random coils do exist. We hypothesized that novel secondary structures may exist in the unsampled space. To test this, we conceived of a spiral shaped secondary structure element not seen in nature. We created in-silico structural models and found amino acid sequences best predicted to stabilize the models. We synthesized designs and used CD and NMR spectroscopy to validate that our novel spiral secondary structure self assembles with an RMSD of ~4.5Å to the in-silico design. This study offers the first glimpse into a potentially vast world of undiscovered secondary structures.
Investigation of Modern Basketball Movement Demands by Film Analysis to Inform Training Interventions
Keywords: Basketball
Demands
Film-Analysis
Movements
Performance
Training Interventions

The feasibility and utility of film-analysis for studying basketball movements completed by NBA guards in the context of performance training was examined.The action type, plane of movement and estimated joint actions of ten NBA guards in five 4th quarter performances were characterized using count data. Athletes made 0.74 + 0.15 movements of interest per minute of performance. Four movements; Change of Direction, Single Leg Bound, Single Leg Jump, and Forward Curvilinear Acceleration, comprised > 80% of observations. Movements were primarily in the sagittal plane. Ankle Plantar Flexion, Knee Flexion, Hip Flexion, and Hip External Rotation were frequently observed. Principal Component Analysis indicated Flexion actions at the hip, knee and ankle were highly linked, while external rotation of the hip was independently important. The film analysis techniques were successfully utilized. Variation in exercise selection for the features of movement plane and joint action may better prepare athletes to meet demands.
Characteristics of Child and Adolescents Hospitalized with Eating Disorder Diagnoses in Ontario Over Time
Keywords: Eating Disorders

Methods: Population-based repeated cross-sectional design using linked health administrative and demographic datasets of individuals aged 5-17 years residing in Ontario between April 2002 and March 2020. Outcomes included rates, and relative changes in rates, of hospitalization overall and by patient sex, age and eating disorder diagnoses. Poisson regression models examined risk ratios of multiple hospitalizations.Results: The largest relative changes in rates per 10,000 population were observed for males (417%, 0.2 to 1.1), individuals aged 12-14 (196%, 2.8 to 8.1) and those with eating disorders other than anorexia or bulimia nervosa (254%, 0.6 to 2.2). Risk ratios of multiple hospitalizations decreased after 2011. Conclusion: Changes over time in the characteristics of hospitalized pediatric eating disorder patients have implications for health service planning, evaluation, clinical research and healthcare provider education.
Analyzing Stability and Protein Interaction of RNA Loaded “OnpattroTM” Lopid Nanoparticle
Keywords: Drug carrier
LNP
NTA
Protein corona
RNA
TEM

RNA medicines show potential to be viable treatments for multiple diseases, although treatments suffer from low bioavailability given the efficiency of the immune system at degrading RNA. This creates an urgent need for delivery systems, and lipid nanoparticles are the leading non-viral delivery systems. The stability and protein interactions of RNA loaded lipid nanoparticles made with the formulation used in OnpattroTM was analyzed. Size measurements were performed to analyze the nanoparticle characteristics as size is a sensitive attribute. Size is often measured initially for release of LNP drugs because it is a good reporter of undesirable traits in a nanoparticle formulation. Size measurements were performed using Nanoparticle tracking analysis, and Cryo-TEM was used to observe size and morphology. This project aims to understand the storage stability of the RNA loaded LNPs to establish better practices for handling and understanding protein interactions to better support future cell and animal studies.
A Low-Cost Low-Power Wide-Area Network For Environmental Sensing
Keywords: Internet of Things
LoRa Mesh Network
LPWAN

Sustainability and climate monitoring efforts create a need for long-term, in-situ sensing of large geographic areas. However, environmental monitoring in developing countries remains impeded by a lack of low-cost, scalable IoT solutions. Most existing IoT systems for in-situ sensing are either low-cost or suitable for large areas, but not both. This thesis presents CottonCandy, a LoRa-based mesh network solution with which nodes self-organize in a spanning-tree topology in a distributed fashion. Scalability is achieved by developing methods that mitigate packet collisions during data collection. Each CottonCandy node runs on a low-cost, custom-built circuit board and can operate for years on 2 AA batteries. Evaluations by simulation show that a CottonCandy network can be scaled to at least 100 nodes across hundreds of square kilometers and achieve a packet delivery ratio of >90%. Measurements of an outdoor deployment with 15 nodes corroborate the high packet delivery ratio in a real-life setting.
Pulmonary Microbial Composition and Density as Prognostic Markers in Lung Transplantation
Keywords: Bronchoalveolar Lavage Fluid
Chronic Lung Allograft Dysfunction
Lung Transplantation
Pulmonary Microbiome

Introduction: Allograft microbial community composition and density are associated with chronic lung allograft dysfunction (CLAD) in lung transplant recipients. Approach & Hypothesis: We assessed the performance of allograft microbiota for prediction of CLAD and hypothesized that quantitative (continuous) microbial predictors of CLAD would outperform categorical composition-only models of the lung allograft microbiota. Methods & Results: 16S rRNA sequencing of bronchoalveolar lavage fluid (BALF) from two cohorts of lung transplant recipients revealed three compositional ‘extremes’ of the lung allograft; community state types (CST). In a case-control study of lung transplant recipients who did or did not develop CLAD, clinical culture and density-normalized relative abundance of Gammaproteobacteria outperformed sequencing-based CSTs for prediction of CLAD. Conclusions: Clinical culture and absolute abundance of BALF microbes may predict CLAD in lung transplantation. The identification of these targets may allow the use of widely available, rapid, and sequencing-independent microbiome analysis for this application.
Demonstration of a Plarization-frequency Hyperentangled Photon Pair Source based on Periodically Poled Silica Fiber
Keywords: Hyperentanglement
Photon pairs
Quantum entanglement

Hyperentangled photons are particles of light that exhibit quantum correlations in multiple degrees of freedom simultaneously. The simultaneous entanglement in these degrees of freedom allows hyperentanglement to provide a distinct advantage over entanglement by increasing the information capacity per particle. Therefore, there is much demand for a high quality hyperentangled source, especially in fiber-based applications such as long distance quantum communication. Periodically poled silica fiber is a strong candidate for directly generating photon pairs in fiber, producing broadband collinear polarization-frequency hyperentangled photon pairs. However, collinear photon pairs cannot be simply accessed for practical applications without reducing their available information capacity. In this thesis, I investigate a method for separating these photon pairs while maintaining their original information capacity. I demonstrate the separation of the photon pairs, measure the degradation of the entanglement quality, and discuss the sources of this degradation as well as possible improvements to avoid degradation.
Mental Health Outcomes in Childhood Survivors of Physical Assault: A Population-Based Study
Keywords: Childhood
Mental health
Physical assault

Objectives: Compare the risk of adverse mental health outcomes and describe patterns of mental illness among children who experienced physical assault vs. non-assaulted children.Methods: Population-based matched cohort study comparing physically assaulted children 0–13 years old (n=5487) and age-matched non-assaulted children (n=27,435). Hazard ratios (HR) were generated for the primary outcome, incident mental illness. Results: Incident mental illness was highest in assaulted children (exposed: 53.3/1000 person-years, unexposed: 32.2/1000 person-years; adjusted HR (aHR) 1.96; 95%CI 1.85-2.08). The greatest risk of mental illness was observed in the first year following assault (aHR 3.08; 95%CI 2.68-3.54). Non-psychotic disorders were the most common mental health disorder in both groups and exposed children more frequently sought acute care compared to unexposed children (14.0% vs. 2.8%). Conclusions: Children who experience physical assault were at high risk of mental illness. Findings suggest there is an opportunity to support children in the first year following assault.
Advances in Mine Pit Wall Geological Mapping using Unmanned Aerial Vehicle Technology and Deep Learning
Keywords: Deep Learning
Drone
UAV

With rising costs and decreasing high-grade reserves, there has been an increased focus in mining operations to improve and to optimize current practices, including pit wall geological mapping. Proper mapping is critical for open pit mining operations since accurately and efficiently identifying the location, spatial variation, and type of geological features on mine faces will greatly decrease dilution and increase geological certainty. Conventional techniques rely on physically examining the pit walls in close proximity and laboratory testing of collected field samples, which are labour-intensive and can expose personnel to hazards such as falling rocks and machineries. Unmanned Aerial Vehicle (UAV) and deep learning (DL) techniques can improve and complement existing practices by efficiently acquiring high-resolution pit wall images and automatically predicting geological units. This thesis investigates the application of geological mapping using UAV-acquired RGB image data with DL models, and also demonstrates the advantages and limitations using these methods.