VictorJuiz/thesis huggingface dataset:
Analysis of Automated Fare Collection Data from Montevideo, Uruguay for Planning Purposes
Keywords: AFC: Automated Fare Collection
Public Transit
Smartcard

Automated Fare Collection (AFC) and smartcard systems have been rapidly adopted by transit systems all over the world. The datasets produced by these systems are extensive and can be analyzed for planning purposes and system evaluation. This thesis analyzes the AFC data from the bus transit system in Montevideo, Uruguay and proposes methods to reconstruct itineraries, identify the alighting locations of transactions, and understand travel behaviour of smartcard users. The methods used successfully build itineraries for 97% of bus runs, identify 87.7% of alighting locations, and recreate 67.5% of complete trip chains of smartcard users. The complete trip chain data is then used to pair smartcards with individuals from the Montevideo travel survey. Only 10 to 15% of individuals from the survey could be paired with smartcards. These findings have important implications for incorporating AFC datasets in transportation planning and evaluating transit systems.
lncRNA-GATA2: The Functional Role of Long Noncoding RNA GATA2 in the Vascular Endothelium
Keywords: Cell Identity
Endothelial
GATA2
Gene Regulation
Hypoxia
Long Noncoding RNA

Long noncoding RNAs (lncRNA) are new, important players in gene regulation. We examined the role of lncRNA-GATA2: a novel, abundant, cytoplasmic, endothelial cell (EC)-enriched lncRNA divergently transcribed from the GATA2 transcription factor (TF). Interestingly, four of the six GATA TFs loci harbor a divergent lncRNA (GATA2, 3, 5 and 6). We investigated whether lncRNA-GATA2 regulates EC phenotype and if this involves a relationship with GATA2. Loss-of-function studies demonstrated that lncRNA-GATA2 regulates 1374 EC genes. Several are EC-enriched, including ESM1, NOTCH4, vWF, and ANGPT2. lncRNA-GATA2 also controlled EC response to hypoxia through contrasting regulation of HIF1a and HIF2a. With respect to GATA2, lncRNA-GATA2 represses GATA2 protein. Importantly, we demonstrate lncRNA-GATA2 in GATA-family cross-talk and controlling the cell-specific GATA program, as lncRNA-GATA2 regulated the GATA TFs and associated lncRNAs. lncRNA-GATA2 regulates the EC phenotype in a context-dependent manner, through the regulation of enriched genes important for EC biology and the GATA family.
Priority Setting in Pediatric Preventive Care Research
Keywords: Health research
James Lind Alliance
Pediatrics
Preventive Care
Priority setting
Research priorities

Objectives: To identify unanswered research questions in pediatric preventive care that are most important to parents and clinicians and to assess differences in priorities between the two groups. Methods: Unanswered research questions were collected from parents of children aged 0-5 years and clinicians via an online questionnaire using a James Lind Alliance-developed methodology. Similar submissions were combined and ranked. Parents and clinicians selected the 10 most important unanswered research questions at a consensus workshop. The categories of questions from parents and clinicians were compared. Results: 1046 submissions were combined into 79 indicative questions. The top 10 unanswered research questions related to mental health, parental stress, physical activity, obesity, childhood development, behaviour management and screen time. Parents were more likely to ask questions about screen time and environmental toxins. Conclusions: The top 10 most important unanswered research questions in pediatric preventive care from the perspective of parents and clinicians were identified.
Hundred Farad-scale Supercapacitor with Monolithic Biochar Electrodes – a Feasibility Study
Keywords: Biochar
Large-scale
Maple-derived Biochar
Monolithic
Supercapacitors

Supercapacitors are high power density electrochemical storage devices that are hindered from widespread adoption by prohibitive material costs, low energy densities for practical applications, and poor scalability. This thesis seeks to solve all three issues by using large-scale monolithic maple-derived biochar as an effective electrode material. Biomass-derived carbon monoliths are pyrolyzed at 800oC and treated with 0.5M nitric acid at room temperature. Two electrode pairs, measuring ~5mm x 5mm x 5mm and ~23mm x 13mm x 10mm respectively, orders of magnitude thicker than typical supercapacitor electrodes, are tested using a suite of electrochemical techniques in 4M KOH electrolyte. Additional testing is done on large electrodes in 1M and 6M KOH, as well as in 1M TEA-TFB organic electrolyte. Capacitive performance of 107 F or 38.2 F/g is observed in the large monolithic electrodes, along with an exceptional energy density of 9.12 Wh/kg.
The Role of Deep Level States in the Optical and Electronic Properties of ZnSe Nanowires
Keywords: defects
microstructure
nanowires
optoelectronics

II-VI semiconductor nanostructures are excellent candidates for next-generation optoelectronic devices, including tunable emitters. ZnSe nanowires can be fabricated easily, and show promise in blue emission applications. However, their practicality is limited by deep level defect states that inhibit their performance. The primary objective of this thesis is to relate the defect structure to the optical and electronic properties of ZnSe nanowires. To this end, a heat treatment procedure to improve the microstructure was identified, and measurements were performed before and after the treatment. Using low temperature photoluminescence spectroscopy, the dominant recombination mechanisms were related to the total defect concentration. The carrier concentration and electron mobility were determined by electron transport measurements on single nanowire transistors. The measured experimental data was used to construct a model describing the type, energies, and ionized fractions of relevant defects, and develop an understanding of how ZnSe nanowires can be tailored for optoelectronic applications.
Food Literacy Education: A Philosophical Perspective
Keywords: Critical Democratic Dialogue
Critical Democratic Education
Food Literacy Education
Philosophical Dialogue
Philosophy Education
Secondary Education

In this thesis, I will argue through a critical democratic education lens for the inclusion of philosophical perspectives in a comprehensive food literacy education program in Ontario high schools. Food is a democratic issue of philosophical concern, requiring critical educational attention. I maintain that if we do not properly deal with food issues in schools we fail to fulfill the democratic social reconstruction aims of education. Utilizing a critical democratic dialogue framework, I combine the work of Laura Pinto and Heesoon Bai, whose approaches to collective communication promote social justice and critical democratic education. To conclude, I offer two concrete pedagogical applications of this framework to high school classrooms. This paper supports initiatives already underway to expand the teaching of food literacy in Ontario high schools, but is significant because of its focus on critical democratic education, and my strong insistence on the inclusion of philosophical perspectives and teachings.
Short-Term and Long-Term Performance of Glass Fibre Reinforced Polymer (GFRP) Bent Bars
Keywords: Bend
Creep
Fibre
GFRP
Stirrups
Sustained

Corrosion-resistant Glass Fibre Reinforced Polymer (GFRP) bars have been growing in popularity as an alternative to steel reinforcement. Newly developed GFRP bent bars were tested in this study, in which strength reduction of the bends in relation to the straight portion was investigated, as well as the long-term behaviour under sustained load. Two test methods were used to determine the instantaneous strength, consisting of 24 stirrups in the standardized testing procedure, and 10 bent bars in the shape of a “J” in a modified direct tension pullout test. The bend strengths ranged from 35% to 55% of the straight portion. Additionally, sustained load levels were applied to eight stirrups to determine the load level the bars could sustain for a 100-year service life. This stress was extrapolated from a logarithmic creep equation developed from regression analysis of the experimental results and found to be 50% of the ultimate short-term capacity.
The Liberal Arts Curriculum in China’s Christian Universities and Its Relevance to China’s Universities Today
Keywords: Christian universities
higher education reform
Liberal arts education
whole person education

This thesis considers the historical background, the development, and the characteristics of China’s Christian universities, with a special focus on their curriculum design. Through the lens of postmodern theory, the thesis explores the concept and essence of liberal arts education as reflected in the curriculum of the Christian universities through a qualitative methodology, focusing on the analysis of historical archival material. The purpose is to find insights for today’s trend towards reviving liberal arts education in China’s elite universities as a way of countering the influence of utilitarianism and neo-liberalism in an era of economic globalization.
Detecting Signals of Coevolution within Immune Response Pathways in the African-American Ancestral Population
Keywords: Evolution
Genetic interactions
Pathway analysis
Population genetics

The natural variation of human populations was shaped by mechanisms of evolutionary selection as our species began their worldwide migration thousands of years ago. Candidate gene and genome-wide association studies have revealed evidence for ancestry-specific positive selection, yet we lack insights regarding the broader biological context of population-driven selection. In this thesis, I describe my efforts to explore how interactions within biological pathways might impact evolution, using a comparative population-based analysis of pathway enrichment and inter-chromosomal allelic association. I compared genetic data from individuals of European-American and African-American ancestry, and identified enrichment for several biological processes, with prominent signals of genetic coevolution in two immune-associated pathways among African-Americans exclusively. Substantiated by considerable experimental-based literature, these findings suggest an effect of population variation on pathway-level selection, in which a global comparative analysis would further the ultimate goal of precision medicine.
Topological Origins of Bound States in the Continuum for Systems with Conical Intersections
Keywords: Born-Oppenheimer
bound states in the continuum
conical intersection
geometric phase
resonance states
stabilization method

Bound states in the continuum (BSCs) were reported in a linear vibronic coupling model with a conical intersection [Cederbaum et al. Phys. Rev. Lett. 2003, 90, 013001]. It was also found that these states are destroyed within the Born-Oppenheimer approximation. We investigate whether a nontrivial topological or geometric phase associated with the conical intersection is responsible for BSCs. To address this question we explore modifications of the original 2D two-state linear vibronic coupling model supporting BSCs. These modifications either add geometric phase effects after the Born-Oppenheimer approximation or remove the geometric phase within a two-state problem. Using the stabilization graph technique we have shown that the geometric phase is crucial for emergence of BSCs.
Borophene and Carbon Nitride Nanosheets for Energy Storage Applications
Keywords: energy storage
hydrogen
lithium sulphur battery
photocatalysis
surface chemistry
two dimensional materials

Borophene phases are a set of two-dimensional (2D) allotropes of boron that are excellent candidates as cathode materials in lithium sulphur (Li-S) batteries. Ab initio calculations were performed to determine stripped borophene and β12-borophene’s applicability as Li-S battery cathode materials. The calculations suggest β12-borophene would sufficiently inhibit the dissolution of lithium polysulphides into the electrolyte, preventing the “shuttle effect”. 2D carbon nitrides including tg-C3N4, hg-C3N4, C2N, and C3N were investigated as potential photocatalyst for solar water splitting, through first principles calculations. Band engineering via n-type, p-type, and isoelectronic doping was demonstrated for tuning the electronic structure, optimizing solar absorption and band alignment for photocatalysis. Among the dopants, Si and Ge dopants can narrow the band gap of carbon nitrides and increase their optical absorption in the visible spectrum. This work expands on the surface chemistry of borophene and comments on the complexities of substitutional doping with group IV elements.
CFD Modeling and Measurements of Jet Properties and Mixing Chamber Flow in a High-pressure Abrasive Slurry Jet
Keywords: Abrasive slurry jet
Aluminum 6061-T6
Computational fluid dynamics (CFD)
Erosion
Micro-machining
Slurry entrainment

Techniques to enhance the performance of a high-pressure abrasive slurry jet micro-machining process (HASJM) were investigated by altering the conditions within the nozzle. The slurry flow rate was controlled using inlet tubes of various diameters, and computational fluid dynamic (CFD) modeling was used to simulate the slurry entrainment process between the high-velocity water from the orifice and low-velocity slurry that occurred within the mixing chamber and mixing tube. The models correctly identified flooding conditions in which there was an increase in the net mass flow rate in the nozzle. Flooding was found to significantly reduce the jet velocity, thus diminishing its erosive efficacy which was assessed by machining blind holes and channels in aluminum 6061-T6. Differences in the centerline erosion rates of holes and channels for a given jet showed clear evidence of incubation and stagnation zone effects.
The Performance of a Zirconium-based Root-Filling Material with Artifact-Reduction Properties in the Detection of Artificially Induced Root Fractures Using Cone Beam CT Imaging
Keywords: Beam hardening artifact
Cone beam CT
Gutta percha
K absorption egde
Zirconium

Objectives: To describe a novel technique for characterizing beam hardening artifact (BHA) using cone-beam computed tomography (CBCT); and to evaluate the influence of the Zirconium-based (Zr) root filling material using CBCT in the detection of artificial root fractures (RF). Material and Methods: The palatal root canals of three phantom teeth were root-filled and subjected to CBCT imaging. The light and dark components of the BHA were quantified. 176 mandibular premolar teeth were divided between Zr and GP. RFs were induced in 44 teeth of each group. All samples were subjected to CBCT images. The images were evaluated by 6 examiners. Results: GP showed a significantly higher measurement of the ‘dark’ artifact (p
Identifying Factors Which Influence Medication Adherence in a Cardiac Rehabilitation Population
Keywords: Cardiac Rehabilitation
Cardiovascular Disease
Cardiovascular risk factors
Medication Adherence
Polypharmacy

Nonadherence to cardiovascular disease medications is a health-related behaviour which increases adverse patient outcomes and healthcare costs. Identification of factors which impact adherence levels in those undergoing cardiac rehabilitation may reduce cardiovascular mortality rates. We hypothesized that use of a greater number of medications and use of acetylsalicylic acid (ASA), beta-blockers and statins would result in lower medication adherence levels. A Poisson regression showed that those who were adherent were taking 1.15 (95% CI, 1.03-1.28, p=0.014) times more medications than those who were nonadherent. An analysis of covariance found the combined use of ASA, beta-blockers and statins was associated with higher adherence levels (F1, 242=5.76, p=0.017). Furthermore, lower cardiopulmonary fitness levels, increased depressive symptoms and forgetfulness were all associated with lower medication adherence levels. These findings suggest that factors other than polypharmacy and medication class – such as cognitive function, depression, or fitness – may negatively influence adherence rates in this population.
Development of a real-time algorithm for the detection of physiological arousal in the presence of motion among children with autism
Keywords: anxiety detection
autism
kalman filter
multimodal kalman filter
presence of motion

Anxiety is a clinical concern among some children with autism, for whom such an emotional onset may exacerbate core symptoms. Current treatment options are challenged as many of these children are unaware of their emotional state, and due to autism some children also have difficulties with language and communication which further complicates anxiety diagnoses. In this thesis, we proposed a novel automated anxiety detection algorithm capable of interpreting heart rate arousal in the presence of physical movements , and intuitively notifying the user to engage in anxiety management techniques. The novelty of our proposed algorithm is based on its ability to detect anxiety in presence of motion; this is a challenge as motion and anxiety influence the heart rate similarly. This algorithm was able to account for the changes in heart rate due to motion and detection anxiety with an accuracy, specificity and sensitivity of 92.7% in children with autism.
The Role of Perineuronal Nets in Learning and Memory
Keywords: generalization
hippocampus
memory
plasticity

The balance between stability and plasticity in the brain determines our ability to learn. A key molecular regulator of this balance includes perineuronal nets. Perineuronal nets are specialized extracellular matrix structures surrounding neurons, and have a presumed function in promoting stability within neural circuits. We investigated the effects of disrupting perineuronal nets, thereby enhancing plasticity, on learning and memory in mice. We found that perineuronal net disruption in the hippocampal CA1 region is associated with faster water maze reversal learning, and increased contextual fear generalization. Moreover, the population of active neurons is larger at retrieval of a contextual fear memory. These results demonstrate that perineuronal nets are important for learning and memory, and that shifts in perineuronal nets is associated with altered circuit level activity.
COMBINATORIALLY CONSTRAINED PORTFOLIO OPTIMIZATION USING MESSAGE PASSING ALGORITHMS
Keywords: Mixed Integer Programming
Portfolio Optimization
Probabilistic Graphical Model

Portfolio optimization aims to find the optimal investment strategy for a series of assets that results in a minimization of the portfolio's variance. Real life portfolio considerations like limiting the number of assets or limiting assets to be traded in lots add combinatorial constraints to the original problem that are computationally expensive for commercial solvers. The aim of this thesis is to explore the use of message passing approaches to solve the portfolio problem with these hard constraints. Message passing represents a class of algorithms used to solve inference problems in graphical models. They are known to recover good sub-optimal solutions and we test this for the posed problem by comparing with branch-and-bound exact methods. Computational results for the portfolio problem with varying cardinality, target return and portfolio size confirm that message passing is a viable method for finding sub-optimal solutions and can return tight bounds around the exact solution.
Characterizing contrast origins and noise contribution in spin-echo BOLD at 3 T
Keywords: Echo-time optimization
Spin-echo BOLD signal
Spin-echo physiological noise contribution

Spin-echo (SE) EPI is generally associated with lower BOLD sensitivity than its gradient-echo (GE) counterpart, limiting the use of SE-BOLD. However, SE-BOLD is less sensitive to physiological noise than GE-BOLD. Yet, unlike for GE, SE-BOLD signal origins and noise contributions haven’t been investigated empirically. In this work, we introduce a two-compartment SE-BOLD model that integrates a physiological-thermal noise model. We fit this model to SE-BOLD fMRI data acquired during hypercapnic manipulations at various echo times (TE) at 3 T in order to characterize SE-BOLD contrast and noise behaviour, and identify optimal contrast-to-noise (CNR) settings for SE-EPI. Our results quantitatively demonstrate that the physiological noise contribution in SE-BOLD signal is lower than that of GE. Importantly, we demonstrate that CNR for SE is maximized at TEs lower than the typically used tissue T2. These findings will lead to improved SE-BOLD sensitivity, making it a more attractive choice for fMRI studies.
Prophylactic Bisphosphonate Therapy to Reduce Glucocorticoid-Induced Osteoporosis in a Mouse Model of Duchenne Muscular Dystrophy
Keywords: Bisphosphonate
Duchenne Muscular Dystrophy
Glucocorticoid
mdx
mouse model
Osteoporosis

Glucocorticoids (GCs) is a standard therapy to prolong muscle function in Duchenne Muscular Dystrophy (DMD) but induce osteoporosis. Bisphosphonates are used prophylactically in adults starting chronic GC treatment but are not in DMD patients until after they sustain fractures. C57BL/10ScSn-mdx mice, a common DMD animal model, was treated with prednisone (0.083 mg/day) from 5-10 weeks of age. Prophylactic pamidronate (8 mg/kg) was administered over 2 or 6 weeks starting at 4 weeks of age to assess the two dosing regimens in ameliorating GCinduced osteoporosis. Pamidronate did not attenuate GC’s improvement on muscle function. GC caused cortical bone loss and decreased cortical bone strength. Two- and 6-week pamidronate treatment improved bone architecture but only 2-week pamidronate improved cortical bone strength. The improvement of bone strength seen only with 2-week pamidronate highlights the importance of when and how much bisphosphonate is administered prior to glucocorticoid exposure, rather than the total cumulative dose.
Compressed Sensing for Diffusion MRI of the Mouse Brain: A Trade-off of Spatial and Directional Information
Keywords: compressed sensing
conjugate gradient
diffusion mri
DTI
HARDI

Diffusion magnetic resonance imaging (MRI) uses loss of signal coherence caused by movement of water molecules to determine how water diffuses in tissue. These scans are known to take a significant amount of time owing to the repeated acquisition of images, each measuring diffusion for a particular direction and weighting. Emerging methods based on collection of increasingly large numbers of diffusion directions and/or weightings promise to provide a more detailed characterization of brain microstructure than previously possible. However, because the time required for these methods can render them impractical, I present a method of acquiring and reconstructing diffusion MRI data based on compressed sensing (CS) that enables flexible trade-off between spatial sampling and diffusion direction/weighting sampling. This method enables the collection of more diffusion data in a given scan time at the cost of extended reconstruction time.