VictorJuiz/thesis huggingface dataset:
Assessing Fish and Zooplankton Species Composition Patterns in Lentic Waterbodies

For ecologists to better analyze and interpret relationships between species and their abiotic and biotic environments, it is useful to study biogeographical patterns of species composition. I examined lentic fish and zooplankton species occurrence patterns and the importance of several predictor variables in relation to these patterns. Fish communities in two Ontario regions exhibited significant nested species composition patterns. Lake size was a significant predictor. One measure of lake isolation explained some residual variation in both regions. Top predator presence was a significant predictor in one region. Through a meta-analysis, I found that crustacean zooplankton communities from across the Americas demonstrated significant negative species co-occurrence patterns. Presence-absence matrix fill and number of sites were the strongest predictors of the departure from random species co-occurrences. Comparisons of species composition patterns and drivers for different taxonomic groups could provide further insight into the level and types of non-random structure in freshwater ecosystems.

Advisor: Jackson, Donald
Hybrid LCC and Multi-terminal Full-bridge Modular Multilevel Converters for HVDC Transmission

This thesis investigates the control and operation of an HVDC hybrid topology utilizing a line commutated converter (LCC) rectifier and a multi-terminal connection of modular multilevel converter (MMC) inverters. The hybrid LCC-MMC system leverage the features of both LCC and MMC technologies. The LCC is more economical, mature, and has a higher power capacity, while the MMC has a smaller footprint, reactive power control, no risk of commutation failure and can connect to weak AC systems. This thesis has four main objectives: (1) development of HVDC characteristic control curves for the proposed hybrid LCC-MMC system which describe operation under normal, DC fault, and AC three-phase-to-ground fault conditions, (2) manage current sharing amongst a multi-terminal connection of inverters, (3) define controls for FB-MMC operation, and (4) demonstrate operation of the proposed system through PSCAD/EMTDC simulations. The hybrid LCC-MMC topology represents a viable candidate to integrate remote energy sources to congested weak AC systems.

Keywords: HVDC
Hybrid
LCC
MMC
Advisor: Lehn, Peter W
Building Networking Applications from a NoC-Enhanced FPGA

An embedded Network-on-Chip (NoC) has been proposed to augment the traditional, fine-grained FPGA interconnect with a fast and efficient system-level interconnect. This thesis aims to build the case for its inclusion by presenting complete applications that can benefit from a NoC-enhanced FPGA, and tools to facilitate their design. The applications chosen – network switches and packet processors – target Software-Defined Networking (SDN), a rapidly growing field in computer networks. The presented network switch architecture uses the NoC as a crossbar and a new buffering scheme, achieving 819 Gb/s 16×16 switching, while being 1.8× and 1.6× more hardware- and power-efficient, respectively, compared to the most efficient previous FPGA-based design. A new packet processor design style is also presented, using the embedded NoC to provide high degrees of efficiency (1.7×-3.2× less area compared to previous work), performance (400G and 800G), and flexibility suitable for programmable computer networks.

Keywords: FPGA
Interconnection Networks
Network-on-Chip
Packet Processing
Software-Defined Networking
Switch Fabric
Advisor: Betz, Vaughn
Optimization of Highly Architectured Stereolithographic Microtrusses

Stereolithography allows architectural freedom which can be used to fabricate optimal architectures with the potential for significant enhancements in structural efficiency. In this study, buckling behaviour of compressive struts is explored. Experimental failure stress values for stereolithographic polymer tubes are found to agree with existing predictive models for Euler and local shell buckling, validating the methodology. Experimental testing on a space frame compressive strut design proposed in literature reveals end constraints between fixed and free, and stereolithographic design freedom is considered to reduce over-engineered features, improving performance. Finally, a novel sandwich wall tubular strut design is introduced: experimental results show successful inhibition of local shell buckling while also enhancing Euler buckling performance (improvements of 45% and 30% in failure strength when compared to equal-mass simple tubes, respectively). A new failure mode termed “wall splitting” is identified, and a preliminary model is developed to predict the increases in failure stress.

Keywords: 3D printing
buckling
space frame
stereolithography
structural optimization
Advisor: Hibbard, Glenn D
Retrieving Leaf Chlorophyll Content in Wheat and Corn using Landsat-8 Imagery

The purpose of this study is to develop a method of modeling crop leaf chlorophyll content (Chlab) using remote sensing data with a physically-based modelling approach. During the 2013 growing season, ground data were collected at 28 corn and wheat sites near Stratford, Ontario. Effective leaf area index, hyperspectral leaf reflectance and transmittance, and chemically extracted Chlab were acquired at each site. A two-step inversion process was developed to model crop Chlab using Landsat-8. In this process, a look-up-table (LUT) was developed using SAIL, a bidirectional radiative-transfer model, to simulate canopy reflectance. The LUT was then utilized to calculate leaf-level reflectance and input into PROSPECT, a leaf-level radiative transfer model, to estimate Chlab. Validation of PROSPECT with ground-based Chlab using simulated Landsat-8 bands shows an R²= 0.83 and RMSE=8.48 μg/cm². Validation using the LUT shows an R²=0.64 at the leaf level and R²= 0.87 at the canopy level.

Advisor: Chen, Jing
Antenna Measurement and Design for the CanX-7 Nanosatellite and the Development of a Global Navigation Satellite System Based Attitude Determination System

This thesis describes and presents solutions to various challenges small satellites may encounter during design and operation, particularly in the areas of communications and attitude determination. The first section of this thesis presents simulation and measurement of communications antennas on a nanosatellite to verify that the antennas have sufficient gain and polarization to enable near-omnidirectional operation. Near-omnidirectional antennas are essential to ensure reliable communication with the spacecraft regardless of its attitude, especially when fine pointing ability is unavailable or inadequate. Next, the following section covers the design of a circularly polarized patch antenna for use on an aircraft tracking payload. Lastly, the final section of this thesis presents the development and analysis of a technique for augmenting a single GPS antenna on a spacecraft to estimate attitude. It is possible for GPS measurements to partially supplement an existing attitude sensor that has been denied operation.

Keywords: Antenna
Attitude Determination
Communications
GPS
Microsatellite
Satellite
Advisor: Zee, Robert E
Consumer Wristband Activity Monitors as a Simple and Inexpensive Tool for Remote Heart Failure Monitoring

Daily physical activity is a strong indicator of heart failure (HF) severity that could help identify at-risk patients before acute decompensation and prevent late readmissions. However, remote-monitoring systems rarely incorporate any activity data. Consumer devices have made continuous activity tracking inexpensive and unobtrusive, but it is not clear whether such devices are suitable for monitoring patients. In this study 50 stable HF outpatients were given Fitbit Flex wristbands activity trackers to wear for two weeks to validate the use of these devices for remote monitoring. We developed metrics of peak activity based on minute-level step data that correlated with clinical cardiopulmonary exercise tests. These consumer devices were also found to be reliable with seamless data collection. Future studies examining the change of these activity metrics over longer periods time in relation to other indicators of HF will help establish the use of consumer devices as a viable remote monitoring tool.

Keywords: consumer
exercise capacity
fitbit
heart failure
physical activity
telemonitoring
Advisor: Cafazzo, Joseph
A Gaze into the Mind’s Eye: Gaze as an Indicator of Cortical Reinstatement during Mental Imagery

When a previously encountered image is visualized, the spatiotemporal pattern of fixations observed during encoding is often recapitulated. Modern theories posit that fixation recapitulation facilitates, and is facilitated by, the retrieval of detailed internal memory representations. However, there currently exists no direct neuroscientific evidence of this claim. Using an fMRI-based measure of neural reinstatement as a proxy for internal memory representations, we found significant correlations between fixation recapitulation and neural reinstatement during visualization. Additionally, we found a strong correlation between memory performance and neural reinstatement, which mediated a non-significant correlation between memory performance and fixation recapitulation. A secondary goal of the discussed research was the development of a fixation similarity measure optimized for visualization tasks. We found that a measure based solely on fixation angle outperformed a traditional location measure, supporting a chunk-based theory of fixation recapitulation. In total, our results support and extend current theories of fixation recapitulation.

Keywords: Cortical Reinstatement
Eye Tracking
fMRI
Memory
Mental Imagery
Scanpath
Advisor: Buchsbaum, Bradley
Investigations of the Expression, Activation and Functional Significance of Platelet-derived Growth Factor Receptor in Pediatric Glioblastoma

Solid tumours arising from malignant transformation of glial cells are one of the leading causes of central nervous system tumour-related death in children. Recurrence in spite of rigorous surgical and chemoradiation therapies remains a major hurdle in management of these tumours. Here, we investigate the efficacy of the second-generation receptor tyrosine kinase (RTK) inhibitor nilotinib as a therapeutic option for the management of pediatric glioblastoma. We have utilised two independent pediatric glioblastoma cell lines with either high expression of platelet-derived growth factor receptor alpha (PDGFRα) or PDGFRβ expression in in vitro assays to investigate the specific downstream effects of nilotinib treatment. We show that nilotinib inhibits ligand-dependent activation of PDGFRα and suppresses AKT signalling. Nilotinib furthermore decreases cell proliferation and colony formation, as well as in vivo growth of xenograft tumours. Our results suggest that nilotinib may be effective for management of a PDGFRα-dependent group of pediatric high-grade gliomas.

Advisor: Zadeh, Gelareh
Investigation of Fuel Nozzle Technologies to Reduce Gas Turbine Emissions

With increasing requirements for reduced emissions from future gas turbines, a multitude of research is being conducted into fuel nozzles by gas turbine manufacturers. This thesis focuses on the development of a novel spill return nozzle, to improve combustion efficiency at starting and low power conditions -where combustion efficiency is often the poorest. The spill return nozzle has the advantage of being able to improve atomization performance and reduce internal coking potential, all while being a simple and durable design. The spill return nozzle tech- nology was subsequently applied to a design for an existing small gas turbine combustor, and its improvements over the existing nozzle were demonstrated. The proposed design was also extended to experimental testing in a simplified form. CAD drawings of the components for testing were made, and prototypes were built in plastic using a high accuracy 3D printer. Future work involves conducting experimental tests to validate results.

Keywords: atomization performance
design methodology
low power
spill return nozzle
Advisor: Groth, Clinton P.T.
Sampath, Parthasarathy
Organizational Learning in the Morbidity and Mortality Rounds

The morbidity and mortality conference (M) is one of many organizational strategies used to address patient safety and quality of care. Organizational learning theory would suggest that learning from error in the M would be optimized by particular organizational and team cultures. The aim of this study was to describe how adverse events are reviewed in the M using an organizational learning framework. I used a qualitative, prospective, multiple Case study design for this study. I selected three Cases, which were running well-structured M All three Cases displayed double-loop learning and utilized organizational memory strategies to ensure that new knowledge stemming from their reviews was being retained within the organization. The presence of a patient safety culture was linked to the promotion of open communication, thereby fostering learning from adverse events. The M can therefore provide a context for organizational learning, allowing optimal learning from adverse events.

Advisor: Baker, G R
Vein-on-a-chip: A Microfluidic Platform for Functional Assessments and Staining of Intact Veins

The ability to perform systematic studies on vein function and structure is of key importance for understanding many vascular diseases and the underlying mechanisms governing transport of cells and macromolecules through the blood vessel wall, both of which are beneficial for drug discovery. Available experimental methods are limited by poor optical access and limited microenvironmental control for in vivo studies, and a partial representation of blood vessel structure in the case of in vitro approaches. In this thesis, I present a microfluidic platform for the in vitro investigation of intact mouse mesenteric vein segment (200-300 μm diameter and 1.5-2 mm length) function under near-physiological conditions. The lumen of the pressurized vein segments are stained on-chip for CD31 to highlight the capacity of our platform for in-situ immunofluorescence staining without the otherwise required tissue processing and sectioning. The selected approach is automatable and reduces the time and staining solution consumption by an order of magnitude compared to traditional methods.

Keywords: blood vessel
function
immunofluorescent staining
Microfluidics
organs-on-a-chip
veins
Advisor: Guenther, Axel
Mechanisms Regulating Intracellular Levels of Helicobacter pylori Cytotoxin Associated Gene A

Helicobacter pylori is a gram-negative pathogen that infects 50% of the population worldwide and is the most important risk factor for the development of gastric cancer, one of the leading causes of cancer-related deaths. I propose a complex interplay between two major virulence factors, CagA and VacA, in mediating disease. VacA is a pore-forming cytotoxin that disrupts the autophagy pathway. Current evidence suggests that the oncoprotein CagA can be degraded by autophagy. I demonstrate that the proteasome is involved in degrading CagA. Furthermore, I show that during chronic infection, VacA-disrupted autophagy promotes CagA accumulation through the concerted efforts of disrupted autophagy and impaired proteasomal clearance. Lastly, I present preliminary evidence of CagA accumulation in infected human gastric organoids, mediated by VacA-disrupted autophagy. Together, these studies provide insights into the mechanisms of regulation of CagA levels in host cells and the synergistic relationship between VacA and CagA during infection and disease.

Keywords: Autophagy
Cancer
Cytotoxin Associated Gene A
Helicobacter pylori
Proteasome
Vacuolating Cytotoxin A
Advisor: Jones, Nicola L
Development of the Structural and Thermal Control Subsystems for an Earth Observation Microsatellite and its Payload

Broad consensus has been reached in the scientific community that climate change is occurring and its cause is anthropogenic. Governments and other regulatory bodies are quickly implementing stricter and further reaching environmental regulations which require companies to regularly report emissions and penalize heavy polluters. To serve private and public end users in emissions monitoring GHGSat Inc. has contracted Space Flight Laboratory to develop Greenhouse Gas Satellite - Demonstration, or GHGSat-D, a remote sensing microsatellite with the mission objective of providing measurements of atmospheric carbon dioxide and methane at emission sources such as power plants and tailings ponds. This thesis presents the author's contributions to the development of the satellite and payload structure as well as the thermal control subsystem from mission concept to system level testing. Each section begins with a discussion of the driving requirements followed by relevant background information. Analysis and design work is then presented followed by noteworthy results.

Advisor: Zee, Robert E
Investigating Accelerated Long-term Forgetting: The Effects of Associative and Item Memory, and Semantic Relatedness on Long-term Retention

We sought to create a test that could delineate memory for semantically related and unrelated associative and item information, for future use with patients with temporal lobe epilepsy in the study of accelerated long-term forgetting. Healthy participants studied semantically related and unrelated object-scene pairs and completed forced-choice recognition tasks for item and associative memory over variable delays. Participants recognized significantly less associative than item stimuli by 6-hours post-study due to degraded memory for associative stimuli. While item memory remained stable, memory was boosted for associative stimuli after a night of sleep but continued to decline thereafter. These effects were particularly robust for pairs that were semantically unrelated, as semantically related pairs demonstrated superior memory across the delays with relatively minimal decay over time. Possible neurobiological correlates of forgetting for the different types of stimuli in the context of current theories of consolidation are discussed, and implications for the phase II patient study are explored.

Keywords: Accelerated Long-Term Forgetting
Consolidation
Hippocampus
Long-Term Memory
Memory
Temporal Lobe Epilepsy
Advisor: McAndrews, Mary Pat
Emergency Department Wait Time Modelling and Prediction at North York General Hospital

At North York General Hospital Yellow Zone (YZ), providers seek real-time forecasts of waiting times to improve communication and prescribe actions to relieve patient crowding. Time series of patient waits to physician assessment (PIA) and to discharge from the YZ (PTE) were collected. Multivariable regression with ARIMA errors was fit to determine the patient-based and systematic predictors of wait times for YZ patients at time of arrival. A regression on occupancy with ARIMA(1,0,0)(0,1,1)24 errors yielded the lowest error in forecasting PIA. Accuracy improved when grouping patients by acuity and complaint. ARIMA methods yielded low accuracy in forecasting PTE, and no correlations were found between PTE and acuity. 90% of patients waited up to 47.88 minutes more than predicted for PIA and up to 118 minutes more for PTE. The results suggest that ARIMA models have utility in forecasting PIA but that alternative models should be used to improve PTE prediction.

Keywords: ARIMA
emergency department
wait time
Advisor: Carter, Michael W
Hemocompatibility of Degradable Polar Hydrophobic Ionic Polyurethane for Blood Contact Applications

Biomaterial hemocompatibility is an important concern in the development of synthetic blood-contacting surfaces, specifically to help mitigate thrombosis which can lead to blood vessel occlusion or device failure. A novel biomaterial, degradable polar hydrophobic ionic polyurethane (D-PHI), is studied for its effect on hemocompatibility. Furthermore, this thesis explores a new subject; changes in hemocompatibility of biomaterials over the course of degradation, using both D-PHI and poly(lactic-co-glycolic) acid (PLGA) as important classes of materials that are finding their way into numerous applications. The key results from this work are that D-PHI elicits a low level of clotting that is likely initiated by complement activation; however, it is anticipated that this activation favours controlled wound-healing. Furthermore, degradation appears to significantly affect hemocompatibility for PLGA suggesting the need for further studies. Finally, this work highlights the importance of including white blood cells (WBCs) in any platelet-biomaterial testing.

Keywords: Biocompatibility
Biomaterial
Degradation
Hemocompatibility
Material characterization
Polyurethane
Advisor: Santerre, J. Paul
Construction Safety Climate in Ontario: A Longitudinal Study

The aim of this paper is to document changes in the relationship between demographics, attitudes, physical symptoms, psychological symptoms, and accidents over time in the construction industry. This longitudinal study compares periodic measures of the construction safety climate in Ontario in 2004/6 and 2014. A total of 442 self-administered questionnaires were collected from 22 construction sites in 2014. The 2014 data were compared to 911 valid questionnaire responses obtained in 2004/06 from 84 construction sites across Ontario. The questionnaire contained 105 questions and took participants 15 minutes to complete. Demographic data remained consistent over time. The participants had an average experience level of 15 years, having spent a median of 2.5 years with their current employer. Considerable attitudinal improvements were observed in the areas of leadership, coworker perception, supervisor perception, management perception, and safety program perception. The prevalence and occurrence of physical symptoms, psychological symptoms, and accidents decreased over time.

Keywords: Construction
Safety
Advisor: McCabe, Brenda
Hyatt, Douglas
Novel Methods to Reduce Muscle Fatigue Using Multi-electrode Functional Electrical Stimulation in Isokinetic Knee Extension Contractions

Muscle fatigue, a major limiting factor in the use of functional electrical stimulation, can be countered through multi-electrode sequential stimulation. To apply this method clinically, our lab developed a generic adapter. The purpose of this thesis project was (1) to test the adapter’s performance and (2) to investigate whether two sequential techniques, namely Spatially Distributed Sequential Stimulation (SDSS) and Sequential Multiple Muscle-Head Stimulation (SMHS), are capable of inducing less fatigue than Single Electrode Stimulation (SES) in isokinetic knee extension contractions. Thirteen able-bodied individuals participated in a three-day study. Performance of the adapter was found to be accurate within acceptable error. Both SDSS and SMHS resulted in significantly less fatigue than SES as measured by fatigue index and torque peak mean. The less low frequency fatigue observed during SDSS and SMHS may explain the lower fatigue. SDSS and SMHS delivered via adapter pose an attractive alternative to SES during clinical applications.

Keywords: Functional electrical stimulation
Isokinetic
Multi-electrode
Muscle fatigue
SDSS
Sequential
Advisor: Masani, Kei