VictorJuiz/thesis huggingface dataset:
Trunk Muscle EMG in a Specially Designed Virtual Reality Motion Simulator
Keywords: Electromyography
EMG
Perception
Roll and Pitch
Seated Balance
Virtual Reality
Simulation
Phasic and Tonic activity
Trunk Muscles
Abdomen and Back Muscles
Seated Posture

Virtual reality (VR) has become an important tool in the study of human balance. It has also been used as a training tool for seated balance and assistive mobility devices. The objective was to design a system that can be used to investigate the effect of VR on trunk muscles during perturbed sitting and perform a preliminary study with two subjects. A spherical system was designed that rotated 26º in the pitch and roll plane at three speeds. The corresponding muscle activity was recorded using EMG in the presence and absence of VR during perturbed sitting. The design was capable of performing the required motions. The results showed a maximum of 31.8% and a minimum of 3.66% muscle activity, relative to maximum voluntary contraction. Our findings suggested that our developed system was successfully able to detect a noticeable effect of VR under perturbed sitting on the subjects’ EMG responses.
Investigating the Mechanisms of Intrinsic Specificity Achievement in SH3 Domains
Keywords: SH3 Domain
Intrinsic Specificity

Protein-protein interactions are an integral part of virtually all aspects of cellular function. Many of these interactions are mediated by small modular units called protein interaction domains (PIDs). We do not yet understand, however, how much functional information is encoded in these modules. It has previously been shown that Nbp2SH3 and Bem1SH3b domains in S. cerevisiae bind several target peptides with the same consensus sequence, yet display finely tuned affinities for each. In this study, I have shown that there exists an evolutionarily conserved ability of orthologous fungal Nbp2SH3, Bem1SH3b, and Abp1SH3 domains to discriminate between target peptides within the same species. In addition, I have developed a method to quantitatively probe SH3 domain specificity using purified SH3 domains and naturally occurring proline-rich constructs (PRRs) in the context of cell lysate from S. cerevisiae. Expansion of this work may yield valuable insights into intrinsic SH3 domain specificity.
The Hawthorne Effect in Hand Hygiene Compliance Monitoring
Keywords: Hand hygiene
Hawthorne effect
Hospital epidemiology

Introduction: The Hawthorne effect, or behaviour change due to awareness of being observed, is believed to inflate directly observed hand hygiene compliance rates, but evidence is limited. Methods: A real-time location system tracked hospital hand hygiene auditors and recorded alcohol-based hand rub and soap dispenses. Rates of hand hygiene events per dispenser per hour within sight of auditors were compared to dispensers not exposed to auditors. Results: The event rate in dispensers visible to auditors (3.75/dispenser/hour) was significantly higher than unexposed dispensers at the same time (1.48) and in prior weeks (1.07). The rate increased significantly when auditors were present compared to five minutes prior to arrival. There were no significant changes inside patient rooms. Conclusions: Hand hygiene event rates increase in hallways when auditors are visible and the increase occurs after the auditors’ arrival, consistent with the existence of a Hawthorne effect localized to areas where auditors are visible.
Phenotypic and Genetic Differentiation Between Sex Chromosome Races of Rumex hastatulus (Polygonaceae)
Keywords: Rumex hastatulus
ecological genetics
population structure
wind pollinated
phenotypic differentiation

Wind-pollinated plants often have little genetic structure owing to high gene flow. However, sex chromosomes evolution promotes divergence, potentially leading to population subdivision. Rumex hastatulus (Polygonaceae) is a wind-pollinated, dioecious coloniser of open disturbed land with two sex chromosome races (SCRs), which occupy different parts of the species’ range in the southern USA. My thesis investigated phenotypic and genetic differentiation between the SCRs, based on a study of 28 populations sampled throughout the range. A glasshouse experiment demonstrated significant differentiation between the SCRs in several life-history traits, several of which exhibited clinal variation. Analysis of population genetic structure, based on 13 nuclear loci, revealed two distinct clusters corresponding to the two SCRs, with an estimated origin of the North Carolina SCR from the Texas SCR between ~5000–15000 generations ago. My results indicate that the SCRs have developed a moderate degree of phenotypic and genetic differentiation despite ongoing gene flow.
Fuel Moisture and Sustained Flaming in Masticated Fuelbeds
Keywords: fuels management
mechanical fuels treatment
chipping

Mastication is a fuel management technique that disrupts the vertical continuity of forest fuels by mechanical shredding of trees and understory vegetation into a highly-compacted surface fuelbed. The particle size distributions, bulk density and arrangements differ from natural and slash fuel types, thus resulting in fuelbeds with potentially different moisture dynamics and fire behaviour. We conducted three experiments, the first of which examined differences in in-stand micrometeorology and fuelbed moisture content between differing levels of stand thinning via mastication. In the second experiment, a fuel moisture model was created, validated with an independent dataset, and compared with pre-existing models that are incorporated in the Canadian Forest Fire Danger Rating System. In the third experiment, we compared the results of standard ignition tests performed on masticated fuelbeds in the laboratory and field to determine probability of sustained flaming, and compared our findings with pre-existing models of ignition for other forest fuels.
Object-based Image Analysis for the Delineation of Canopy Gaps and Individual Tree Crowns using Multi-source Data: A Case Study in Haliburton Forest, Ontario
Keywords: remote sensing
GIS

This thesis assessed object-based image analysis techniques using multi-source remote sensing data in order to automatically delineate canopy gaps and individual tree crowns (ITCs). Image segmentation is much more complex when conducted on data covering deciduous, un-even aged forests like those in Central Ontario. To delineate canopy gaps high spatial resolution multispectral ADS40 aerial imagery and a LiDAR CHM were assessed both separately and jointly. To delineate ITCs two commonly used segmentation approaches were assessed – region growing and watershed segmentation. Ground based measurements and manually delineated data were used as reference to evaluate results. Using multi-source data to delineate canopy gaps produced an average overall accuracy of 99.35%, whereas using the imagery and CHM individually resulted in average overall accuracies of 81.41% and 82.45%, respectively. For the delineation of ITCs, the watershed and region growing segmentations resulted in average overall accuracies of 67.5% and 65.5%, respectively.
Pain and Psychological Outcomes Following Traumatic Musculoskeletal Injury
Keywords: Traumatic musculoskeletal injury
Pain
Anxiety
Depression
Posttraumatic Stress Disorder

Background: Traumatic musculoskeletal injury (TMsI) often leads to chronic pain and post-traumatic stress disorder (PTSD). This study examined factors of a modified diathesis-stress model in the development of PTSD symptoms following TMsI. Methods: 205 patients were recruited in this prospective, observational study. Within 14 days of injury, participants completed an in-hospital questionnaire investigating acute symptoms of anxiety, depression, pain, and PTSD. Results: Logistic regression identified multiple factors associated with symptoms of PSTD (p<.0001). Neuropathic pain (odds ratio[OR]=1.091, 95% confidence interval[CI] 1.020-1.168), general anxiety (OR=1.176, 95%CI 1.046-1.318), pain anxiety (OR=1.056, 95%CI 1.018-1.094), and pain catastrophizing (OR=1.168, 95%CI 1.016-1.348) were associated with acute symptoms of PTSD. Conclusions: The results support the modified diathesis-stress model indicating that neuropathic pain, general anxiety, pain anxiety, and pain catastrophizing are associated with symptoms of PTSD. Future studies should examine the influence of these acute factors on the development of chronic pain and PTSD following TMsI.
Propulsion System Development for the CanX-4 and CanX-5 Dual Nanosatellite Formation Flying Mission
Keywords: aerospace
microsatellite
nanosatellite
propulsion
formation flying
canx4
canx5
canx-4
canx-5
canx-4/-5
SFL
UTIAS
cold-gas thruster
satellite
CNAPS
NANOPS
nano
sulfur hexafluoride
SF6
vibration testing
spacecraft environmental testing
propulsion testing
low earth orbit
canx2
canx-2
station keeping
orbit maneuver
orbital station-keeping
liquefied cold-gas propulsion
micropropulsion
engineering
space
canadian
space flight laboratory
canadian advanced nanospace experiment
PSLV
micro-propulsion
thruster
interferometry
ground moving target indicator
on-orbit servicing and inspection

The Canadian Nanosatellite Advanced Propulsion System is a liquefied cold-gas thruster system that provides propulsive capabilities to CanX-4/-5, the Canadian Advanced Nanospace eXperiment 4 and 5. With a launch date of early 2014, CanX-4/-5's primary mission objective is to demonstrate precise autonomous formation flight of nanosatellites in low Earth orbit. The high-level CanX-4/-5 mission and system architecture is described. The final design and assembly of the propulsion system is presented along with the lessons learned. A high-level test plan provides a roadmap of the testing required to qualify the propulsion system for flight. The setup and execution of these tests, as well as the analyses of the results found therein, are discussed in detail.
Development of a Free Lime Monitoring System for the Kraft Recovery Process using Zeta Potential
Keywords: Zeta Potential
Liming Ratio
Free Lime
Kraft Recovery
Causticizing Plant
Green Liquor
White Liquor
Reburned Lime
Pulp and Paper

The presence of Ca(OH)2 (or free lime) in lime mud can cause many problems in the recovery process of kraft pulp mills. Conventional free lime analyses require extensive laboratory work and give inconsistent results. A systematic study was performed to determine if zeta potential, a quickly measurable dispersion characteristic, can be used to indicate the presence of free lime in the recovery process. Measurements were made on synthetic wet lime mud to simulate samples collected after the white liquor clarifier in pulp mills. The results show that zeta potential increases from negative to positive when the free lime content in the lime mud exceeds a critical threshold. This change from negative to positive zeta potential of the lime mud slurry can be used as a basis for developing an on-line monitoring system that effectively detects free lime in the lime mud in order to avoid problems associated with overliming in the recovery process.
Evaluation of Test Methods for Determining the Water to Cement Ratio of Fresh and Hardened Concrete
Keywords: concrete
cement

The purpose of this research was to determine the accuracy of two test methods used in measuring the water to cement ratio (w/c) of fresh and hardened concrete. The microwave oven test based on a current ASTM Draft was used in determining the w/c of fresh concrete while the modified Norwegian PF-method was used to determine the w/c of hardened concrete. The microwave oven evaporates the water of a 1500 gram sample of fresh concrete to determine a w/c and can accurately measure the w/c within 0.05 of the true value. The modified PF-method uses an absorption method similar to ASTM C97 and Powers’ hydrations models to determine the w/c of hardened concrete. 100mm diameter concrete cores were prepared from slabs and 50mm thick concrete cylinders were tested. The results from this hardened concrete test had a large degree of variability; however, it was a useful indicator of concrete segregation.
Reliable Writeback for Client-side Flash Caches
Keywords: Client-side Caching
Flash Storage
Performance
Consistency
Durability

Modern data centers are increasingly using shared storage solutions for ease of management. Data is cached on the client side on inexpensive and high-capacity flash devices, helping improve performance and reduce contention on the storage side. Currently, write-through caching is used because it ensures consistency and durability under client failures, but it offers poor performance for write-heavy workloads. In this work, we propose two write-back based caching policies, called write-back flush and write-back persist, that provide strong reliability guarantees, under two different client failure models. These policies rely on storage applications such as file systems and databases issuing write barriers to persist their data, because these barriers are the only reliable method for storing data durably on storage media. Our evaluation shows that these policies achieve performance close to write-back caching, while providing stronger guarantees than vanilla write-though caching.
Automated Vitrification of Mammalian Embryos on a Digital Microfluidic Platform
Keywords: microfluidics
vitrification

This thesis presents the development of a digital microfluidic system to achieve automated sample preparation for the vitrification of mammalian embryos for clinical in vitro fertilization (IVF) applications. This platform included micro devices fabrication, an imaging system, a high voltage control system, and a LabVIEW interface. Individual micro droplets manipulated on the digital microfluidic device were used as micro-vessels to transport a single embryo through a complete vitrification procedure. The device showed cell survival and development rates of 77% and 90%, respectively, which are comparable to the control groups that were manually processed. Technical advantages of this approach, compared to manual operation and channel-based microfluidic vitrification, include automated operation, cryoprotectant concentration gradient generation, and feasibility of loading and retrieval of embryos.
High Level Debugging Techniques for Modern Verification Flows
Keywords: RTL Debugging
FPGA
Triage
Clustering

Early closure to functional correctness of the final chip has become a crucial success factor in the semiconductor industry. In this context, the tedious task of functional debugging poses a significant bottleneck in modern electronic design processes, where new problems related to debugging are constantly introduced and predominantly performed manually. This dissertation proposes methodologies that address two emerging debugging problems in modern design flows. First, it proposes a novel and automated triage framework for Register-Transfer-Level (RTL) debugging. The proposed framework employs clustering techniques to automate the grouping of a plethora of failures that occur during regression verification. Experiments demonstrate accuracy improvements of up to 40% compared to existing triage methodologies. Next, it introduces new techniques for Field Programmable Gate Array (FPGA) debugging that leverage reconfigurability to allow debugging to operate without iterative executions of computationally-intensive design re-synthesis tools. Experiments demonstrate productivity improvements of up to 30 x vs. conventional approaches.
Influence of Biogenic Silica from Terrestrial Vegetation on Riverine Systems and Diatom Evolution
Keywords: Biogenic Silica
Vegetation
Diatoms
Soils
Rivers
Leaching

Presently within the scientific literature no terrestrial biogenic silica models exist that compare by magnitude, processes transporting silica. Change in vegetation type has the potential to alter dissolved concentrations of Si in rivers and ultimately the oceans. Diatoms greatly depend on Si concentrations for growth, and as a result land cover change may have influenced onset diatom radiation during the Cenozoic. To expand our understanding of this cycle, a terrestrial biogenic silica model is proposed. This model accounts for biogenic silica production, dissolution and leaching through soils, as well as providing estimates for annual silica soil storage. A case study performed using the constructed biogenic silica model, showed an increase in oceanic DSi concentration during the Miocene (period of diatom diversification). However, this increase does not appear to have been sufficient to trigger global diatom radiation, suggesting multiple geographically isolated locations for this diversification.
Modeling the Reaction Kinetics of the Enzymatic Hydrolysis of Lignocellulosic Biomass
Keywords: biofuel
enzymatic hydrolysis
reaction kinetics
modeling
bioconversion
reaction kinetics modeling
enzymatic hydrolysis optimization

Maximizing enzymatic hydrolysis performance can be achieved through the combination of experimental work and modeling. The present work utilizes an enzymatic hydrolysis model based on reaction kinetics, Langmuir adsorption isotherms, and product inhibition of enzymes (β-glucosidase, cellobiohydrolase, and endoglucanase). The model was developed from a 10% w/w corn stover system. Glucose yield sensitivity to changes in parameter values was assessed and linked to biomass and enzyme characteristics. A commercial enzyme cocktail (CEC) was subsequently characterized by FPLC and gel electrophoresis to identify key enzymes/activities, and the CEC was used in the enzymatic hydrolysis of 20% w/w steam-exploded hardwood. The model was applied to experimental data from the enzymatic hydrolysis of the steam-exploded hardwood, which provided characteristic reaction rate and inhibition parameters consistent with cellulose and xylan hydrolysis. These model-based analyses enhanced understanding of hydrolysis at commercially relevant solids loadings, while identifying pathways to improve enzyme cocktails and enhance biomass conversion.
Probing the Hydration of Ultrathin Antifouling Adlayers using Neutron Reflectometry
Keywords: Neutron Reflectometry
Antifouling
Biosensors
Hydration
Ultrathin film

Adverse interaction and subsequent adsorption of biomolecular species (i.e. fouling) pose a great hindrance for medical and clinical applications (e.g. biosensors). Research into the mechanism behind antifouling coatings have shown a strong link between surface hydration and antifouling behaviour due to the existence of a ‘water barrier’ which prevents proteins from adsorbing onto the surface. In a previous study, a short, mono(ethylene-glycol) silane adlayer (MEG-OH) showed significantly different antifouling behaviour in comparison to its homolog – lacking the internal ether oxygen (OTS-OH). In the present work, neutron reflectometry (and modeling) was used to investigate the water density profiles at MEG-OH and OTS-OH silane adlayers on quartz and Si/SiO2 to determine whether the internal ether oxygen affects the adlayers’ interaction with water. Despite the limitations of studying such ultrathin organic films, the two systems showed different hydration profiles supporting the link between surface hydration and antifouling.
Characterization of Nedd4 Function and its Interaction with Angiomotin
Keywords: Nedd4
Angiomotin
Ubiquitin ligase
biochemistry

The HECT E3 ubiquitin ligase Nedd4-1 was previously shown to regulate diverse processes such as cell and animal growth, insulin signaling, and lysosomal trafficking. To further elucidate the cellular functions of Nedd4-1, Nedd4-1 knockout mouse embryonic fibroblasts were characterized relative to their wild type counterparts. Immunofluorescence experiments revealed an altered lysosomal distribution in the knockout cells, although their lysosomal proteolytic function appeared normal. Transmission Electron Microscopy revealed striking morphological differences, especially regarding the lysosome and endoplasmic reticulum of the knockout cells. Another aspect of my studies examined the interaction between Nedd4-1 and Angiomotin (p130-AMOT), which involves the same motifs required to sequester transcriptional co-activators YAP and TAZ in the cytoplasm. To test either a competitive or non-competitive mode of binding, co-immunoprecipitation experiments involving p130-AMOT, the Nedd4 proteins, and YAP or TAZ were performed, with results not supporting a competitive mode of interaction. Overall, my results demonstrate new Nedd4-1 cellular functions.
Extrinsic Substrate Stiffness Regulates Chondrocyte Phenotype through Actin Remodeling and MRTF Mechanotransduction Pathway
Keywords: Tissue Engineering
Cartilage
MRTF
Actin
dedifferentiation

To obtain a cell source for cartilage tissue engineering primary cells are passaged on polystyrene dishes to increase cell number however, this stiff environment results in dedifferentiation. This study evaluates the role of microenvironment stiffness on regulation of passaged chondrocyte phenotype. Results show passaged cells on soft polyacrylamide gels (0.5kPa) become round, less proliferative, less contractile, have higher levels of globular actin (g-actin) compared to filamentous actin (f-actin), MRTF localization in the cytoplasm and down-regulation of MRTF associated genes such as type I collagen, alpha-smooth muscle actin, transgelin, tenascin C and vinculin. This suggests that the chondrogenic phenotype during passaging is regulated by actin polymerization and activation of MRTF signaling that induces expression of non-chondrogenic genes, and has functional effects as the cells become proliferative and contractile. Modulating substrate stiffness maybe a way to influence aspects of the chondrogenic phenotype in order to obtain sufficient cells suitable for cartilage tissue engineering.
The Effects of Serum from Obese Patients and Adipocyte-derived Cytokines on Growth of Prostate Cancer Cells In Vitro
Keywords: oncology
urology
cancer
prostate
obesity
adipokines
prostate cancer
cytokines
adipocytes
adiponectin
resistin
fat cells
tumor
malignancy
neoplasm
body mass index
in vitro
wnt
proliferation
migration
invasion
LNCaP
PC3
overweight
fat
adiposity
beta-catenin
glycogen synthase kinase-3beta

Obesity has been related to a greater incidence of more aggressive, advanced stage prostate cancer. It is expected that serum adipokines related to obesity will promote a more aggressive phenotype in PC cells in vitro. Patient serum (n = 80) was obtained for analysis and divided into four patient groups based on obesity and prostate cancer status. Characteristics of serum-treated PC cells in vitro were measured. In a separate set of analyses, LNCaP and PC3 cells were treated with adiponectin and resistin in vitro, and cell characteristics were analyzed. Serum from obese PC patients induces greater amounts of cell migration and lower amounts of cell proliferation and invasion in vitro. Exogenous treatment of adiponectin on PC cells in vitro does not affect cell migration or invasion. However, adiponectin modulates cytosolic protein levels of soluble β-catenin and GSK-3β, indicating that its mechanism of action may be through the Wnt signalling pathway.
Determining Tree Water Acquisition with Stable Isotope Analysis in a Temperate Agroforestry System
Keywords: agroforestry
water

The water acquisition strategies of trees in agroforestry systems may affect adjacent crops through competition for resources. This study characterizes the water uptake zones of Juglans nigra (walnut) and Populus sp. (hybrid of Populus deltoids X Populus nigra clone DN-177) (poplar) in a temperate agroforestry system. Isotopic analysis (δ18O) of soil water and tree xylem water occurred in early season and late season samples from the Agroforestry Research Station in Guelph, Ontario, Canada. Direct inference and multiple source mass-balance approaches showed that poplar exhibited a primary soil water uptake zone at 20 cm in early season, while walnut uptake was higher in the soil profile at 10 cm. Late season water uptake zones shifted to lower in the soil profile (40-70 cm) for both poplar and walnut trees. This study indicates: i) species dependent water acquisition zones, and ii) a shift to lower in the soil profile later in the growing season.