VictorJuiz/thesis huggingface dataset:
Effects of Model Salivary Esterases and MMP Inhibition on the Restoration's Marginal Integrity and Potential Degradative Contribution of Cariogenic Bacteria

Enzyme-catalyzed degradation of the restoration-tooth interface compromises interfacial integrity, thereby contributing to secondary caries, which is a major cause of resin-based restoration failure. It is hypothesized that in addition to salivary esterases, the cariogenic bacterium Streptococcus mutans has specific esterases that degrade the resin-dentin interface, releasing biodegradation by- products (BBPs) such as bis-hydroxy-propoxy-phenyl-propane (BisHPPP). In turn, BisHPPP affects S. mutans by stimulating the expression of esterases. Another hypothesis is that the biostability of the resin-dentin interface is affected by simulated salivary esterases, dentinal matrix metalloproteinase (MMP) inhibition, and restorative materials. To test the first hypothesis, putative esterase genes in S. mutans UA159 were identified, purified, and characterized. SMU_118c was identified as the dominant esterase in S. mutans UA159 and showed a similar hydrolytic activity profile to salivary esterases. BisHPPP upregulated expression of the SMU_118c gene and related protein in a concentration-dependent manner. This positive feedback process could accelerate the degradation of the restoration-tooth interface and lead to premature restoration failure. To test the second hypothesis, an in vitro model was established to evaluate the effects of salivary esterases, MMP inhibition and restorative materials on interfacial integrity. It was confirmed that interfacial integrity was compromised with time and was further deteriorated by simulated salivary esterases, as indicated by the greater depth of bacterial ingress and more bacterial biomass of biofilm along the interface. However, this process could be modulated by using different restorative materials and MMPs inhibition.This project elucidated the mechanistic interaction between oral bacteria and restorative materials and established a new, in vitro, and physiologically relevant model to assess the effect of material chemistry, properties, and application modes on bacterial penetration and biofilm formation. These findings offer the oral health community practical ways to reduce secondary caries by altering material composition and restorative procedures.

Keywords: biodegradation
esterase
gene response
resin composite
secondary caries
Streptococcus mutans
Advisor: Finer, Yoav
Cvitkovitch, Dennis
Home Caregiver Safety when Assisting with Bathing and Toileting

Home care workers who assist with personal care have much higher rates of musculoskeletal disorders (MSDs) of the back and shoulder than the general working population. This thesis identifies and describes activities that are likely to contribute substantially to the development of MSDs, then identifies and evaluates ways to reduce risk. Physically demanding activities and aspects of the home care context that contribute to MSD risk are identified through a literature review and through focus groups with home care providers, leading to a focus on toileting and bathing. An observational study was used to analyze providers’ postures and related lower back loads while assisting with these activities in a simulated home care scenario. During toileting, exposures to MSD risk factors were highest when managing clothing, providing posterior perineal care and during transfers. One third of providers’ exposure to severely flexed trunk postures, which are powerful predictors of lower back MSD risk, could be eliminated if bidet seats were used for perineal cleaning. During bathing, the highest exposures to MSD risk factors were observed during transfers and while providing lower limb care. Four tools to reduce exposures were evaluated in a follow-up study. Shoulder muscle activity and exposure to non-neutral postures were reduced when using a short-handled leg-lifter to transfer the legs, while sitting to lift the legs improved back postures but increased demands on the shoulders. A sliding, rotating bench reduced back muscle activity despite an increased use of awkward postures. All participants judged the leg-lifter and sliding, rotating bench to be feasible and desirable for use in the community. The identified tools reduce providers’ exposure to MSD risk factors when assisting with two of the most demanding homecare activities. There is a need to improve access to assistive devices to ensure providers’ occupational safety while preserving their ability to provide client care.

Keywords: aging in place
assistive devices
ergonomics
home care provider
Advisor: Fernie, Geoff R
Habits of Peace: The Foundations of Long-Term Regional Cooperation in Southeast Asia and South America

The regions of Southeast Asia and South America are often cited as puzzling cases of long peace among nation-states. Absent hard power balancing behaviours, liberal democratic development, and economic interdependence, both present unlikely cases for prolonged periods of time absent large scale inter-state violence. This research begins with an inquiry into the foundations the long peace of each region: practices of conflict management. More narrowly, this project asks: How can we understand cooperation and community building alongside persistent militarized violence? Upon what foundations have these largely illiberal states been able to build relative but lasting peace despite pervasive territorial disputes? In answering these questions, this research argues that distinct and diplomatic habits shape the management of peace and conflict in each region. The underlying argument of this work is that the habitual and dispositional qualities of regional diplomatic practice inform the long peace of these regions and regional relations more generally. In each region, distinctive and discrete qualities of regional relations shape crisis response, but also shape how crises, themselves, are understood by regional diplomatic officials. These â habits of peaceâ make possible long-term regional cooperation and relative peace alongside persistent intra-regional violence. After articulating the conflictual nature of peace in each regional case, I suggest that existing understandings of regional long-peace overlook the practical and tactical foundations upon which interstate cooperation rest. I offer a theoretical framework and particular set of methods attentive to the habitual and dispositional qualities of inter-state relations. In the subsequent empirical cases I demonstrate the existence and effect of a particular regional habitual disposition in each region, with a particular focus on episodes of regional crisis including the 2011 Preah Vihear border dispute in Southeast Asia and the 1995 Cenepa conflict between Peru and Ecuador.

Keywords: Constructivism
Diplomacy
Habit
Practice Theory
South America
Southeast Asia
Advisor: Hoffmann, Matthew J.
Children's and adolescents' judgments about social responsibility: Moral identity and the public good

The current research sought to assess children's (10-11 years), adolescents' (13-14 years), and adult's (Psy100 students) perceptions regarding the importance and obligation to engage in various civic activities. Drawing from previous research on the topic of civic obligation, participants were presented with five different types of civic acts (voting, volunteering, charity work, clubs sports, and petitions/protests) and were asked to assess the extent to which these acts were important, obligatory, and legally mandatory. Of interest was also participants' justifications for their responses, which were coded according to moral reasoning, personal choice, or practical factors which mitigated responses. Finally, measures of moral identity were administered to explore the extent to which individual differences in the personal importance of moral qualities influenced responses. Results suggested that younger participants rated charitable endeavors as more obligatory and legally mandatory than did the young adults. Conversely, the young adults tended to prioritize voting more highly relative to the younger participants. Supplementing these findings were the justification analyses, which suggested that younger participants used more moral reasoning in their responses to questions about charitable organizations compared to the young adults. Results also suggested that moral identity was related to the quantitative evaluations of the different civic activities. Moral identity was also positively associated with the use of moral reasoning within morally salient activities across all situations. Regression models indicated that this link between moral identity and moral cognition persisted when age effects were controlled.

Keywords: Identity development
Moral development
Moral reasoning
Political Psychology
Political socialization
Advisor: Helwig, Charles
Investigating the Metal-like Optical Behavior of Boron Nitride

Recent advances in scanning near-field optical microscopy (SNOM) have led to rapid growth of the field of phonon polaritonics. Due to strong vibrational resonances, which are responsible for negative permittivity in the mid-infrared (mid-IR) region, hexagonal boron nitride (hBN) is of high interest in the field. Here, we investigate the metal-like optical properties of hBN governed by phonons. We demonstrate one of the first experimental observations of surface phonon polaritons (SPhPs) in boron nitride nanotubes (BNNTs), which exhibits a very high effective index (neff ~70), yet a long propagation length. We show that the apparent periodicity can be controlled by varying the nanotube size and the supporting substrate. We also observed IR polaritonic interaction between graphene plasmons and surface phonon polaritons of BNNT, which are capable of coherently exchanging their energies at the nanoscale. 2D hBN films were also studied, and we report a metal-free method of launching phonon polaritons by making use of the intrinsic property of the material itself. To support these studies, we also developed and implemented an opto-mechanic stabilization mechanism for the SNOM and showed improved phase stability. Our reported modification of the SNOM setup to work with 2 IR continuous wave (CW) lasers opens further doors for studying inter-mode energy transductions by performing IR pump-probe CW spectroscopy.

Keywords: boron nitride
graphene
Phonon polariton
SNOM
surface waves
Advisor: Walker, Gilbert C
Circuits, Architectures, and CAD for Low-Power FPGAs

Field Programmable Gate Arrays (FPGAs) are becoming an ever more prominent platform for the implementation of digital systems. In contrast to traditional processors that map computations onto a series of predefined instructions, an FPGA maps a computation onto a custom tailored digital circuit, thus yielding performance benefits. FPGAs can also provide cost and time-to-market benefits compared to Application Specific Integrated Circuits (ASICs). However, these advantages do not come for free as FPGAs typically have higher power consumption than the aforementioned platforms. FPGA power consumption is specifically of great concern presently given the growing demand for compute power in power constrained environments such as in mobile devices and data centres. To that end, in this thesis we explore circuit and architectural techniques to reduce power dissipated in FPGAs, and present the necessary CAD tools to implement our proposed power optimization schemes. First, we present a technique to reduce the dynamic power dissipation that arises because of glitches. For this technique we designed a programmable glitch filter which we propose to augment a conventional FPGA; the proposed circuit can be configured to eliminate glitches for a range of different pulse-widths. Our second power reduction technique is motivated by observing that there exists an abundance of unused routing conductors in FPGAs. We show that by tri-stating these unused routing conductors we can reduce the effective wire capacitance seen by adjacent conductors, thereby reducing dynamic power. Moreover, we show how tri-stated wires also results in reduced routing leakage. The third power reduction technique also seeks to leverage unused routing conductors; in this case we employ the unused routing conductors as charge reservoirs to enable a charge recycling technique to reduce dynamic power. Finally, this thesis presents a technique to aggressively reduce leakage power dissipated in the routing network of an FPGA by tri-stating both used and unused routing buffers; the used routing buffers in this case are temporarily activated when they are needed â i.e. when they are in the process of transmitting data. Ensuring that all circuits are effectively shut-off at all other times allows us to reduce leakage power.

Keywords: CAD
Circuit design
FPGA
Interconnect
Low Power
Reconfigurable Computing
Advisor: Anderson, Jason H
Confirmation bias in visual attention

This dissertation evaluates the proposal that visual attention is biased towards stimuli that could potentially verify a perceptual hypothesis, compared to stimuli that might falsify it. To do so, I use a visual search task with two, mutually exclusive, coloured targets (e.g., a red p or a blue p). Before each set of searches, one target colour is designated positive, or confirmatory, information and one is designated negative information by requiring affirmative responses or negative responses to one of the two targets (e.g., press Z if the p is red, press M if it is not). The first set of experiments, reported in Chapter 2, showed that confirmatory search patterns were observed for both novel and practiced hypotheses, were observed despite instructions to the contrary, and were mitigated by a search colour-preview. Chapter 3 measured the ocular correlates of the search bias, showing that more fixations indeed go towards confirmatory stimuli, but showed that when stimulus inspections took longer, search became les confirmatory and more efficient. Finally, Chapter 4 demonstrated that confirmatory search did not occur when hypotheses referred to visually heterogeneous stimuli and also did not occur when hypotheses included a negation, suggesting that a visual matching bias underlies confirmatory search. Confirmation bias thus appears to be a side-effect of goal-directed cognition in general, and the present results are discussed in relation to theories likening reasoning to foraging and information search.

Keywords: Attention
Cognition
Confirmation bias
Decision making
Vision
Advisor: Pratt, Jay
(Sparse) Exchangeable Random Graphs

Many common statistical models for network valued datasets fall under the remit of the graphon (cf. dense exchangeable) framework. These models are defined by a multi-dimensional analogue to de Finetti style exchangeability that provides a natural formalization of the requirement that the labels of a random graph carry no information about its structure. This seemingly innocuous assumption implies that the corresponding networks are densely connected: a property that rarely holds for real-world networks of practical interest. This thesis develops the statistical theory for network valued data; in particular, generalizing the dense exchangeable models to the sparse graph regime. The key ingredient is a novel notion of exchangeability for graphs based on a point process representation of networks. The main results are: The construction of a new modeling framework through a de Finetti style representation theorem. The characterization of several important sampling distribution properties of the resulting random graphs. The introduction of a generic non-parametric estimator (analogous to the empirical measure) for these models. And, finally, the recasting of the core exchangeability concepts in the language of sampling, which leads to a clear articulation of the sampling design naturally associated with the models, as well as a unification with the theory of limits of large (sparse) graphs.

Keywords: Exchangeability
Machine learning
Network science
Random graphs
Sampling
Statistics
Advisor: Roy, Daniel M.
Investigating brittle rock failure and associated seismicity using laboratory experiments and numerical simulations

Rock failure process is a complex phenomenon that involves elastic and plastic deformation, microscopic cracking, macroscopic fracturing, and frictional slipping of fractures. Understanding this complex behaviour has been the focus of a significant amount of research. In this work, the combined finite-discrete element method (FDEM) was first employed to study (1) the influence of rock discontinuities on hydraulic fracturing and associated seismicity and (2) the influence of in-situ stress on seismic behaviour. Simulated seismic events were analyzed using post-processing tools including frequency-magnitude distribution (b-value), spatial fractal dimension (D-value), seismic rate, and fracture clustering. These simulations demonstrated that at the local scale, fractures tended to propagate following the rock mass discontinuities; while at reservoir scale, they developed in the direction parallel to the maximum in-situ stress. Moreover, seismic signature (i.e., b-value, D-value, and seismic rate) can help to distinguish different phases of the failure process. The FDEM modelling technique and developed analysis tools were then coupled with laboratory experiments to further investigate the different phases of the progressive rock failure process. Firstly, a uniaxial compression experiment, monitored using a time-lapse ultrasonic tomography method, was carried out and reproduced by the numerical model. Using this combination of technologies, the entire deformation and failure processes were studied at macroscopic and microscopic scales. The results not only illustrated the rock failure and seismic behaviours at different stress levels, but also suggested several precursory behaviours indicating the catastrophic failure of the rock. Secondly, rotary shear experiments were conducted using a newly developed rock physics experimental apparatus ERDÎź-T) that was paired with X-ray micro-computed tomography (ÎźCT). This combination of technologies has significant advantages over conventional rotary shear experiments since it allowed for the direct observation of how two rough surfaces interact and deform without perturbing the experimental conditions. Some intriguing observations were made pertaining to key areas of the study of fault evolution, making possible for a more comprehensive interpretation of the frictional sliding behaviour. Lastly, a carefully calibrated FDEM model that was built based on the rotary experiment was utilized to investigate facets that the experiment was not able to resolve, for example, the time-continuous stress condition and the seismic activity on the shear surface. The model reproduced the mechanical behaviour observed in the laboratory experiment, shedding light on the understanding of fault evolution.

Keywords: Acoustic emission
Fault evolution
FDEM
micro-CT
Microseismicity
Rotary shear test
Advisor: Grasselli, Giovanni
Tisato, Nicola
Quantification of Belowground C Flow from Root Exudation of Peatland Sedges and Shrubs

A large range of labile organic compounds are secreted by roots into the soil, which inevitably leads to changes in nutrient availability and C cycling. Little is known about root exudation variability among species, or at the individual root level, hampering estimates of total C deposition. Environmental controls are believed to influence root exudation at the single root scale, yet are rarely accounted for. Quantifying exudation heterogeneities within the root system permits more accurate upscaling to the whole plant and landscape level, provided the sites of exudation and belowground biomass are well quantified. Root exudate composition was characterized in two model organisms - Eriophorum vaginatum and Rhododendron groenlandicum utilizing localized sampling of root segments. E. vaginatum roots were distinguished into three classes by age, and R. groenlandicum into four classes by fine root abundance and root diameter. Considerable variations in the total efflux, as well as the composition of exudates, was documented at both the species and root class level, confirming that exudation is not homogenous within the root system. Existing root biomass data has little correlation with the vertical gradients of exudation. Whole plant root systems were excavated and digitally mapped at sufficient detail to explicitly distinguish the depth distribution of the roots associated with exudation. Measurements of the normalized root length fraction per depth interval were tested against a variety of density distribution models to infer a suitable function to represent roots for upscaling a single root to the landscape scale. The abundance of key species such E. vaginatum that deposit C directly into the anoxic zone are poorly mapped in peatlands. A new detection methodology, based on phenological timing and the spectral contrast of decomposing litter, was investigated utilizing an expanded version of PROSAIL. Close range imagery indicated the calibrated model was capable of quantifying decaying monocot litter as a unique class, which bodes well for detection at the landscape scale. The studies presented in this thesis document root exudation rates and root distribution data necessary to conduct a simple upscaling from the single root to the landscape level. Collectively, they permit the C flow via the exudation pathway to be estimated, with consideration for vertical gradients that partition exudation into the oxic and anoxic zone.

Keywords: Radiative transfer modelling
Root depth distribution
Root exudation
Simulation model
Advisor: He, Yuhong
Diagnosing and Treating Infectious Diseases and Antimicrobial Resistance Using Gold Nanoparticles

The continued emergence of infectious diseases and the development of antimicrobial resistance represent a major global health challenge in the 21st century. Rapid and accurate diagnosis of infectious pathogens is vital for both the treatment and prevention of new forms of antimicrobial resistance. The current advances in nanotechnology have afforded the development of new simple and rapid diagnostic assays as well as novel therapeutic technologies. This thesis presents new and original work that exploits the physical and chemical properties of gold nanoparticles to diagnose and treat infectious diseases. The contributions to the field are two-folds. Earlier work was aimed at developing a rapid, sensitive and simple platform for the detection of infectious diseases and antimicrobial resistance, where signal readout could be observed with the naked eye. Second, the photo-thermal characteristics of gold nanoparticles were used to create a novel plasmonic thermogel that disinfected antimicrobial resistant bacteria in surgical wounds, preventing the use of a broad-spectrum antibiotic. It is anticipated that the contribution of this thesis will continue to advance the implementation of gold nanoparticles for the development of commercial diagnostics and therapeutics. Collectively, this work should improve the mitigation of infectious diseases and reduce the risk of the development of further antimicrobial resistance.

Keywords: Antimicrobial resistance
Clinical Diagnosis
Gold nanoparticles
MNAzyme
Nucleic acid detection
Photothermal therapy
Advisor: Chan, Warren