VictorJuiz/thesis huggingface dataset:
Impact of Pretreatment Methods on Enzymatic Hydrolysis of Softwood

Bioethanol is an appealing alternative to petroleum-based liquid fuel due to drivers such as environmental regulations and government mandates. Second generation lignocellulosic feedstocks are abundant, but their resistance to hydrolysis continues to be problematic. Different pretreatments have been proposed to increase cellulose reactivity. Softwood pine autohydrolyzed at different severities was subjected to further treatment to increase fibre reactivity. Liquid hot water is most effective at removing barriers, with the highest increase in sugar yield after enzymatic hydrolysis. Alkaline (NaOH) is found to be the worst option compared to dilute acid and organosolv. In addition, higher chemical concentrations and longer treatment times do not guarantee higher enzymatic hydrolysis yield. Process modifications such as fiber washing and multistage enzymatic hydrolysis are observed to be effective at increasing yield. However, more research is required to bring the enzymatic hydrolysis yield to a level where commercialization is feasible.

Keywords: Biomass
Pretreatment
Enzymatic Hydrolysis
Autohydrolysis
Steam Explosion
Multistage
Lignocellulose
Softwood
Bioethanol
Advisor: Saville, Bradley
Characterization of an Electrospray with Co-flowing Gas

In mass spectrometry an electrospray is commonly used as an ion source. At high sample flow rates a sheath co-flow of gas around the electrospray emitter is employed. The co-flow of gas reduces contamination and increases signal sensitivity in the mass spectrometer’s results. This work characterizes the operation of an electrospray with co-flowing air for various operating conditions. It is found that a co-flowing air has a negligible effect on droplet size for the spindle and cone jet modes while it only reduces the droplet size marginally in the unstable mode. In the high flow rate unstable mode, the addition of air seems to have no real effect on droplet size. In summary, the electrospray with co-flowing air produces a denser and more focused spray with similar droplet size and distribution than that of the un-nebulized spray. This explains why using co-flowing air in mass spectrometry applications improves the signal quality, since it allows for the focusing of droplets produced into the inlet and also aids in the breakup of larger droplets.

Keywords: Electrospray
Characterization
Co-Flowing Gas
Nebulizer
Droplet Size
Cone Jet
Mass Spectrometry
Spray
Advisor: Ashgriz, Nasser
Investigating the Hippo Signaling Pathway using High-throughput Protein-protein Interaction LUMIER Screens

The Hippo pathway plays a key role in controlling organ growth and size. In mammals, core pathway components include the Lats1/2 and Mst1/2 kinases, which phosphorylate the transcriptional regulators, Taz and Yap. To identify novel upstream pathway regulators high throughput protein-protein interaction screens, called LUMIER (LUminescence-based Mammalian IntERactome) were performed together with a functional screen using a luciferase reporter that examines Hippo pathway responses. The screens revealed 1103 protein-protein interactions and 227 transcriptional regulators, which were particularly enriched in cytoskeletal regulators. A subset of these hits including BTK, Dvl1, Dvl2, Dvl3, Ing2, Magi2, Mark4 and Trip6 were validated by manual LUMIER assays and co-immunoprecipitation (Co-IP). Of particular interest was the microtubule dynamics regulatory protein MARK4. Loss of Mark4 prevents Taz activity demonstrating its role as a potential negative regulator of the Hippo pathway. Further studies could help decipher mechanisms of how Mark4 and the other cytoskeletal hits act to modulate the Hippo pathway.

Keywords: Biochemistry
Molecular Biology
Advisor: Attisano, Liliana
Differential Effects of NMDA Receptor Antagonism on Spine Density

Recent studies have demonstrated that an acute, low dose of ketamine, a non-competitive NMDA receptor antagonist, provides rapid and sustained antidepressant effects in patients with major depressive disorder. Studies in rodents have shown that the antidepressant properties of ketamine are due to an increase in dendritic spine density in the cortex. Our goal was to determine whether these effects are specific to ketamine and whether they are dependent on dose, drug regimen and brain region. We observed that the effects of ketamine on spine density were dependent on dose and drug regimen and were also brain region specific. In addition, MK-801, another NMDA receptor antagonist, did not demonstrate the same effects on spine density as ketamine. Furthermore, genetic NMDA receptor hypofunction significantly reduced spine density. Our studies demonstrate that while acute ketamine treatment leads to an increase in cortical spine density, chronic administration has opposite and potentially detrimental effects.

Keywords: NMDA receptor antagonism
Ketamine
MK-801
Spine density
Depression
Advisor: Ramsey, Amy J.
Grant, Denis M.
A Comparative Analysis of Long-term Care Policies and Placements

The objective of this study was to determine whether provincial health policies influence the supply of long-term care in a province, and the care received by residents that require it. This was achieved by first conducting a comprehensive review and comparative analysis of the long-term care policies of Alberta and Ontario, and then comparing health conditions of long-term care and assisted living/retirement home residents in both provinces. The latter comparisons used information collected from comparable versions of the Resident Assessment Instrument – Minimum Data Set (RAI-MDS) and the RAI-MDS Home Care. The study hypothesis was that provinces with health policies favouring institutional over community care would have a higher proportion of residents with lower care requirements in institutional settings. The results show that this is not the case, and that institutional settings house those with high care needs in both provinces.

Keywords: Long-Term Care
Policies
Advisor: Wodchis, Walter
The Use of Information and Communication Technologies for Knowledge Translation in a Mentoring Network of Physicians to Optimize Roles in the Management of Chronic Pain

This study seeks to understand how collaborative information communication technologies (cICT) are used to support knowledge translation and optimize physician’s roles in chronic pain management. A survey was developed and distributed to 170 physicians in two chronic pain mentoring networks in Ontario and Nova Scotia. With a response rate of 74.1% the study identified the use of a broad variety of cICTs; with email as the most used. A majority of respondents (85.0%) used email to support discussions and 69.8% found it to be valuable in learning about chronic pain management. A higher frequency of email (adjusted OR=10.70, 95% CI: 2.84-40.33) and number of cICTs (adjusted OR=2.93, 95% CI: 1.19-7.21) used to communicate in the networks were associated with more interactions. These results highlight how cICTs can support the interactions and learning that are part of the knowledge translation process in optimizing the roles of physicians in chronic pain management.

Keywords: knowledge translation
chronic pain
information and communication technologies
role optimization
mentoring
communities of practice
physicians
Advisor: Jadad, Alejandro R.
Diversity and Dynamics of Algal Viruses in the Bay of Quinte

To initiate algal virus research in the Bay of Quinte, three stations were sampled biweekly throughout 2011. By targeting algal virus DNA polymerase, major capsid protein genes (MCP), and a Microcystis aeruginosa cyanophage (Ma-LMM01) tail sheath protein gene, PCR amplification revealed diverse and unique Phycodnaviruses (viruses of eukaryotic algae) and cyanophage. When analysed statistically, patterns of virus abundance suggested that the seasonality of any one virus cannot be generalised to predict that of other viruses, even among closely related viruses. This study also demonstrated a strong relationship between algal virus abundance and host biomass. It was found that despite the apparent heterogeneity of virus abundance across the Bay, virus abundance patterns clustered by sampling date and geographic location. By providing evidence for diverse algal viruses with complex seasonality, this work highlights significant gaps in the current understanding of Bay of Quinte phytoplankton ecology.

Keywords: Algal viruses
Bay of Quinte
Phycodnaviruses
DNA polymerase
major capsid protein gene
Sheath protein gene
Microcystis aeruginosa
freshwater
Lake Ontario
Cyanophage
abundance
seasonality
Algal bloom
Quantitative PCR
Chlorophyll a
Advisor: Short, Steven
Insular Thinking: Ideology and Memory in the Japan-China/Japan-Korea Maritime Territorial Disputes

Territorial disputes between Japan and South Korea (Dokdo/Takeshima) and Japan, Taiwan, and China (the Senkaku/Diaoyu Islands) are characteristic of post-war East Asian diplomacy. This thesis explores these ongoing territorial disputes, problematizing Realist arguments by which these disputes are analyzed as matters of territorial or resource nationalism, or as the result of legal complications or security concerns. Instead, it is argued that we should look to ideologies of nationalism to understand seemingly extreme emotional reactions over these 'rocks' which threaten to destabilize Northeast Asia. These islands are treated as 'sublime' symbols of the nation and irredentist arguments which support the Japanese, Korean, and Chinese positions read history through a lens of essentialized notions of 'a people' or 'a nation', and in the process help define both.

Keywords: Japan
China
Korea
Territory
Senkaku
Takeshima
Diaoyu
Dokdo
Cold War
Territoriality
Irredentism
Zizek
Advisor: Yoneyama, Lisa
Genetic Dissection of Virulence and Immune-eliciting Functions and Characterization of the Immune Response of the Pseudomonas syringae HopZ1 Type III Effector Family

Successful pathogens like Pseudomonas syringae translocate type III effector proteins (T3SE) into host cells. Plant hosts react by specifically recognizing these effectors via R proteins that trigger defense responses. The T3SE family HopZ1 has evolved into three allelic forms as a result of diversifying selection. In this thesis, I investigated how virulence and immune-eliciting functions are determined in HopZ1a and HopZ1b in Arabidopsis. Mutational analysis of HopZ1a identified ten residues important for immune elicitation and at least three are involved in virulence functions. These results suggest that distinct key amino acid residues in HopZ1a mediate the two activities. The closely related HopZ1b T3SE elicits an inconsistent immune response in Arabidopsis. We found that HopZ1b-triggered immune response involves a TIR-type R protein and plastid-derived SA. Together, these results highlight an uncharacterized ETI response to the HopZ1 family of T3SEs.

Keywords: HopZ1
Pseudomonas syringae
type III effector
Advisor: Guttman, David S.
Desveaux, Darrell
The Impact of Engineering Halide/Thiol Methyltransferase-mediated Cl– volatilization on Salt Tolerance of Tomato Plants

Many higher plants can synthesize methyl chloride gas via a common metabolic route, also known as the biological chloride methylation. The reaction is catalyzed by an S-adenosyl-L- methionine (AdoMet) dependent halide/thiol methyltransferase (H/TMT). It is speculated that plants use chloride methylation to remove excess chloride via volatilization and hence maintain homeostatic levels of cytoplasmic chloride ion, suggesting a role of H/TMT in salt tolerance. In this project, the effect of engineering a Brassica oleracea thiol methyltransferase (BoTMT) into tomato was studied to determine the physiological relevance of this enzyme in conferring salt tolerance. Transgenic tomato plants acquired the ability to release methyl chloride in response to NaCl treatment, but exhibited no greater tolerance to NaCl, based on several morphological and physiological measurements, as compared to the wild-type plants. The results indicate that AdoMet dependent chloride methylation is unlikely to contribute to an increase in salt tolerance in higher plants.

Keywords: Halide/Thiol methyltransferase
Thiol Methyltransferase
Halide methylation
salinity
Tomato
AdoMet
Salt tolerance
H/TMT
Advisor: Saini, Deep
Physiological Synchrony as Manifested in Dyadic Interactions

Children with severe disabilities have limited ability to communicate with their environment. Understanding how and to what extent these children connect with the environment can be an insurmountable challenge for their caregivers. In this thesis we investigated the degree of interactions between a pair of individuals using their physiological signals. It was hypothesized that stronger social interaction induces greater physiological synchrony. We introduced a multivariate index of synchrony to relate various physiological correlations into the degree of social interaction. 18 able-bodied individuals participated in a study to measure the extent of synchrony between two intimate individuals vs. two strangers during conversation. Stronger correlation was detected for intimate participants in comparison with the strangers. The physiological alignment also increased as the dyad interacted more. A generalization of our method can be used for the study of children with disabilities to understand the degree of their non-verbal interaction with their social environment.

Keywords: Physiological correlation
Sociophysiology
Social interaction
Advisor: Chau, Tom
Examining Trends in the Incidence of Asthma in Children in Ontario

Background: The causes of trends in asthma incidence are not fully understood. Objectives: This study examined trends in age and severity at asthma diagnosis for Ontario children. Methods: Multiple birth cohorts of Ontario children between 1992-2000 were created using health administrative data. Descriptive statistics and multivariable logistic regression examined changes in age and severity of asthma at diagnosis over time. Results: Age at asthma diagnosis decreased (p<0.0001) with a higher relative risk of asthma in children under age three (RR=1.5, 95% CI:1.47, 1.54). Predictors of asthma diagnosis before three included male sex, lower income quintile, and maternal asthma. ‘Severe onset asthma’ increased over time (p<0.0001), its predictors being male sex, lower income quintile, rural residence, comorbidity, low birth weight and age less than three. Conclusions: Observed trends in asthma incidence are not confined to mild disease and are secondary to variations in asthma rates in children under age three.

Keywords: asthma
incidence
age of onset
children
severity
Ontario
Advisor: To, Teresa
Short-term Saccadic Adaptation in Patients with Amblyopia

This thesis investigates sensorimotor adaptive mechanisms that maintain the accuracy of goal-directed saccades in amblyopia, a developmental disorder characterized by impairment of spatiotemporal visual processing. Saccadic adaptation was induced by displacing the visual target toward initial fixation during the saccade. Eleven visually normal controls and seven patients with amblyopia were tested binocularly and monocularly with the amblyopic and fellow eye (non-dominant and dominant eye in controls) in three separate sessions. Patients with amblyopia exhibited reduced adaptation of saccadic gain compared to controls when viewing with the amblyopic eye and binocularly. Initiation of saccades was also delayed in patients when viewing with the amblyopic eye. It is proposed that the adaptive ability to modify the initial saccadic motor commands for maintaining short-term saccadic accuracy is impaired in amblyopia due to imprecise error signals. Moreover, this thesis reaffirms the notion that the error signals driving saccadic adaptation are visual in nature.

Keywords: Amblyopia
Saccadic eye movements
Motor adaptation
Eye movement accuracy
Advisor: Wong, Agnes Ming-Fong
Goltz, Herbert
Parallel, Block-based, Adaptive Mesh Refinement, Finite-volume Scheme for Solution of Three-dimensional Favre-averaged Navier-Stokes Equations

A parallel, block-based, adaptive mesh refinement, finite-volume scheme is developed and validated for the solution of the Favre-Averaged Navier-Stokes equations governing three-dimensional flow of a polytropic gas. The two-equation k-omega turbulence model is used to model the unresolved turbulent scales and their influence on the mean solution. The finite-volume spatial discretization is accomplished by using a finite-volume procedure on multiblock, body-fitted, hexahedral mesh. The inviscid flux functions make use of Roe's approximate Riemann solver. The viscous flux is evaluated using a diamond path reconstruction procedure on each cell boundary. Verification and validation of the solution method is accomplished through the application of the algorithm to a number of flow problems. The results from the application of the solution method to the flow problems are in good agreement with available experimental data. Therefore, the validity of the solution method for solving three-dimensional, turbulent flows is confirmed.

Keywords: CFD
turbulence modeling
aerospace
RANS
Advisor: Groth, Clinton P. T.
Responses of Ground Beetles (Coleoptera: Carabidae) to Variation in Woody Debris Supply in Boreal Northeastern Ontario

The maintenance of downed woody debris supplies is increasingly being recognized as an integral part of forest management. In order to better manage this resource, it is important to assess its role in supporting biodiversity. In this thesis, I investigate the responses of carabid communities to variation in woody debris availability in an experimental manipulation of woody debris volume in closed canopy forests and following a biomass harvest in a clearcut. Within closed-canopy forests, total carabid abundance and the abundances of eight species increased significantly with increasing volumes of various types of woody debris, particularly large diameter, late-decay conifer wood. Similarly, a strong affinity with woody debris was observed in the clearcut. These findings suggest that reductions in woody debris will have negative consequences for carabids and indicate the need to ensure a diverse and abundant supply of woody debris during stand development.

Keywords: Carabidae
beetle
manipulation
woody debris
dead wood
slash
boreal
clearcut
forest
Advisor: Malcolm, Jay R.
Smith, Sandy
Applications of Principal Component Analysis of Fluorescence Excitation-emission Matrices for Characterization of Natural Organic Matter in Water Treatment

Quantification of natural organic matter (NOM) in water is limited by the complex and varied nature of compounds found in natural waters. Current characterization techniques, which identify and quantify fractions of NOM, are often expensive and time consuming suggesting the need for rapid and accurate characterization methods. In this work, principal component analysis of fluorescence excitation-emission matrices (FEEM-PCA) was investigated as a NOM characterization technique. Through the use of jar tests and disinfection by-product formation tests, FEEM-PCA was shown to be a good surrogate for disinfection by-product precursors. FEEM-PCA was also applied in order to characterize differences in humic-like, protein-like, and Rayleigh scattering between multiple source waters and due to differing treatment processes. A decrease in Rayleigh scattering influence was observed for a deep lake intake, and multiple processes were found to significantly affect humic-like substances, protein-like, and Rayleigh scattering fractions.

Keywords: natural organic matter
principal component analysis
fluorescence excitation-emission matrices
disinfection by-products
Advisor: Andrews, Robert C.
Extension of the ADjoint Approach to a Laminar Navier-Stokes Solver

The use of adjoint methods is common in computational fluid dynamics to reduce the cost of the sensitivity analysis in an optimization cycle. The forward mode ADjoint is a combination of an adjoint sensitivity analysis method with a forward mode automatic differentiation (AD) and is a modification of the reverse mode ADjoint method proposed by \citet{Mader:2008:B}. A colouring acceleration technique is presented to reduce the computational cost increase associated with forward mode AD. The forward mode AD facilitates the implementation of the laminar Navier--Stokes (NS) equations. The forward mode ADjoint method is applied to a three-dimensional computational fluid dynamics solver. The resulting Euler and viscous ADjoint sensitivities are compared to the reverse mode Euler ADjoint derivatives and a complex-step method to demonstrate the reduced computational cost and accuracy. Both comparisons demonstrate the benefits of the colouring method and the practicality of using a forward mode AD.

Keywords: Laminar Navier-Stokes
adjoint
automatic differentiation
Advisor: Martins, Joaquim R. R. A.
Plasmonic Enhancement for Colloidal Quantum Dot Photovoltaics

Colloidal quantum dots (CQD) are used in the fabrication of efficient, low-cost solar cells synthesized in and deposited from solution. Breakthroughs in CQD materials have led to a record efficiency of 7.0%. Looking forward, any path toward increasing efficiency must address the trade-off between short charge extraction lengths and long absorption lengths in the near-infrared spectral region. Here we exploit the localized surface plasmon resonance of metal nanoparticles to enhance absorption in CQD films. Finite-difference time-domain analysis directs our choice of plasmonic nanoparticles with minimal parasitic absorption and broadband response in the infrared. We find that gold nanoshells (NS) enhance absorption by up to 100% at λ = 820 nm by coupling of the plasmonic near-field to the surrounding CQD film. We engineer this enhancement for PbS CQD solar cells and observe a 13% improvement in short-circuit current and 11% enhancement in power conversion efficiency.

Keywords: photovoltaics
colloidal quantum dots
plasmonics
Advisor: Sargent, Edward H.
The Costs and Benefits of Deep Brain Stimulation Surgery for Patients with Parkinson’s Disease at Different Stages of Severity – An Initial Exploration

Objectives: To estimate the incremental cost per QALY in patients with Parkinson’s Disease (PD) with varying disease severity and to ascertain which patient subgroup would accrue the greatest net monetary benefits to Ontario’s public health perspective as a result of Deep Brain Stimulation (DBS). Design: A cost-utility study and a net monetary benefit framework approach were applied to 37 PD patients with varying disease stages who underwent DBS treatment. Results: DBS resulted in cost savings of $2,686.3, $2,752.4, and $7348.4 and QALY gains of 0.33, 0.09 and 0.04 in patients with mild, moderate and severe PD. The ICER was $16,076.2/QALY. At $50,000/QALY, the greatest net monetary benefits accrued to Ontario’s MOHLTC were from treating patients with mild PD with DBS. Conclusions: DBS surgery was found to be a cost-effective PD treatment compared to pharmacotherapy. The greatest net monetary benefits were from treating patients with mild PD severity.

Keywords: Health Economics
Parkinson's Disease
Advisor: Coyte, Peter C.