VictorJuiz/thesis huggingface dataset:
Substrates and Inhibitors of Enzymes Involved in Exopolysaccharide Dependent Biofilms
Keywords: Biofilms
Carbohydrate
Chemoenzymatic
PNAG

Many biofilm-forming bacteria produce a similar partially de-N-acetylated β-1,6-N-acetyl glucosamine homopolymer (dPNAG) to facilitate bacterial adhesion. In many medically important biofilm forming bacterial strains, including Escherichia coli, Staphylococcus epidermidis and Staphylococcus aureus, de-N-acetylation of the β-1,6-N-acetyl glucosamine homopolymer (PNAG) is catalyzed by a metal dependent de-N-acetylase. Sixty-five percent of all human persistent bacterial infections are considered to be biofilm related. In vivo studies have implicated the production and subsequent de-N-acetylation of PNAG is essential to bacterial virulence. In this work, methods of monitoring and targeting PNAG-dependent biofilm processes are explored. A novel chromogenic glycosidase substrate based on a glycosyl carbamate was developed and used to effectively monitor the activity of Dispersin B (DspB), an enzyme capable of degrading PNAG/dPNAG. Additionally, an array of potential deacetylase inhibitors were synthesized with the goal of targeting the essential de-N-acetylase enzymes PgaB and IcaB, from E. coli and S. epidermidis respectively, for biofilm formation. These inhibitors were based on a carbohydrate scaffold containing either a metal chelating moiety or a transition state mimic. Finally, a novel coumarin based substrate was developed to monitor in vitro de-N-acetylase activity of PgaB and IcaB. Using this substrate, the potency of the synthesized inhibitors was evaluated through a competitive fluorogenic assay. The most effective inhibitor, a chemoenzymatically-synthesized pentasaccharide derivative showed a Ki value of 280 µM.
The Biological Identity of Nanoparticles
Keywords: Drug Delivery
Nanomedicine
Nanoparticles
Nanotechnology
Pharmaceuticals
Proteomics

Understanding and controlling the biological response to nanoparticles is essential to designing safe and effective formulations to diagnose and treat disease and for mitigating toxicological risks resulting from incidental or accidental exposure. Because cells are the basic functional units of the body, nanoparticle-cell interactions are a critical determinant of the overall biological response to nanoparticles. In the past, it was assumed that the form of a nanoparticle that comes into contact with cells is the same as the form it had following synthesis. However, when a nanoparticle enters a biological environment, it immediately comes into contact with a complex and highly concentrated mixture of proteins. A subset of these proteins will interact with the surface of a nanoparticle and adsorb to it. The adsorbed proteins form a protein `corona' that defines, in part or in whole, the bioactive interface of a nanoparticle within a biological system. Protein-nanoparticle interactions can also lead to nanoparticle aggregation. The formation of the protein corona and aggregation within a biological environment give the nanoparticle a `biological identity' that is distinct from its `synthetic identity'. It is ultimately the biological identity of a nanoparticle that is `seen' by cells and other components of a biological system and determines the biological response. Yet, it is not clear how the physical and chemical properties of a nanoparticle determine the composition and structure of the protein corona and, in turn, downstream cellular interactions and responses. In this thesis, I elucidate fundamental relationships between nanoparticle design, the composition of the protein corona, and downstream cell interactions within static and dynamic biological environments. These relationships will enable nanoparticle-cell interactions within a biological system to be predicted and controlled and will act as a guide for the design of safer, more effective nanoparticle formulations for nanotechnology applications.
The Crossover Effects of Morphological Awareness on Literacy Outcomes among Children in French Immersion
Keywords: cross-language transfer
French immersion
morphological awareness
reading comprehension
second-language learners
vocabulary

This dissertation comprised three studies examining the cross-language effects of morphological awareness on literacy outcomes among early elementary school children in a French immersion program. Two aspects of morphological awareness were investigated: inflectional awareness and derivational awareness. Study 1 explored the bidirectional cross-language effects between morphological awareness and vocabulary development in English and French over one year. Participants included 156 students in Grades 1 and 2. Regression analyses revealed that English inflectional awareness predicted unique variance in French vocabulary among Grade 1 students. Among Grade 2 students, cross-lagged analyses showed that both English inflectional and English derivational awareness predicted gains in French vocabulary between Grades 2 and 3. Moreover, French derivational awareness measured at Grade 2 was associated with Grade 3 English vocabulary.Study 2 examined the role of cognates in mediating the relations between English morphological awareness and French vocabulary. Participants included 108 first and second grade students. Results indicated that English morphological awareness was a unique predictor of French cognate but not non-cognate vocabulary. This suggests that the transfer of morphological awareness across languages is facilitated when the words to be learned in the children's additional language bear similarities to words in their primary language. Finally, Study 3 evaluated the longitudinal contributions of English morphological awareness to French reading comprehension skills among the sample from Study 1. The effects of children's knowledge of the systematic relations between English and French derivational suffix pairs on their French reading comprehension skills were additionally explored. Results showed that English inflectional awareness significantly predicted French reading comprehension among the Grade 1 students, whereas English derivational awareness predicted variance in French reading comprehension among the Grade 2 students. Children's awareness of the systematic relations between English and French derivational suffix pairs predicted changes in French reading comprehension from Grades 2 to 3.Taken together, these results add to the extant corpus of research to substantiate that children can leverage morphological awareness from their primary language to facilitate their vocabulary learning as well as reading comprehension in their additional language. These results are discussed in light of current reading and transfer models.
Applied Stochastic Control in High Frequency and Algorithmic Trading
Keywords: Algorithmic Trading
Hawkes Process
High Frequency Trading
Market Making
Stochastic Control

In this thesis, problems in the realm of high frequency trading and optimal market making are established and solved in both single asset and multiple asset economies. For an agent that is averse to holding large inventories for long periods of time, optimal high frequency trading strategies are derived via stochastic control theory and solving the corresponding Hamilton-Jacobi-Bellman equations. These strategies are analyzed and it is shown that both inventory control and accounting for adverse selection play critical roles in the success of an algorithmic trading strategy. In the single asset problem, a market maker actively modifies her limit quotes in an economy with asymmetric information. She attempts to keep her inventory small and posts her limit orders in the limit order book at a depth that mitigates her adverse selection risk, while not posting too deep in the book as to generate no trade flow. In addition to this behaviour, a profit maximizing investor trading in multiple assets also seeks out statistical arbitrage opportunities and acts aggressively via the submission of market orders when it is deemed optimal to do so.Throughout this thesis, numerical and practical considerations are made a priority. Full scale calibration and estimation methods are given in detail, as well as dimensional reductions for large scale numerical procedures, where appropriate. The bridge from abstract mathematical theory to practical real-time implementation is made complete as an entire chapter is dedicated to applications on real data.
Evaluation of Oil Sands Projects and their Expansion Rate using Real Options
Keywords: Dynamic programming
Financial modeling
Oil sands
Real options analysis
Uncertainty
Valuation

The rapidly expanding oil sands of western Canada, the third largest reserves in the world, are creating serious challenges, such as ecological harm, labour shortages, and extensive natural gas consumption. This thesis develops three practical real options models to evaluate the feasibility of oil sands projects and to stimate the optimal rate of oil sands expansion, while accounting for the stated concerns. The first model estimates the value of an oil sands plant, while accounting for oil price uncertainty, in a single-agent setting. The model shows that, in the current bullish oil market and with the long life of oil sands projects, once constructed, oil sands plants are highly unlikely to close unless the price of oil drops substantially. Unsanctioned projects with little capital spentare susceptible to delay/cancellation. The second model estimates the value of a plant, while accounting for oil and natural gas price uncertainties, in a single-agent setting. The results show that oil price is the key driver of oil sands growth in Alberta. Becauseof the current low natural gas price, the importance of natural gas price uncertainty in the valuation is low. The third model evaluates the rate of oil sands expansion under different environmental tax/cost policies, while accounting for the oil price uncertainty,in a multi-agent setting . This model also accounts for labour shortages in Alberta. The results show that a stricter environmental tax policy delays investment but leads to a higher rate of expansion once investment begins. The first two models provide a framework for oil companies to value new oil sands plants and to gauge the optimum time to construct, given the current state of uncertainty in the industry. The third model allows oil companies and government policy makers to gauge the impact of policy strategies on oil sands expansion rates.
High-pressure Soot Formation and Diffusion Flame Extinction Characteristics of Gaseous and Liquid Fuels
Keywords: diffusion flame
flame extinction
liquid fuels
soot formation

High-pressure soot formation and flame stability characteristics were studied experimentally in laminar diffusion flames. For the former, radially resolved soot volume fraction and temperature profiles were measured in axisymmetric co-flow laminar diffusion flames of pre-vaporized n-heptane-air, undiluted ethylene-air, and nitrogen and carbon dioxide diluted ethylene-air at elevated pressures. Abel inversion was used to re-construct radially resolved data from the line-of-sight spectral soot emission measurements. For the latter, flame extinction strain rate was measured in counterflow laminar diffusion flames of C1-4 alcohols and hydrocarbon fuels of n-heptane, n-octane, iso-octane, toluene, Jet-A, and biodiesel.The luminous flame height, as marked by visible soot radiation, of the nitrogen- and helium-diluted n-heptane and nitrogen- and carbon dioxide-diluted ethylene flames stayed constant at all pressures. In pure ethylene flames, flame heights initially increased with pressure, but changed little above 5 atm. The maximum soot yield as a function of pressure in nitrogen-diluted n-heptane diffusion flames indicate that n-heptane flames are slightly more sensitive to pressure than gaseous alkane hydrocarbon flames at least up to 7 atm. Ethylene's maximum soot volume fractions were much higher than those of ethane and n-heptane diluted with nitrogen (fuel to nitrogen mass flow ratio is about 0.5). Pressure dependence of the peak carbon conversion to soot, defined as the percentage of fuel's carbon content converted to soot, was assessed and compared to previous measurements with other gaseous fuels. Maximum soot volume fractions were consistently lower in carbon dioxide-diluted flames between 5 and 15 atm but approached similar values to those in nitrogen-diluted flames at 20 atm. This observation implies that the chemical soot suppression effect of carbon dioxide, previously demonstrated at atmospheric pressure, is also present at elevated pressures up to 15 atm, but fades off beyond 15 atm.In flame stability experiments, the extinction strain rates increased with decreasing dilution. In general, the fuels with higher carbon number and fuels with more compact structures were found to be more prone to extinction. Counterflow laminar diffusion flames established at the impingement of reactants with a top-hat (axially uniform) velocity profile were found to be more resistant to extinction than those with a parabolic exit velocity profile. Multiple solutions to the flame stability were observed for certain hydrocarbons.
Practicality of Quantum Information Processing
Keywords: Ion trap
Quantum computer
Quantum cryptography
Quantum information

Quantum Information Processing (QIP) is expected to bring revolutionary enhancement to various technological areas. However, today's QIP applications are far from being practical. The problem involves both hardware issues, i.e., quantum devices are imperfect, and software issues, i.e., the functionality of some QIP applications is not fully understood.Aiming to improve the practicality of QIP, in my PhD research I have studied various topics in quantum cryptography and ion trap quantum computation. In quantum cryptography, I first studied the security of position-based quantum cryptography (PBQC). I discovered a wrong assumption in the previous literature that the cheaters are not allowed to share entangled resources. I proposed entanglement attacks that could cheat all known PBQC protocols.I also studied the practicality of continuous-variable (CV) quantum secret sharing (QSS). While the security of CV QSS was considered by the literature only in the limit of infinite squeezing, I found that finitely squeezed CV resources could also provide finite secret sharing rate. Our work relaxes the stringent resources requirement of implementing QSS.In ion trap quantum computation, I studied the phase error of quantum information induced by dc Stark effect during ion transportation. I found an optimized ion trajectory for which the phase error is the minimum. I also defined a threshold speed, above which ion transportation would induce significant error.In addition, I proposed a new application for ion trap systems as universal bosonic simulators (UBS). I introduced two architectures, and discussed their respective strength and weakness. I illustrated the implementations of bosonic state initialization, transformation, and measurement by applying radiation fields or by varying the trap potential. When comparing with conducting optical experiments, the ion trap UBS is advantageous in higher state initialization efficiency and higher measurement accuracy.Finally, I proposed a new method to re-cool ion qubits during quantum computation. The idea is to transfer the motional excitation of a qubit to another ion that is prepared in the motional ground state. I showed that my method could be ten times faster than current laser cooling techniques, and thus could improve the speed of ion trap quantum computation.
The Full Day Kindergarten Classroom in Ontario: Exploring Play-based Learning Approach and Its Implications for Child Development
Keywords: Child Development
Early Years Education
Full Day Kindergarten
Ontario FDK
Play-based Learning
Teaching Practices

Children have the right to fulfill and expand on all their potentials and desires to learn. In 2010, the Ontario Ministry of Education introduced Full-Day Kindergarten (FDK) in Ontario and aimed at providing quality Kindergarten programs for children. The implementation of FDK is expected to be implemented in all public schools by 2015/16. The literature and research on early years education affirms that children benefit from quality early years educational programs as they are important in developing neurons in the brain before the age of six. This qualitative study focuses on understanding early years' educational philosophies and examining teachers' perspectives on FDK teaching and learning practices. The case studies are informed by the narratives of eight Kindergarten teachers through data collected from interviews, observation, classroom visits, and artifacts. The most significant findings of the study are that quality FDK teaching and learning practices are based on the following features: (a) learning through play-based, inquiry-based and experiential-based exploration; (b) making the educational experiences child-centred and authentic; (c) building on childrens' past experiences, nurturing self-expression and identity; (d) strengthening relationships and connections; and (e) creating stimulating environments, both indoor and outdoor, for children's learning and development. Teachers' perspectives and specific FDK classroom practices are described, analyzed and discussed. Theory informed practice and practice informed theory, as models were developed and designed during this research journey. The theoretical framework served as a holistic lens and was instrumental in examining FDK practices in each case study. The Integrated Child Development Model was created, later modified and named the Early Years Education Model (EYE Model). The EYE Model identified important aspects of quality FDK and named developmental domains. The models served as a tools and conceptual frameworks in evaluating and analyzing classroom practice. Research implications that resulted from this study included improving class size, providing more teacher training, and greater opportunities for quality and varied play experiences were identified as essential moving forward. The Kindergarten years lay a strong foundation for success in future schooling and looking closer at teaching and learning practices in the Kindergarten classroom brings awareness to best practices.
Partisan Manipulation of the Democratic Process and the Comparative Law of Democracy
Keywords: Comparative Law
Election Law
Electoral Management Bodies
Judicial Review
Law of Democracy
Partisanship

This dissertation argues for institutionally focused judicial oversight of the law of democracy in order to minimize partisan manipulation of the democratic process. Elected representatives have incentives to distort for partisan gain campaign finance, political party funding, electoral boundaries, and the other rules shaping democratic political competition. While representatives are elected to act in the best interests of voters, they can entrench themselves and reduce their electoral accountability by altering the rules that structure elections and democratic politics. In other words, political representation is beset by a principal-agent problem. I trace the implications of the principal-agent problem for judicial review of the comparative law of democracy. I argue that leading accounts of judicial review of the law of democracy have failed to account for the presence of electoral management bodies (EMBs), such as election commissions and redistricting commissions, and the role played by majoritarian constitutional structures. If the goal is to reduce partisan self-dealing then judicial oversight must be institutionally sensitive, because the risk of partisan self-dealing varies depending on the type and characteristics of the institution whose actions are under review. I argue that courts should show different degrees of deference based on the risk that the institution is likely to have distorted the democratic process. EMBs are likely to be independent and impartial and the risk of partisan self-dealing by these institutions is therefore reduced. To the extent that they are independent and impartial, then these institutions are entitled to deference. Courts must be aware, however, of the variation in institutional design of EMBs, which range from independent and impartial to partisan and captured. Where the EMB has been captured by partisan interests, then deference is not warranted. Where it is the decisions of legislatures and not EMBs that are under review, then courts should engage in vigilant oversight because of the incentives elected representatives possess to manipulate the democratic process. I develop doctrine to aid courts in limiting partisan self-dealing and assessing the proper degree of deference to grant, including a test to assess the independence and impartiality of EMBs. Where legislative action is under scrutiny, I argue that motive-based judicial review is a way forward for courts to prevent partisan self-dealing. The majoritarian democracies of Canada, Australia, India, and the United States are considered in depth in order to make these claims.
Recovering the Classic: Twelfth-Century Latin Epic and the Virgilian Tradition
Keywords: Aeneid
Alexandreis
Anticlaudianus
Architrenius
Vergil
Ylias

This dissertation considers how ancient and medieval commentaries on the Aeneid can give us new insights into four twelfth-century Latin epics--the Ylias by Joseph of Exeter, the Alexandreis by Walter of Ch창tillon, the Anticlaudianus by Alan of Lille, and the Architrenius by John of Hauville. Virgil's influence on twelfth-century Latin epic is generally thought to be limited to verbal echoes and occasional narrative episodes, but evidence is presented that more global influences have been overlooked because ancient and medieval interpretations of the Aeneid, as preserved by the commentaries, were often radically different from modern readings of the Aeneid. By explaining how to interpret the Aeneid, these commentaries directly influenced the way in which twelfth-century Latin epic imitated the Aeneid. At the same time, these Aeneid commentaries allow us a greater awareness of the generic expectations held by the original readers of twelfth-century Latin epic. Thus, this dissertation contributes to our understanding of ancient and medieval perceptions of the Aeneid while exploring the importance of commentaries in shaping poetic composition, imitation, and reading. The first chapter presents evidence that the allegorical interpretation of the Aeneid, as presented by Servius, Fulgentius, and Bernard Silvestris, served as an important structural model for the plots of the Anticlaudianus and the Architrenius. The second chapter examines how the twelfth-century understanding of history and myth in the Aeneid influenced the Alexandreis and the Ylias. The final chapter explores how these medieval epics respond to the twelfth-century ethical reading of the Aeneid and suggests possible links to modern `pessimistic' interpretations of the Aeneid, building on the work done by Craig Kallendorf in The Other Virgil and Richard Thomas in Virgil and the Augustan Reception.