VictorJuiz/thesis huggingface dataset:
Mechanisms of Decarboxylation: Internal Return, Water Addition, and Their Isotope Effects

2-(2-mandelyl)thiamin (MTh), the adduct of benzoylformate and thiamin, is an accurate model of 2-(2-mandelyl)thiamin diphosphate, the initial covalent intermediate in the decarboxylation of benzoylformate by benzoylformate decarboxylase (BFDC). The first order rate constant for spontaneous decarboxylation of MTh is about 106 times smaller than the enzymic rate (kcat) for the BFDC reaction. Based on the similarities of MTh and the corresponding enzymic intermediate, as well as the inherent nature of the intermediate, it is not obvious why the enzyme-catalyzed reaction is so much faster. However, earlier studies showed that the decarboxylation of MTh is catalyzed by protonated pyridines and this was proposed to occur through a preassociation mechanism. If this explanation is correct, then the observed 12C/13C kinetic isotope effect (CKIE) will increase in the presence of the catalyst as a more favorable forward commitment is made possible. This provides a specific model for the enzyme-catalyzed process. We developed a technique using headspace analysis and compound specific isotope analysis (CSIA) to determine the CKIE for the decarboxylation of MTh in the presence and absence of pyridinium. We found that the CKIE increases in the presence of the catalyst, as predicted for the preassociation mechanism. In a related study, we investigated the kinetics of decarboxylation of pyrrole-2-carboxylic acid, which was known to be subject to acid catalysis in highly acidic solutions. In the expected mechanism, protonation of the pyrrole ring at C2 destroys the aromaticity of the ring. C-C bond cleavage in the process of decarboxylation will re-establish the aromatic pyrrole. However, the overall reaction rate would not increase as it is counteracted by a larger concentration of the undissociated carboxyl group compared to carboxylate ion necessary for decarboxylation. Since the reaction occurs readily, there must be an alternative pathway for the acid-catalyzed reaction. This can be achieved in an associative mechanism that is initiated by addition of water to the carboxyl group of the carboxyl-protonated reactant. C-C bond cleavage results in formation of pyrrole and protonated carbonic acid, a species that has been recognized as a viable intermediate in related processes. Protonated carbonic acid is spontaneously converted to H3O+ and carbon dioxide. The associative mechanism is consistent with solvent-deuterium kinetic isotope effects and 12C/13C kinetic isotope effects.

Keywords: Decarboxylation
Isotope effects
Internal return
hydrolytic
Advisor: Kluger, Ronald
Exploring the Role of 'Slowing Down When You Should' in Operative Surgical Judgment

Context: The study of expertise in medical education has tended to follow the traditions of describing either the analytic processes or the non-analytic resources that experts acquire with experience. We argue that a critical function of expertise is the ability to transition from the automatic mode to the more effortful mode when required – a transition referred to as ‘slowing down when you should’. Objectives: To explore the phenomenon of ‘slowing down when you should’ in operative surgical practice and its role in intra-operative surgical judgment, and to develop conceptual models of the factors involved in the display of this transition in surgical operative practice. Design: In Phase 1A, 28 surgeons were interviewed about their views of surgical judgment in general and their perceptions of the role of this phenomenon in operative judgment. In Phase 1B, a subset of surgeons from Phase 1A was re-interviewed to explore their perceptions of automaticity in operative practice. In Phase 2, observational sessions (and brief interviews) were conducted of surgeons in the operating room to explore the nature of this phenomenon in its natural environment. Results: The surgeons in this study recognized the phenomenon of ‘slowing down’ in their operative practice and acknowledged its link to surgical judgment. Two main initiators were described and observed: proactively planned ‘slowing down’ moments occurring intra-operatively initiated by critical events anticipated pre-operatively and situationally responsive ‘slowing down’ moments initiated by emergent cues intra-operatively. Numerous influences of this transition were uncovered. A control dynamic emerged as surgeon’s negotiated ‘slowing down’ moments through trainees in their supervisory academic practice. Numerous manifestations of this phenomenon were observed in the operating room and considered using a cognitive psychology attention capacity model. Conclusions: This study offers a conceptual framework for understanding the role of ‘slowing down when you should’ in operative surgical practice, providing a vocabulary that will allow more explicit consideration of what contributes to surgical expertise. Consideration of this framework with its consequent ability to make surgical practices more explicit has implications for self-regulation in practice, surgical error, and surgical training.

Keywords: surgical judgment
education
cognitive
slowing down
judgment
surgery
Advisor: Regehr, Glenn
Lingard, Lorelei
MacRae, Helen
Structure-based Design and Characterization of Genetically Encoded PhotoactivableE DNA-binding Proteins Based on S. cervisiae GCN4 and Hr. halophila PYP

Halorhodospira halophila photoactive yellow protein (PYP) is a promising candidate to act as a photoswitching domain in engineered proteins due to the structural changes that occur during its photocycle. Absorption of a photon of wavelength 446 nm triggers trans to cis isomerization of its 4-hydroxycinnamic acid chromophore leading to large structural perturbations in the protein, particularly in the N-terminus. In the dark, a slower cis to trans reisomerization of the chromophore restores the protein’s native fold. The fusion of proteins to PYP’s N-terminus may therefore enable photomodulation of the activity of the attached protein. To test this hypothesis, this thesis descibes genetically encoded photoswitchable DNA-binding proteins that were developed by fusing the prototypical leucine-zipper type DNA-binding protein GCN4 bZIP to the N-terminus of PYP. Five different fusion constructs of full length or truncated GCN4 bZIP and full length PYP as well as fusion constructs of full length GCN4 bZIP and N-terminally truncated PYP mutants were designed in a structure-based approach to determine if the dimerization and DNA binding activities could be controlled by the PYP photocycle. Extensive biophysical characterization of the fusion constructs in the dark and under blue light irradiation using electronic absorption, circular dichroism and fluorescence spectroscopic techniques were performed. As all the fusion proteins could complete photocycles, the DNA binding abilities of the dark and light-adapted states of the proteins were characterized using spectroscopic techniques as well as by the electrophoretic mobility shift assay. All the fusion constructs maintained DNA-binding abilities, however they each differed in their affinities and the extent to which they were activated by blue light irradiation. The reasons for these differences in DNA-binding abilities and photoactivation are explored. Using the results from the characterization of these constructs, proposals are also made to develop more robust genetically encoded photoactivatable DNA-binding proteins of the same type.

Keywords: Photoactive Yellow Protein
PYP
GCN4
leucine zipper
bZIP
photo-control
photo-isomerization
photo-activation
Advisor: Woolley, Andrew
A Consistent Numerical Method for Simulating Interfacial Turbulent Flows

A mathematically consistent algorithm for simulating interfacial turbulent flows is devised in this work. To minimize numerical errors for imposing dynamic boundary conditions at the interface locations, piezometric pressure is used to limit the effect of gravity forces in a flow field. Consequently, suitable and consistent numerical schemes are designed to accurately implement the new forms of interfacial forces. The proposed numerical methods are challenged for low Froude number flows which tend to trouble conventional algorithms. To capture the effect of turbulence on the interface, standard large eddy simulation techniques are reviewed and discussed. It is shown the standard filtered flow equations encounter numerical and mathematical inconsistencies. To remedy the irregularities of the conventional methods, a new framework for large eddy simulations is grounded. Purely mathematical models are derived and correlated with the conventionally more physical models. Semi implicit SIMPLE method is used to discretize the final flow equations. Taking advantage of the implicit feature of SIMPLE algorithm, an error correction technique is devised by which numerical cost of a turbulent simulation is substantially reduced. The entire framework is finally discussed toward simulating a turbulent interfacial flow.

Keywords: Turbulence
Multiphase
Advisor: Mostaghimi, Javad
Characterization of NimA-related Kinase 10 (NEK10): A Role in Checkpoint Control

Deregulation of the cell cycle is a hallmark of neoplastic transformation and plays a central role in both the initiation and progression of cancer. Members of the NimA-related kinase (NEK) family of protein kinases are emerging as important players in regulation of the eukaryotic cell cycle during normal cell cycle progression and checkpoint activation in response to genotoxic stresses. The focus of this thesis is NEK10, a previously uncharacterized member of the NEK family. While little is known about the biology of NEK10, recent cancer genomics studies have identified NEK10 as a candidate susceptibility gene at chromosome 3p24 in cancer. Work herein describes a role for NEK10 in the cellular response to ultraviolet (UV) irradiation. NEK10 was required for the activation of ERK1/2 signaling upon UV irradiation, but not in response to mitogens, such as the epidermal growth factor. NEK10 interacted with Raf and MEK and enhanced MEK activity through a novel mechanism involving MEK autoactivation. Significantly, appropriate maintenance of the G2/M checkpoint following UV irradiation required NEK10 expression and ERK1/2 activation. In support of a conserved role for NEK10 in the cellular response to UV irradiation, nekl-4, the NEK10 C.elegans homologue, affected embryonic sensitivity to UV-irradiation. In search of regulatory inputs into NEK10, using mass spectrometry, our laboratory identified 19 distinct sites of NEK10 phosphorylation. Characterization of a number of these sites revealed a role for intermolecular autophosphorylation in achieving full NEK10 catalytic activity through activation loop phosphorylation on S684 and S688. Further, a C-terminal phosphorylation site on NEK10, S933, was found to be a 14-3-3 binding site, and was essential for NEK10 cytoplasmic to nuclear translocation following UV irradiation. Taken together, my studies have discovered a role for NEK10 in the engagement of the G2/M cell cycle checkpoint and provided a mechanistic insight into the relationship between NEK10 and the Raf/MEK/ERK cascade, and the control of NEK10 subcellular localization. This work will serve as a foundation for future studies aimed at understanding the molecular mechanism of NEK10 action and its function in development and tumourigenesis.

Keywords: kinase
cell cycle checkpoint
phosphorylation
UV
Advisor: Stambolic, Vuk
Learning Distributed Representations for Statistical Language Modelling and Collaborative Filtering

With the increasing availability of large datasets machine learning techniques are becoming an increasingly attractive alternative to expert-designed approaches to solving complex problems in domains where data is abundant. In this thesis we introduce several models for large sparse discrete datasets. Our approach, which is based on probabilistic models that use distributed representations to alleviate the effects of data sparsity, is applied to statistical language modelling and collaborative filtering. We introduce three probabilistic language models that represent words using learned real-valued vectors. Two of the models are based on the Restricted Boltzmann Machine (RBM) architecture while the third one is a simple deterministic model. We show that the deterministic model outperforms the widely used n-gram models and learns sensible word representations. To reduce the time complexity of training and making predictions with the deterministic model, we introduce a hierarchical version of the model, that can be exponentially faster. The speedup is achieved by structuring the vocabulary as a tree over words and taking advantage of this structure. We propose a simple feature-based algorithm for automatic construction of trees over words from data and show that the resulting models can outperform non-hierarchical neural models as well as the best n-gram models. We then turn our attention to collaborative filtering and show how RBM models can be used to model the distribution of sparse high-dimensional user rating vectors efficiently, presenting inference and learning algorithms that scale linearly in the number of observed ratings. We also introduce the Probabilistic Matrix Factorization model which is based on the probabilistic formulation of the low-rank matrix approximation problem for partially observed matrices. The two models are then extended to allow conditioning on the identities of the rated items whether or not the actual rating values are known. Our results on the Netflix Prize dataset show that both RBM and PMF models outperform online SVD models.

Keywords: statistical language modelling
collaborative filtering
neural networks
distributed representations
machine learning
Advisor: Hinton, Geoffrey
Bayesian Methods in Gaussian Graphical Models

This thesis contributes to the field of Gaussian Graphical Models by exploring either numerically or theoretically various topics of Bayesian Methods in Gaussian Graphical Models and by providing a number of interesting results, the further exploration of which would be promising, pointing to numerous future research directions. Gaussian Graphical Models are statistical methods for the investigation and representation of interdependencies between components of continuous random vectors. This thesis aims to investigate some issues related to the application of Bayesian methods for Gaussian Graphical Models. We adopt the popular G-Wishart conjugate prior WG(δ, D) for the precision matrix. We propose an efficient sampling method for the G-Wishart distribution based on the Metropolis Hastings algorithm and show its validity through a number of numerical experiments. We show that this method can be easily used to estimate the Deviance Information Criterion, providing a computationally inexpensive approach for model selection. In addition, we look at the marginal likelihood of a graphical model given a set of data. This is proportional to the ratio of the posterior over the prior normalizing constant. We explore methods for the estimation of this ratio, focusing primarily on applying the Monte Carlo simulation method of path sampling. We also explore numerically the effect of the completion of the incomplete matrix Dν, hyperparameter of the G-Wishart distribution, for the estimation of the normalizing constant. We also derive a series of exact and approximate expressions for the Bayes Factor between two graphs that differ by one edge. A new theoretical result regarding the limit of the normalizing constant multiplied by the hyperparameter δ is given and its implications to the validity of an improper prior and of the subsequent Bayes Factor are discussed.

Keywords: Gaussian Graphical Models
DY-conjugate prior
Markov Chain Monte Carlo
Model Selection
Normalizing constant
Metropolis Hastings
Bayes Factors
Deviance Information Criterion
Advisor: Escobar, Michael
Massam, Helene
Patients' Perceptions of the Primary Care Characteristics in a Model of Interprofessional Patient-centred Collaboration between Chiropractors and Physicians

Background: Considerable attention has been paid to evaluating the roles and relationships of professionals participating in team-based or collaborative practice; however, less attention has been paid to exploring the patients’ views and impact of such practice despite claims of it being patient-centred. Objectives: To examine the relationship between patient and provider characteristics and patients’ ratings of measures of quality of care and integration, and to explore the patient views of care delivered in a patient-centred collaborative study involving chiropractors and physicians. Design: Cross-sectional survey. Method: A mixed methods sequential approach with a quantitative priority was used in data analysis. Quantitative data were collected from 2597 patients participating in a collaborative study involving chiropractors and physicians and 530 patients attending chiropractors not involved in collaborative care. All participants presented with musculoskeletal pain. The Primary Care Assessment Survey (PCAS) was modified and scores from six of its scales were used to assess attributes of quality patient-centred care between the two study groups. Qualitative transcript-based data from six purposefully selected focus groups was analyzed using an interpretivist approach. Results: The revised PCAS demonstrated acceptable psychometric properties. Patients in both study groups received quality, patient-centred care. Patients’ reporting being completely satisfied and feeling improved by their care was positively associated with rating chiropractors as high performers on all scales. Survey findings were confirmed in focus groups of study patients. Patients appreciated positive interpersonal interactions, sharing in the treatment decision-making process, having a choice in provider and treatment, and the provision of holistic care. Patients perceived that collaboration between chiropractors and physicians varied, favouring those who were co-located. Patients with chronic or co-morbid conditions desired greater involvement in their care. Patients felt sharing of clinical information was more important than co-location as facilitating coordination and integration of collaborative care. Conclusion: The study suggests that patients suffering from musculoskeletal pain benefit from interprofessional collaborative care that includes improved access to and choice of providers and treatment options, as well as enhanced interprofessional communication and coordination of care.

Keywords: patient-centred care
patient satisfaction
outcome assessment
interprofessional relations
chirpractic
primary care
Advisor: Cockerill, Rhonda
Relationships among Span, Time Allocation, and Leadership of First-line Managers and Nurse and Team Outcomes

Comparisons of raw span (i.e., number of staff who report directly to a manager) within and across organizations can misrepresent managerial capacity to support staff because managers may not allocate the same amount of time to staff contact. The purpose was to examine the influence of alternative measures of managerial span on nurse satisfaction with manager’s supervision and on multidisciplinary teamwork. The alternative measures were (a) raw span as a measure of reporting structure and (b) time in staff contact as a measure of closeness of contact by the manager. The main effects of the alternative measures, leadership, hours of operation, and other covariates on outcomes were examined. The interaction effects of the alternative measures with leadership and hours of operation were investigated. The study framework was based on Open System Theory and the boundary spanning functions of managers. A descriptive, correlational design was used to collect survey and administrative data from employees, managers, and organizations. Managerial time allocation data were collected through self-logging and validated through observation. Acute care hospitals were selected through purposive sampling. For supervision satisfaction, the final sample size was 31 first-line managers and 558 nurses. For teamwork, the final sample size was 30 first-line managers and 754 staff. The Leadership Practices Inventory, the Satisfaction with my Supervisor Scale, and the Relational Coordination Scale were used. Hierarchical linear modeling was the main type of analysis conducted. Raw span interacted with leadership and hours of operation to explain supervision satisfaction. Teamwork was explained by leadership, clinical support roles, hours of operation, total areas, and non-direct reports, but not by raw span or time in staff contact. Large acute care hospitals can improve satisfaction with supervision and teamwork by modifying first-line management positions.

Keywords: nurse managers
leadership
span of control
timing study
supervision satisfaction
teamwork
Advisor: O'Brien-Pallas, Linda
Agency and Institutional Transformation: The Emergence of a New Corporate Governance Model

This research examines institutional transformation of the board of directors in Canada to a collaborative model in which the board, in addition to its monitoring function, provides a service role by acting as a sounding board to management and providing advice and counsel to management on strategic issues. This thesis also examines how director search, likely initiated by the ‘Enron’ scandals, led to some boards adopting a new model of practice that directors deemed more efficacious and possessing legitimacy, bringing together the old and the new institutionalism in institutional change processes. Legitimacy was drawn from guidance from a professional association for directors that outlined how boards could become strategic asset to the firm that was consistent with a stewardship model of governance that saw boards collaborative with management. It is also argued in this thesis that following the Enron scandal, directors searched for a model of practice that would be more efficacious such that their fears of liability were reduced. In searching for and adopting a new model of practice, the collaborative board, it is also argued that adoption requires coupling to the technical core (enacted), as opposed to symbolic, if it is to be effective. This research studies directors and senior management of public firms of the TSX Composite by way of survey methods. The findings provide support that the board is evolving in Canada to a new collaborative model and that the model of practice appears to be enacted (coupled) as opposed to symbolic (decoupled). Further, the results did not find that collaborative boards are impaired in their monitoring function and support is found that the board’s monitoring role may actually be enhanced. These results are discussed as well as future research directions and limitations of the study.

Keywords: Corporate Governance
Institutional Theory
Institutional Change
Agency Theory
Stewardship Theory
Advisor: D'Cruz, Joseph
Amburgey, Terry
Kirzner, Erik