VictorJuiz/thesis huggingface dataset:
Metal Binding and Response of Helicobacter pylori HypB and Escherichia coli YjiA

The biosynthesis of [NiFe]-hydrogenase and urease in Helicobacter pylori requires several accessory proteins for proper assembly of the nickel-containing active sites. Critical to the maturation of both enzymes in H. pylori is the GTPase HypB. In this work, the metal-binding properties of H. pylori HypB (HpHypB) were investigated and a link between metal binding and the other biochemical properties of HpHypB was established. HpHypB binds stoichiometric nickel or zinc with nanomolar affinities, in partially overlapping sites located between two major GTPase motifs. Upon metal binding, the GTP hydrolysis activity and oligomeric properties of the protein are modulated. Furthermore, the stoichiometry and affinity of the nickel is altered when HpHypB is bound to nucleotide, a change not observed for zinc. Mutagenesis of the metal ligands suggest that a conserved cysteine is responsible for transducing the metal-bound state to altered GTPase activity and a conserved histidine is a required nickel ligand only in the nucleotide-bound state. Together, these results suggest that the metal-binding and GTP hydrolysis properties of HpHypB are intimately linked and may comprise a mechanism through which the [NiFe]-hydrogenase and urease maturation pathways can discriminate between Ni(II) and Zn(II). Characterization of the Escherichia coli GTPase YjiA, a member of the same GTPase family as HpHypB, demonstrated that YjiA can bind Ni(II), Zn(II), or Co(II) at a site in a similar location as in HpHypB. Metal binding also regulates the GTPase activity and oligomerization of YjiA. This finding suggests that metal-responsive GTPase activity may be a trait of this family of GTPases. Together, this work describes a unique link between the metal-binding and biochemical properties of the G3E GTPases and provides insight into the role of HpHypB in [NiFe]-hydrogenase and urease maturation.

Keywords: bioinorganic
nickel
nickel homeostasis
[NiFe]-hydrogeanse
GTPase
metal homeostasis
metal binding
Advisor: Zamble, Deborah
Regulation Of Long-Range Planar Cell Polarity By Fat- Dachsous Signaling

Planar cell polarity (PCP) is the organization of cellular characteristics within the plane of a tissue. PCP manifests both structurally, as in the directionality of insect bristles or mammalian skin hair, or dynamically, as in vertebrate neurulation, gastrulation, and oriented cell division in the kidney. Two well-conserved pathways are known to regulate PCP in invertebrates and in vertebrates: the Frizzled/PCP pathway and the Fat-Dachsous (Ft-Ds) pathway. The latter consists of the cadherins Ft and Ds, along with the Golgi kinase Four-jointed (Fj) and the transcriptional co-repressor Atrophin (Atro). Ft and Ds can bind each other, suggesting a mechanism for signal transduction. Fj phosphorylates Ft and Ds, modulating their binding affinities for each other. Atro is proposed to link Ft-Ds signaling with downstream events in the nucleus during eye development. The details of Ft-Ds binding, and the consequences of their interactions with other members of the pathway are poorly understood. In this work, I quantitatively analyzed Ft-Ds pathway mutant clones for their effects on ommatidial polarity in the Drosophila eye. My findings suggest that the Ft-Ds pathway regulates PCP independently of asymmetric cellular accumulation of Ft or Ds. I found that Atro has a position-specific role in regulating polarity in the eye, that Fj dampens clonal polarity signals, and that asymmetric accumulation of the atypical myosin Dachs is not essential for production and propagation of a long-range PCP signal. My observations suggest that Ft and Ds interact to modulate a secondary signal that regulates long-range polarity, that signaling by the Ds intracellular domain is dependent on Ft, and that ommatidial fate specification is genetically separable from long-range signaling.

Keywords: polarity
fat
dachsous
atrophin
four-jointed
planar cell polarity
pcp
drosophila
genetics
clones
epithelia
ommatidia
eye
photoreceptor
Advisor: McNeill, Helen
The Integration of Metabolite and Hormone Signalling Drives Seedling Development

Sugars have a profound impact on plant biology, acting as structural components, signalling molecules, and sources of energy. As such, the availability of sugars has important implications for plant growth and development. Sugar levels rise and fall as part of a daily cycle, while cues from other environmental stimuli are also in flux. As sessile organisms in an ever-changing environment, plants must integrate signals from multiple pathways in order to promote the appropriate developmental responses. To uncover pathways that interact with sugars during seedling development, a chemical screen was performed in search of compounds that modify responses to sucrose. This screen identified an interaction between the folate inhibitor sulfamethoxazole (SMX) and sucrose that resulted in changes to auxin signalling and distribution. Synergy between sucrose and SMX was used to explore the effect of metabolic cues on auxin signalling during hypocotyl elongation. A second line of investigation explored whether sucrose and folates influence root meristem activity. Sucrose induced hormone signalling pathways that promote cell division and differentiation. Treatment with SMX perturbed the effect of sucrose on hormone networks that mediate growth, and resulted in a loss of meristem integrity. This study highlights the influence of metabolism on hormone signalling at the root apex, and its role in maintaining balance of a complex signalling network that drives root growth. These studies characterise an interaction between metabolic pathways that is integrated with hormone signalling during plant development. Taken together, they highlight a mechanism through which plant growth might be regulated by metabolism.

Keywords: Sugar
Folate
Chemical Genetics
Auxin
Development
Advisor: Campbell, Malcolm M.
Experimental and Numerical Studies for Soot Formation in Laminar Coflow Diffusion Flames of Jet A-1 and Synthetic Jet Fuels

In the present doctoral thesis, fundamental experimental and numerical studies are conducted for the laminar, atmospheric pressure, sooting, coflow diffusion flames of Jet A-1 and synthetic jet fuels. The first part of this thesis presents a comparative experimental study for Jet A-1, which is a widely used petroleum-based fuel, and four synthetically produced alternative jet fuels. The main goals of this part of the thesis are to compare the soot emission levels of the alternative fuels to those of a standard fuel, Jet A-1, and to determine the effect of fuel chemical composition on soot formation characteristics. To achieve these goals, experimental measurements are constructed and performed for flame temperature, soot concentration, soot particle size, and soot aggregate structure in the flames of pre-vaporized jet fuels. The results show that a considerable reduction in soot production, compared to the standard fuel, can be obtained by using synthetic fuels which will help in addressing future regulations. A strong correlation between the aromatic content of the fuels and the soot concentration levels in the flames is observed. The second part of this thesis presents the development and experimental validation of a fully-coupled soot formation model for laminar coflow jet fuel diffusion flames. The model is coupled to a detailed kinetic mechanism to predict the chemical structure of the flames and soot precursor concentrations. This model also provides information on size and morphology of soot particles. The flames of a three-component surrogate for Jet A-1, a three-component surrogate for a synthetic jet fuel, and pure n-decane are simulated using this model. Concentrations of major gaseous species and flame temperatures are well predicted by the model. Soot volume fractions are predicted reasonably well everywhere in the flame, except near the flame centerline where soot concentrations are underpredicted by a factor of up to five. There is an excellent agreement between the computed and measured data for the numbers of primary particles per aggregate and the diameters of primary particles. This model is an important stepping-stone in the drive to simulate industry-relevant and multi-dimensional flames of practical liquid fuels, with detailed chemistry and soot formation.

Keywords: Combustion
Jet Fuel
Soot
Numerical Modeling
Experimental Measurements
Flames
Advisor: Thomson, Murray J.
The Role of Cell-polarity in Development and Disease

From the simplest unicellular organisms to complex metazoans, cell polarity is a widespread characteristic that is essential for almost every aspect of biology. Proper polarization of cells is crucial for the establishment and maintenance of higher order structures such as tissue and organs. Cell polarity refers to the asymmetric distribution of various macromolecules and cellular structures, resulting in polarized architecture and function of the cell. Defects in cell polarity lead to various phenotypes, ranging from aberrant signaling, proliferation, cell adhesion and migration, cell fate determination and pluripotency, as well as embryonic lethality, neoplasia and cancer. Given the various roles for cell polarity in development and disease, the characterization of the components involved in polarity and their mechanisms of function is of great importance. My thesis work has encompassed three major projects, each of which is focused on understanding the role of cell polarity in development and disease. Although genetic screens in invertebrates have led to the identification of a number of cell-polarity proteins, similar systematic approach have not been undertaken in mammalian systems. The goal of my first project was to design and implement a high-throughput screen to systematically knockdown individual genes using siRNA, and then assess cell junction integrity as a measure of cell polarity. Given the importance of cell polarity to signaling pathways, I next sought to determine the mechanism by which cell polarity affects TGFβ and Hippo pathways, two important signaling pathways involved in development and disease. Lastly, by studying the acquisition of pluripotency by somatic cells, I uncovered a central role for cell polarity in the establishment and maintenance of pluripotency. Here I will present and discuss our discovery pertaining to the role of cell polarity in cell signaling and pluripotency.

Keywords: Polarity
Cancer
Pluripotency
Reprogramming
TGF-beta
Hippo
Advisor: Wrana, Jeffrey
Hyperthermia Mediated Drug Delivery using Thermosensitive Liposomes and MRI-Controlled Focused Ultrasound

The clinical efficacy of chemotherapy in solid tumours is limited by systemic toxicity and the inability to deliver a cytotoxic concentration of anticancer drugs to all tumour cells. Temperature sensitive drug carriers provide a mechanism for triggering the rapid release of chemotherapeutic agents in a targeted region. Thermally mediated drug release also leverages the ability of hyperthermia to increase tumour blood flow, vessel permeability, and drug cytotoxicity. Drug release from thermosensitive liposome drug carriers in the tumour vasculature serves as a continuous intravascular infusion of free drug originating at the tumour site. However, localized drug release requires precise heating to improve drug delivery and efficacy in tumours while minimizing drug exposure in normal tissue. Focused ultrasound can noninvasively heat millimeter-sized regions deep within the body, and can be combined with MR thermometry for precise temperature control. This thesis describes the development of strategies to achieve localized hyperthermia using MRI-controlled focused ultrasound, for the purpose of image-guided heat-triggered drug release from thermosensitive drug carriers. First, a preclinical MRI-controlled focused ultrasound system was developed as a platform for studies of controlled hyperthermia and drug delivery in rabbits. The feasibility of using ultrasound hyperthermia to achieve localized doxorubicin release from thermosensitive liposomes was demonstrated in normal rabbit muscle. Second, strategies were described for using MR thermometry to control ultrasound heating at a muscle-bone interface based on MR temperature measurements in adjacent soft tissue, demonstrating localized drug delivery in adjacent muscle and bone marrow. Third, fluorescence microscopy was employed to demonstrate that increased overall drug accumulation in rabbit VX2 tumours corresponds to high levels of bioavailable drug reaching their active site in the nuclei of tumour cells. The results of this thesis demonstrate that image-guided drug delivery using thermosensitive liposomes and MRI-controlled focused ultrasound hyperthermia can be used to noninvasively achieve precisely localized drug deposition in soft tissue, at bone interfaces, and in solid tumours. Clinical application of this work could provide a noninvasive means of enhancing chemotherapy in a variety of solid tumours.

Keywords: hyperthermia
drug delivery
focused ultrasound
magnetic resonance imaging
MR thermometry
thermosensitive liposomes
image-guided therapy
cancer
Advisor: Chopra, Rajiv
Bayesian Optimization and Semiparametric Models with Applications to Assistive Technology

Advances in machine learning are having a profound impact on disciplines spanning the sciences. Assistive technology and health informatics are fields for which minor improvements achieved through leveraging more advanced machine learning algorithms can translate to major real world impact. However, successful application of machine learning currently requires broad domain knowledge to determine which model is appropriate for a given task, and model specific expertise to configure a model to a problem of interest. A major motivation for this thesis was: How can we make machine learning more accessible to assistive technology and health informatics researchers? Naturally, a complementary goal is to make machine learning more accessible in general. Specifically, in this thesis we explore how to automate the role of a machine learning expert through automatically adapting models and adjusting parameters to a given task of interest. This thesis consists of a number of contributions towards solving this challenging open problem in machine learning and these are empirically validated on four real-world applications. Through an interesting theoretical link between two seemingly disparate latent variable models, we create a hybrid model that allows one to flexibly interpolate over a parametric unsupervised neural network, a classification neural network and a non-parametric Gaussian process. We demonstrate empirically that this non-parametrically guided autoencoder allows one to learn a latent representation that is more useful for a given task of interest. We establish methods for automatically configuring machine learning model hyperparameters using Bayesian optimization. We develop Bayesian methods for integrating over parameters, explore the use of different priors over functions, and develop methods to run experiments in parallel. We demonstrate empirically that these methods find better hyperparameters on recent benchmark problems spanning machine learning in significantly less experiments than the methods employed by the problems' authors. We further establish methods for incorporating parameter dependent variable cost in the optimization procedure. These methods find better hyperparameters in less cost, such as time, or within bounded cost, such as before a deadline. Additionally, we develop a constrained Bayesian optimization variant and demonstrate its superiority over the standard procedure in the presence of unknown constraints.

Keywords: bayesian optimization
machine learning
autoencoders
assistive technology
Advisor: Alex, Mihailidis
Support Exchange on the Internet: A Content Analysis of an Online Support Group for People Living with Depression

Online support groups have shown a strong potential to foster resourceful environments for people living with depression without restrictions of time, space, and stigma. Research has found that users of those groups exchange various types of support. However, due to the scarcity of research, many other aspects of depression online support groups remain inconclusive. In particular, how the support exchange contributes to the everyday lives of users living with depression remains unclear. To contribute to filing some of the knowledge gaps, the present study explored what kinds of support were requested and provided in a depression online support group. By doing so, this study aimed to examine the roles of the depression online support group in the management of depression. Mixed methods were employed with a concurrent triangulation strategy. A sample of 980 posts were selected systematically from the support group. Demographic and clinical information of the users who made those posts were recorded. Quantitative and qualitative content analyses were conducted to examine the types of support being exchanged through those posts. Inter-coder reliability was calculated to ensure the consistency of the coding process. The results indicate that users sought informational support, various types of emotional support and coaching support, and social companionship. Users not only sought listening ears, but also practical advice to cope with the situations they were going through. The group appeared to serve its users as a place to meet others with similar experience; to manage loneliness; to discuss what they could not discuss elsewhere; to "just vent"; to gain advice from multiple perspectives on an issue that had been magnifying the impact of depression; to share the experience with formal care provision systems; to express immediate support needs; to share useful discoveries, accomplishments, and creative ways to manage depression; and to experience the value of helping others. This study supports the idea that depression online support groups have the strong potential to contribute to the everyday lives of people living with depression in a way that is not available elsewhere and in a way that complement to the overall framework of existing care provision systems.

Keywords: Content Analysis
Online Support Group
Social Media
Major Depressive Disorder
Health Information
Information Seeking Practice
Advisor: Dilevko, Juris B.
The Emergence of Regional Cultures and Practices: A Comparative Study of Canadian Software Entrepreneurship

Despite the ‘cultural turn’ in economic geography, the discipline has yet to conclusively describe the processes through which culture influences actors’ daily economic and social practices. Without a better understanding of the role of culture, it is difficult to explain the emergence and influence of the heterogeneous landscapes of regional business culture we readily observe. This problem is particularly acute in the study of entrepreneurial environments, where regional culture is theorized to play an important role in the local entrepreneurship process. This dissertation proposes an alternative approach to culture which draws on the work of Pierre Bourdieu to reveal the underlying social processes connecting culture with entrepreneurial action. Through qualitative case studies of software entrepreneurs in three Canadian cities — Kitchener- Waterloo, Ontario; Ottawa, Ontario and Calgary, Alberta — this dissertation examines the emergence and evolution of regional cultures and how they have helped to create distinct contexts which encourage unique forms of entrepreneurial practices, outlooks and strategies. This new perspective allows for a more detailed and dynamic analysis of regional cultures and provides new tools for researchers and policy makers to understand the role of cultures within regional economic development.

Keywords: Economic Geography
Entrepreneurship
Regional Culture
Advisor: Bathelt, Harald
Through the Social Web: Citizen-led Participation in Ontario Policy-making

In the mid to late 1990s, many states developed eGovernment programs that included the use of consultation technologies. More recently, the social characteristics of the web have emerged as offering an alternative means for citizen participation, promising more openness and inclusion. In this dissertation I draw upon studies of the policy-making process and media design, to examine the implications of citizen-led production of infrastructures for public participation in policy-making through the social web and within the context of open government discourse. My research methods for this research project were ethnographically informed. I participated in the design and use of social web infrastructures for participation in policy-making as a contributor to open government communities in Ontario, Canada. I also analyzed Hansard records as well as the popular press, and interviewed 15 citizen designers who created social web based infrastructures for public participation in the policy-making of four bills in Ontario. In my research, I develop and use the term citizen designer drawing on the more common phrase of citizen journalist. Both terms suggest that citizens can engage in creative practices to encourage institutions such as government or the mass media to become more participatory. The citizen designers in my project were found to act as policy entrepreneurs, sometimes for particular bills, but more generally for the broader ideal of open government that includes citizen participation. The major finding of this work is that citizens are using an integrated mix of social web tools across multiple policy windows to promote openness and participation. This work contributes to the policy, information and the internet studies literatures on the roles and experiences of internet-savvy policy entrepreneurs who are situated in civil society networks, which are not always tied to formal organizations. This work also expands our understandings of citizenship to include the design and use of the social web in everyday political life.

Keywords: social media
internet
policy
Canada
science and technology studies
information
Advisor: Clement, Andrew
Building Trust in a Private School: Formal and Informal Practices of Principals

Today’s contemporary challenges of educating students place responsibility on school principals that may be unmatched by any other generation. Principals in their early years of the portfolio face an even greater task as they become comfortable with the portfolio and the school community which they lead. Drawing from the leadership literature that emphasized the importance of trust for effective school leadership and improvement, this qualitative study examines the formal and informal leadership practices of seven principals/ headmasters with less than eight years of experience in private high schools in Ontario. The study focuses on the practices that these leaders identify as being crucial to building trust. Their responses reveal that trust building includes personal and professional honesty, transparency and clear communication and a sharing of decision-making powers which all help to minimize the micropolitics that arise in a school, engenders better relationships with faculty members, increases capacity of faculty members more effectively, and ultimately provides support for the principal and decreases personal stress. This study contributes to the Canadian literature on school leadership and the literature on private school leadership and concludes with recommendations for both research and practice.

Keywords: Trust
Secondary Private Schools
Principals
Advisor: Flessa, Joseph