VictorJuiz/thesis huggingface dataset:
Probing the Link between Ni(II) Binding and GTP Hydrolysis by the Escherichia coli Metal Chaperone HypB

Nickel enzymes are virulence factors in some human pathogens. Oftentimes the maturation machinery that forms these enzymes includes a nickel chaperone that is also an NTPase. In [NiFe]-hydrogenase maturation, this NTPase factor is HypB, which hydrolyzes GTP, binds nickel, and in the GDP state delivers nickel to the partner protein HypA. One metal-binding residue, C198 in Escherichia coli, is in the Switch II GTPase motif, and possibly connects the metal-binding, nucleotide-binding, and GTP hydrolyzing activities of HypB. A C198T mutation, made in an effort to disconnect these processes, prevented HypB from maturing [NiFe]-hydrogenase in E. coli. C198T HypB could bind nickel with low ÂľM KD, hydrolyze GTP, and GTP hydrolysis remained unexpectedly metal sensitive. The C198T mutation may have affected nucleotide-dependent metal affinity, or GDP-dependent complex formation with HypA; however, these possibilities need to be further explored. This work contributes to our understanding of the role of the NTPase in metallocenter assembly.

Keywords: Bioinorganic chemistry
Escherichia coli
GTPase
Hydrogenase
Nickel
Nickel enzyme
Advisor: Zamble, Deborah B
Pressures of Isomorphism on the External Institutional Diversity of Ontario College Activity and Performance

This study examined the external institutional diversity of the Ontario college system, while also examining the degree of diversification or isomorphism that would exist if all plans in the Strategic Mandate Agreements are realized. Analysing the state of diversification has important public policy relevance, particularly in light of Ontarioâ s Differentiation Policy Framework for Postsecondary Education. College activity and performance were measured across a series of variables, and these findings were triangulated with an abductive document analysis of Strategic Mandate Agreements and annual reports. Two additional dimensions were identified by this research that extend beyond the seven dimensions presented by Birmbaum (1983): aspirational diversity, and evaluative diversity. The results show that institution size is highly diversified and this corresponds with diversity in institutional activity. At the regional level, Toronto-area colleges have the highest degree of activity. The findings also conclude that, if all plans were implemented, there would be considerable isomorphism.

Keywords: Colleges
Differentiation
Diversification
Isomorphism
Strategic Mandate Agreement
Advisor: Wheelahan, Leesa
Childs, Ruth
Past History of Substance Misuse Impedes Attentional Recovery After Moderate to Severe Traumatic Brain Injury

Degree of cognitive recovery from a moderate-severe traumatic brain injury (TBI) will affect the extent of permanent disability sustained; therefore, it is critical to understand which factors may enhance or impede recovery. Since attentional impairments affect 40-60% of moderate-severe TBI patients, and elevated use of psychotropic substances can have lasting effects on attention and attention-related structures, the role of pre-injury substance misuse on attentional recovery was examined. Attentional recovery from 2 to 5 months post-injury in moderate-severe TBI patients was compared in those with versus without self-reported high levels of substance misuse. Those with high substance misuse recovered significantly less on an aggregate score of attention, and on 4 of the 8 individual tests of attention that comprised the aggregate: Trail-Making Test A, Stroop Colour-Word, Stroop Word, and Verbal Fluency Test (Phonemic). This is the first study to demonstrate that pre-injury substance misuse may reduce attentional recovery after moderate-severe TBI.

Keywords: alcohol
attention
marijuana
recovery
substance misuse
traumatic brain injury
Advisor: Green, Robin
The Role of Voltage Regulation in Power Integrity for Multi-Gbps Parallel I/O Interfaces

Strategies for power supply distribution in high speed I/O interfaces including the design of low dropout regulators (LDOs) and allocation of decoupling capacitance are proposed to minimize power supply induced jitter (PSIJ) in load circuits (aggressors and victim circuits) sharing the same supply. Different LDOs should be used for the aggressor and victim circuits and it is preferable to allocate available decoupling capacitance to the aggressor circuit. A prototype is developed in 28nm CMOS with the aggressors - 4 transmitters (aggressors) and the victim circuit - 1 injection locked oscillator (ILO) sharing a common supply but operating under separate LDOs. LDO1 employs a conventional topology with a bandwidth of 10MHz for the transmitters and LDO2 employs tri-loop topology with a worst-case PSR of -15dB at 400MHz for the ILO. The resulting simulated transmitter jitter is 3.5ps-pp at 20Gbps and the ILO jitter is 710fs-pp at 10GHz.

Advisor: Chan Carusone, Tony
The Effects of Uremic Serum from Hemodialysis Patients on Hepatic Cyochrome P450 and VKORC1 Gene Expression in Primary Human Hepatocytes

Warfarin is frequently prescribed to patients with atrial fibrillation (AF) who are on hemodialysis (HD) for stroke prevention regardless of conflicting evidence showing unclear benefits of warfarin, as shown in the systematic review conducted as part of this thesis. We believe an increased variability in INR, correlated with increased adverse events, can be explained by uremic effects on the vitamin K cycle through the downregulation of Cytochrome P450 2C9 (CYP2C9), 4F2 (CYP4F2), and vitamin K epoxide reductase complex subunit 1 (VKORC1) expression. We examined the transcriptional regulation of CYP2C9, CYP4F2 and VKORC1 by human uremic serum, isolated from patients on hemodialysis who are anticoagulated with warfarin for AF, in primary human hepatocytes. We observed no difference in CYP2C9, CYP4F2 and VKORC1 mRNA expression between uremic serum and non-uremic serum treated PHHs. Further studies are warranted to confirm the effects of uremic serum on translational regulation.

Keywords: Cytochrome P450
Hemodialysis
VKORC1
Warfarin
Advisor: Battistella, Marisa
Adaptation of Commercial Off-the-shelf Camera Technology for Deployment Imaging and Inspection on Small Satellites

Commercial off-the-shelf camera technology is frequently adapted for use onboard small satellites to aid in the validation of deployment mechanisms. Commercial off-the-shelf cameras are not designed with this application nor the constraints of a small satellite in mind, however, and as a result often perform poorly on-orbit. To address this problem on the Miniature Visual Inspection Camera - a commercial off-the-shelf derived deployment imaging and inspection camera under development at the Space Flight Laboratory - a set of requirements were derived. Their verification revealed that this camera was initially incapable of producing neither video nor properly exposed images at the start of this research project. This thesis develops and discusses the measures undertaken to correct these problems in the context of the CanX-7 and NORSAT-2 small satellite missions, on which the Miniature Visual Inspection Camera will fly.

Keywords: imaging science
microsatellites
nanosatellites
radiometric calibration
radiometry
small satellites
Advisor: Zee, Robert E
City Indicator Consistency Analysis: An Approach to Inconsistency Detection

Cities use a variety of metrics to evaluate and compare their performance. The ISO 37120 standard provides a definition for city indicators that measure a cityâ s quality of life and sustainability. A problem that arises in indicator-based comparisons, is whether the comparison is invalid due to inconsistencies in the data used to derive them? In this thesis we present three types of inconsistency analysis for automating the detection of inconsistencies in open city data. Namely, definitional consistency analysis that evaluates if data used to derive a city indicator is consistent with the indicatorâ s definition (e.g., ISO 37120); transversal consistency analysis that evaluates if city indicators published by two different cities are consistent with each other; and longitudinal consistency analysis that evaluates if an indicator published by a city is consistent over different time intervals. City indicator consistency analysis enable the possibility of consistently measuring and comparing performances of cities.

Keywords: City Indicator
Consistency
Global City Indicators
Inconsistency detection
Knowledge Representation
Ontology
Advisor: Fox, Mark S
Structural and Functional Characterization of Aminoglycoside N-Acetyltransferases from Environmental Microbiomes

Aminoglycoside N-acetyltransferases (AACs) are widespread enzymes that catalyze the acetylation at amino groups of the aminoglycoside antibiotics. Significant number of AAC encoding genes have been identified in diverse microbial (meta)genomes. Such a prospect necessitates a study of AACs from environmental microbiomes in order to anticipate the rise of corresponding resistance elements in the clinic. Accordingly, I performed both functional and structural characterization of putative AACs identified in soil microbiomes, which we named ENV enzymes. Four ENV enzymes demonstrated robust AAC activity and conferred aminoglycoside resistance. Among them, ENV0020 was identified as a novel member of AAC family that catalyzed the acetylation reaction at the prime ring of the antibiotic substrate. The crystal structures of the ENV0020 enzyme obtained in my study provided the molecular framework of its substrate recognition mechanism, which could be useful in the design of novel drug variants less prone to modification by AACs.

Advisor: Savchenko, Alexei
Winter Road Salting on Parking Lots: Permeable Pavements vs. Conventional Asphalt

Permeable pavements have been widely used in stormwater attenuation, water balance, and stormwater quality control. Recent studies suggested that the usage of permeable pavement may offer the possibility to reduce the frequency and application rates of road salt during winter time, while simultaneously maintaining required skid resistance on pavement surfaces. This research summarizes the winter performance assessment study of a heavily used permeable pavement parking lot in St. Catharines, Ontario. The purpose of this monitoring study is to evaluate the safety and environmental benefits of permeable pavements, by comparing them to a traditional asphalt pavement. This thesis will present the results and findings from winter 2015/2016 for the pervious concrete and porous asphalt pavements.

Keywords: Low Impact Development
Permeable Pavement
Winter Road Salting
Advisor: Drake, Jennifer
Building and Using Virtual FPGA Clusters in Data Centers

This thesis presents a framework for creating network FPGA clusters in a heterogeneous cloud data center. Our main objective is to abstract away the details of creating inter-FPGA fabrics, by automating the FPGA network connections and the networking to connect multiple FPGA clusters together. The FPGA clusters are created using a logical kernel description describing how a group of FPGA kernels are to be connected, and an FPGA mapping file. This work lastly looks at acquiring FPGAs as virtual resources from the data center using the cloud managing software OpenStack. This work first partitions the user circuit onto multiple FPGAs using a user-specified mapping, creates the FPGA fabric for inter-FPGA connection, generates the OpenStack calls to reserve the compute devices, create the network connections, generate the bitstreams, programs the devices, and configure the devices with the appropriate MAC addresses, creating ready-to-use network device that can interact with other network device in the data center.

Keywords: Cloud Computing
Datacenters
FPGAs
Virtualization
Advisor: Chow, Paul
Examining the use of Digital Technology by Four Literacy Teacher Educators

The purpose of this study is to understand the use of digital technology by four literacy teacher educators through examining their backgrounds, visions, and practices. Three semi- structured interviews were conducted with each participant over a three-year period. The analysis of the interviews suggests four important areas to consider when examining digital technology use. They are: attitudes toward literacy instruction, attitudes toward digital technology, goals for using digital technology, and supports and barriers to using digital technology. The literacy teacher educators highlight innovative uses of digital technology, which are influenced by their multimodal approach to teacher education pedagogy and strong belief that digital technology belongs in the classroom. This research contributes to our understanding of the professional lives of teacher educators and the use of digital technology in teacher education programs.

Keywords: Digital Technology
Multiliteracies
Teacher Education
Advisor: Kosnik, Clare
Parents' Experiences with Learning to Manage Medications in Pediatric Rehabilitation

Introduction: There is a significant amount of risk associated with the transition from hospital to home due to the fact that care can become fragmented and discontinuous. Children with chronic complex conditions are particularly susceptible to this risk because of their multiple health care needs, including complicated medication regimens. Methods: Qualitative interviews were used to capture a description of parentsâ experiences with learning to manage their childâ s medications prior to discharge from a pediatric rehabilitation hospital. Results: Two key thematic categories emerged from the interviews: 1) learning to manage the technical aspects of medications and 2) learning to integrate medication management into everyday life. Conclusions: More research is needed to identify effective models of care where hospitals partner with the community to improve the integration of medication management into home life.

Keywords: Care Transitions
Medication
Patient Education
Patient Experience
Patient Safety
Pharmacy
Advisor: Baker, Ross
Minimizing Dispersion in FDTD Methods with CFL Limit Extension

The CFL extension in FDTD methods is receiving considerable attention in order to reduce the computational effort and save the simulation time. One of the major issues in the CFL extension methods is the increased dispersion. We formulate a decomposition of FDTD equations to study the behaviour of the dispersion. A compensation scheme to reduce the dispersion in CFL extension is constructed and proposed. We further study the CFL extension in a FDTD subgridding case, where we improve the accuracy by acting only on the FDTD equations of the fine grid. Numerical results conrm the efficiency of the proposed method for minimising dispersion.

Keywords: Finite difference time domain (FDTD)
numerical stability
perturbation
subgridding
Advisor: Triverio, Piero
Attachment and Communication: Softening the Demands for Intimacy with Avoidantly Attached Individuals

Three samples examined the influence of attachment avoidance on positively receiving messages of affection during couple conversations about love. The interactions were coded for speaker and listener behaviours to determine which actions were most effective when communicating affection. Factor analyses yielded a two factor solution of speaker behaviours: positive involvement and directness. Positive involvement included speaker engagement, expressiveness, enjoyment and love, while directness included speaker emotion, authenticity and deflecting. Results indicated that there was a speaker involvement by listener avoidance interaction on how loved the listener looked and self-reported positive emotion, such that avoidant listeners showed significantly more behavioural love when the speaker was high relative to low in positive involvement. There was no speaker directness by listener avoidance interactions. These results suggest that being involved rather than direct with an avoidant partner may be one way to lower their emotional defenses and accept the speaker's messages of affection.

Keywords: attachment
avoidance
communication
love
nonverbal behaviour
verbal behaviour
Advisor: MacDonald, Geoff
Impett, Emily
Pilot Study to Investigate the Mineral-Inducing Effect of AMELOTIN in an Experimental Rat Model

Periodontal diseases are high prevalence infections of the periodontium that might lead to tooth loss. Even though several approaches have been implemented to stimulate periodontal regeneration, they are still unable to restore the periodontium in humans. The main challenge is the rapid apical migration of junctional epithelium, which prevents periodontal regeneration. Our approach employs a novel mineral-inducing protein “Amelotin” that has consistently induced mineralization in several in vitro systems. Therefore, maintaining a “closed healing” environment that prevents the apical migration of epithelial cells to the wound site can be achieved through the use of “Amelotin”. This study investigated the in vivo mineral-inducing effect of Amelotin in experimental rat models, using a collagen membrane designed in our lab. Results showed that Amelotin probably stimulates mineral formation in vivo and might have a “time-dependent” effect in mineral formation. In addition, the protein did not stimulate any immune response in all rats analyzed.

Keywords: Tissue Engineering
Advisor: Ganss, Bernhard
Development and Usability Testing of a Smartphone Technology for the Self-management of Pediatric Concussion

Noticeable gaps continue to exist in the management of pediatric concussion that can lead to poor health outcomes. This research describes the development, and usability evaluation of a smartphone application to aid youth in self-managing concussion. An agile user-centered design approach was used to develop the technology, followed by a formative usability study for assessment and improvement proposals. Seven youth ages 10 to 18 years with a history of concussion, and seven healthcare professionals were recruited for this study that included, participants performing 11 tasks using the â think aloudâ protocol, administration of the System Usability Scale (SUS) questionnaire, and a semi-structured interview. The mean SUS score was 83, mean task success rates were >90% for 92% of tasks, and mean task completion times were

Keywords: concussion
mobile health
pediatric
self-management
smartphone application
usability testing
Advisor: Mihailidis, Alex
Development of Digital Microfluidics Platform for 2D and 3D Chemosensitivity Assays

In this project, the potential of digital microfluidics (DMF) platform in chemosensitivity was explored and evaluated. A new DMF device architecture (laser-cut PET-ITO top plate) was developed. The fabrication and operation of these devices were optimized for device performance and lifetime, which may be useful for multiple future applications. After developing the platform, the responses of one breast cancer cell line, MDA-MB-231, to two chemotherapeutic drugs, 5-fluorouracil and paclitaxel, were measured for both 2D culture and 3D culture, respectively, and we demonstrated the feasibility of the platform to generate credible chemosensitivity curves. Furthermore, the data shows preliminary evidence that the ratio of cell media volume to cell number should be considered in future experiments. In sum, this work represents the initial step towards the establishment of a new chemosensitivity platform.

Keywords: chemosensitivity
digital microfluidics
DMF
microfluidics
tumour testing
Advisor: Wheeler, Aaron R
Study on the Effect of Surface Energy of Polypropylene/Polyamide12 polymer Hybrid Matrix Reinforced with Virgin and Recycled Carbon Fiber

The presented work is focused on characterization of thermal treated recycled and virgin carbon fibers. Their thermal performances, chemical surface composition and its influence on interfacial adhesion phenomena on PP/PA12 hybrid matrix were compared using TGA, FTIR and XPS analysis. Additionally, differences between hybrid matrix structural performances of PP/PA12 using both surface modifiers PMPPIC and MAPP were investigated. Final mechanical properties improvements between 8% up to 17% were reached by addition of PMPPIC in PP/PA12 hybrid matrix. For PP/PA12 matrix reinforcement using virgin and recycled carbon fibers, impact energy was improved up to 98% compared with MAPP modified matrix leading to a novel composite with good energy absorption. Finally, wettability studies and surface free energy analysis of all materials studied support the effect of the addition of PMPPIC, MAPP and carbon fibers in final composite surface thermodynamics bringing important data correlation between interfacial adhesion mechanisms and final composite performance.

Keywords: Carbon Fiber
Composites
Polymers
Surface Energy
Surface Modifiers
Themoplastics
Advisor: Sain, Mohini
Tjong, Jimi
A Comparative Study of Camelina, Canola and Hemp Seed Processing and Products

Processes for the production of protein isolates from Camelina sativa and Cannabis sativa were developed by modifying the procedure used for Brassica napus. Due to the high concentration of mucilage in camelina a water-to seed ratio of 30 had to be used instead of the conventional ratio of 18. A rapid mucilage extraction process using hot, 55â °C water was developed. The final products were compared to the isolates made from Estonian rapeseed flour and canola. Recovery of the isolates was the highest from the Estonian rapeseed (67%), followed by hemp (65%), canola (29%) and camelina (22%). The hemp PPI had the highest protein concentration, 97%, and favourable colour, texture and flavour. Camelina SPI and mucilage absorbed water and oil completely. Viscosity measurements of dried and redissolved mucilage showed the highest values at natural pH and the viscosity increased rapidly above 1% solids concentration.

Keywords: Camelina isolates
Colour analysis
Extraction of camelina mucilage
Hemp isolates
Membrane processing
Viscosity of camelina mucilage
Advisor: Diosady, Levente L
Trass, Olev
Patterns in the Temperature Selection and Occupancy of Brook Trout in Algonquin Park

Temperature is a key environmental factor affecting habitat selection of many freshwater fishes as it controls physiological processes including growth and metabolism. Many species face potential threats due to rising temperatures and cold-water species, including Brook Trout, are thought to be particularly vulnerable. Much of our knowledge about selection of Brook Trout thermal habitat is from work estimating upper thresholds and optimal or selected temperatures within experimental settings. Broadening our understanding of thermal selection beyond laboratory experiments is a necessary next step in order to accurately identify and conserve important thermal habitat for this and other potentially threatened species. I first review the literature on Brook Trout temperature relations in order to summarize our current state of knowledge and compare between the lab- and field-based studies. Field estimates of Brook Trout thermal selection from 37 Algonquin Park lakes are then studied, followed by models of Brook Trout occupancy and detection probability.

Keywords: Algonquin Park
Brook Trout
Detection Probability
Physiology
Temperature Selection
Thermal Habitat
Advisor: Jackson, Don
Ridgway, Mark