VictorJuiz/thesis huggingface dataset:
A Gate Sinking Threshold Voltage Adjustment Technique for High Voltage GaN HEMT
Keywords: GaN
HEMT
metal inter-diffusion
Power
Process
Recessed gate

GaN-based power electronics receive many interests because of its wider bandgap, higher electron mobility and higher critical electrical field than silicon. However, the intrinsic AlGaN/GaN-based HEMT is a "normally-on" device. This thesis proposes a gate sinking method during the metal gate deposition to adjust the VT towards enhancement mode operation. This recessed gate process relies on the chemical reaction between Ta and AlGaN using a simple RTA procedure rather than the more complicated RIE method. This eliminates the need for etching with nanometer precision. During the Ta sputtering process, both Ar and N2 carrier gases are used to form TaN with work function in the range of 4.15 to 4.7 eV. The fabricated HV GaN HEMTs exhibit VT shift from -5 to -2 V. Moreover, the proposed device is compatible with silicon-CMOS technology to ensure cost-effective implementation of future high performance smart power ICs.
Pathogenesis of Anti-integrin αIIb-mediated Fetal and Neonatal Alloimmune Thrombocytopenia: Establishment of Novel Murine Models in αIIb Deficient and Human αIIb Transgenic Mice
Keywords: Animal models
Fetal and neonatal illumine thrombocytopenia
Hematology
Platelets
Thrombocytopenia
Thrombosis

Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is a life threatening bleeding disorder caused by maternal antibodies targeting fetal/neonatal platelets. The incidence is approximately 1:1000 live births, but the frequency of FNAIT associated miscarriage has not been adequately investigated. FNAIT targeting the β3 subunit of integrin αIIbβ3 occurs in approximately 85% of reported cases, whereas αIIb-mediated-FNAIT only accounts for approximately 5% of reported cases although frequencies of polymorphisms in αIIb and β3 polypeptides are similar in the human population. It is unknown whether immune responses to these two subunits differ and currently no animal model exists to address this question. We hypothesize that αIIb-mediated-FNAIT causes a severe form of FNAIT (e.g. miscarriage), which may account for this discrepancy. Here, two new murine models of αIIb-mediated-FNAIT were established. Severe FNAIT (e.g. miscarriage and intracranial hemorrhage) is frequently observed, and we conclude that the severity of anti-αIIb-FNAIT may mask the clinically reported incidence of disease.
Studies on MITE amplification in Saccharomyces cerevisiae and the de novo characterization of MITEs in the genome of Solanum lycopersicum
Keywords: bioinformatics
inverse PCR
Miniature inverted-repeat transposable elements
MITE amplification
Transposable elements
yeast

Miniature inverted-repeat transposable elements (MITEs) have been found to reach high copy numbers in eukaryotic genomes. The underlying mechanisms of their transposition and the characterization of existing and novel MITEs are highly sought after. An IPCR-based system was developed to detect the copy number of the T7-neo MITE in the yeast genome. However, this system resulted in minimal detection of the MITE. Using bioinformatics programs MITE Digger and Mite Analysis Kit, MITE families were characterized in the genome of Solanum lycopersicum. Thirty-seven MITE families were classified and characteristic of DNA transposon superfamilies Tc1/mariner, CACTA, PIF/Harbinger, hAT and Transib. Divergence of the MITE families was calculated and of those least diverged, four showed evidence of transcription. Some were identified in the related genomes of Solanum pimpinellifolium, Solanum tuberosum, and Nicotiana tabacum. Overall, an experimental MITE amplification system and de novo characterization of MITEs contributes to understanding MITE amplification in eukaryotic genomes.
Gene-environment Interplay on Oviposition Site Selection in Drosophila melanogaster
Keywords: choice
decision-making
Drosophila melanogaster
foraging gene
oviposition
social environment

The underlying mechanisms of decision-making behaviour are poorly understood. Oviposition site selection (OSS) in the Drosophila melanogaster fruit fly provides a useful system for studying simple decision-making. OSS is influenced by both genetic and environmental variation. Variation of the foraging gene (for) is known to affect OSS. Given a choice of high- and low-nutrient oviposition sites, groups of rovers (forR) lay significantly more of their eggs on low-nutrient sites than sitters (fors) and sitter mutants (fors2). I examined the roles of choice, female density, and for expression in gustatory neural circuitry in rover/sitter differences in OSS. I found a role of choice and female density in rover/sitter differences, and a role of for in response to glycerol, an indicator of yeast. However, driving for-mRNA expression in gustatory neurons using the GAL4/UAS system did not alter OSS. These findings suggest a central role of for in decision-making during OSS.
Patched-1 Intracellular Domains Interact with E3 Ubiquitin Ligases Smurf2 and Itch
Keywords: Itch
Ptch1
Smurf2

Patched-1 (Ptch1) is the primary receptor of the Hedgehog signalling pathway and mediates both canonical and non-canonical signalling. Previously our lab identified a group of proteins that interact with the C-terminus of murine Ptch1 that possessed SH3- and WW- binding domains, chief among them being C2-WW-HECT E3 ubiquitin ligases. Using a molecular-based approach, we showed that E3 ligases Smurf2 and Itch bind through sequences within the large intracellular middle loop and C-terminus of murine Ptch1 (mPtch1). We further demonstrated that mPtch1 is ubiquitinated in the presence of Smurf2 and Itch and this requires the middle loop and C-terminus. We also showed that mPtch1 can oligomerize and that the stability of mPtch1 is affected when the middle loop and C-terminus are deleted. Together, these data reveal a role for E3 ubiquitin ligases in mediating protein turnover of mPtch1 and show that the intracellular domains of mPtch1 interact with distinct protein factors.
Ore-skin Design to Control Sloughage in Underground Open Stope Mining
Keywords: Design Optimization
DFN-3DEC
Dilution
Open Stoping
Ore-skin
Sloughage

In open stope underground mines, stope hangingwall (HW) sloughage is typically the main source of ore dilution. In cases where the immediate stope HW consists of a weak rock mass, the HW sloughage can be substantial and can result in increased dilution rates which have significant economic impact on the mine operation. This thesis presents an alternative design method which requires leaving a certain thickness of ore unmined (i.e., an ore-skin) to support the weak adjacent/overlying hangingwall. The ore-skin design approach is presented in the context of a hypothetical open stope mine to determine the feasibility of implementing this alternative design method to control HW sloughage. Both the economics and the geomechanical aspects of the ore-skin design are investigated. This study aims to determine the importance of considering alternative design approaches to optimize the open stope mining process.
Broadband Optical Three Wave Mixing in AlGaAs Waveguides
Keywords: bandwidth
Bragg Waveguides
Compound Semicondutors
Difference frequency generation
Etching
Three wave mixing

This thesis presents Bragg reflector waveguide based AlGaAs tapered waveguides as means of achieving broadband difference frequency generation (DFG). Different fabrication processes are developed and optimized to fabricate devices with design specifications. In particular, the dry and wet etching recipes are optimized using design of experiments approaches (DOE). Response surface method is implemented to improve the etch quality and process robustness. The dry etching process is implemented to fabricate laterally tapered DFG devices. From nonlinear frequency conversion experiments, DFG bandwidth of some of the tapered devices showed a 3-fold bandwidth enhancement when compared to straight waveguides. DOE is also implemented for establishing an equirate wet etching process for beveled waveguides. DFG bandwidth of some of these beveled devices showed a 6-fold bandwidth enhancement when compared to straight waveguides. This enhancement in conversion bandwidth will benefit numerous devices that offer tuneable wavelength sources for applications in sensing and imaging.
Arrestin Interactions with Rhodopsin in the Squid Visual System
Keywords: arrestin
phosphorylation
rhodopsin
squid
vision

Light activation of squid rhodopsin results in stimulation of the Gq signalling cascade. Activated rhodopsin (metarhodopsin) is a target for squid arrestin and squid rhodopsin kinase which are involved in the inactivation of metarhodopsin. The aim of this project is to characterize the interaction between squid rhodopsin and arrestin, and the role of phosphorylation on their interactions. We determined the affinity of arrestin for metarhodopsin to be 32nM. Two mutations to the polar core did not decrease the affinity of arrestin for metarhodopsin, suggesting a difference in basal structure of squid arrestin compared to other arrestins. Serine392 and Serine397 in the C-terminus of squid arrestin were phosphorylated by squid rhodopsin kinase. Arrestin phosphorylation decreased the affinity of arrestin binding to metarhodopsin, while metarhodopsin phosphorylation increased the dissociation of the two proteins. Further studies are required to identify mechanisms of metarhodopsin and arrestin dephosphorylation in the squid visual system.
Developing an In vitro Model of the OAF-CEP Interface: Towards Tissue Engineering the Intervertebral Disc
Keywords: Annulus Fibrosus
Bovine
Cartilage Endplate
Interface
Intervertebral Disc
Tissue Engineering

Bioengineering a biologically relevant interface is an essential element toward developing an intervertebral disc (IVD) replacement for the treatment of low back pain. To this end, this study further characterized the native outer annulus fibrosus (OAF)/cartilage endplate (CEP) interface of adolescent bovine and fetal human disc by immunohistochemical and mechanical methods. Secondly, a model of the interface was developed in vitro using a 3-dimensional contact co-culture system between in vitro-formed cartilage tissues and a trilamellar AF tissue formed using OAF cells and polycarbonate urethane (PU) scaffolds. The native bovine OAF-CEP interface showed mechanical stability up to peak forces of 2.5 + 0.8 MPa. The in vitro generated tissues integrated themselves to form an AF-cartilage interface with some characteristics that mimic native fetal and adolescent bovine interface. Col II was absent from the in vitro-formed OAF but present in the interface which contained aggrecan and calcific deposits and demonstrated alkaline phosphatase activity (ALPa). Cells at the in vitro-formed interface were surrounded by Col I, Col II, Col III, versican, biglycan and decorin. Intermittent compression load of tissue cultures improved tissue integration, matrix accumulation and altered the spatial organization of Col X and ALPa at the interface suggesting that these tissues may respond to loading when implanted in vivo. These data convey that tissue engineered disc replacements have the potential to integrate following implantation. Furthermore, this model is anticipated to be valuable to investigate conditions that will promote in vivo integration and to study AF and cartilage interactions.
Development of In Vivo Lung Perfusion Strategy for the Treatment of Lung Metastases
Keywords: In Vivo Lung Perfusion
Isolated Lung Perfusion
Locoregional Therapy
Lung Metastases
Pulmonary Metastasectomy
Sarcomas

In Vivo Lung Perfusion (IVLP) can potentially enhance the treatment of lung metastases by allowing the delivery of elevated doses of chemotherapy to the lungs without systemic exposure. Previously, experimental and clinical studies reported questionable efficacy and frequent lung toxicity, hindering the broad application of this technique. We have developed a modified IVLP strategy that avoids acute lung injury using a protective mode of ventilation/perfusion. Our IVLP strategy enabled an extended perfusion time using chemotherapy doses usually given intravenously to patients. Additionally, we successfully administered higher chemotherapy levels in a safe manner and found higher lung tissue levels of chemotherapeutic drugs compared to previous studies. Importantly, these findings were possible without acute lung injury, demonstrating a likely protective effect of our IVLP strategy. This is a significant step towards a safer and more effective IVLP technique to help patients with pulmonary metastases, minimizing the adverse effects of chemotherapy to the lungs.
A Bibliometric Analysis of the Field of Records Management: A Case Study of Records Management Journal, 1989-2013
Keywords: Bibliometrics
Citation Preference
Collaboration
Gender
Records Management
Subject Dispersion

This study profiles the characteristics of the scholarship published in one of the central journals in the field of Records Management in order to identify salient aspects of the evolution of that field. Through a bibliometric analysis of the contents of the first twenty-five years of Records Management Journal (RMJ), the study presents a multi-dimensional view of published research and opinion articles in Records Management in the period 1989-2013. Key aspects examined are: the nature of authorship (including gender, country and institutional affiliations, and degree of collaboration); and citation practices (including commonly cited authors, commonly cited journals, and degree of cross-disciplinarity). Records Management scholarship provides a structural framework for Records Management as a discipline, which in turn influences Records Management practice. The publication patterns found in RMJ can therefore serve as a mirror of the history of the scholarship of Records Management as it was presented to practitioners in the field during the examined time period.
Light Harvesting Strategies of Cryptophyte Algae
Keywords: Cryptophyte
Energy Transfer
NPQ
Phycobiliprotein

Cryptophyte algae employ a unique system of free floating phycobiliproteins that shuttle photosynthetic excitations to membrane bound chlorophyll a/c complexes which are connected to the photosystem reaction center (Larkum, 2010). Using absorption, emission and excitation spectroscopy, we attempt to determine, firstly, the manner in which the algae absorb incoming photons and then shuttle the excitation from the outlying peripheral proteins to the core complex reaction centers and secondly, how efficient this process is within the organism. The complex relationship between light harvesting efficiency and the antenna proteins was examined by performing experiments on organisms that varied in antenna structure both energetically and structurally. The adaptability to varying environmental conditions was also studied by exposing organisms to varying ambient light intensity, a factor which is known to influence photosynthetic efficiency (Falkowski Owens, 1980). Contributions of alternate dissipative pathways were determined by chemically decoupling key systems in the electron transport chain.
A Study of Underground Stormwater Detention Chambers and the Creation of the Model for Underground Detention of Sediment
Keywords: Sedimentation Modeling
Stormwater Management
Stormwater treatment
Underground Stormwater Detention Chamber

This thesis investigates the hydraulic and runoff treatment capabilities of Underground Stormwater Detention Chambers (USDC) and compares them to stormwater management ponds, the industry standard system for runoff detention and treatment. Runoff characteristics were monitored at a USDC in Markham, Ontario. Characteristics include: total suspended solids, turbidity, nutrients, metals, bacteria, temperature, and hydrocarbons. The Model for Underground Detention of Sediment (MUDS) was created to predict the removal of suspended solids by a USDC. The results indicate that the Markham USDC meets all provincial hydraulic requirements and most water quality requirements. Also, the Markham USDC provides equivalent or improved level of service compared to stormwater management ponds for runoff treatment in most cases. MUDS was proven capable of accurately predicting USDC hydraulics and suspended solids removal for both event based and continuous based simulations.
The Use of Social Media in a Physical Activity Campaign: MoveU
Keywords: Evaluation
Facebook
Health promotion
Physical activity
Social marketing
Social media

This study used mixed methods to explore the role of a social media platform (Facebook) in supporting a social marketing physical activity (PA) campaign ("MoveU") targeting first year undergraduate females. It comprised one-on-one interviews with nine key partners involved in the campaign's development and implementation; six focus groups with the target audience; and analytic data combined with a content analysis of posts delivered by MoveU on the Facebook page. This evaluation highlights that Facebook can be used to assist in some PA campaign goals such as reaching a target audience while simultaneously promoting existing opportunities to be physically active. However, campaign partners had unrealistic expectations about how "social media" could be used to engage the audience in multi-way conversations, as seen in modest engagement with MoveU's Facebook page. The meaning behind engagement metrics, as well as theoretical and methodological implications of the findings, are discussed.
Drift Recovery and Station Keeping for the CANX-4 and CANX-5 Nanosatellite Formation Flying Mission
Keywords: Control
Formation Flight
Guidance
Microsatellite
Nanosatellite
Navigation

Canadian Advanced Nanospace eXperiments 4 5 (CanX-45) are a pair of formation flying nanosatellites that demonstrated autonomous sub-metre formation control at ranges of 1000 to 50 m. To facilitate the autonomous formation flight mission, it is necessary that the two spacecraft be brought within a few kilometres of one another, with a low relative velocity. Therefore, a system to calculate fuel-efficient recovery trajectories and produce the corresponding spacecraft commands was required. This system was also extended to provide station keeping capabilities In this thesis, the overall drift recovery strategy is outlined, and the design of the controller is detailed. A method of putting the formation into a passively safe state, where the spacecraft cannot collide, is also presented. Monte-Carlo simulations are used to estimate the fuel losses associated with navigational and attitude errors. Finally, on-orbit results are presented, validating both the design and the error expectations.
Biogeography of the Weakly Electric Knifefish Gymnotus carapo (Teleostei: Gymnotidae) in the Guianas
Keywords: biogeography
Guiana Shield
Gymnotidae
ichthyology
species complex

The electric knifefishes (Gymnotiformes) are widely distributed across South and Central America, with the highest species concentrations occurring in the Amazon and Orinoco basins. Riverine features such as waterfalls and rapids can cause disjunct populations to form between highland and lowland areas in these basins. The Guiana Shield provides a good model to study the genetic differences between populations precisely because it has upland and lowland areas with extant populations of Gymnotiformes. To examine genetic divergence between highlands and lowlands, mitochondrial (cytochrome b) and nuclear (S7) DNA was sequenced for members of the Gymnotus carapo species complex (Gymnotidae). Population and phylogenetic analysis indicate a distinct split between upland and lowland populations, with those species in the highlands showing greater genetic similarity to populations from the Amazon basin.
An Examination of Benders' Decomposition Approaches in Large-scale Healthcare Optimization Problems
Keywords: Benders
large-scale
optimization
planning

Benders' decomposition is an important tool used to solve large-scale optimization problems found in healthcare. Radiation therapy and operating room planning and scheduling are two areas in which Benders' decomposition have been applied to solve difficult problems. In radiation therapy, we develop two novel Benders' algorithms, including a classical Benders' algorithm and a combinatorial Benders' algorithm, to solve the sector duration and optimization problem efficiently. In operating room planning and scheduling, we implement an existing logic-based Benders' algorithm for tactical operating room planning and scheduling and analyze the effect of changes to the input data on various output statistics.
Clinicopathological Correlates of Pituitary Adenoma
Keywords: clinicopathological
Intracranial
mTOR
Pituitary
RAD001
xenograft

Our current understanding of pituitary adenoma (PA) pathobiology is limited. Thus, the purpose of this project is to gain a better understanding of PA biology through the completion of two aims: 1) conducting a retrospective review of PA patients and 2) establishing and characterizing an intracranial xenograft mouse model of PA and using the model to identify novel targeted therapies. With respect to our first aim, several tumor- and patient specific factors were correlated to PA growth and recurrence. In our second aim, our tumor models were found to express growth hormone (GH) and prolactin as well as proteins in the mTOR pathway. These PA models were responsive to mTOR inhibition using RAD001 and resuted in a reduction in tumor growth rate and the expression of mTOR and GH. A preclinical and clinical study of PA provides a robust understanding of the clincopathologic factors contributing to PA and may ultimately help improve treatment and outcome.
Development of a Real-time System to Measure Foot Clearance Based on Inertial Sensors
Keywords: Accelerometer
Foot clearance
Gyroscope
Intertial measurement unit

Certain patient populations such as amputees are at a higher risk of falling when walking due to the diminished ability to maintain a safe Foot Clearance (FC). Current research in FC measurement focuses on developing systems that can be worn by the patient in the community, providing a tool for clinical assessment of gait outside a laboratory to provide users with feedback about FC. In this project, an inertial measurement unit (IMU) was used and an algorithm was developed for estimating FC during walking. Experiments were conducted whereby five health adults walked under different conditions while their foot movements were tracked using the IMU-based system, and concurrently with an Optical Motion Capture System for comparison. Pearson Correlation coefficient and error in peak values were used to determine the system accuracy, while the processing time was measured during every trial to determine the delays in the system.
Role for the Red Nucleus in Motor Control during REM Sleep
Keywords: DREADDs
Muscle atonia
Phasic Twitches
Red Nucleus
REM Sleep
REM Sleep Behaviour Disorder

During rapid eye movement (REM) sleep the brain exhibits activity similar to waking. Despite this activity, the motor system is forced into a state of paralysis called REM sleep atonia. Though muscle tone is highly suppressed, this atonia is punctuated by phasic twitches. Here, the red nucleus (RN), a predominantly glutamatergic motor center in the midbrain, is identified as a potential region involved in the control of REM sleep twitches. Using a pharmacogentic technique termed Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), the RN was stimulated during REM sleep to determine its effect on muscle tone. I found that activation of the RN and its glutamatergic neurons increases muscle activity during REM sleep by increasing the number of phasic twitches. This increase disrupts the normal pattern of muscle activity seen during REM sleep. These results bring to light a new area of motor control during REM sleep.