VictorJuiz/thesis huggingface dataset:
Why Bring Students to the Theatre? An Exploration of the Value of Professional Theatre for Children

Experienced by thousands of children every year, professional theatre for young audiences TYA) is still a relatively new and understudied phenomenon in Canada. The purpose of this research has been to learn why teachers bring their students to the theatre, specifically Young People’s Theatre (YPT), and to determine how these connect to the perceptions of those who work at and with the theatre. In order to understand the complexities of the impetus to bring students to YPT, the limitations and successes teachers encounter in doing so, this ethnographic study was situated at the intersection of spatial and curriculum theories and has included surveys, interviews and participatory observation. This research provides greater understanding of the challenges and benefits of including theatre-going in one’s educational repertoire. These new insights contribute to contemporary scholarship on aesthetic education and arts-based community building and provide opportunities for further research about teaching and learning through theatre.

Keywords: curriculum studies
theatre education
drama education
spatial theory
theatre
drama
theatre for young audiences (TYA)
ethnography
aesthetic education
Advisor: Gallagher, Kathleen
Characterization of Metal-binding P-loop GTPases: E. coli YeiR and M. thermoacetica AcsF

Organisms express metal-binding proteins in order to deal with essential metal ions that can be potentially toxic. A common trend of bacterial metal homeostasis pathways is the presence of a GTPase, and several of these proteins are members of the G3E family of P-loop GTPases. In this work we focused on E. coli YeiR, member of the under-characterized COG0523 subfamily, and on M. thermoacetica AcsF. The in vitro metal-binding properties of isolated YeiR are presented. The protein binds Ni2+ and Zn2+ with low micromolar affinity, and oligomerizes in the presence of metal. The GTPase activity of YeiR is similar to that measured for other members of the group and is enhanced by Zn2+. In the case of AcsF, it was not possible to establish concluding evidence that the protein binds metal. This study helps shed light upon members of the under-characterized subfamily of G3E P-loop GTPases.

Keywords: P-loop GTPase
metallochaperone
Advisor: Zamble, Deborah
Interferon Regulatory Factor-9 (Irf-9) Mediates Short Term Host Protection, But Promotes Long Term Immune Injury in Evolution of Myocarditis Leading to Dilated Cardiomyopathy

Evolution of viral myocarditis to dilated cardiomyopathy (DCM)represents a delicate balance between host innate immunity and T-cell acquired immunity. IRF-9 is a key member of a transcription factor family that regulates type I interferon (IFN) production, critical for innate antiviral protection. RESULTS: IRF9-/- mice showed dramatically increased mortality compared to the wildtype littermates (0% WT vs 72% IRF-9-/- on day 14, P<0.0001). On day 42, there was less cardiac hypertrophy and inflammation in IRF-9-/- mice compared to WT controls (p<0.05). Onn day 42 there was a dramatic increase in the number of cytotoxic and helper T-Cells in the wild-type mice that was not observed in the IRF-9-/- spleens (p<0.05). CONCLUSIONS: These data suggest a novel dual role of IRF-9 in not only regulating interferon in acute stage of viral infection in myocarditis, but also late acquired immunity activation, including CD4/8 populations, contributing to the development of chronic cardiomyopathy.

Keywords: viral myocarditis
dilated cardiomyopathy
Genome-wide Analysis of Nucleosome Occupancy Surrounding Saccharomyces cerevisiae Origins of Replication

The Saccharomyces cerevisiae origin recognition complex (ORC) binds to replication origins at the ARS consensus sequence (ACS), serving as a scaffold for the assembly of replication complexes needed for the initiation of DNA synthesis. I generated a genome-wide map of nucleosome positions surrounding replication origins because the precise locations of nucleosomes may influence replication. My map revealed a nucleosome-free region surrounding the ACS that is bordered by two well-positioned nucleosomes. I was able to explain differences in origin properties by clustering nucleosome profiles. I found an association between the replication time and nucleosome profile for a given origin cluster. An ORC depletion mutant nucleosome map indicated a shift in nucleosomes towards the ACS. I present the first genome-wide view of origin nucleosome architecture, indicate a relationship between chromatin structure and replication timing, and suggest a model whereby the interplay between DNA sequence and ORC binding defines the nucleosome occupancy pattern.

Keywords: nucleosome
yeast
Advisor: Nislow, Corey
Brown, Grant
Genome-scale Dynamic Modeling of the Competition Between Rhodoferax and Geobacter in Anoxic Subsurface Environments

In situ bioremediation by Fe(III) reducers is a strategy for clean-up of ground water through reductive immobilization. The dynamics of the community involved is complex and needs to be understood better for improving the bioremediation. Here, we have created a dynamic genome-scale metabolic model of Geobacter sulfurreducens and Rhodoferax ferrireducens, the two primary iron-reducers in subsurface environments, in order to understand the community competition prior to and during uranium- bioremediation. The simulation results suggest that the community competition is modulated by two factors: the ability of G. sulfurreducens to fix nitrogen under ammonium limitation, and a rate vs. yield trade-off between these two organisms. This model will be an important tool for the analyses of more complex microbial communities and the design of effective uranium-bioremediation strategies.

Keywords: systems biology
model
Advisor: Radhakrishna, Mahadevan
Design and Development of a Modular Platform for Remotely Testing DC Motors via the Internet

This thesis presents the design of a platform for testing DC motors over the Internet. The system allows customers to test multiple DC motors under the specific loading conditions of the real world application for which the motor is required. This provides more information than the motor performance charts alone, therefore allowing the user to make a more-informed decision. The architecture is divided into three subsystems: the Motor Test Platform, the Target Software Application and the Server Software Application. A proof-of-concept prototype was built using this architecture. This implementation was evaluated against benchmark tests to determine its capabilities as a simulation and evaluation tool. The positioning system performed well and was able to connect to different Test Motors with any proximal human operation. The positioning system did introduce some error compared to emulation done with manual coupling.

Keywords: motor testing
hardware-in-the-loop
emulation
torque/speed
Advisor: Emami, Mohammad Reza
Analog Front-end Design for 2x Blind ADC-based Receivers

This thesis presents the design, implementation, and fabrication of an analog front-end (AFE) targeting 2x blind ADC-based receivers. The front-end consists of a combination of an anti-aliasing filter (AAF) and a 2-tap feed-forward equalizer (FFE) (AAF/FFE), the required clock generation circuitry (Ck Gen), 4 time-interleaved 4-b ADCs, and DeMUX. The contributions of this design are the AAF/FFE and the Ck Gen. The overall front-end optimizes the channel/filter characteristics for data-rates of 2-10 Gb/s. The bandwidth of the AAF is scalable with the data-rate and the analog 2-tap feed-forward equalizer (FFE) is designed without the need for noise-sensitive analog delay cells. The test-chip is implemented in 65-nm CMOS and the AAF/FFE occupies 152×86 μm2 and consumes 2.4 mW at 10 Gb/s. Measured frequency responses at data-rates of 10, 5, and 2 Gb/s confirm the scalability of the front-end bandwidth. FFE achieves 11 dB of high-frequency boost at 10 Gb/s.

Keywords: High-speed signaling
chip-to-chip communication
analog front-end
equalization
clock and data recovery
feed-forward equalization
receiver
ADC-based receiver
blind receiver
channel
Advisor: Sheikholeslami, Ali
A 5Gb/s Speculative DFE for 2x Blind ADC-based Receivers in 65-nm CMOS

This thesis proposes a decision-feedback equalizer (DFE) scheme for blind ADC-based receivers to overcome the challenges introduced by blind sampling. It presents the design, simulation, and implementation of a 5Gb/s speculative DFE for a 2x blind ADC-based receiver. The complete receiver, including the ADC, the DFE, and a 2x blind clock and data recovery (CDR) circuit, is implemented in Fujitsu’s 65-nm CMOS process. Measurements of the fabricated test-chip confirm 5Gb/s data recovery with bit error rate (BER) less than 1e−12 in the presence of a test channel introducing 13.3dB of attenuation at the Nyquist frequency of 2.5GHz. The receiver tolerates 0.24UIpp of high-frequency sinusoidal jitter (SJ) in this case. Without the DFE, the BER exceeds 1e−8 even when no SJ is applied.

Keywords: high-speed signaling
decision-feedback equalizer (DFE)
blind sampling
ADC-based receiver
speculative
look-ahead
clock and data recovery (CDR)
blind oversampling
CMOS
jitter tolerance
eye diagram
equalizer
Advisor: Sheikholeslami, Ali
VLSI Implementation of Digital Signal Processing Algorithms for MIMO Detection and Channel Pre-processing

The efficient high-throughput VLSI implementation of Soft-output MIMO detectors for high-order constellations and large antenna configurations has been a major challenge in the literature. This thesis introduces a novel Soft-output K-Best scheme that improves BER performance and reduces the computational complexity significantly by using three major improvement ideas. It also presents an area and power efficient VLSI implementation of a 4x4 64-QAM Soft K-Best MIMO detector that attains the highest detection throughput of 2 Gbps and second lowest energy/bit reported in the literature, fulfilling the aggressive requirements of emerging 4G standards such as IEEE 802.16m and LTE-Advanced. A low-complexity and highly parallel algorithm for QR Decomposition, an essential channel pre-processing task, is also developed that uses 2D, Householder 3D and 4D Givens Rotations. Test results for the QRD chip, fabricated in 0.13um CMOS, show that it attains the lowest reported latency of 144ns and highest QR Processing Efficiency.

Keywords: MIMO Communication
VLSI Implementation
Digital Signal Processing
MIMO Detection
Channel Pre-Processing
QR Decomposition
K-Best Algorithm
Error Correcting Codes
High Speed
Low Power
Advisor: Gulak, P. Glenn
Decidual Leukocyte Involvement in Human Spiral Artery Remodeling

The decidualized endometrium harbors abundant leukocyte populations that are proposed to regulate critical processes at the maternal fetal interface including transformation of decidual spiral arteries. The work in this thesis investigated the leukocyte subtypes in the decidua throughout the course of this vascular transformation. A particular focus was the role of the uterine Natural Killer (uNK) cells and macrophages in an in vitro model of vascular remodeling. A significant infiltration of uNK cells and macrophages, matrix metalloproteinase-2/9 activity, and evidence of apoptosis and phagocytosis were observed in remodeling arterioles. From first to second trimester, FACS analysis demonstrated dramatic changes in the decidual leukocyte subpopulations, including the decline of uNK cells and macrophages and substantial increase in T lymphocytes and neutrophils. These data demonstrate an integral role of uNK cells and macrophages in early vascular remodeling and provide evidence of unique and complex immune interactions in the decidual microenvironment during human pregnancy.

Keywords: uNK cells
macrophages
flow cytometry
dendritic cells
lymphocytes
Advisor: Lye, Stephen J.
Verdazyl Radicals as Substrates for the Synthesis of Novel Nitrogen-containing Heterocycles

The emergence of verdazyl radicals as starting materials for organic synthesis is providing a unique opportunity to create a variety of distinctive heterocyclic scaffolds. These stable radicals have previously been used as spin probes, polymerization inhibitors, mediators of living radical polymerizations, and as substrates for molecular-based magnets. However, verdazyl radicals have never been employed to fulfill an organic synthetic role until recently. In an effort to pioneer the chemistry behind verdazyl radicals as novel organic substrates, our lab has been inspired to expand and explore the scope of reactions involving their synthetic utility. This thesis assesses the synthetic versatility of verdazyl radicals by constructing a library of structurally complex and diverse verdazyl-derived heterocycles in an approach called diversity-oriented synthesis. The synthetic versatility was further expanded to the preparation of a biphenyl-stacked biphenylophane, which exhibited interesting structural and conformational features as highlighted herein.

Keywords: Verdazyl radicals
1,3-dipolar cycloaddition
azomethine imine
heterocyclic syntheses
pyrazolotetrazinanone
Advisor: Georges, Michael
Investigating the ERBB Protein Interactome

The erythroblastoma (ErbB) receptor family consists of four members that are implicated in many human cancers. To gain insight into their biological function, we investigated their interacting partners to derive a comprehensive protein interaction network. Using the membrane yeast two-hybrid (MYTH) system we probed the ErbB2, ErbB3, and ErbB4 interaction space and validated a subset of interacting partners using the luminescence-based mammalian interactome mapping (LUMIER) system. The integrated use of these two complementary protein interaction technologies generated high confidence data and identified many novel ErbB binding partners, a subset of which was supported by co-immunoprecipitation in the breast adenocarcinoma cell line Sk-Br-3 including the GPCR GPRC5B, the cysteine protease CAPN1, and WIF1, a secreted protein containing 5 EGF domains that may represent a novel ErbB ligand. Our systematic approach offers an unbiased systems level view that may identify novel drug targets and contribute to therapeutic research.

Keywords: ErbB receptors
LUMIER
Advisor: Stagljar, Igor
microRNAs in the Drosophila Egg and Early Embryo

Posttranscriptional regulation plays a very important role in animal oocytes and embryos. Maternally synthesized mRNAs and proteins control early animal development up until the maternal-to-zygotic transition (MZT). This is the point when the zygotic genome takes control. The maternally deposited mRNAs are posttranscriptionally regulated right from the time they are produced during oogenesis, through egg activation, and in the embryo. microRNAs (miRNAs) are posttranscriptional regulators that have been shown to play a role in both RNA stability and translation. I examined miRNA abundance in Drosophila stage 14 oocytes, activated unfertilized eggs, and embryos and have grouped all the then known Drosophila miRNAs into four distinct temporal classes. Class I and III appear to be maternally deposited, while Class II appears to be both maternally and zygotically transcribed, and Class IV appears to be strictly zygotically transcribed. Follow-up experiments validated three of the four classes.

Keywords: Drosophila
egg
microRNA
embryo
oocyte
miR-309
Advisor: Lipshitz, Howard
Translational Regulation of smaug mRNA

In Drosophila, early embryonic development is controlled by maternally loaded RNAs and proteins. For proper development to occur it is vital these maternal transcripts are post-transcriptionally regulated. SMAUG, a major post-transcriptional regulator, has been found to be responsible for the destabilization of two thirds of the unstable maternal transcripts upon egg activation (Tadros et al., 2007). smg mRNA is translationally repressed in stage 14 oocytes, but its translation is activated upon egg activation in a PAN GU kinase dependent manner. Here I show that redundant translational repression elements reside in the smg 3’UTR, and PUMILIO mediates repression through one of these elements. I also show that these elements are sufficient to cause translational repression in stage 14 oocytes. smg mRNA appears to be regulated post-initiation in stage 14 oocytes in a large repression complex which is similar to smg mRNA repression in a png mutant.

Keywords: Translation
mRNA
Pumilio
Smaug
Drosophila
maternal mRNA
oocyte
embryo
Advisor: Lipshitz, Howard
Matrix Supplemented Stem Cell Microencapsulation for Regenerative Medicine

Previous studies reported that matrix protein supplementation (fibronectin/fibrinogen, FN/FG) of agarose gel microcapsules enhances survival and pulmonary retention of syngeneic rat multipotent stromal cells (MSCs). I hypothesized that additional supplementation of microcapsules with osteopontin (OPN) and transglutaminase 2 (TG2) would enhance cell survival, while stabilizing the provisional matrix. Using monomeric OPN or OPN polymerized with TG2, I examined human MSC adhesion, morphology, focal contact formation and apoptosis. Polymeric OPN induced greater adhesion than monomeric OPN (84.5±10.7 vs. 44.3±10.0cells/field), and also significantly enhanced focal contact formation (351.5±21.2 vs. 45.6±17.6 focal contact sites/cell) and cell spreading (2.7x103±0.20x103μm2 vs. 1.2x103±0.26x102μm2) while preserving MSC pluripotency. Microcapsules supplemented with FN/FG, polymeric OPN and TG2 demonstrated significantly less apoptotic cells than FN/FG microcapsules (14.0±2.34% vs. 28.2±3.22%). Reduced apoptosis was attributed to matrix stabilization by TG2 and the synergistic activity of matrix proteins. It is anticipated that this enhanced survival will maximize the therapeutic potential of MSCs.

Keywords: Biomedical Engineering
Cell Biology
Medicine and Surgery
0564
0379
Advisor: Courtman, David
Stewart, Duncan John
The Transmembrane Receptor UNC-40 Directs Muscle Arm Extension in Caenorhabditis elegans

In Caenorhabditis elegans, body muscles extend muscle arms in a chemotropic fashion to the nearest nerve cord and serves as a model for the investigation of guided cell migration. I found that the transmembrane receptor UNC-40/DCC is required, and functions cell-autonomously to regulate muscle arm extension. Surprisingly, both the canonical ligand of UNC-40 (UNC-6/Netrin) and the extracellular domains of UNC-40 are dispensable, suggesting that UNC-40 relies on a co-receptor or other polarizing pathways to direct muscle arm extension. Furthermore, through double mutant analyses and the use of a neomorphic phenotype induced by UNC-40 over-expression, I define a distinct UNC-40 pathway in which UNC-73/Trio, the WAVE actin polymerization complex, and components of the dense body likely act downstream of UNC-40 to regulate muscle arm extension. Distinct modes of UNC-40’s function in muscle arm extension compared to its role in neurons provide a more complete understanding of how this conserved guidance receptor functions.

Keywords: UNC-40
C. elegans
muscle arms
cell guidance
membrane extension
Advisor: Roy, Peter John
Effects of Bilateral and Unilateral Deafness Observed from Cortical Responses Evoked in Children with Bilateral Cochlear Implants

This study examined the effects of bilateral and unilateral deafness by measuring cortical auditory evoked potential (CAEP) responses in children at initial stages of bilateral cochlear implant (CI) use. We recorded cortical responses evoked by right and left CI stimulation in 127 children with early onset (< 12 months) deafness, with 72 children receiving the two devices in the same surgery (simultaneously implanted) and 55 children receiving the devices in separate procedures (sequentially implanted). Three different types of responses were identified in children with bilateral CIs. No significant effects of duration of deafness, age at implantation, or duration of unilateral CI use were found on response latencies and amplitudes within each type of cortical response, but there were clear differences in responses types between groups and ears. In the context of these findings, the effects of bilateral and unilateral deafness to the auditory pathways were discussed.

Keywords: Cortical Development
Hearing
Deafness
Bilateral Deafness
Unilateral Deafness
Cochlear Implants
Neural Development
Neural Plasticity
Advisor: Gordon, Karen A.
Harrison, Robert
Invasive bacteria induce cellular stress that alters the cytoplasmic dynamics of the SMN complex

The course of pathogenic bacterial infection is dependent on the interactions between the host immune response and the bacterial virulence mechanisms. Our lab previously discovered that the Survival of Motor Neuron (SMN) protein complex undergoes a change in subcellular localization during infection with invasive Shigella bacteria, forming novel cytoplasmic aggregates called "U bodies". Similar results were obtained with other intracellular bacterial pathogens suggesting that these U bodies are a fundamental entity in microbial pathogenesis. Notably, the SMN complex normally plays a key role in the assembly of the spliceosomal U snRNA. We have shown during infection that there are changes in U snRNA maturation and splicing patterns. Importantly, we have found that U bodies are downstream of a stress pathway involving the stress-inducible ATF3 protein. Altogether, intracellular bacterial infection induces novel cellular stress pathways that disrupt normal SMN complex function and leads to changes in U snRNA associated functions.

Keywords: SMN complex
Invasive Bacteria
Advisor: Girardin, Stephen
Efficiency Enhancement Techniques for Switched Mode Power Electronics

In the design of the state-of-the-art electronic products, power management circuits play a very important role for the enhancement of overall system efficiency. Switched mode DC-DC converter is an increasingly popular power management circuit due to its superior power conversion efficiency. This thesis introduces two efficiency optimization techniques for switched mode power electronic circuits. One is dead-time optimization. This technique can automatically adjust the dead-time on-the-fly according to the circuit operating conditions. Second, an energy conservation based high-efficiency dimmable multi-channel LED driver is discussed. An auxiliary power switched is use to allow free wheeling of the inductor current during the load disconnect period. The sequential burst mode PWM current sharing scheme with dimming capability can effectively reduce design complexity and cost. The proposed LED driver provides a practical solution for the realization of LED BLU in the flat panel TVs with local dimming capability according to the video content.

Keywords: power management circuit
power efficiency
DC-DC converter
dead-time
LED driver
contrast ratio
energy conservation
Advisor: Ng, Wai Tung
The Role of Septin 5 in Exocytosis

Septins are an evolutionarily conserved family of proteins that have been implicated in a multitude of cellular processes. Septin 5 is mainly expressed in the nervous system and it has been linked to regulated secretion through its binding to the SNARE protein syntaxin 1. However, the exact mechanism of septin 5 function in localized exocytosis remains unknown. Over-expression of septin 5 is known to lead to lower levels of secretion in HIT-T15 cells. Interestingly, in the current study, the knock-down of septin 5 also results in reduced levels of regulated secretion in PC12 cells, suggesting a more complex role of septin 5 that includes both negative and positive effects on exocytosis. Septin 5 knock-down data point to a possibility of septin 5 facilitating formation of a tether between the vesicles and their site of secretion.

Keywords: Septins
Septin 5
Exocytosis
TIRF
Secretion assay
Advisor: Trimble, William S.