VictorJuiz/thesis huggingface dataset:
Characterizing Novel ATRX-Associating Proteins – CCDC71 and FAM207A

ATRX is an ATP-dependent chromatin remodeling/helicase protein with a number of established cellular functions that depend on its protein-protein interactions, notably with DAXX, a histone chaperone. ATRX maintains heterochromatin stability and repression over repetitive DNA elements, including pericentric heterochromatin and telomeres. According to current models, ATRX resolves aberrant DNA structures and then enforces heterochromatin stability through DAXX-dependent deposition of histone variant H3.3. How ATRX further promotes chromatin compaction and telomere homeostasis is not well understood. To investigate this, we defined the ATRX interactome and identified two novel and uncharacterized interactors of ATRX: CCDC71 and FAM207A. Here, I show that FAM207A locates to the nucleolus, where it associates with nucleolar proteins. CCDC71 is, however, chromatin-bound and dispersed across the nucleus. It associates with Heterochromatin Protein 1 (HP1), suggesting that ATRX likely functions with CCDC71 to maintain heterochromatin.

Keywords: ATRX
BioID
CCDC71
FAM207A
Heterochromatin
HP1
Advisor: Campos, Eric
Fast Packet Scheduling for Hierarchical Fairness

Hierarchical link sharing addresses the demand for fine-grain traffic control at multiple levels of aggregation.Currently deployed scheduling algorithms for hierarchical link sharing are effective with upholding rate guarantees to classes, but perform poorly when distributing excess capacity to classes in need of additional capacity. This leads to counterintuitive allocations and leaves the allocation of capacity vulnerable to manipulation, whereby classes in one branch of the hierarchy can obtain bandwidth at the cost of classes in another branch. We present HLS, a strategy-proof scheduler for hierarchical link sharing, which ensures rate guarantees and provides isolation between classes in the hierarchy. HLS is designed to satisfy a hierarchical version of max-min fairness. We evaluate our implementation of HLS in the Linux kernel with respect to rate allocation and overhead, and compare the results obtained for the CBQ and HTB Linux qdiscs.

Advisor: Liebeherr, Jörg
The Effect of Cell to Cell Communication on Differentiation and Integration of Human Induced Pluripotent Stem Cell-derived Neural Progenitor Cells

Spinal cord injuries (SCI) have devastating impacts due to paralysis and lack of spontaneous repair. It has been shown in a rat model of cervical SCI that forelimb function can be improved by transplanting neural progenitor cells (NPC) obtained from human-induced pluripotent stem cells (hiPSCs). However, molecular mechanisms behind NPC-mediated recovery remain unclear. To overcome this knowledge gap, we have engineered hiPSC-NPCS with inducible tetanus toxin light chain expression to prevent cellular communication via blocking neurotransmitter and/or growth factor release. The resulting NPC line retained progenitor cell properties and the NPCs were able to differentiate to functional neurons, astrocytes, and oligodendrocytes. TeTxLC expression didn’t have a significant effect on NPC differentiation, reduced neuronal soma size and neurite length, and was successful in abolishing synaptic function in vitro. A preliminary proof-of-concept study showed that the inducible expression was successful in vivo as well as in vitro, highlighting the potential for this cell line to be used to study the effect of cellular communication between transplanted NPCs on NPC-mediated functional recovery after spinal cord injury.

Keywords: neural stem cells
regenerative medicine
spinal cord injury
Advisor: Fehlings, Michael G
Recapitulating Nutritionally Regulated Human Muscle Protein Metabolism In vitro using Humanized Cell Media

Most in vitro models used to study the effects of nutrients on skeletal muscle protein metabolism use supraphysiological concentrations of nutrients and amino acids, making translation of their findings to humans difficult. Therefore, there is a need to develop an in vitro model that uses physiological nutrient concentrations. This study used a humanized fasted and fed media, modeled after human plasma fasted and fed amino acid concentrations, to study in vitro protein metabolism and anabolic signalling following nutrient withdrawal and refeeding compared to typical supraphysiological withdrawal and refeeding. In all outcomes measured, there was a similar knockdown of protein synthesis and anabolic signalling in both models. Further, refeeding generally resulted in similar phosphorylation responses in the proteins measured despite protein synthesis differing between the two models. These findings suggest that a humanized media may be a useful tool to study skeletal muscle physiology in vitro.

Keywords: Amino acids
Anabolism
mTOR
Muscle
Nutrition
protein synthesis
Advisor: Moore, Daniel R
Comparative Analysis and Demonstration of Monolithic Integration in High-voltage Gallium Nitride Processes

Gallium Nitride (GaN) power e-HEMT, a popular alternative to Si in high temperature and high voltage power applications, can be monolithically integrated with low-voltage HEMTs, passive components and diodes. Through comparative analysis between the experimental performance of LV circuits, fabricated using ON Semiconductor’s 650-V GaN-on-Si and imec’s 200-V GaN-on-SOI process, and simulated results from their BCD-counterparts, this thesis identifies the types of circuits that are suitable for monolithic GaN integration based on the processed-power and operating frequency of an application. Using the GaN-on-SOI technology, a binary-weighted segmented gate-driver is fabricated with a power-HEMT, controlling the HEMT’s voltage slew-rate and overshoot. The power-HEMT has embedded current and temperature sensing structures. A monolithic high-voltage floating level-shifter and a programmable deadtime generation circuit, as building blocks to a GaN half-bridge IC controlled using a single low-side gating signal, are built and tested.

Keywords: Gallium Nitride
gate-driver
HEMT
PMIC
power converter
power electronics
Advisor: Trescases, Olivier
Size Characterization of Biofiltration-related N-nitrosodimethylamine (NDMA) Precursors

Previous studies have reported variable removals or even contributions of N-nitrosodimethylamine (NDMA) precursors during biofiltration. To better understand the source of these biofiltration-related NDMA precursors, it is imperative to quantify their state (i.e., dissolved or particulate). This study characterized biofiltration-related NDMA precursors according to their size as well as quantified their removal by examining them in backwash remnant water. Biofiltration-related particulate precursors were the primary contributor (43-64%) to the total NDMA precursor level in the influent, while dissolved precursors were the dominant size fraction (56-83%) in the effluent. Although near-complete removal (80-91%) of particulate precursors was observed during filter ripening, dissolved precursors were removed to a lesser extent (22-31%), indicating their greater potential for a breakthrough. In the event of a breakthrough of dissolved NDMA precursors, turbidity may not be an effective parameter to evaluate backwash performance.

Keywords: Backwash
Biofiltration
Dissolved NDMA precursors
Filter ripening
N-nitrosodimethylamine (NDMA)
Particulate NDMA precursors
Advisor: Andrews, Robert C
Andrews, Susan A
Designing a Synthetic Biology Modulator using Structural Mimicry of Homeodomain-zipper Proteins

In synthetic biology, an organism’s genome can be re-engineered to produce substances outside of its natural capabilities. This is achieved by incorporating exogenous DNA circuitries into the host. We designed a minimalist “franken-protein” termed HinZip that binds to a unique DNA sequence comprising two 12 base-pair half-sites. HinZip combines motifs from eukaryotic and prokaryotic proteins to structurally mimic homeodomain-zipper (HD-Zip) proteins, which is a transcription factor family observed only in plants. HinZip has shown good binding affinity and DNA sequence specificity in vivo. These results provide a promising start to designing synthetic biology circuitries controlled by HinZip.

Keywords: Biology
DNA-binding
Modulator
Synthetic
Advisor: Shin, Jumi JAS
Field Trips From Home: Exploring how Online Museum-based Learning can Help International Graduate Students Meet their Language Goals in the Time of COVID-19

Museums are known as exemplary sites of informal learning and more recently are understood to foster positive social outcomes for visitors, like reduced social isolation and improved wellbeing. As museums and university campuses are closed due to COVID-19 provincial lockdown measures, this thesis asks: how might online museum-based learning support international graduate students in their language learning goals, at a time of physical and social isolation? Using a grounded theory approach, I draw on existing literature on museum-based learning and social outcomes, and bring informal learning theories to bear on the online museum experience. The interviews and group discussions with eight participants revealed that online museum experiences supported formal language improvement, self-reflection and enjoyment, but fell short of supporting informal language practice. The research identifies that a critical pedagogical approach to the development of online museum programs could more robustly meet the needs of international students and language learners alike.

Keywords: Informal learning
Language learning
Museum-based learning
Online museum
Social isolation
Virtual exhibits
Advisor: Sumner, Dr. Jennifer
Semantic Processing in Children with ASD: Differences in underlying Neural Processing in Children with High Language vs. Low Language Capabilities

The primary objective was to investigate semantic neural processing in children with autism spectrum disorder (ASD) as impairments in this domain have been shown in this patient population. Typically developing (TD) children and children with ASD with varying language ability did an auditory semantic categorization task. Only children with ASD with low language ability had semantic neural processing deficits, indexed by a late onset and smaller N400 component compared to TD children when the N400 component was evoked, although it was not evoked to all auditory stimuli. There were negligible neural processing differences between children with high language ability and TD children. In children with ASD, the smaller N400 component predicts lower language ability and the smaller N400 component is predicted by deficits in cortical auditory processing indexed by a smaller P1 component. Thus, language deficits in children with ASD are predicted by semantic and cortical auditory processing deficits.

Keywords: auditory
Austim
children
EEG
language
semantics
Advisor: Pang, Elizabeth
Gordon, Karen
Development, Validation, and Implementation of a Clinical Decision Tool for Blood Pressure Management in Patients on Hemodialysis

Hypertension is a strong risk factor for cardiovascular disease and remains uncontrolled in a large proportion of patients on hemodialysis. Management requires a multifactorial approach involving optimization of hemodialysis specific factors and medications. The objective of this study was to develop, validate, and implement a clinical decision tool to help improve blood pressure control for patients on hemodialysis. A clinical decision tool was developed and assessed for face and content validity. The tool was then implemented in a cohort of patients on hemodialysis. Blood pressure control was similar pre and post implementation and without a greater incidence in adverse events compared to the control group. A number of blood pressure related interventions were made including the discontinuation and dose reduction of antihypertensive medications. Implementation of the tool in a larger cohort of patients for an extended time period is required to further assess implications of the tool in clinical practice.

Keywords: Clinical decision tool
Hemodialysis
Hypertension
Advisor: Battistella, Marisa
Aqueous Proton Conducting Polymer Electrolytes as Gate Dielectrics for Organic Field-effect Transistors

The vast majority of solid electrolyte-gated field-effect transistors (EGFETs) use ionic liquid or lithium ion conducting electrolytes. However, other classes of solid electrolytes have seen little attention for use in EGFETs despite their promising properties. In particular, proton conducting polymer electrolytes have great potential due to their high ionic conductivity, specific capacitance, and environmental stability. In this work, strong acid based proton conducting polymer electrolytes comprised of either phosphoric acid (H3PO4) or sulphuric acid (H2SO4) in a polyvinyl alcohol (PVA) polymer host were investigated as potential gate dielectrics. The resulting proton conducting polymer electrolyte gated EGFET devices exhibited promising performance with sub 1 V operation, a high ON/OFF ratio >105 and a low subthreshold swing of 90 mV/decade, which demonstrates the viability of using proton conducting polymer electrolytes as gate dielectrics in organic thin-film transistors (OTFTs).

Keywords: organic thin film transistor
phosphoric acid
polymer electrolyte
Printed electronics
proton conducting
transistor
Advisor: Lian, Keryn
Chu, Ta-Ya
Embodied Energy and Reaction Calorimetry of Boron Subphthalocyanine Derivatives

This thesis is a culmination of my work in advancing the fields around boron subphthalocyanine materials and their applications. First, it details the methods and results from modelling the embodied energy of chloro-boron subphthalocyanine using an established baseline reaction. It then analyzes the opportunity to reduce the embodied energy through process and solvent modifications by swapping from 1,2-dichlorobenzene to 2,4-dichlorotoluene (2513 MJ/kg versus 64 MJ/kg, respectively). Second, this thesis provides calorimetry results for a variety of bromo- and chloro-boron subphthalocyanine reactions. An alternative method for chloro-boron subphthalocyanine was proposed and tested that incorporated scale-up design principles. These pathways were assessed on their applicability for scale-up based on the measured reaction enthalpy and criticality classes. The work compiled in this thesis serves to highlight the positive aspects of boron subphthalocyanines from an environmental viewpoint through embodied energy modelling and provides strong evidence for their near-term ability for scale-up to commercial reaction sizes.

Keywords: boron subphthalocyanine
embodied energy
reaction calorimetry
Advisor: Bender, Timothy P
Modelling and Experimental Validation of a Sponge Filter in a Column System

Oil spills can damage the marine environment, local populations, and impact tourism. By adding an in-situ filtration step to the existing skimming process, it is possible to improve the oil spill response times dramatically. This thesis examines surface engineered sponges implemented in a flow through column configuration as a potential filtration technology for this application. A lab scale column system is developed to investigate the impact of temperature, flow rate, and emulsion concentration on the oil adsorption. The results of the experiments are used to develop a computational fluid dynamics model. Results show that the column system can achieve a maximum adsorption of 0.0022 kg/g and adsorption rate of 1.1 g/(kg-s) when run at a flow rate of 300 ml/min. The computational fluid dynamics model shows that the technology can be scaled for skimming vessel operation, increasing utilization by 75% over current practice when implemented in a continuous processing mode.

Keywords: adsorption
applied engineering
column system
computational fluid dynamics
oil spill
porous media
Advisor: Bilton, Amy AB
Decentralized Oracles and Network Economics in Modern Blockchain Systems

As blockchain technology opens up opportunities with the popularization of decentralized applications, many problems are left to address. Firstly, blockchain systems rely on oracles to bridge external information to the decentralized applications. However, many existing oracle designs either express strong dependency on trusted third parties, or limit the query to very specific formats such as a web API. This thesis describes a novel oracle protocol based on the Astraea protocols and a peer-prediction mechanism. The proposed oracle is capable of extracting subjective data truthfully and discouraging Sybil attacks. Secondly, Proof-of-Work blockchains depend on proper economic incentive designs for miners to faithfully maintain the network in a sustainable way. This thesis describes how the economic engineering of the Conflux Network, a high throughput proof-of-work blockchain, leads to sound economic incentives that support desirable and sustainable mining behavior.

Keywords: Blockchain
Blockchain oracle
Advisor: Veneris, Andreas
A High-efficiency Three-level Integrated Boost Converter with a Flying Capacitor for Mobile Application

The Organic Light Emitting Diode (OLED) display in modern smartphones requires a high voltage power supply capable of providing 26 V and a driving current of up to 100 mA. In this thesis, an integrated, highly efficient three-level boost converter is designed to address the above challenges. Comparison with the conventional topology boost converter topology is carried out in detail. This study includes an in-depth analysis on the operation and tradeoffs between device voltage ratings and efficiency. In addition, various unwanted power losses are identified, and the approaches to reduce them are applied in both topologies. The proposed three-level integrated boost converter has a peak efficiency of 81%. A 2 to 8% efficiency improvement over the conventional boost converter topology across a wide range of load currents is achieved. The three-level boost converter topology is also designed in an integrated form for the first time.

Advisor: Ng, Wai Tung
From Bathtubs to Bloodfeeders: An Evolutionary Study of the Aphaproteobacterial Gellertiella (formerly Ca. Reichenowia)

Many leeches are blood feeders and host bacteria within specialized organs. One example is Placobdella which hosts the alpha-proteobacterial Candidatus Reichenowia. It is assumed that Reichenowia provisions Placobdella with B vitamins. Although Reichenowia consistently places within Rhizobiaceae, its free-living relative remains a mystery. By obtaining genome sequences of the endosymbiotic bacteria of six species of Placobdella, I address questions regarding the role of Reichenowia and its origin. B vitamin synthesis pathways remain largely intact across all taxa with many gaps likely representing a lack of knowledge concerning alternate synthesis routes. I find robust and consistent support for the nesting of the free-living Gellertiella hungarica within Reichenowia, necessitating the dissolution of Reichenowia. The topology of this clade suggests two independent origins of endosymbiosis from a G. hungarica-like ancestor. These findings clarify the ecology of the system and point towards a potentially novel model system for investigating the early stages of endosymbiosis.

Keywords: B vitamin synthesis
Endosymbiosis
Leech
Metabolic pathways
Nutrient provisioning
Phylogenomics
Advisor: Kvist, Sebastian
Manzano Marín, Alejandro
Race and Contemporary (Post)feminism: Expanding Theory and Feminist Practice in Gender-based Violence Media Activism

This study focuses on recent public calls for a sex strike made by actress and activist Alyssa Milano and other contemporary resistance strategies by public female figures like Me Too founder Tarana Burke and executive producer of Surviving R. Kelly dream hampton. This study explores how race, class and access to the public sphere shape contemporary counter violence in the United States and Global North. This study uses a variety of published, publicly-accessible documents including interviews, social media posts and articles to qualitatively analyze the racial and class politics of contemporary counter violence strategies. Employing a conceptual framework grounded in intersectional feminist theory and existing literature regarding gendered and sexual violence, this study conveys the limitations of contemporary (post)feminist and white celebrity pop cultural counter violence media activism. This study contextualizes the politics of violence beyond a gender-only lens to expand feminist theory and practice within contemporary counter violence activism.

Keywords: counter violence
feminist resistance
gendered violence
intersectionality
media activism
postfeminism
Advisor: Todorova, Miglena
Improving the Performance of Membrane Electrode Assembly CO2 Electrolyzers

Detrimental ohmic and mass transport overvoltages experienced by the membrane electrode assembly (MEA) CO2 electrolyzer pose critical barriers to the transition from lab scale to large scale operation. The operating temperature was found to be a critical parameter for improving the performance as the power density was reduced by up to 35 % when increasing the temperature from 25 °C to 60 °C. At low current densities, increasing temperature also led to a 7 fold reduction in ohmic resistance. At higher current densities, overvoltages were dominated by distinct mass transport limitations at the gas diffusion electrodes. Additionally, a high current density of 755 mA/cm2 was reached by fully humidifying the reactant CO2. The power density was reduced by up to 30 % as a result of a 4-fold decrease in ohmic losses. The findings of this thesis provide valuable insights for achieving higher current densities at low cell voltages for CO2 electrolyzers.

Keywords: Carbon dioxide electrolyzer
Membrane electrode assembly
Neutron imaging
Overvoltages
Synchrotron X-ray imaging
Advisor: Bazylak, Aimy
Chondrocyte Migration from Bioengineered Cartilage

Platelet-rich plasma (PRP) treatment enhances the integration of bioengineered cartilage to host cartilage, which involves cell migration into host cartilage. This study hypothesizes that PRP treatment of bioengineered cartilage supports chondrocyte migration and matrix accumulation by these cells in an in vitro 3D co-culture model. Osteochondral-like constructs were developed by culturing primary bovine or passaged human chondrocytes on a bone substitute which were then soaked in PRP and placed in co-culture with native osteochondral plugs. Controls were not pretreated with PRP. Cells from bovine and human bioengineered cartilage migrated onto fibre networks formed by PRP. However, only the bovine cells had the ability to form hyaline cartilage-like tissue, but this required cell migration from the bone. Cells did not migrate out from the human osteochondral plugs. This thesis demonstrates that cartilage implant integration is likely a complex process. This model system can be used to facilitate future investigations.

Keywords: Articular Cartilage
Cartilage Integration
Cell Migration
Chondrocyte
Platelet-Rich Plasma
Tissue Engineering
Advisor: Kandel, Rita
Investigating the Role of Crumbs in Tissue Growth Regulation of Drosophila Imaginal Wing Discs

Crumbs (Crb) is an apical determinant which also causes neoplastic overgrowth when overexpressed in imaginal disc epithelia. My work shows that both the conserved binding sites within the Crb cytoplasmic tail, the FDB and PDB, contribute to the Crb-induced neoplastic phenotype. Downstream of Crb overexpression, the JAK/STAT proliferative pathway, and excessive division in general are required for mediating not only the excess tissue growth but also the loss of epithelial integrity, a key feature of the neoplastic phenotype. Finally, my work uncovered a novel role of Crb overexpression levels in eliciting distinct JNK signaling responses. Moderate Crb overexpression levels caused JNK-dependent overproliferation as was anticipated based on previous findings. In contrast, high levels of Crb overexpression had JNK-dependent pro-apoptotic activity. These findings reveal Crb as a unique tumour oncogene among polarity factors, and open avenues for further investigations into Crb ability to direct downstream proliferative or apoptotic responses.

Advisor: Tepass, Ulrich