VictorJuiz/thesis huggingface dataset:
A Tellurium-Based Probe for Monitoring the Rates of Protein Synthesis

The ability to monitor rates of protein synthesis is important in understanding protein equilibrium and perturbations induced by disease and experimental conditions. Insight into the rates of protein synthesis will report on the tightly-regulated proteome, rendering a physiopathological snapshot of cells and tissues. As such, there exists many tools for studying the rates of protein synthesis. Despite the wide range of current probes on the market, these probes are faced with many limitations. To overcome the challenges that limit the current methods for monitoring the rates of protein synthesis, we describe the development of a phenylalanine analogue containing the heavy metal isotope tellurium that is amenable to mass cytometry. We show that it is successfully taken up by Jurkat cells and incorporated into proteins, thereby highlighting the potential of this tool as protein synthesis probe.

Keywords: Mass cytometry
Protein synthesis
Tellurium
Advisor: Nitz, Mark
Power Minimization in Wireless Network Virtualization with Massive MIMO

This thesis aims to study wireless network virtualization and particularly its challenges when it is applied to massive MIMO technology. Virtualization has been well studied in the wired networks and computational resources. However, when it comes to wireless networks new challenges arise. We consider virtualization in the context of massive MIMO technology and develop a novel precoding schemes to abstract and share a massive MIMO base station with the objective of minimizing power. This problem is investigated when perfect channel information is available and when is not. Furthermore, we show that our formulation is general enough to be easily extended to multi-cell and address some concerns of the service provider. We obtain optimal precoding when perfect channel information is available and a nearly optimal solution when the channel information is corrupted.

Keywords: Massive MIMO
Precoding
Virtualization
Wireless networks
Advisor: Liang, Ben
Modelling and Energy Management for DC Microgrid Systems

Greenhouse Gas (GHG) emissions and climate change has generated a need for renew able energy sources. DC microgrids require less complex power conversion and commu nication equipment, making it a promising candidate for renewable energy integration. This thesis investigates modelling techniques to demonstrate modularity and scalabil ity of DC microgrid systems. SpeciďŹ cally, a ďŹ exible state-space modelling technique is developed to accurately represent a complete DC microgrid system to investigate the eďŹ ects additional energy storage media and generation sources have on stability. An autonomous energy management scheme is proposed to further DC microgrid robustness and reliability. The goal of the thesis is to further prove that DC microgrids can operate as an alternative to the traditional AC grid infrastructure.

Keywords: DC
Energy Management
Microgrid
Modelling
Power Scalability
Advisor: Lehn, Peter W
Inhibition and enhancement of quantized, interference-driven, ultrafast-laser cleaving and intra-film ejection with angle and polarization control

Optical interference and ultra-fast laser interaction within micro-scale transparent films offer a novel means for nonlinear confinement of dissipated energy to facilitate high resolution three-dimensional (3D) nanostructuring. Recently, study of thin-film interference has allowed the formation of thin (~40 nm) nanoscale plasma disks stacked on half wavelength spacing, 位/2nfilm (film refractive index, nfilm ) in dielectric media. This thesis presents angle and polarization control as methods to manipulate the fringe visibility of 1 碌m thick SiOx thin-films on silicon substrates, also exploring the coherence of film interference effects in tight focusing through modelling of Gaussian beam effects. In doing so, an enhancement or diminishment of the quantized intra-film processing has been definitively demonstrated according to s- and p-polarization states, respectively, opening viable quantized intra-film structuring to previously unsuitable low-contrast thin-film systems. The resulting novel 3D topographies and intra-film stacked micro- and nano-cavity formation represents significant advancement of this field.

Keywords: Femtosecond Laser
laser processing
micro-topographies
nano-structured
surface structuring
Thin-film
Advisor: Herman, Peter R
Discovery and Biochemical Characterization of New CAZymes from PULs and Metagenome Sequences

(methyl)-Glucuronoxylan, a main hemicellulose in hardwood trees, has a broad range of potential applications, ranging from biofuels to bio-based coatings and packaging films. It is substituted with (methyl)glucuronic ((Me)GlcpA) and acetic acids, which affect polymer solubility, rheology, interaction with other polymers, and accessibility of the polymer to enzymes. To date, there are no known esterases that are able to deacetylate internal xylose residues that are both 3-O-acetylated and 2-O substituted with (Me)GlcpA (Xyl-3-Ac-2MeGlcpA). In this study a protein of unknown function, which was named FjoAcXE, was produced and characterized to be an acetyl xylan esterase capable of deacetylating xylose residues at all positions, including Xyl-3-Ac-2MeGlcpA. Additionally, FjoAcXE was shown to display synergism with α-glucuronidases from glycoside hydrolase (GH) 67 and GH115 families. Synergistic action between FjoAcXE with α-glucuronidases was further tested with three recombinantly produced α-glucuronidases from metagenomic sequences of the Canadian beaver (Castor Canadensis) droppings enriched on poplar hydrolysate.

Keywords: acetylation
glucuronic acid
metagenomes
polysaccharide utilization loci
protein characterization
xylan
Advisor: Master, Emma
From Smuggling to Social reproduction: Migration and Livelihood Strategies of Young Somali Men in Toronto, Canada

This research paper traces the methods, modes and networks that young Somali men between the ages of 25-30 have used in order to migrate, gain entry and seek asylum in Toronto, Canada from Somalia. This thesis goes further to analyze the ways in which this group of young men seek to carve out a livelihood once they arrive in Canada. Using in depth interviews with a group of 9 young men in the Toronto area, I explore how legal status, statelessness, race and gender norms, clan affiliations and masculine kinship obligations intersect to produce a particular migratory and settlement experience for these young men. Furthermore, I suggest that these networks do not just structure the migration experience for this group of young men but they play an important role in shaping these men’s access to work and ability to survive once they arrive in Canada.

Keywords: Citizenship
Intersectionality
Migration Studies
Somali Studies
Advisor: Buckley, Michelle
The Temporal Expression Patterns of CREB Governing Long-Term Memory Formation

The cyclic adenosine monophosphate (cAMP)-response element binding protein (CREB) is a nodal transcription factor that has been hypothesized to be a molecular switch governing the formation of long-term memories in the mammalian brain. The present thesis takes advantage of a novel optogenetic regulator of CREB, applying it for the first time in an in vivo system, to present the first evidence showing that a temporally-restricted elevation in CREB function, in a small proportion of neurons in the lateral amygdala (LA), is sufficient to enhance the formation of long-term memories in a living mouse. Specifically, a restricted spike in CREB function in a small proportion of LA neurons one hour before learning is sufficient to enhance the encoding of an auditory fear memory. These results, in combination with the existing literature, suggest that the timing of variations in endogenous CREB function govern the formation or forgetting of long-term memories.

Advisor: Josselyn, Sheena A
RNA Interference Pathways In Shiga toxin-treated Human Endothelial Cells

Shiga toxins (Stxs) are a family of bacterial-derived protein exotoxins, implicated in the pathogenesis of Hemolytic Uremic Syndrome (HUS). Stxs have profound effects on endothelial cell (EC) gene expression. These effects include increase in the mRNA stability and translational efficiency of select mRNAs (e.g. CXCR4/SDF-1, ET-1). Here we examined whether Stx has a global effect on post-transcriptional gene regulation in ECs via RNA interference (RNAi) pathways. Microarray analysis revealed changes in microRNA expression due to Stx, most of which were downregulated. Accordingly, we observed reduction in Dicer and Drosha, key enzymes in microRNA biogenesis. In silico analysis revealed that many of the down-regulated microRNAs target ATF3, which is highly induced by Stx. Consistent with this data, We find that Stx induction of ATF3 protein and mRNA expression is associated with an increase in ATF3 mRNA stability. These data identify an important role for Dicer and microRNA biogenesis in Stx-mediated HUS.

Advisor: Marsden, Philip A
The Development Of A Novel Chimeric Antigen Receptor Specific For Syndecan-1

The adoptive transfer of T lymphocytes expressing chimeric antigen receptors (CARs) has become a promising treatment for various cancers. CARs have been shown to redirect the cytotoxicity of T lymphocytes towards cancerous cells independent of the interactions between T cell receptors and major histocompatibility complexes. Given that CARs tie together an extracellular recognition domain with intracellular signaling domains of immune cells, there exists flexibility in designing CARs specific for different antigens in order to target different malignancies. Here, we established murine antibodies specific for CD138 with the goal of designing a novel CAR. We designed a 2nd generation CAR using a single chain variable fragment derived from the 3E9B6 monoclonal antibody as the extracellular recognition domain. The expression of the 3E9B6 HL CAR specifically enhanced the cytotoxicity of the NK-92 cell line against CD138+ cells. Downstream activation of ZAP70 in NK-92 3E9B6 HL CAR cells was also dependent on the presence of CD138+ target cells. This work shows that the 3E9B6 HL CAR is functionally able to recognize CD138 and to initiate the CD3Îś activation pathway.

Keywords: Cancer
Gene Therapy
Immunotherapy
Advisor: Medin, Jeffrey A
Yeast Genetic Modeling of Pbp1/ATXN2-linked Neurodegenerative Diseases

The polyglutamine expansion of the human gene ATXN2 is associated with neurodegenerative diseases including Amyotrophic Lateral Sclerosis (ALS) and Spinocerebellar Ataxia type 2 (SCA2). Work in our lab demonstrated that deletion of the Saccharomyces cerevisiae ATXN2 orthologue Pbp1 results in the accumulation of RNA-DNA hybrids. Here I demonstrate that hybrid accumulation in pbp1Î cells triggers aberrant recombination within the ribosomal DNA (rDNA) repeats and shortening of replicative lifespan. These deleterious phenotypes can be rescued by caloric restriction. To better model disease I created a yeast genetic model of human ATXN2-linked diseases by generating cells expressing polyglutamine-expanded Pbp1. These cells also had shorter replicative lifespan. However, hybrid accumulation or aberrant recombination within the rDNA repeats was unaffected. Instead, these strains demonstrate gross chromosomal rearrangement more substantial than those observed in pbp1Î cells suggesting that replicative lifespan is impacted by distinctive mechanisms in strains lacking Pbp1 or expressing polyglutamine-expanded Pbp1.

Keywords: ALS
ATXN2
rDNA Repeats
Replicative Lifespan
SCA2
Advisor: Mekhail, Karim
Two Novel Photoactivatable Phosphodiesterases to Independently Hydrolyze cAMP and cGMP

cAMP and cGMP are universal second messengers and have been implicated in synaptic plasticity underlying learning and memory. Pharmacological and genetic manipulations highlight the role of postsynaptic cAMP/cGMP in synaptic plasticity; however these techniques alone lack the precision to understand their rapid and dynamic spatiotemporal roles. To non-invasively control the rapid molecular activity in living neurons, I developed genetically engineered photoactivatable PDE4 (PhPDE4) and PDE5 (PhPDE5) to independently degrade cAMP/cGMP by light. To optimize their light-dependent activities, I validated their single-photon and two-photon photoactive properties in vitro. These enzymes showed substrate specificity and rapid millisecond level photoactivation. For in vivo application, I demonstrated the suppression effect of cAMP in synapse structural plasticity by two-photon photoactivation of PhPDE4. In combination with bacterial photoactivatable enzymes (PAC, BLGC) to enhance cAMP/cGMP signaling, these novel light sensitive enzymes will enable us to understand the rapid spatiotemporal role of cAMP/cGMP in synaptic plasticity and brain function.

Keywords: cAMP
cGMP
Optogenetics
Phosphodiesterases
Synapse
Two-Photon Microscopy
Advisor: Okamoto, Kenichi
High Throughput Screening of Kinase Inhibitor Drugs on Cardiac Function using Engineered Heart Tissue Constructs

Protein kinase inhibitors (KIs) are used as highly specific cancer targeting agents for their ability to prevent kinase molecules from activating signalling pathways that regulate cellular behaviour, however they have recently been linked to toxicities on the heart that were not detected during clinical trials. We hypothesize that a high-throughput, high-fidelity screening platform for evaluating the physiological effects of KIs on human myocardium could be established using high-content screening assays on hiPSC-derived cardiomyocytes (hiPSC-CM), and engineered heart tissue constructs termed BiowiresTM. 80 KIs were screened using high-content screening assays and artificial neural network modelling, and the least detrimental inhibitor on cardiac function was examined on the Biowire. 3D Biowire tissues were less sensitive to functional improvements and detrimental effects on viability of KIs compared to 2D monolayer cultures. In conclusion, we propose a system linking high throughput screening with empirical modelling to observe the effects of KIs on cardiac tissue.

Keywords: Engineered cardiac tissue
Kinase inhibitors
Pre-clinical drug screening
Advisor: Radisic, Milica
Investigating the Effectiveness of Android Privacy Policies

Smartphones are nowadays an indispensable tool for people around the world. Privacy issues, however, arise along with the increasing capabilities equipped on smartphones. Privacy policies are the main mechanism through which users are informed about data practices performed by smartphone applications. In this thesis, we investigate the effectiveness of privacy policies of Android applications through a series of three studies on policy accuracy, policy understandability, and policy template usage. In our study, almost 60% of apps provided inaccurate policies describing data collection. We found the majority of Android privacy policies likely difficult to read for 26% of the US population. Furthermore, we estimate that 25% of app developers use policy template services to generate pre-written policy text, and most of such services offer poor coverage for Android-related data practices, contributing to policy inaccuracy.

Keywords: accuracy
Android
policy
privacy
template
understandabilty
Advisor: Lie, David
Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings

Natural stack action affects all types of buildings, but it becomes a significant driving force and imposes adverse impacts on tall buildings. Traditional approaches such as corridor pressurization system, revolving doors, and airtight exterior envelope to mitigate stack-action induced problems may not be effective for tall residential buildings; hence, an alternative mitigation strategy is required. Compartmentalization is one potential solution which can be used to effectively control stack induced pressures and airflows. However, there exists little information in the academic literature about the effectiveness of using compartmentalization. This thesis begins by looking at the difficulties faced when assessing the effectiveness of compartmentalization. Then, using computer simulation, a quantitative analysis on the potential improvement resulting from implementing compartmentalization is presented. The simulation results showed that compartmentalization is an effective means of controlling contamination air movements, improving building serviceability, providing sufficient ventilation, and reducing the total energy consumption related to conditioning air.

Keywords: Compartmentalization
Computer Simulation
Stack Effect
Tall Residential Buildings
Advisor: McCabe, Brenda
Pressnail, Kim
Temporal Patterns in Biomass Size Spectra in the Upper Bay of Quinte, Lake Ontario

Aquatic ecosystems are sensitive to environmental changes on long-term and seasonal scales. Normalized biomass size spectra (NBSS) are often used to quantify changes in these communities. In this study, I used data on plankton and fishes from the Upper Bay of Quinte, Lake Ontario spanning over forty years to construct NBSS. I hypothesized that NBSS heights (indicator of overall biomass) and slopes (indicator of trophic energy transfer) would vary in response to significant environmental change in the Bay (Pre-phosphorus control, Post-phosphorus control, and Post-Dreissenid mussel periods), and that they would also vary seasonally. Linear mixed effects models indicated that community heights and slopes changed across seasons, but only heights changed across periods. NBSS for phytoplankton, zooplankton, and fishes showed differing responses to seasonal and periodical changes. Overall, NBSS were able to detect community changes across seasons and periods, and I recommend the continued use of NBSS for aquatic ecosystem assessments.

Keywords: aquatic ecology
Bay of Quinte
fisheries
size spectra
Advisor: de Kerckhove, Dak T.
Chu, Cindy
Quantification and Characterization of Coated Materials on Refractory Black Carbon Particles with a Soot Particle – Aerosol Mass Spectrometer

The Soot Particle – Aerosol Mass Spectrometer (SP-AMS) is a valuable instrument for the study of atmospheric aerosol species such as black carbon. Although the addition of a laser vaporizer for the study of black carbon is a step forward, questions remain about the functionality of the laser vaporizer, two of which are probed in this work. In particular, the use of Aerosol Mass Spectrometers (AMSs) for on-line elemental analysis of organic aerosols is a useful method for obtaining the elemental ratios of samples. Use of the laser vaporizer for obtaining elemental ratios comparable to those obtained on the thermal vaporizer is demonstrated. As well, the response of the instrument to black carbon particles has been shown to vary in sensitivity in the SP-AMS when coated with varying amounts of an organic species. This trend and the differences in sensitivity between the laser and thermal vaporizers of the SP-AMS are investigated.

Advisor: Abbatt, Jonathan
"Never Had I Known Such Sorrow": Death and Emotional Standards in Heian Japan

Death is perhaps the only universal human experience, yet emotional reactions to it are neither natural nor universal. Although every person experiences emotions, socially constructed standards shape how an individual conceives, perceives, and expresses a given emotion. As failing to comply with a society’s standards is a serious and damaging social mistake, researching standards of emotion provides an opportunity to bring forward new aspects of complex social relationships. In this thesis, the aristocratic society of Heian Japan (794-1185 CE) is studied from the perspective of emotional history, focusing upon expressions of sadness in response to death as described in nikki, a popular form of literature. After establishing the emotional standards of departures for the purpose of comparison, the thesis moves on to establish the standards for the deaths of loved ones and of the emperor. Compared to other aspects of life, death allowed for far more extreme expressions of sadness.

Keywords: Emotion
Heian
Japan
Sadness
Advisor: Keirstead, Thomas
Metallization and Characterization of Nanocrystalline Nickel Coated Jetted Photopolymer Structures

Nanocrystalline nickel can be electrodeposited on a structurally efficient polymer core to create lightweight load bearing structures. The polymer core is made by jetted photopolymer, a type of additive manufacturing that can produce polymer parts of almost any geometry with a high degree of feature resolution. Electrodeposition has the advantage of being able to coat complex structures in metal since it does not rely on coating apparatus line-of-sight. However, the electrodeposition of nickel on a polymer core is challenging because of surface anisotropy effects and the polymer metallization step. In this study, a technique for coating jetted photopolymer parts with nanocrystalline metal is developed and its complications are explored. Simple polymer parts including rods, tensile coupons, and microtrusses are characterised and mechanically tested to investigate the capabilities of the developed metallizing technique for producing high performance hybrid structures.

Keywords: electrodeposition
hybrid materials
jetted photopolymer
metallization
Advisor: Hibbard, Glenn D
Evaluating the accumulation of dual-modal indocyanine green-containing liposomes in pre-clinical models for visualizing human lung cancer

This thesis explores CF800, a multimodal nanoliposomal contrast agent that co-encapsulates a near infrared agent indocyanine green, and a computed tomography (CT) agent iohexol in pre-clinical human lung cancer models for intraoperative visualization. Pre-clinical models rely heavily on a basement membrane extract, Matrigel, for the localization and formation of orthotopic lung xenografts. Matrigel has been suspected of altering pre-clinical models with a negative affect on the accumulation of nanoparticles. Mice were injected with human lung adenocarcinoma cancer cells with 0%, 50% and 100% Matrigel concentrations. Mice were injected with CF800 after tumor formation and optical images were acquired. CF800 significantly increased the visual fluorescence of the tumors but not CT enhancement. Xenografts with Matrigel exhibited lower fluorescence and CF800 accumulation, although not significantly. The tumor rate of growth and size had a significant effect on nanoparticle accumulation, showing that factors other than Matrigel affect visualization and accumulation of CF800 intraoperatively.

Keywords: ICG
lung cancer
nanoparticles
NIR contrast agent
pre-clinical model
Advisor: Yasufuku, Kazuhiro
The Effect of Viscous and Non-Viscous Fibre Supplementation on Glycemic Control in Individuals with Diabetes Mellitus

This thesis project includes two systematic reviews and meta-analyses (SRMA) of randomized controlled trials (RCTs) to assess the effect of viscous and non-viscous dietary fibre supplementation on glycemic control in individuals with diabetes mellitus. In study one, including 31 trials (n=1428), diets supplemented with viscous fibre isolates significantly lowered HbA1c, fasting glucose and HOMA-IR. In the second study, which included 13 trials (n=545), diets supplemented with non-viscous fibre significantly lowered HbA1c, fasting glucose and fasting insulin. Although both SRMA revealed significant improvements in glycemic control, the effect of viscous fibre supplementation appears to be stronger and with higher quality evidence as assessed by the GRADE tool. Overall, the results suggest that supplementing diet with fibre leads to modest improvement in conventional markers of glycemic control in diabetes mellitus, especially in T2DM. More research is needed to address the limitations of our analyses raised by GRADE.

Advisor: Vuksan, Vladimir