VictorJuiz/thesis huggingface dataset:
Inhibition and enhancement of quantized, interference-driven, ultrafast-laser cleaving and intra-film ejection with angle and polarization control
Keywords: Femtosecond Laser
laser processing
micro-topographies
nano-structured
surface structuring
Thin-film

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.
Discovery and Biochemical Characterization of New CAZymes from PULs and Metagenome Sequences
Keywords: acetylation
glucuronic acid
metagenomes
polysaccharide utilization loci
protein characterization
xylan

(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.
From Smuggling to Social reproduction: Migration and Livelihood Strategies of Young Somali Men in Toronto, Canada
Keywords: Citizenship
Intersectionality
Migration Studies
Somali Studies

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.
The Development Of A Novel Chimeric Antigen Receptor Specific For Syndecan-1
Keywords: Cancer
Gene Therapy
Immunotherapy

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.
Yeast Genetic Modeling of Pbp1/ATXN2-linked Neurodegenerative Diseases
Keywords: ALS
ATXN2
rDNA Repeats
Replicative Lifespan
SCA2

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.
Two Novel Photoactivatable Phosphodiesterases to Independently Hydrolyze cAMP and cGMP
Keywords: cAMP
cGMP
Optogenetics
Phosphodiesterases
Synapse
Two-Photon Microscopy

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.
High Throughput Screening of Kinase Inhibitor Drugs on Cardiac Function using Engineered Heart Tissue Constructs
Keywords: Engineered cardiac tissue
Kinase inhibitors
Pre-clinical drug screening

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.
Investigating the Effectiveness of Android Privacy Policies
Keywords: accuracy
Android
policy
privacy
template
understandabilty

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.
Using Compartmentalization to Mitigate the Impacts of Stack Effect in Tall Residential Buildings
Keywords: Compartmentalization
Computer Simulation
Stack Effect
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.
Temporal Patterns in Biomass Size Spectra in the Upper Bay of Quinte, Lake Ontario
Keywords: aquatic ecology
Bay of Quinte
fisheries
size spectra

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.
"Never Had I Known Such Sorrow": Death and Emotional Standards in Heian Japan
Keywords: Emotion
Heian
Japan
Sadness

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.
Metallization and Characterization of Nanocrystalline Nickel Coated Jetted Photopolymer Structures
Keywords: electrodeposition
hybrid materials
jetted photopolymer
metallization

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.
Evaluating the accumulation of dual-modal indocyanine green-containing liposomes in pre-clinical models for visualizing human lung cancer
Keywords: ICG
lung cancer
nanoparticles
NIR contrast agent
pre-clinical model

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.
Investigating the Influence of D4 Receptor Modulation on Alcohol Addiction-Relevant Behaviours
Keywords: Alcohol
D4 Receptor
Dopamine

The recent development of selective dopamine D4 receptor ligands has made it possible to further examine their effects on addiction-relevant behaviours. This study investigated the effects of D4 receptor modulation, using the selective antagonist L-745,870 and agonist PD 168,077, on alcohol self-administration and reinstatement induced either by cue or stress. Although activation of the D4 receptor was ineffective, inactivation attenuated alcohol self-administration without affecting food self-administration. Initial analyses of reinstatement experiments found no significant effects, but by distilling for robust responders, alcohol-seeking was reduced by D4 receptor inactivation under stress-induced reinstatement. The culmination of this work deepens existing lines of evidence that the D4 receptor is involved in addictive disorders, and suggests that D4 receptor blockade diminishes motivation for alcohol-taking without influencing natural food rewards. Furthermore, there appears to be a plausible effect of D4 receptor blockade interfering with stress- but not cue-induced alcohol-seeking.
Shared Enemies and the Competitive Ability of Native Plants in Populations of an Invasive Plant (Cirsium arvense)
Keywords: Cirsium
community
invasion
microbe
plant
soil

Shared enemies commonly mediate interactions between plant species. Here, I investigated how two guilds of enemies can indirectly affect native plant communities through interactions with an invading plant, Cirsium arvense (Canada thistle). First, I assessed how soil microbes in invaded areas can limit the establishment of native plant species. Microbes from invaded soils reduced germination or growth for three of the eight native plant species surveyed, but did not affect Cirsium, which suggests that soil microbial interactions may benefit Cirsium, potentially facilitating its invasion. Second, I assessed the influence of Cirsium invasion on damage by aboveground insect enemies. Based on plants' association with Cirsium, I observed inconsistent and very minor patterns in insect damage, which suggests that other ecosystem factors influence damaging insects more strongly than Cirsium invasion. Together, these results indicate that soil microbial enemies, but not aboveground insect enemies, may be influential in the invasion of Cirsium arvense.
Multiple Mutualist Effects in an Ant-Plant-Bacteria System
Keywords: Ants
Ecology
Legume
Multiple Mutualist Effects
Mutualism
Rhizobia

Plants simultaneously partake in multiple mutualisms, and partner species that share a focal host are capable of indirectly affecting one another, potentially affecting the outcome of mutualisms. Context-dependence is thought to largely determine the nature of these multiple mutualist effects as well as focal host resource allocation in each partner. We factorially manipulated the ant "bodyguards" and nitrogen-fixing rhizobia that associate with the legume Chamaecrista fasiculata in a field experiment to determine how each mutualistic partner affected the other. Rhizobia treatment impacted the identity and abundance of ants. Both rhizobia treatment and ant treatment impacted plant survival. Additionally, ant and rhizobia treatment affected the weight of nodules housing rhizobia, but in a way that depended on plant size. Our results show that belowground mutualists can influence plant interactions with aboveground mutualists, and vice versa. This study highlights the importance of incorporating multiple mutualist effects in to our understanding of mutualisms.
Towards Practical Driver Cognitive Workload Monitoring via Electroencephalography
Keywords: Cognitive Workload
Driving
eDREAM
EEG
Machine Learning
nBack

Monitoring of Driver Cognitive Workload is an active area of research and has gained traction in recent years. This study pertains towards the development of an Automated Driver Cognitive Workload Prediction System using the Electroencephalography modality. In this experiment, the driver cognitive workload has been modelled using a secondary n-back task. This study aims to answer the question if a consumer-grade 2-channel EEG modality can be used to discriminate between the granular cognitive workloads induced on the driver as it is measured by the n-back test. Statistical Learning Models are generated while taking into account the practical data-partitioning schemes as would be feasible in real world implementation. It is found that individual Beta and Gamma bands provide good discriminating performance while using a combined set of 32-features provides the best overall performance. Non-Linear Classifiers outperform the linear classifiers and dimensionality reduction techniques assist in producing practical prediction models.
Hepatocyte Growth Factor-Preconditioned Neural Progenitor Cells Attenuate Astrocyte Reactivity and Promote Neurite Outgrowth
Keywords: central nervous system injury
glial scar
hepatocyte growth factor
neural progenitor cells
reactive astrocytes
regeneration

The astroglial scar is a defining hallmark of secondary pathology following central nervous system (CNS) injury that significantly obstructs neuroregeneration. Neural progenitor cell (NPC) therapies for repair and regeneration have demonstrated favourable outcomes not only via cell replacement, but trophic support. In an effort to strategically enhance this secretory potential, we utilized the regenerative aptitude of hepatocyte growth factor (HGF) as a cellular preconditioning agent and assessed the capacity of modified secretome to attenuate astrocyte reactivity in vitro. HGF-preconditioned NPCs demonstrated increased levels of tissue inhibitor of metalloproteinases-1 and reduced vascular endothelial growth factor compared to untreated NPCs. In reactive astrocytes, HGF-enhanced NPC secretome reduced glial fibrillary acidic protein expression and chondroitin sulfate proteoglycan deposition to a greater extent than either treatment alone, and enhanced neurite outgrowth of co-cultured neurons. These findings have important translational implications for modification of the post-injury milieu and optimization of cell-based strategies for CNS injury.
Investigating the Role of Glycogen Synthase Kinase-3 (GSK-3) in Pathological Progression of Alzheimer’s Disease
Keywords: Alzheimer's Disease
CRND8
Dementia
Morris Water Maze

Alzheimer’s Disease (AD) is characterized by development of beta amyloid (Aβ) plaques and hyper-phosphorylation of tau in the brain. Glycogen Synthase Kinase-3 (GSK-3) dysregulation has been highlighted as a potential contributor to the onset of disease, and is therefore being investigated as a new therapeutic to ameliorate pathological progression of AD. This research focuses on the GSK-3α isoform and its involvement in Aβ plaque formation and hyper-phosphorylation of tau in mouse models of disease. This research confirms the presence of soluble Aβ in mouse models of AD. Soluble Aβ is accompanied by behavioral deficits. Insoluble Aβ plaques are not abundant, suggesting that soluble Aβ is the culprit in the behavioral deficits. Tau hyper-phosphorylation is present in mouse models of frontotemporal dementia (FTD). Most of these insults are rescued upon partial or full deletion of GSK-3α suggesting that GSK-3α deletion is protective against AD onset.