VictorJuiz/thesis huggingface dataset:
Eroticizing Egypt: Voyeurism and Commodification at the Petrie Museum of Egyptian Archaeology

The collecting of “erotic” artifacts in 19th century Egyptology reveals the ways in which museums constructed knowledge around sex and grappled with sexual content in relation to the perceived value of artifacts. By looking at two types of artifacts, those with an overt sexual nature or meaning, and those which have been transformed to have an erotic intention in the context of a museum collection, this thesis explores how the commodification of museum objects impact perceptions and treatment of ancient Egyptian “erotic” material culture. This thesis uses the Petrie Museum of Egyptian Archaeology in London, England as a case study for synthesizing an erotohistoriographic analysis into the biography of an object due to its unique context of colonial intervention, Victorian sexual mores, collecting habits and motivations of its founders, Amelia Edwards and Sir W.M Flinders Petrie, at a moment in Egyptology’s infancy as a “scientific” field. Centering pleasure in the study of erotic artifacts reveals new epistemological potential in both Egyptology and Museology.

Keywords: Colonialism
Commodification
Egyptology
Erotohistoriography
Ethnopornography
Petrie Museum
Advisor: Mihalache, Irina D
Keilty, Patrick
Development of Cell4D, a Spatial Stochastic Cell Simulator, and Applications towards CEACAM1 Pathway Modelling

Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) are known to be involved in biological functions such as metabolism, apoptosis, receptor signaling, and tumorigenesis. However, some mechanisms of CEACAM1 activation are still poorly understood from a systemic point of view, partially due to the complexity of the pathway. Here I present Cell4D, a graphical stochastic spatial cell simulator that I have developed to simulate hypothetical CEACAM1 pathways. Cell4D is more robust and complex than other publicly available meso-scale simulators with similar capabilities. I applied Cell4D to create computational models of CEACAM1 signaling systems and made functional predictions about the system through model perturbations. The simulation models predict that clustering increases the effective concentration of CEACAM1, and these clusters can self-propagate upon reaching a critical concentration threshold. In summary, the aim of this thesis is to further investigate mechanisms of CEACAM1 signalling in the context of T cells through computational modelling.

Keywords: Calmodulin
CEACAM1
Cell4D
Computational modeling
Spatial stochastic simulation
T cell
Advisor: Parkinson, John
Using Micro-ultrasound to Investigate the Effectiveness of Short-term Rehabilitation following Focal Ischemic Stroke

Ischemic stroke leaves 40% of survivors with moderate to severe impairment. Understanding how rehabilitation affects brain structure and function will be critical in its effective application to individual patients and in its combination with promising new interventions. In this work we investigated the impact of two weeks of skilled reaching rehabilitation on motor function, cerebrovascular tortuosity, cerebral blood flow and neuronal activity on a rodent model. Micro-ultrasound, intracerebral array electrophysiology and Montoya staircase testing were used to characterize changes in the brain and motor function following stroke. Perilesional vessels were significantly more tortuous than vessels in the contralesional cortex with a further abolishment of hypercapnia-elicited homogenization of microbubble velocities in perilesional arterioles. Rehabilitation significantly improved skilled reaching and elevated neuronal power ratios. This current project highlights functional motor recovery and neuronal plasticity in the subacute stage following stroke in the absence of cerebrovascular changes using a dual imaging modality setup.

Keywords: Imaging
Rehabilitation
Stroke
Ultrasound
Advisor: Stefanovic, Bojana
Fabrication of Multi-chamber Graphene Liquid Cell and Characterization of Liquid

In this study, a graphene/anodic aluminum oxide (AAO)/graphene liquid cell was fabricated. Five nanometer gold nanoparticles dispersed in trisodium citrate buffer were used as a test system to prove the quality of the liquid cell. The liquid was observed and characterized using a Hitachi HT7700 TEM. A two-stage liquid dynamical process was discovered when the liquid was irradiated by the electron beam, and the first stage is dependent on the amount of liquid. Besides, liquid droplets were observed in the liquid cell which could be explained by the surface effect of AAO membrane and graphene. The sandwiched nanopore liquid cell showed a self-closing effect and a good sealing quality of liquid sample, which would possibly enable a true single particle imaging and reconstruction in the future.

Keywords: anodic aluminum oxide
bubble evolution
graphene liquid cell
liquid droplet
liquid phase TEM
two-stage evolution
Advisor: Howe, Jane
Miller, Dwayne
Who's Zooming Who

This thesis examines playwright Deb Margolin’s (2007) play O Yes I Will (I will remember the spirit and texture of this conversation) and her radical feminist approach of care in contrast to the chance-based operations utilized by surrealists John Cage, Andre Breton and Joseph Cornell. Ten disparate individuals perform selected dialogue through their experiential engagement with Margolin’s play via the application Zoom. Zoom's meta format is compared to surrealist interventions against a dearth of physical human interaction across the SARS-CoV-2's global backdrop of disenfranchisement. Margolin’s work reconsiders chance-based operations, reformulating this methodology into change-based practice, demonstrating how theatrical engagement with a one-woman show through this divergent group of people encourages healing and compassion.

Keywords: Artistic Practices
Covid-19 Pandemic
Radical Feminist Care
Surrealism
Zoom Application
Advisor: Schotzko-Cesare, Nikki
The Impact of Fan-type Rapid Palatal Expanders on Speech in Patients with Unilateral Cleft Lip and Palate

Fan-type rapid palatal expanders (RPEs) can affect tongue movement and speech because of their position and size. The present study investigated the effects on the speech of 25 patients with unilateral cleft lip and palate. Speech questionnaires (patients and parents) and standardized speech recordings (patients) were analyzed prospectively for psychosocial burden, vowel space, fricative articulation, and oral-nasal balance before insertion, after insertion, during expansion, during retention, after removal, and at 3-months follow-up after removal. RPE insertion resulted in an increase in dysfunction and distress, no change for the vowel /a/, an increase in the first formant for the vowel /i/ with a decrease in the second formant for the vowels /i/ and /u/, a decrease in the spectral means for the fricatives /s/, /ʃ/, and /z/, as well as no change in nasalance. All measures returned to baseline levels before removal. Speech was adversely, albeit transiently, affected by an RPE.

Keywords: cleft lip and palate
palatal expander
speech
Advisor: Bressmann, Tim
Stevens, Kyle
Patterns and Predictors of Growth in English Language Learners’ Vocabulary, Word Reading and Non-word Reading Fluency: A Longitudinal Perspective

This study modeled vocabulary, word, and non-word reading fluency trajectories in 260 English Language Learners (ELL) from Mandarin, Cantonese, Portuguese, and Spanish home-language backgrounds from Grades 1-4. Longitudinal relations between early phonological awareness (PA) and rapid automatized naming (RAN) and the growth trajectories of the outcome variables were examined. Multilevel modeling revealed quadratic trajectories for all outcome variables, with differences in growth rates between language groups on vocabulary and word reading fluency, but not for non-word reading fluency. Regardless of home language, those with lower Grade 1 vocabulary and/or word reading fluency caught up to their ELL peers by Grade 4, but those with low non-word reading fluency did not. Grade 1 PA was the best predictor of growth in vocabulary, and Grade 1 RAN was the best predictor of growth in word and non-word reading fluency. Results are discussed in terms of implications for early identification and intervention.

Keywords: ELL
English Language Learner
Non-word Reading Fluency
Vocabulary
Word Reading Fluency
Advisor: Geva, Esther
The Relationship between Homocysteine, Oxidative Stress, and Cognition in Mild Vascular Cognitive Impairment

Homocysteine (Hcy) generates reactive oxygen species and has been associated with cardiovascular disease and impaired cognition. While the relationship between Hcy and cognition has been studied in other disorders, it has not been well characterized in mild vascular cognitive impairment (mVCI), the prodromal stage of vascular dementia. This cross-sectional study investigated the relationship between elevated Hcy, oxidative stress markers, and cognition in this at-risk population. 30 mVCI patients were assessed for cognition, plasma Hcy, and plasma oxidative stress markers. No intergroup difference was observed in executive function or verbal memory. Glutathione-S-transferase (GST), an oxidative stress product modulator, had elevated log transformed activity in the high Hcy group (mean(SD) =-0.11(0.15)) compared to the normal Hcy 0.15(0.24) group (F(1,12)=6.15, p=0.029, partial ƞ2=0.339. While there were non-significant results for primary and secondary hypotheses, findings suggest that elevated Hcy may be related to compensatory increased GST activity in mVCI.

Advisor: Lanctôt, Krista L
High Stiffness Glass Flake Reinforced Composites Produced using Inverted Stereolithography

High aspect ratio glass flakes were introduced as the composite reinforcement in inverted stereolithography (ISLA). Due to flow-induced fiber alignment transverse to the intended loading direction, past attempts to produce high modulus composites by reinforcing the matrix with short fibers failed. Flake reinforced composites, however, reinforce the composite in all directions in the plane. Flake reinforced composites were successfully produced with good planar alignment and exhibited increasing elastic moduli and toughness with increasing flake volume fraction. Despite these promising results, viscosity limited the range of flake loading severely. The tradeoff between flake aspect ratio and the reinforcement efficiency was investigated by grinding flakes. Higher volume fractions of ground flakes were incorporated into the matrix.In summary, the results presented in this work show that adding flakes to the resin in ISLA may create a new path for the production of high performing, stiff composites using 3D printing.

Keywords: Additive Manufacturing
Composites
Glass Flakes
Inverted Stereolithography
Advisor: Kortschot, Mark T
About Explicit Variance Minimization: Training Neural Networks for Medical Imaging with Limited Data Annotations

We proposed the Variance Aware Training (VAT), the novel method of training well-generalized Deep Neural Networks with limited data annotations. Our method requires selecting only one hyper-parameter and matching or improving the performance of state-of-the-art self-supervised methods while achieving an order of magnitude reduction in the GPU training time. We validated VAT on three medical imaging datasets from diverse domains and for various learning objectives and compared VAT with state-of-the-art self-supervised methods. These included a Magnetic Resonance Imaging (MRI) dataset for the heart semantic segmentation (MICCAI 2017 ACDC challenge), fundus photography dataset for ordinary regression of diabetic retinopathy progression (Kaggle 2019 APTOS Blindness Detection challenge), and classification of histopathologic scans of lymph node sections (PatchCamelyon dataset). Our code is available at https://github.com/DmitriiShubin/Variance-Aware-Training.

Keywords: Artificial Neural Nets
Bias-variance Trade-off
Deep Neural Networks
Generalization
Medical Imaging
Advisor: Goodfellow, Sebastian D.
Eytan, Danny
A Kinetic Exploration of the [3+2] Nitrone-Olefin Cycloadditions as a Bioconjugative Tool

Chemical modification of biologically relevant molecules to: improve visualization, modulate the function, or allow for purification is key to chemical biology. Useful bioconjugation reactions specifically couple the desired partners while avoiding off target functionalities. The bonds formed should be stable and the reactions should proceed at rates compatible with physiological concentrations. We describe a biorthogonal reaction cascade reaction which involves the formation of a nitrone followed by trapping with a pendant alkene in a [3+2] cycloaddition. The reaction rate is evaluated under physiological conditions to determine if the reaction meets the requirements of a useful bioconjugation tool. An aldehyde-alkene small molecule binding partner with a UV active analytical handle was synthesized, and its reaction with N-methyl hydroxylamine gave the desired bicyclic isoxazole product. Determination of the kinetic rate constants under physiological conditions through TLC, 1H NMR, and HPLC showed a reaction rate constant of 2.64 M-1 s-1 at pH 7, which is comparable to other known useful bioconjugation reactions.

Advisor: Nitz, Mark
Neurophysiological Features of Working Memory Performance and their Relationships with Demographic, Clinical, Genetic, Neurochemical, and Neuro-structural Characteristics in Older Adults at Risk for Dementia

Theta gamma coupling (TGC) is a neurophysiological mechanism of working memory (WM). However, the relative contributions of TGC and clinical, demographic, and biological characteristics to WM performance, and the relationship between TGC and these characteristics, remains unclear. Older participants at-risk for Alzheimer’s dementia completed N-back-EEG, genetic testing, PET scan and brain MRI. Linear regressions were used to assess the relationships among 2-back WM performance; demographic and clinical variables; TGC; ApoE4 carrier status; β-amyloid SUVR; and regional cortical thickness, subcortical volumes, and white matter fractional anisotropy. Our results demonstrate that TGC and age are strongly associated with 2-back WM performance. Analyses with additional WM features- theta event-related synchronization (ERS) and alpha event-related desynchronization (ERD)- revealed that neither theta ERS nor alpha ERD were associated with WM performance or any other characteristics. Our findings underline the strong association between WM and TGC, which may represent a mechanism of cognitive reserve.

Keywords: Alzheimer's
Cognitive Reserve
EEG
Mild Cognitive Impairment
Theta-gamma coupling
Working Memory
Advisor: Rajji, Tarek K
Automation of Real-time Three-dimensional Image-based Visual Servo Control for Single Cell Surgery

Micromanipulation of biological cells is a challenging task that requires levels of precision and repeatability which are difficult to achieve by most human operators. Automation of these processes presents an alternative approach which is capable of high precision task execution and much higher throughput, yet with its own limitations. In this thesis, we propose automation methods for the image-based visual servo control feedback and tracking of both blastomeres’ motion and the motion of micromanipulators, in real-time, for blastomere micromanipulation. An automation procedure is developed for the microinjection or blastomere biopsy of an embryonic cell. These steps involve blastomere Z-stack image acquisition, 3D image processing to identify blastomere feature (X, Y, Z) coordinates, and real-time image-based visual servo control of micropipettes to hold and immobilize the embryo while a micropipette injects or biopsies the target blastomere.

Keywords: automated manipulation
embryo manipulation
image segmentation
micromanipulation
single cell surgery
visual control
Advisor: Mills, James K
Variational Autoencoders for Volatility Surfaces

The implied volatility surface is an important tool used by financial practitioners. It shows how the market price of an option varies as a function of its strike price and maturity. It conveys important information about market conditions and is typically used for risk management or as an input to exotic option pricing models. However, market data is sparse and incomplete, requiring trading desks to infer unobserved prices. Conventional methods used to complete volatility surfaces are often not flexible enough to adapt to rapidly evolving markets. This thesis demonstrates how variational autoencoders (VAEs) can be used to model volatility surfaces. We show how VAEs provide a flexible and entirely data-driven approach which is both computationally faster and conceptually simpler than traditional methods. We illustrate how VAEs can complete, explore, and generate synthetic volatility surfaces. Our methodology is demonstrated using S 500 index and foreign exchange options.

Keywords: Quantitative Finance
Variational Autoencoders
Volatility Surfaces
Advisor: Veneris, Andreas
The Impact of Frailty on Outcomes after Spine Surgery

Background: It remains unclear how best to treat elderly patients with spinal pathologies. Aim: The aim of this thesis was to investigate the impact of frailty on outcomes after spine surgery. Methods: A systematic review on frailty and spine surgery was done. A study investigating the impact of frailty on morbidity in patients treated for degenerative lumbar spondylolisthesis was performed. The National Surgical Quality Improvement Program (NSQIP) database was used for this study. The primary outcome was major complications. Results: Thirty-two studies were included in the systematic review. Regardless of how frailty was measured, frailty was associated with an increased risk of morbidity and mortality. There were 15 648 patients in the study on patients treated for degenerative lumbar spondylolisthesis. Frailty was significantly associated with increased risk of morbidity. Conclusion: There is strong evidence that frailty is an independent predictor of morbidity and mortality after spine surgery.

Keywords: aging
degenerative spine disease
elderly
frailty
outcomes
spine surgery
Advisor: Fehlings, Michael G
Disentangling the Influence of Blood on Brain Parametric Maps and Volumetry

Caffeine, the most commonly used psychoactive substance in the world, leads to changes in cerebral blood flow (CBF). Recent research has shown that changes in CBF can bias regional estimates of brain volume and cortical thickness as measured by magnetic resonance imaging (MRI). In addition, recent studies have shown that quantitative MRI parameters that are indicative of tissue microstructure (T1, R2* and QSM) may also be sensitive to acute CBF changes. Here, we used an ecologically valid manipulation of CBF (caffeinated vs decaffeinated coffee) to assess whether our estimates of brain volume and qMRI maps are sensitive to caffeine-induced changes in CBF, in moderate caffeine users. Furthermore, an improved method for multi-parametric mapping was proposed and assessed in this study. As expected, CBF was significantly reduced after caffeine, however of all structural metrics explored, only R2* maps were sensitive to changes in CBF in this preliminary dataset of 5 subjects.

Keywords: Brain Imaging
Caffeine
Cerebral Blood Flow
Hemodynamics
MRI
Quantitative MRI
Advisor: Chavez, Sofia
A Multimodal Assessment of Adults with Dravet Syndrome

Dravet Syndrome (DS) is treated as a developmental and epileptic encephalopathy. Several comorbidities in DS exist such as motor and cognitive abnormalities. Aging is not well characterized in these patients, and parents complain about their adult children losing previously acquired skills. We aimed to identify if DS adults experience a premature aging process. A systematic review was performed to characterize the adult phenotype. In our first study, we performed an instrumental gait analysis and evaluation of parkinsonisms. In our second study, we assessed gait, parkinsonisms, adaptive behaviours, screening for autism, and other clinical factors in a larger cohort. The review identified a 1:7 ratio of adult to children studies exclusively, and a lack of overall clinical adult studies. We identified worsening of physical and adaptive behaviours with age in our studies. Our studies show a progressive deterioration of most clinical manifestations, in keeping with an accelerated ageing process. A holistic approach to care is necessary in DS.

Keywords: accelerated aging
adults
Dravet syndrome
gait
natural history
parkinsonism
Advisor: Andrade, Danielle M
The Effect of Virion-Incorporated Host Proteins on the Expression and Conformation of the HIV-1 Envelope Protein

The envelope (Env) glycoprotein of human immunodeficiency virus type 1 (HIV-1) is the sole target for the development of an HIV-1 vaccine. However, due to the extensive glycosylation and the metastable nature of Env, targeting the viral Env glycoprotein is very challenging. Recently, several host proteins have been described to be incorporated on the viral surface and to alter the course of HIV-1 infection, suggesting virion-incorporated host proteins could be a potential target for therapeutics and vaccine development. This thesis examined the impact of a panel of virion-incorporated host proteins on the infectivity of HIV-1. Our results showed that the incorporation of host proteins, CD162 and α4β7, significantly decreased the infectivity of HIV- 1. Furthermore, we found that virion-incorporated host proteins can alter the conformation of Env and affect the amount of Env incorporated onto the surface of viral particles. Taken together, our work shows that selected virion-incorporated host proteins can have an impact on the infectivity of HIV-1 and defining the effects of host proteins on the viral Env glycoprotein could be useful for designing new antiviral strategies.

Keywords: Envelope glycoprotein
HIV-1
Virion-incorporated host proteins
Advisor: Guzzo, Christina
Mathematical Modelling of Rodent Circadian Rhythms Involving Photic and Non-photic Inputs

We develop models that describe the effects of photic and food input on the mouse and rodent respectively. In the former, we construct a similar model to the Kronauer model. We fit the parameters to mouse phase response curve data. We deduce model parameter ranges using sensitivity analysis and parameter distributions. Applications of the model indicate the relation between parameter choice and aspects of rhythm generation/control. In the latter, we employ a population of Kuramoto oscillators to describe food anticipatory activity (FAA). The model captures the main features of FAA, such as multiple meals and meals of different periodicities. We explore the model by conducting a continuum approximation of the oscillators using the Ott-Antonsen ansatz. Finally, we suggest some interesting experiments that reveal important properties about the characteristics of FAA. The models developed provide insight and testable predictions to further our understanding of various circadian processes.

Keywords: circadian pacemaker
food anticipatory activity
Kuramoto oscillators
parameter estimation
phase response curve
phenomenological model
Advisor: Stinchcombe, Adam