VictorJuiz/thesis huggingface dataset:
Targeting the CFTR Locus for Human CFTR Gene Correction using the CRISPR-Cas9 System

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated nuclease 9 (Cas9), a gene editing tool, is being explored as a possible therapy for CF. Our strategy is to use helper dependent adenoviral (HD-Ad) vectors to deliver the CFTR transgene and the CRISPR-Cas9 system targeting the CFTR locus to human cells. In vitro experiments, using a lacZ donor plasmid, were performed to validate genome targeting efficiency, integration and expression in human embryonic kidney (HEK293) cells. The information gained from these proof-of-concept experiments allowed for the design of HD-Ad vectors. Future experiments using these HD-Ad vectors will allow us to examine CFTR expression and channel activity in CF corrected cells. Overall, these studies will contribute to the development of a long-lasting effective treatment for all CF patients.

Keywords: CFTR locus
CRISPR-Cas9
Cystic Fibrosis
Gene editing
HD-Ad vectors
Advisor: Hu, Jim
Oscillatory Mechanisms of Schematic Processing

Schematic processing requires activating and sustaining a schema template, which is later used to flexibly interact with incoming information. This is accomplished by schema reinstatement (activation) and instantiation (interaction). Previous work has neglected direct analysis of these processes, resulting in a lack of definitive neural mechanisms that distinguish them from other forms of prior knowledge. We hypothesize that these processes are modelled in the brain as the interaction between the vmPFC and posterior neocortical areas. We indexed schematic processing behaviourally and neurally and compared it with categorical processing. Under EEG recording, 10 vmPFC patients and 13 controls were instructed to determine stimuli belongingness to a given schema or category. Pre-stimulus low-frequency coherence desynchronization between the vmPFC and posterior neocortex, followed by post-stimulus power decreases in the vmPFC correlated with better performance for schema trials. Our results suggest that these patterns of oscillatory activity may serve as mechanisms for schematic processing.

Keywords: category
EEG
schema
schema instantiation
schema reinstatement
vmPFC
Advisor: Gilboa, Asaf
Moscovitch, Morris
Health and Climate Impacts of Electric Vehicle Deployment – A Case Study of the Greater Toronto and Hamilton Area

The transportation sector is a big source of greenhouse gas and air pollution emissions. Though studies generally agree that introducing electric vehicles (with no exhaust emissions) brings environmental benefits, an accurate assessment requires detailed analysis of emissions from electricity generation, vehicle travel patterns, and air pollutants transport. By operationalizing the concept of marginal emission factors and simulating charging patterns using person-level travel activity data, this thesis first developed a framework to evaluate the emission reduction potential of EV deployment in the Greater Toronto and Hamilton Area (GTHA). Then, to assess the health and economic impacts, an integrated model was built by combining a high-resolution chemical transportation model with an emission inventory that included traffic and electricity generation details. According to the results, EV deployment in the GTHA can achieve substantial health and climate benefits, and there is a need for policies to promote EV uptake and manage rising electricity demand.

Keywords: air pollution
electric vehicles
emission reduction
greenhouse gas emissions
health impact assessment
life cycle assessment
Advisor: Hatzopoulou, Marianne
Posen, I.Daniel
The Role of microRNAs in the Regulation of Cardiomyocyte Proliferation in the Early Postnatal Period

The regenerative capacity of the mammalian heart is lost quickly after birth when CM stop dividing and undergo cell cycle arrest. CM were shown to only proliferate in the first 12 hours following birth, with proliferative arrest occurring at 1d. A differential expression of cell cycle genes was found during this time. Cell cycle genes have been shown to be regulated by microRNAs (miRNAs). Therefore, we hypothesized that a differential expression of miRNAs exists in the first hours after birth and manipulation of these miRNAs will provide the potential to promote cardiomyocyte (CM) proliferation. Profiling of miRNAs from wild type murine hearts revealed a differential expression of miRNAs that were enriched for cell cycle gene targets. The use of antagomirs was effective in significantly increasing the degree of proliferation in neonatal rat CM cytokinesis, suggesting a role for these miRNAs in the control of CM cell cycle arrest.

Keywords: Cardiology
Cardiomyocyte proliferation
Cell Cycle
microRNA
Advisor: Billia, Filio
Molecular Analyses of the Mouse Anorexia Mutation

The mouse anorexia (anx) mutant displays food restriction leading to emaciation and may represent an animal model of anorexia nervosa. To date, the causative anorexia gene(s) remain to be identified. Our lab’s previous analyses found early deficits in glutamatergic and GABAergic synapses in the cerebella of anx/anx mice at postnatal day 10 (P10). Gene expression analyses of P10 anx/anx cerebella identified two genes within the anx critical interval with notable expression differences: Pla2g4d was ~7-fold downregulated, while Pla2g4e was ~10-fold upregulated. These phospholipases are involved in the synthesis of arachidonic acid, a key endocannabinoid precursor. Endocannabinoids have widespread roles in synaptic plasticity and in the reward mechanisms of feeding and activity and may influence risk of developing Anorexia Nervosa. We anticipate that further research into the roles of these phospholipases will contribute to better understanding of the endocannabinoid system and its roles in anorexia nervosa.

Keywords: anorexia
cannabinoid
endocannabinoid
mouse
mutation
Pla2
Advisor: Cordes, Sabine
The Role of Napthenic Acids and Asphaltenes on the Phase Behavior of Bitumen-water Systems

In this thesis, the behavior of naphthenic acids and asphaltenes in bitumen-water systems is explored. The bifunctional model was developed to characterize polar oils in surfactant-oil-water systems. This model incorporated the HLD equation and the Langmuir adsorption isotherm to determine the interfacial adsorption of surface-active compounds. For the first time, the amphiphilic behavior of naphthenic acids was characterized by an EACN and a Cc, simultaneously. Furthermore, it was concluded that in the presence of a surfactant, asphaltene molecules are rejected from the interface of the bicontinuous phase due to their large size, and thus have little effect on the curvature of the system. Consequently, the bifunctional model predicted the phase behavior of bitumen-water systems from naphthenic acids’ surfactant-like and oil-like behavior at different pH values. This resulted in the prediction of the phase inversion point, at which the properties of the system reach minimum interfacial tensions and emulsion stability.

Keywords: asphaltene
characteristic curvature
EACN
HLD-NAC
microemulsions
polar oils
Advisor: Acosta, Edgar
PHIP1: A Novel Regulator of Diabetes

Diabetes is characterized by impaired glucose homeostasis due to loss/dysfunction of β-cell mass; therefore, maintaining functional β-cell growth and survival is fundamental for diabetes treatment. Moreover, PHIP1 as a novel downstream transcriptional co-regulator of insulin signaling shows a potential role in regulating β-cell biology. Our in vitro experiments showed that PHIP1 protects INS-1 cells against IFN-γ/IL-1β-induced apoptosis through STAT1 and SOCS3 genes. Accordingly, our preliminary data from β-cell-specific knockout mice generated by LoxP-Cre system either during development or at adult ages (Tamoxifen-induced expression of Cre in PHIP1Flox/Flox: MIP1-CreERT), imply to an essential role of pancreatic PHIP1 in maintaining glucose homeostasis through enhancing insulin sensitivity and improving glucose tolerance. To better explore the role of PHIP1 in initiation, development, and progression of diabetes, we have successfully constructed a β-cell-specific transgene for nuclear microinjection and then generated, genotyped and characterized two transgenic mice models (NOD-PHIP1-tg and C57BL/6-PHIP1- tg) of β-cell specific overexpressing of PHIP1.

Keywords: Apoptosis
Diabetes
Epigenetic
PHIP1
Advisor: Adcock, Dr. Maria R
Neural Correlates of Content-general Reactivation and Vividness: A Meta-analysis

Recollection reflects retrieval of qualitative episodic details. This is accompanied by a subjective level of vividness and neural reinstatement, whereby the brain state at encoding is reactivated upon retrieval. Vividness and reinstatement are positively associated, suggesting judgments of vividness may be a subjective correlate of objective neural reactivation. St-Laurent, Abdi, and Buchsbaum (2015) investigated neural networks supporting vividness and reactivation and reported a substantial overlap between regions. The current study extended this work by performing a meta-analysis on neural correlates of vividness and reinstatement from five studies (100 participants total). Results largely converge with what was reported by St-Laurent and colleagues, but reliable relationships were now found within the hippocampus. Regions underlying reinstatement contributed to retrieval of memory details, whereas vividness was associated with regions related to subjective judgments. The current analysis elucidates the networks underlying both reactivation and vividness in recollection to understand their commonalities and differences.

Advisor: Buchsbaum, Bradley R
The Formula of Race and Racism: White Supremacy +Anti-blackness + Non-white, Non-black = less (

This thesis argues that white supremacy and anti-Blackness are always deployed together. White supremacy and anti-Blackness is the foundational structure that allows for race and racism to operate and racism is a superstructure that is built on the foundational structure of white supremacy and anti-Blackness. A formula for race and racism is forwarded: white supremacy + anti-Blackness = non-white, non-black groups as less (

Keywords: Anti-Blackness
Intermediate groups
Polarity
Proximity
Race and racism formula.
White supremacy
Advisor: Titchkosky, Tanya
Walcott, Rinaldo
The Impact of Estrogen Deprivation on Associative Memory and Functional Brain Activation During Encoding in Spontaneous and Surgically-Induced Menopause

There is little understanding of the influence of 17β-estradiol (E2) depletion on associative memory following bilateral salpingo-oophorectomy (BSO) prior to spontaneous/natural menopause (SM). Using functional magnetic resonance imaging (fMRI), recognition performance and brain activity during face-name pair encoding were assessed in women who underwent BSO who were taking E2-based hormone therapy (BSO+E2), those taking no hormone therapy (BSO), age-matched premenopausal control (AMC), and SM women. Results demonstrated no group differences in recognition accuracy. Partial least squares analysis revealed differences in brain-behaviour correlations between the BSO and SM groups: with higher accuracy, the SM group showed increased activation of regions commonly thought to subserve memory. Alternatively, with higher accuracy, the BSO group exhibited decreased activation of these regions. Further, activation in regions of interest in the frontal, parietal, and temporal lobes was positively correlated with estrogen levels. These findings extend our understanding of the impact of E2 deprivation on the brain.

Keywords: Aging
Alzheimer's Disease
Associative Memory
Estrogen
Menopause
Oophorectomy
Advisor: Einstein, Gillian
Grady, Cheryl
Event Boundaries Change Hippocampal Representations of Time and Space during Navigation

Extended spatiotemporal representations are a critical feature of navigation. Navigation is not always a continuous experience and can be segmented by boundaries. Research suggests that boundaries during navigation might affect the hippocampus similarly to boundaries in non-spatial tasks. To test whether the neural representations of time and space differ across contexts during navigation, we employed a navigation task in which participants were scanned while they navigated a virtual environment. Using instructed navigational goals, we segmented participants’ experience into different goal contexts. We calculated the neural distance between pairs of TRs within the same goal context and across goal contexts. We found that across goal contexts, neural distance increases, and that changes in neural distance within a goal context are related to navigational strategies employed by participants. Our findings suggest that during navigation there are not objective representations of temporal and spatial distances but instead these representations are modulated by context.

Keywords: event boundaries
fMRI
navigation
neural distance
space
time
Advisor: Barense, Morgan D
Moscovitch, Morris
Reinforcement and Reproductive Isolation in Willow Flycatchers (Empidonax traillii) and Alder Flycatchers (Empidonax alnorum) from Southern Ontario

Reinforcement -- the evolution of increased pre-mating isolation driven by selection against maladaptive hybridization -- could represent a key step in the speciation process. Reinforcement may be more likely to persist in sympatric populations, since they are less susceptible than parapatric populations to gene flow swamping from allopatric regions. I tested for patterns expected by reinforcement in Willow (Empidonax traillii) and Alder flycatchers (E. alnorum) from southern Ontario. They are an ideal system to search for signatures of reinforcement, as their breeding ranges are mostly parapatric but eastern populations are broadly sympatric. My results suggest that extensive gene flow occurred after secondary contact was established, and gene flow ceased during the Holocene. I found two genomic regions that were substantially more differentiated in sympatric than allopatric populations. One of these regions presents the classic hallmarks of reinforcement, as it contained two genes potentially important for pre- mating and post-zygotic isolation respectively.

Keywords: Coalescent modelling
Empidonax
Gene flow
Reinforcement
Single-nucleotide polymorphisms
Advisor: Weir, Jason T
Effect of Thermal Stress on the Intracellular Localization of the Constitutively Expressed Heat Shock Protein HSPA8 (Hsc70) in Differentiated and Undifferentiated Cultured Human Neuronal Cells

Heat shock protein HSPA8 (Hsc70) is a constitutively expressed member of the Hsp70 multigene family that is abundantly expressed in neuronal cells. Previous studies in our laboratory suggest that HSPA8 may play an important role in neuronal pre-protection against cellular stress. This thesis highlights the importance of HSPA8 and its role as a fast responder to cellular stress in differentiated human SH-SY5Y neuronal cells. The effect of thermal stress on the intracellular localization of HSPA8 is compared in differentiated and undifferentiated neuronal cells. HSPA8 rapidly translocated into the nuclei of differentiated neuronal cells after heat shock and co-localized at transcription sites with DNAJB1 (Hsp40) and HSPH1 (Hsp105α) components of the protein disaggregation/ refolding machine. The rapid targeting and assembly of an HSPA8 based disaggregation/ refolding machine acts as a nuclear protective mechanism in differentiated neurons without the time lag needed to induce stress-inducible Hsp70.

Keywords: Differentiated
Heat shock proteins
HSPA8 (Hsc70)
Human neuronal cells
Thermal stress
Undifferentiated
Advisor: Brown, Ian R
Decreased Periaqueductal Gray Size and Sex-specific Alterations in Rostrocaudal Subregion Size and Astrocyte Counts in a Mouse Model of Pain Priming

Mice that receive a hindpaw incision in the first post-natal week display enhanced hypersensitivity (pain priming) after an additional incision in adulthood compared with mice that receive a first-time incision as adults. In whole brain MRI scans, the volume of the periaqueductal gray was robustly different between primed and non-primed mice. I used immunohistochemistry to quantify the size and cell counts of the whole and rostrocaudal subregions of the periaqueductal gray to determine whether there are differences between primed and non-primed mice after adult incision. I observed that the whole periaqueductal gray in primed mice was smaller than in non-primed mice and that female primed mice had a larger subregion four (found within the intermediate periaqueductal gray) with more astrocytes than male primed mice and female non-primed mice. My results demonstrate that astrocytes within the intermediate periaqueductal gray may be responsible for the sex-specific volume difference observed in pain priming.

Keywords: Neonatal Pain
Pain
Periaqueductal Gray
Advisor: Salter, Michael W
Scavenging Reactive Oxygen Species Mimics the Anoxic Response in Goldfish Pyramidal Neurons

The common goldfish is one of the few species able to avoid cellular damage during month-long periods in anoxic environments. By suppressing action potentials in excitatory glutamatergic neurons, the goldfish brain decreases its overall energy expenditure. Reductions in O2 availability results in a decrease in reactive oxygen species (ROS) generation, which has been proposed to function as part of signal transduction pathway. Therefore, I propose that low [ROS] contributes to the anoxic response. Using live-tissue fluorescence microscopy and whole-cell patch-clamping, I measured anoxic changes in [ROS] and electrophysiological parameters of cortical pyramidal goldfish neurons in response to ROS modulators. I found that the general scavenger N-acetyl cysteine and mitochondrial-specific scavenger MitoTEMPO were sufficient to depolarize the membrane, increase whole-cell conductance and decrease firing frequency similar to the anoxic response, while addition of hydrogen peroxide reversed it. Together, this implies that ROS plays a signaling role in anoxia.

Keywords: anoxia
goldfish
reactive oxygen species
Advisor: Buck, Leslie T
The Development of Small Manganese(III) Porphyrins as Blood Pool Agents for Magnetic Resonance Angiography and the Analyses of their Binding to Human Serum Albumin

Magnetic Resonance Angiography (MRA) allows for the visualization of the vascular system and the diagnosis of various pathologies. A contrast agent (CA) is often used to enhance tissue contrast. Currently, gadolinium-based CAs (GBCAs) are most widely used but due to the emerging issues related to Gd-toxicity and suboptimal r1 at high field, there is an increasing need to replace GBCAs. To overcome these limitations, we have developed water-soluble Manganese(III) porphyrins (MnPs) as alternatives to conventional GBCAs. In this thesis, the design, synthesis and characterization of MnTriCPP, a small MnP is reported to show high relaxivity (21.0 mM-1s-1 at 31.6 MHz and 14.8 mM-1s-1 at 3T) upon non-covalent interaction with Human Serum Albumin (HSA). Furthermore, to understand the mechanism of HSA binding, Isothermal Titration Calorimetry (ITC) was chosen to study the binding properties of MnTriCPP in comparison with previously synthesized MnPs, and all exhibit detectable entropy driven affinity to HSA.

Keywords: blood pool agents
contrast agents
human serum albumin
Magnetic resonance imaging
manganese
porphyrin
Advisor: Kerman, Kagan
Zhang, Xiao-an
Structure-guided Substrate Design for Carbohydrate Esterase Family 4 (CE4) de-N-acetylase Enzymes Implicated in Microbial Pathogenesis

Carbohydrate esterases are enzymes that catalyze the hydrolysis of acetyl esters or acetamides on various glycosides. Carbohydrate Esterase family 4 (CE4) contains numerous enzymes involved in microbial pathogenesis. These carbohydrate esterases use a divalent metal to catalyze the deacetylation of the saccharide substrates.

Keywords: Esterases
Saccharide Synthesis
Advisor: Nitz, Mark
FPRaker: Exploiting Fine-grain Sparsity to Accelerate Neural Network Training

sis presents FPRaker, a processing element for composing training accelerators. Training manipulates floating-point data and multiply-accumulate (MAC) operations constitute the bulk of its computations. FPRaker boosts performance and energy-efficiency by skipping ineffectual computations during training. FPRaker processes the operands’ significand of each MAC as a series of signed-powers-of-two, or terms. This exposes ineffectual work that can be skipped: encoded values have few terms and some can be discarded as they would fall outside the accumulator's precision. Over 9 studied networks, FPRaker is 1.5x faster and 1.4x more energy-efficient compared to a baseline accelerator with conventional TensorCore-like tiles under iso-compute-area constraints. We demonstrate that FPRaker delivers additional benefits when training incorporates pruning, quantization and methods that use a different accumulator precision per layer. Finally, we propose a memory compression technique for exponents of floating-point values that exploits the narrow value distribution during training using base-delta compression reducing off-chip memory bandwidth.

Keywords: Accelerators
Bit-serial Processing
Deep Learning Training
Hardware Acceleration
Memory Compression
Advisor: Moshovos, Andreas
An Immunological Epitope Selective for Misfolded Immunoglobulin Light Chains or Diagnosis and Treatment of AL Amyloidosis

AL amyloidosis is a disease in which a single plasma cell clone undergoes unregulated expansion and produces above-normal amounts of light chain (LC) protein. This increase renders the LCs prone to aggregate and accumulate as amyloid in vital organs including the heart and kidneys. Diagnosis is complicated as signs are often masked by symptoms of more common etiologies with shared symptomatology. Treatments target the plasma cell clone, and a number of patients maintain significant organ burden and low quality of life. Thus, there is a critical need to develop tools that target these mis/unfolded LCs for detection and removal. We designed an isotype-specific antibody that should be specific for these pathogenic LCs but evade the native protein. We used in vitro and in vivo methodologies that confirmed the specificity of our antibodies to the mis/unfolded recombinant protein, its pre-amyloid aggregates, LC presence in the blood sera of patients and amyloid in human tissue.

Keywords: amyloid
amyloidosis
immunotherapy
light chain
organ failure
protein misfolding
Advisor: Chakrabartty, Avijit
Magnetic Twisted String for Powerful Wireless Actuation of Robotic Tools

Untethered microrobots have greatly evolved in terms maneuverability and autonomy, at increasingly small scales. Nonetheless, generating enough usable force, especially for minimally invasive surgery, remains a challenge, as most millimeter-size microrobots achieve forces of less than 0.100 N. In this work, we present a novel magnetic twisted string microtransmission that amplifies force by up to 3500%, compared to direct magnetic actuation. We model the transmission analytically to predict its behaviour, perform tests that validate the analytical model in terms of the maximum achievable force, and quantify the transmission’s performance over numerous cycles, the effect of string materials, of the rate of force transmission and the impact of hysteresis and viscoelasticity. Finally, we integrate the transmission in a surgical gripper prototype that can fit through a 3 mm endoscopic hole and we achieve gripping forces of 1.09 N, a drastic increase from the previous magnetic gripping force of 0.018 N.

Advisor: Diller, Eric