VictorJuiz/thesis huggingface dataset:
The Role of Transforming Growth Factor Beta Signalling in Regulating the Sphingolipid Rheostat in Intrauterine Growth Restriction

Disruptions of sphingolipid metabolism contribute to the onset of several human pathologies. Herein, I examined sphingolipid metabolism in intrauterine growth restriction (IUGR), a pregnancy-related disorder that is commonly due to placental insufficiency. Lipid mass spectrometry revealed increased levels of pro-death sphingosine (SPH) in IUGR placentae relative to pre-term control placentae. This was accompanied by increased acid ceramidase (AC) expression and reduced sphingosine kinase 1 (SPHK1) expression and activity. Exposure of human choriocarinoma JEG3 cells to TGF1 and 3 recapitulated the sphingolipid regulatory enzyme expression profile observed in IUGR. Pharmacological inhibition of activin receptor-like kinase 5 (ALK5) in human villous explants and JEG3 cells reversed the TGF1 and 3 stimulatory effect on AC expression; whereas exposure of JEG3 cells to ALK1 inhibitor, Dorsomorphin, further suppressed SPHK1 expression. Of clinical significance, ALK5 expression and Smad2 activation is increased in IUGR placentae. Hence, altered TGF signalling may contribute to SPH accumulation in IUGR.

Keywords: Acid Ceramidase
Intrauterine Growth Restriction
Placenta
Sphingolipids
Sphingosine Kinase
Transforming Growth Factor Betas
Advisor: Caniggia, Isabella
Using Intraoperative Audio to Predict the Presence of Surgical Errors in Operating Room Black Box Recordings

Recording and review of surgeries can increase safety by allowing researchers to identify errors and analyze their root causes. Watching a surgical can be time consuming. There is a need to make this process more efficient. The research aims to use intraoperative audio to create a machine learning algorithm that can identify times in a surgical recording where an error has been committed. Audio can create effective features due to subtleties in communication, known to change under times of stress. An alternating decision tree is generated using 19 features and a training set of 31 surgeries. The algorithm was tested on 21 surgeries, yielding a sensitivity of 80.8% and overall accuracy of 41.1%. By changing algorithm parameters, an accuracy of 68% was also achieved. The algorithm demonstrates the feasibility of a machine learning algorithm for surgical error prediction. The algorithm should be tested with raters to test its helpfulness.

Keywords: Safety
Surgery
Advisor: Grantcharov, Teodor
Investigating the Effects of Temporal Duration Structure on Recognition Memory

In order to function optimally within our environment, we continuously extract temporal patterns from our experiences and formulate expectations that facilitate adaptive behavior. Given that our memories are embedded within spatiotemporal contexts, an intriguing possibility is that mnemonic processes are sensitive to the temporal structure of events. To test this hypothesis, we manipulated interval duration at encoding in a series of behavioral experiments. Our findings revealed enhanced recognition memory (d’) for stimuli that were explicitly encoded within a temporally structured versus unstructured framework. Encoding information within a temporally structured framework was also vital in reducing the negative effects of proactive interference and was linked to a greater ability to recollect contextual details associated with the study event. Rhythmic temporal structure also enhanced recognition memory for incidentally encoded information. Collectively, these results support the possibility that we possess a greater capacity to learn and subsequently remember temporally structured information.

Keywords: Duration
Hippocampus
Memory
Rhythm
Temporal Structure
Timing
Advisor: Lee, Andy
Beads: Symbols of Indigenous Cultural Resilience and Value

My intention for this paper is to explore the cultural relevance of the influence that beads have had on Indigenous people in North America. By exploring the inherent cultural values that beads possess in Indigenous culture, I hope to illuminate how beads have come to represent Indigenous resiliency after the effects of colonialism and the residential school system. I aim to illustrate how important this art form has been in the past and will continue to be in the future. Beads should not be portrayed as simple trinkets that Indigenous people have sought to trade in the past, instead, they are integral elements to the greater Indigenous society both prior to and concurrent with European contact. Beads are playing an integral role in repairing cultural ties and spiritual beliefs to Indigenous artists. Beadwork has been, and will continue to be significant in representing Indigenous resiliency as well as highlighting the distinct cultural value of Indigenous peoples.

Keywords: Beads
Beadwork
Cultural Value
First Nations
Indigenous
Resilience
Advisor: Muehlebach, Andrea
Kalmar, Ivan
The Role of Toll-like Receptor 4 in the Pathogenesis of Experimental Subarachnoid Hemorrhage

Subarachnoid hemorrhage (SAH) accounts for 5-7% of strokes worldwide and is associated with high mortality and morbidity. In addition to brain damage from the initial hemorrhagic events, secondary complications are observed in patients as well as animal models. Inflammation is being increasingly implicated in the presentation of secondary complications of SAH. This study was designed to investigate the contributions of Toll-like receptor 4 (TLR4) to secondary pathologies after SAH in mice. SAH was induced in TLR4- deficient animals, animals treated with a pharmacological inhibitor of TLR4 (TAK-242) and their respective controls; the degree of behavioral disruption, histological vasospasm, neuronal damage, reactive gliosis and demyelination was assessed. Disruption of TLR4 signaling was found to improve behavioral scores, and reduce neuronal damage and reactive gliosis, but did not affect histological vasospasm and demyelination after SAH. These data suggests that inhibition of TLR4 signaling could be a promising new therapeutic strategy for SAH patients

Keywords: Delayed Cerebral Ischemia
Inflammation
Subarachnoid hemorrhage
Toll-like receptor 4
Advisor: Macdonald, R. L.
Importance of Cell Specific Transcription Factors in Sox2 Regulation, Conservation and Reprogramming

Importance of Cell Specific Transcription Factors in Sox2 Regulation, Conservation and Reprogramming By Nakisa Malek-Gilani Master of Science, 2016 Cell and Systems Biology, University of Toronto The Sox2 gene is a transcription factor critical for the self-renewal and pluripotency of embryonic stem cells. While Sox2 is expressed in ES cells, the cell-type specific regulation of Sox2 transcription is only recently investigated; with a distal Sox2 Control Region (SCR) discovered. I demonstrated the importance of two clusters of ES cell specific transcription factor binding motifs in conferring enhancer activity to functional regions within the SCR. Mutation of a single motif results in significant loss of enhancer activity suggesting formation of TF complexes. Using these motifs studied in mice, I located a putative functionally conserved SCR region in human. The putative human Sox2 control region (hSCR) demonstrates high sequence conservation of ES cell specific TF motifs and two distinct clusters as seen in mouse. Overall, these results suggest TF binding at Sox2 distal enhancers is vital for activity and could be conserved across species.

Advisor: Mitchell, Jennifer A
The Role of Ryanodine Receptor on Neurite Outgrowth under Physiologic and Oxygen and Glucose-deprived Conditions

Ca2+ can enter a neuron from outside or can be released from internal stores, including endoplasmic reticulum (ER). Ryanodine receptor (RyR) is one of Ca2+ releasing channels present on the ER. They were first recognized in skeletal muscles, and later discovered throughout the brain but their role here needs to be further elucidated. Considering the importance of Ca2+ signaling and its contribution to neuronal maturation, it is likely that RyRs contribute to growth. Our goal was to better understand the role of RyR in neurite outgrowth. I report that RyRs mediate intracellular Ca2+ signaling, under physiological and hypoxic stress conditions. Blocking RyRs interfered with neurite outgrowth in the earlier stages of development. RyRs contributed to the abnormal neurite outgrowth following hypoxic stress. Neurons with a mutation that causes an enhanced RyR activity displayed stalled neurite elongation. Our findings support that RyRs facilitate neuronal maturation although exact mechanisms involved remain unknown.

Advisor: Feng, Zhong-Ping
Regulation of Cisplatin-induced Programmed Cell Death In Vivo

Cisplatin [ cis-PtCl2 NH3)2 ] is a widely utilized chemotherapeutic agent. Its proposed mechanism of action involves DNA-platinum adduct formation that triggers DNA damage responses, cell cycle arrest and p53-mediated cell death. In vivo treatment of murine embryos with cisplatin caused widespread cellular injury consistent with induction of apoptosis. Caspase-3 knockout embryos exhibit complete inhibition of cell death 24 hours following cisplatin treatment in a variety of tissues. Examination at later time points revealed an alternate form of programmed cell death in the absence of caspase-3 exhibiting features of necroptosis, suggesting coordinated regulation of these disparate pathways is critical to control PCD signaling in vivo. These results demonstrate caspase-3 is necessary and sufficient to regulate cisplatin- mediated PCD in numerous embryonic tissues and could hold implications towards the maintenance of normal and malignant cells in a variety of solid tissues in the presence of cisplatin.

Keywords: Apoptosis
Caspase-3
Cisplatin
DNA damage
Necroptosis
PCD
Advisor: Henderson, Jeffrey T
Organic Anion Transporter Blockade to Improve Beta Cell Function in Diabetes

The furan fatty acid metabolite 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) is elevated in Type 2 Diabetes. CMPF delivery to diabetic levels in mice causes glucose intolerance, impairing glucose-stimulated insulin secretion (GSIS). CMPF enters the β cell through Organic Anion Transporters (OATs). Here, we investigate whether OAT blockade represents a therapeutic target for diabetes prevention, blocking CMPF action on the β cell. First, we block CMPF transport in vivo using pharmacological OAT inhibition. CMPF impairs glucose tolerance, and islets isolated from CMPF-treated mice showed impaired GSIS, while co-treatment with pan-OAT inhibitor probenecid rescues glucose tolerance and islet function. Next, we developed Oat3 knockout (Oat3KO) mice which were also protected against the negative effects of CMPF in vivo, and remarkably, Oat3KO mice were more glucose tolerant than Wildtype controls. These novel studies demonstrate the requirement of OAT transport for CMPF to alter β cell function, and highlight potential for OAT inhibition to improve diabetes.

Keywords: Beta Cell
CMPF
Diabetes
OAT3
Organic Anion Transporter
Probenecid
Advisor: Wheeler, Michael B
The Spatiotemporal Accumulation of Myeloid Lineage Cells Is Mapping Out Fibrosis in the Liver after Acute and Chronic Injury

Liver fibrosis is known to become problematic after persistent injury. However, little is known about its response after an acute insult. Myeloid lineage cells, specifically, macrophages have been implicated in the promotion and resolution of inflammation and fibrosis. We investigated the role of myeloid lineage cells in the liver after acute injury. Our data show that thermal injury in mice induces fibrosis predominantly around portal venules whereas myeloid cells are enriched throughout the liver. The fibrosis peaks 1-2 weeks post injury and resolves by week 3. Depletion of myeloid cells led to lower fibrosis. Microarray analysis revealed an inflammatory signature and modulation of components of the serotonin (5-HT) pathway in myeloid cells. Antagonizing the 5HT2A/2C receptor decreased fibrosis in thermally injured mice, likely through promoting an anti-fibrotic phenotype in macrophages. Treating mice with a 5HT2A/2C receptor antagonist promotes an anti-fibrotic effect, through modulating the phenotype of macrophages.

Keywords: fibrosis
Kupffer
liver
macrophage
myeloid
serotonin
Advisor: Jeschke, Marc G
Phenotypic and Transcriptional Consequences of Shwachman-Bodian-Diamond Syndrome (SBDS) Deficiency during Hematopoietic Development

Shwachman-Diamond syndrome (SDS) is a genetic disorder characterized by exocrine pancreatic and hematological dysfunction. As hematological complications are major concerns for mortality with limited treatment options, the mechanisms underlying the SDS hematopoietic defects need to be elucidated to advance the development of effective treatments. We hypothesized that the onset of SDS hematopoietic defects occurred in a certain hematopoietic developmental stage. In this study, definitive hematopoietic differentiation of SDS compared to normal hiPSCs showed reduced CFU-GM and BFU-E formation, increased venous and endothelial potential, and reduced viability in embryoid bodies containing hemogenic and vascular endothelia. Over-representation analysis of dysregulated genes in SDS compared to normal hiPSCs showed enrichment for pathways including histones, glycosaminoglycan metabolism, and WNT signaling. This study offers insight into the onset of SDS hematopoietic defects and potentially disrupted pathways in SDS hiPSCs, and provides patient hematopoietic cell resources for drug screening and the potential to improve patient outcome.

Keywords: definitive hematopoietic differentiation
human induced pluripotent stem cells (hiPSCs)
RNA-seq
Shwachman-Diamond Syndrome (SDS)
Advisor: Dror, Yigal
Genetic Polymorphisms in Fructokinase and Aldolase B, and Biomarkers of the Metabolic Syndrome

In the absence of consistent clinical evidence, concerns have been raised regarding the potential role of fructose in the development of the Metabolic Syndrome (MetS). We determined whether common polymorphisms in the genes involved in fructose metabolism (Fructokinase (KHK), and Aldolase B (ALDOB)) modify the association between fructose intake and biomarkers of the MetS (waist circumference, blood pressure, triglyceride, HDL-cholesterol and blood glucose). Fructose intake was measured using a food frequency questionnaire and genotyping was completed using real-time PCR. We found no association between the KHK (rs2119026) and fructose intake or biomarkers of the MetS. The ALDOB (rs1929480) was associated with decreased HDL-cholesterol in East Asians, while the ALDOB (515313) modified the association between dietary fructose and serum triglyceride in South Asians. The results suggest that partial and incomplete metabolism of fructose in the liver may have adverse metabolic effects.

Advisor: Sievenpiper, John
El-Sohemy, Ahmed
Using the Unpredictable Chronic Mild Stress Model in Mice to Understand the Involvement of DNA/RNA Oxidation in Major Depressive Disorder

Major Depressive Disorder (MDD) is a debilitating illness, associated with chronic development and a highly heterogeneous etiology. Despite unclear mechanisms, chronic stress is implicated in its development and/or progression. Previous studies in patients with MDD have reported chronic stress and elevated levels of oxidative stress, including increased DNA/RNA oxidation in post-mortem analyses in brain regions associated with cognitive and emotional processing. Using a preclinical model of chronic stress, this thesis investigates: 1) whether unpredictable chronic mild stress (UCMS) in mice induces neuronal DNA/RNA oxidation in the frontal cortex (FC) and basolateral amygdala (BLA), and 2) correlations between levels of neuronal DNA/RNA oxidation with depressive-like behaviors. We predicted that mice subjected to UCMS, relative to mice not subjected to the stress would present higher levels of neuronal DNA/RNA oxidation, and this would be associated with anxiety/depressive-like behaviors. This work provides a translational perspective for the involvement of DNA/RNA oxidation in MDD.

Keywords: Behavioral assays
Chronic Stress
Cortical neurons
DNA/RNA Oxidation
Immunohistochemistry
Major Depressive Disorder
Advisor: Andreazza, Ana C
Banasr, Mounira
The Optimal Distribution of a Perishable Item with Quality Requirements and Delivery Time Windows

Food quality deteriorates continuously over time at a speed depending on the storage temperature, and therefore they have to be stored in low temperature to prolong the shelf life, increasing the storage cost significantly. In this thesis, we study a distribution problem in which a temperature controlled warehouse is responsible for supplying a dairy product, using a fleet of homogenous capacitated vehicles, to multiple customers with minimum quality requirements and delivery time windows. The objective is minimizing the sum of the energy cost at the warehouse to maintain the storage temperature low and the transportation cost to deliver the product. Decisions include the storage temperature at the warehouse and the routing of vehicles among customers. We formulate the optimal distribution problem as a mathematical model, and solve it in various scenarios by changing environmental temperature, quality requirements and delivery time windows imposed by customers, energy cost, and transportation cost.

Advisor: Lee, Chi-Guhn
Modulating Autophagy in a Murine Model of Severe Malnutrition Enteropathy

Severe acute malnutrition (SAM) remains pervasive in developing countries. It is associated with enteric dysfunction, but its pathophysiology is poorly understood. Evidence suggests that dysregulated autophagy contributes to the intestinal dysfunction in SAM. A novel murine model of SAM was induced in male weanling C57Bl6 mice through a protein deficient diet (1% protein) and compared to mice fed a control diet (18% protein). Malnourished mice showed significant weight loss, a significant decrease in villous height in the small intestine and a significant decrease in crypt depth, and goblet cell density were observed in the colon. Malnourished mice had increased intestinal permeability assessed via FITC-dextran uptake and upregulation of Claudin 2. Induction of autophagy in malnourished mice through intraperitoneal rapamycin injections restored the increase in intestinal permeability and Claudin 2 levels. This study will help characterize intestinal pathology associated with severe acute malnutrition, and potentiallyÂ identify new targets for intervention.

Keywords: Autophagy
Enteropathy
Intestinal Barrier
Malnutrition
Mouse
Tight Junction
Advisor: Bandsma, Robert
Biocompatibility of Bone Allograft Toughened with a Novel Sterilization Method for Critically-Sized Segmental Defects: An In Vivo Rabbit Study

PURPOSE: Bone allografts often undergo γ-irradiation to decrease infection risk. This consequently degrades bone collagen and makes the bone brittle. Our laboratory found pre-treatment with ribose could protect the bone. This thesis aimed to determine if ribose-treated γ-irradiated allografts were biocompatible in vivo. MATERIALS AND METHODS: Using the New Zealand White rabbit (NZWr), we first aimed to establish a proper in vivo model to test the graft using intramedullary wire fixation (Study 1), and then tested the biocompatibility of ribose-treated grafts (compared to untreated and conventionally-irradiated grafts) (Study 2). Healing/union was assessed with radiographs, μCT, histomorphometry, backscatter electron microscopy, and torsion testing. RESULTS: Intramedullary fixation achieved stable reconstructions. All grafts achieved bony union. No differences were found in radiographic and biomechanical parameters tested. However, irradiated grafts had less bone volume (p=0.000) but greater bone forming properties (p

Keywords: Biocompatibility
Bone allograft
Bony union
New Zealand White rabbit
Ribose
Îł-irradiation
Advisor: Grynpas, Marc
The Alzheimer's Spectrum: Diagnostic Challenges and Nosology in a Clinically Heterogeneous Disease

Hypothesis: Alzheimer's disease (AD) is not a unitary condition but a phenotype spectrum. Rationale: Mounting evidence suggests AD is more complex than previously thought. A new AD conceptualization accounting for this biologic and clinical complexity is needed. Aim: To review existing evidence for, provide a specific example of, and investigate the nosological impact of AD heterogeneity. Methods: Three studies were done using (1) literature review, (2) imaging analysis case series, and (3) systematic chart review. Results: AD is heterogeneous and sub-syndromes exist. Extreme heterogeneity results in syndrome mimicry with blending of imaging markers. Wide variation in diagnostic classification occurs even with standardized application of consensus criteria. Conclusions: AD is not a single disease but a spectrum of sub-syndromes (core phenotype and atypical sub-syndromes). The AD conceptual framework must evolve to acknowledge, define, and anticipate this complexity, harnessing it to improve diagnostic precision and facilitate treatment discovery.

Keywords: Alzheimer's disease
Brain imaging
Clinical criteria
Diagnosis
Heterogeneity
Phenotype
Advisor: Black, Sandra E
The Contribution of IgG Fc Glycans on Antibody-mediated Immune Suppression (AMIS) to Murine Erythrocytes

The ability of anti-D to prevent hemolytic disease of the fetus and newborn (HDFN) is an example of antibody-mediated immune suppression (AMIS). A recombinant monoclonal antibody to replace anti-D is desired, however, none of the developed therapies have been as effective and some antibodies have unexpectedly led to enhanced immune responses. The requirement for IgG glycosylation for AMIS was analyzed for five antibodies reactive with erythrocytes in a murine model. The antibodies recognized the HOD (hen egg lysozyme [HEL] linked to ovalbumin and the human Duffy transmembrane protein) antigen. It was observed that glycosylation in the Fc region of polyclonal AMIS-inducing antibodies was not essential for complete suppression. In contrast, monoclonal AMIS-inducing antibodies were partially sensitive to removal of the glycan structure. These results may help explain the superiority of polyclonal antibodies to monoclonal therapeutics for AMIS induction and could influence the development of effective therapies to replace anti-D.

Keywords: alloimmunization
AMIS
anti-D
HDFN
red cell antibodies
Advisor: Lazarus, Alan
Life Cycle External Cost Evaluation of Crude Oil Transportation Options

Widespread concerns associated with crude oil transportation which could drive decision-making motivate the life cycle evaluation of crude oil transportation options. This thesis integrates life cycle assessment, economic input output life cycle assessment, and life cycle costing to examine the internal and external costs of pipeline, rail, and tanker transportation. The case studies used in this work illustrate the difference in impacts and costs between pipeline and rail transport for similar original-to-destination routes (including tanker, where relevant). Results show that pipeline costs are lower for each of case studies compared to the equivalent rail routes. No changes within the plausible ranges of input values for transport operation, greenhouse gas emissions, health impact, volume transported and discount rate would change the overall outcome from a preference for pipelines to rail (tanker costs included where relevant), however, cross-over between favoring pipeline over rail is possible with varying changes in the capital costs.

Keywords: Life Cycle Assessment
Life Cycle Costing
Pipeline
Transportation Externalities
Advisor: MacLean, Heather L