VictorJuiz/thesis huggingface dataset:
Power Level Control in High-Density Cellular Communication Systems: a Deep Learning Based Approach

Effective power control, while essential for the operation of cellular communication systems, is most challenging in high-density cellular systems as the computational complexity for determining optimal base station transmission power levels grows exponentially with the number of system base stations and channel variation rate. A power level control scheme for high-density cellular systems, based on recent advances in machine learning and neural networks, is proposed in this thesis. Optimal power levels are computed using a greedy search in an offline phase to train a neural network predicting optimal power levels during the online phase. Multiple neural network structures are studied, along with regularization and optimization methods for fast and efficient training, the effect of the training size on the performance and effect of granularity of transmission power levels. Provisions for improving user quality of service are also introduced through a modified optimization objective function targeting minimum user throughput rates.

Keywords: Cellular
Deep Learning
Interference
Machine Learning
MIMO
Small Cells
Advisor: Sousa, Elvino S
Direct-writing and Quantitative Characterization of Soft Material Tubes

Soft materials tubes and their formation have important implications in a wide range of applications across the field of tissue engineering. Presented here are improvements and further characterization made using a microfluidic-based platform for the continuous formation of collagen tubes with gelation timescales up to several minutes and write speeds ranging from 3-7mm/s. A bioprinting cartridge consisting of three microfluidic channel layers are aligned by a unifying radial outlet that, when infused, forms cylindrical sheaths of concentric flow to extrude tubular constructs. Tubes can vary in sizes by manipulating focusing fluid flow rates to yield tubes of various dimensions, which can be approximated using analytical models. Assessment of gelation timescales can be performed via in situ measurements by translating optical measuring units to measure pH gradient, turbidity and diameters. This platform could have the potential of extruding cell-laden tubes to bioprint tubular microtissues.

Keywords: Biomaterials
Bioprinting
Collagen
Microfluidics
Advisor: Guenther, Axel
The Community of Inquiry as a Social Reform: Challenging Standardization in Schools through a Juxtaposition of Aquinas' Notion of Connatural Learning, Dewey's Centrality of Experience and Buber's Concept of Dialogue

Education imbibes the processes of drawing from within and connecting with the world. Schools which practice standardization have not become a place where students are provided with connections and experiences that enable them to learn and link with the environment, impeding the cultivation of critical thinking and the students' abilities to exercise `knowing-how and knowing-why'. I strongly argue against standardization in schools. Education must be a critical field where learning comes from questioning, discovery and flourishing with the vast tapestry of life experiences that is imbibed through the community of inquiry - collaboration among the students and teachers. I aim to explore the possibility of resolving the problem of standardization in schools through the community of inquiry as a social reform. As a means of social reform, I characterize the community of inquiry through a juxtaposition of Aquinas' notion of connatural learning, Dewey's centrality of experience and Buber's concept of dialogue.

Keywords: Centrality of Experience
Community of Inquiry
Connatural Learning
Democracy in Schools
Dialogue
Advisor: Portelli, John P
Engineering Red Blood Cell Progenitors to Achieve Greater Proliferative Potential

Increased proliferative potential of mouse bone marrow derived erythroid progenitor cells was achieved by ectopic over-expression of the transcription factor c-Myc. This was enabled by stable gene transfer of a novel all-in-one lentivirus transfer vector allowing for tight doxycycline (dox) inducible gene expression. These cells maintained a surface marker expression profile, and responsiveness to both stem cell factor (SCF) and erythropoietin (EPO) similar to colony-forming unit-erythroid (CFU-E) cells for more than 6 weeks. Upon removal of ectopic c-Myc expression, the cells lost the c-kit, and CD71 surface markers, expressed Ter119, hemoglobinized, reduced in size, and enucleated. Although further work is needed to ensure the method to create these cells is reproducible, achieved results are evidence that support a novel method to produce large quantities of enucleated red blood cells (RBCs). This method may provide a platform to produce universal donor-type RBCs for traditional blood transfusions and novel cellular therapeutics.

Keywords: Cell Engineering
Cellular Therapy
Erythroid
Progenitor Cell
Proliferation
Red Blood Cell (RBC)
Advisor: Audet, Julie
A Safety Assessment of Dexamethasone for Chemotherapy-Induced Nausea and Vomiting in Children Receiving Hematopoietic Stem Cell Transplantation

Though life-saving, hematopoietic stem cell transplantation (HSCT) carries significant risk for morbidity and mortality. Children receiving chemotherapy to prepare for HSCT also often suffer from poorly controlled chemotherapy-induced nausea and vomiting (CINV). Dexamethasone is an effective antiemetic, but the lack of safety data, especially during HSCT, presents barriers to its routine use. Three projects were undertaken to better understand the safety of dexamethasone in children: (1) a systematic review of the literature; (2) post-hoc analysis of its immediate adverse events during HSCT; and (3) a framework to assess its impact on transplant-related mortality. Overall, we identified few high quality studies evaluating the safety of dexamethasone for CINV. Adverse events were transient and of minor clinical significance in the immediate setting. Our framework was designed to feasibly collect and analyze data from multiple centers. Future efforts will refine the overall risk of dexamethasone given as an antiemetic to children undergoing HSCT.

Keywords: Children
Dexamethasone
Hematopoietic Stem Cell Transplantation
Nausea
Vomiting
Advisor: Dupuis, L. Lee
PERIPHERAL BLOOD MARKERS INDICATING SUBCORTICAL ISCHEMIC VASCULAR DISEASE AND THE RELATED STRUCTURAL AND COGNITIVE CHANGES

White matter hyperintensities (WMH), indicative of small vessels disease (SIVD), are common in the elderlies with or without Alzheimer’s disease (AD). Lipid peroxidadtion (LP) and soluble epoxide hydrolase (sEH) metabolites are thought to contribute to the development of AD and SIVD. This thesis compares serum concentrations of lipid peroxidation markers (lipid hydroperoxides [LPH], 8-isoprostane [8-iso] and 4-hydroxynonenal), as well as sEH related metabolites, between four groups with or without AD and SIVD, and explores their relationships with cognitive performance. LPH, 8-iso, and ratios of sEH derived linoleic acid (LA) diol to the epoxides, were elevated in SIVD. LPH mediated the effect of hypertension on deep WMH. The ratio was associated with poorer processing speed, attention and executive function, which is explained 37% by periventricular WMH volume. Peripheral LP and sEH oxylipins were related to SIVD. Lipid peroxidation markers indicated structural brain changes, while oxylipins had additional effects on cognitive performance.

Keywords: Alzheimer's Disease
Biomarker
Oxidative Stress
Soluble Epoxide Hydrolase
Subcortical Ischemic Vascular Disease
Vascular Cognitive Impairment
Advisor: Swardfager, Walter
Black, Sandra E
Influence of Ethnicity on Circulating Biochemical Markers in a Healthy Pediatric Cohort (CALIPER)

Accurately established pediatric reference intervals (RIs) are essential for correct laboratory test interpretation and subsequent clinical decision making. Numerous studies have established sex- and age-specific RIs for several biomarkers of health and disease. However, little is known of the influence of ethnicity on RIs. It was hypothesized that a limited number of biochemical markers exhibit major ethnic differences, warranting ethnic-specific RIs. Serum samples were collected from a large cohort of healthy children and adolescents (5-

Keywords: CALIPER
Ethnicity
Laboratory Markers
Laboratory Medicine
Pediatric
Reference Intervals
Advisor: Adeli, Khosrow
Development of Supercritical Fluid Extraction for Urban Mining of Rare Earth Elements and for Purifying Recycled Plastics

Supercritical fluid extraction is an emerging green technology with a wide range of applications. The full technical potential of supercritical fluid extraction has yet to be discovered. This study put the emphasis on discovering technical potential of supercritical fluid extraction application and developing the supercritical fluid extraction process for both urban mining of rare earth elements from end-of-life Nickel Metal Hydride battery, and for purification of recycled waxes from waste plastics. The novel, environmental sustainable supercritical fluid extraction process is proven to be successful in both urban mining of rare earth elements from Waste Electrical and Electronic Equipment and purifying recycled polymeric waxes from waste plastics.

Advisor: Azimi, Gisele
Method Development for Measuring Black Carbon (BC) Using a Smartphone Camera

Black carbon (BC) is one of the major components of the atmospheric particulate matter (PM), which can cause adverse health impacts and contribute significantly to climate change. Poor understanding of BC sources and concentrations is the main obstacles to reduce BC emissions. Current commercial BC sensors remain too costly to deploy widely. A fast, cost-effective, and easily accessible deployment of smartphone camera was used to quantify colour information of PM collected on filters to estimate BC and elemental carbon (EC) loading. When applied to 1266 PM2.5 ambient samples collected from six sites across Ontario, Canada, the RGB-based BC model showed powerful predictability with R2=0.95 between predicted and measured BC concentrations from an aethalometer. The RGB-based EC model was trained using 478 personal PM2.5 samples collected from pre-diabetic subjects in Beijing with an R2=0.91 between predicted and measured EC concentrations from OC/EC analyzer.

Keywords: black carbon
smartphone camera
Advisor: Chan, Arthur W.H.
Population genomics of the Medicago lupulina and Ensifer mutualism in North America

Species interactions such as mutualisms are a key process affecting evolution. One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and rhizobia Ensifer, I explored whether coevolution is locally structured and differs between separate populations, or is broadly structured and is similar across large geographic scales. I found higher proportions of E. meliloti in southeast populations and higher proportions of E. medicae in northwest populations but no genetic differences between M. lupulina plants hosting different species of rhizobia. M. lupulina and Ensifer populations showed different spatial genetic structure. In particular, I detected very little genetic variation in both Ensifer species. My findings suggest there is little evidence of coevolution in the M. lupulina and Ensifer mutualism or coevolution is occurring on a large geographic scale.

Advisor: Stinchcombe, John
Light-assisted Selective Chemical Synthesis on Plasmonic Nanoparticles: Titanium Dioxide on Gold Nanostars

In this thesis, light-assisted crystallization of TiO2 on gold nanostars was investigated by using gold plasmonic nanoparticles as a nano-source of heat to induce forced hydrolysis of TiCl4 precursor. The frequency of localized surface plasmon resonance and absorption cross-sections were investigated using COMSOL. Using a multi-laser Raman setup, in-situ crystallization of TiO2 was observed under various laser frequencies and intensities on four different shapes of gold nanoparticles each with a unique plasmonic resonance frequency. The correlation between laser intensity, precursor concentration, and plasmonic resonance frequency of the nanoparticles with crystallization nature of TiO2 was investigated. Through careful control over the experimental conditions we demonstrate localized crystallization of anatase TiO2 in the valleys of gold nanostars as confirmed by transmission electron microscopy. Our findings offer a new approach to the synthesis of partially covered gold-TiO2 core-shell nanocomposites with promising implications for visible light photocatalytic applications.

Advisor: Kherani, Nazir P
Cost-effectiveness of Donor Milk versus Preterm Formula for Neurodevelopment and Necrotizing Enterocolitis in Very Low Birth Weight Infants

Awareness of the benefits of mother’s milk for very low birth weight (VLBW) infants has led to a rise in donor milk (DM) use despite limited data evaluating its efficacy or cost-effectiveness. Studies estimate DM reduces hospital costs compared to preterm (PTF), but none were conducted using prospectively collected patient-level data in an RCT that reflects the actual costs of resources used. This study investigated the cost-effectiveness of DM versus PTF as a supplement to mother’s milk from a societal perspective from birth to 18 months. There was no difference in costs between groups, with median (IQR) costs of $193 404 ($129 656-$283 359) in the DM group and $189 819 ($129 343-$264 237) in the PTF group. While DM compared to PTF reduced the incidence of necrotizing enterocolitis, it did not result in cost savings nor was it cost-effective for improving neurodevelopment at 18 months corrected age.

Keywords: Donor Human Milk
Economic Evaluation
Infant
Newborn
Very Low Birth Weight
Advisor: O'Connor, Deborah L
Effects of Vitamin D, K1, K2 and Calcium on Bone Formation by Osteoblasts in Vitro

Bone loss is a major health problem that most people will face and thus research focusing on enhancing bone formation is of great importance. Although there have been many cell biology articles focusing on the effects of vitamin D, K1 or K2 on bone formation in vitro, there has yet to be a consensus amongst the literature. Through the use of several meta-analyses of past vitamin studies, we found that supplementation of vitamin D, K1 and K2, along with the combination of K2 + 1,25D, increased mineralization, while not consistently changing all of the other parameters associated with bone formation. In addition we quantified the area of von Kossa stained bone nodules in calcium, vitamin K1, vitamin K2, 25D and 1,25D treated human and mouse osteoblast cultures and found that mineralization levels varied depending on the presence of ascorbic acid or the organism from which the cell lines were derived.

Keywords: Bone
Calcium
Meta-analysis
Mineralization
Osteoblast
Vitamins
Advisor: Harrison, Rene E
Evaluation of Organic Rankine Cycle Systems for Low Power Combined Heat and Power Applications

Four Combined Heat and Power (CHP) generation system prototypes comprising an Organic Rankine Cycle (ORC) that uses R245fa as a working fluid, and a standard residential air handler were designed and fabricated. Each prototype served as the performance evaluation test bench for a different volumetric-type expander. With focus on the expander, the performance of each cycle component was evaluated and consequentially, the overall cycle efficiency was determined. With an average heat source temperature of 220° C, the cycle achieved a maximum of 400 W and 600 W of electrical and mechanical power output, respectively. The highest achieved thermodynamic efficiency of the cycle was 6.5%. The design cycle conditions weren’t achieved due to various component inefficiencies. Moving forward, the focus should be on modifying non-hermetic scroll compressors to operate as expanders and tackle the issues related to the heat exchangers to be able to produce a higher performing prototype.

Advisor: Wallace, Jim
Droplet Microfluidics for Additive Screening in Enhanced Oil Recovery

Enhanced oil recovery is a set of methods used to increase the productivity of a reservoir after it is not possible to economically produce oil using hydrostatic reservoir pressure, artificial lift devices, waterfloods or gas floods. Droplet microfluidics, the study and utilization of ordered multiphase flows in closed microchannels, is predominantly used for biological or chemical reaction screening and particle fabrication. This thesis focuses on using droplet microfluidics to inform enhanced oil recovery. A platform was developed to assess the effect of a set of additives on droplet deformation. Droplets were found to become more deformable with an increase in pH and less deformable with an increase in ionic strength and salinity. These trends agree with behaviour reported in the literature.

Keywords: additive
alkaline
droplet microfluidics
EOR
heavy oil
Advisor: Sinton, David A
Modeling Atrial Fibrillation using Human Embryonic Stem Cells

Background: Atrial fibrillation (AF) is the most common clinical arrhythmia and is associated with significant morbidity and mortality. Hypothesis: “Atrial” cardiomyocytes generated from hESCs will recapitulate the key hallmarks of human AF in a 2 dimensional tissue model, as well as demonstrate the expected electrophysiologic changes in response to drugs. Methods and Results: Our “atrial” cardiomyocytes were 80-90% positive for cardiac troponin, were enriched for the atrial markers ANF and KCNJ3, and lacked ventricular markers (MYL2 and IRX4). The “atrial” cells mimicked the human electrophysiologic phenotype with the majority (90%) demonstrating atrial like action potentials. Optical mapping of multicellular cell sheets was performed on rotors at baseline, after induction of rotor formation and with the addition of commonly employed antiarrhythmic drugs. Conclusions: We have successfully generated a human model of AF in vitro and demonstrated its utility in screening for known, and unpredicted effects of commonly employed anti-arrhythmics.

Keywords: atrial fibrillation
human pluripotent stem cells
Advisor: Backx, Peter
Genetic Analysis of Gata3 and Runx1 in Mammary Tumor Formation

Genomic analysis of breast cancer (BC) has revealed the existence of recurrent copy number losses and mutations in GATA3 and RUNX1. Interestingly, these are predominantly found in luminal tumors. GATA3 and RUNX1 are transcription factors that help specify mammary luminal lineages. To test whether BC-associated genetic aberrations of GATA3 and RUNX1 contribute to luminal-like tumorigenesis, I generated cohorts of female mice in which Gata3 and Runx1 were deleted in mammary epithelium. In addition, I have successfully generated transgenic mice that express a breast tumor-derived Gata3 mutant. To date, twelve-months old females with copy number loss of Gata3 and Runx1 are mostly tumor-free (approximately 3% and 13% of Gata3 and Runx1 conditional heterozygous have developed mammary tumours, respectively).

Keywords: Breast Cancer
Gata3
Mouse Models
Runx1
Advisor: Egan, Sean E
Correlated Evolution of Teleost Fish Rhodopsin with Habitat: Linking Molecular Changes to Ecology

A critical challenge in molecular evolutionary biology is to determine how changes in protein coding sequence correlate with ecology, physiology, or morphology. While statistical approaches aiming to investigate signatures of selection at the molecular level have been developed, methods designed to correlate these findings with macroscopic traits remain understudied. Here, I investigated amino acid replacements in the visual pigment rhodopsin (RH1) of teleost fishes that show significant association with shifts in habitat, using both existing phylogenetic comparative methods, as well as novel implementation of sequence simulations and ancestral reconstructions. Through an unbiased examination of amino acid sites in RH1, I found several substitutions that are known to affect spectral sensitivity or other properties of rhodopsin. Thirteen additional control genes showed markedly weaker associations between amino acid substitutions and habitat compared with teleost RH1. The framework established in this thesis can similarly be used to study other genes and macroscopic traits.

Advisor: Chang, Belinda SW
Pilot Study of Engineered Biofiltrations as Pretreatment for Ultrafiltration: Effects on Fouling and Disinfection By-products

This study focused on biological treatment of river and lake water to mitigate ultrafiltration fouling. Biofiltration, consisting of dual-media filtration in the absence of chlorine backwash, produced an effluent with lower turbidity and less variability than coagulation and settling alone. Biofiltration’s ability to lower turbidity, reduce biopolymer and humic concentration, and decrease membrane fouling when compared to untreated water was improved by in-line addition of low coagulant doses (

Keywords: Biofiltration
Biopolymers
Drinking water
Fouling control
Ultrafiltration
Advisor: Andrews, Robert C
Identifying Genetic Causes of Specific Phenotypes by Whole-genome Sequencing Analysis

The advent of next-generation sequencing (NGS) makes it more practicable to extract genetic information from biological systems. Whole-genome sequencing analysis has become one of the major approaches to identify genetic causes of specific phenotypes, with the help of well-developed mapping and annotation tools. My project is aimed to identify causative mutations for some mutant Saccharomyces cerevisiae strains. One class of mutants belong to Ctf strains, with increased rate of chromosome loss in mitosis. Exploration of Ctf genes is helpful to understand cellular causes and consequences of chromosome instability (CIN), thereby elucidating mechanisms of some human diseases. Another class of mutants are strains that adapted for stronger growth in His- medium in a yeast two-hybrid assay (“papillation strains”). Papillation strains could harbor spontaneous genetic modifiers of protein-protein interactions (PPIs). By computational analysis of whole-genome sequencing data, I identified some candidate genes responsible for these two phenotypes, respectively, and validated some candidate Ctf genes experimentally.

Keywords: Chromosome instability
Whole-genome sequencing
Yeast
Yeast two-hybrid assay
Advisor: Roth, Frederick
Visual Scanning Behaviour in Patients with Alzheimer's Disease

Alzheimer's disease (AD) is characterised by memory loss and is often accompanied by psychiatric disorders. Since there are difficulties administering standard cognitive and psychiatric tests to patients with AD, it is desirable to develop objective tests of such functions. Novel tests to assess memory loss and apathy in AD were developed. The tests are based on the analysis of visual scanning behaviour (VSB) when participants look at visual stimuli. Differences between the VSBs of patients and controls are used for the assessments. When compared to controls, patients with AD had significantly reduced differences between their VSBs on novel and previously shown images. This was used to assess memory loss and to accurately classify patients with AD from elderly controls. Also, apathetic patients with AD showed more uniform VSBs on images with different arousal. The results suggest that analysis of VSB can help to assess memory and psychiatric functions in AD.

Keywords: Alzheimer's Disease
Apathy
Cognition
Eye Tracking
Visual Scanning Behaviour
Advisor: Eizenman, Moshe