VictorJuiz/thesis huggingface dataset:
Investigation of the influence of heterogeneous and anisotropic nature of rock mass on blast-induced outcomes - a case study at Detour Lake mine
Keywords: blast-induced fragmentation
blast-induced rock movement
blasting
data analytics
rock mass characteristics
statistical analysis

Blasting is the initial stage of comminution in mining. It has significant influence on the cost and efficiency of downstream operations. A highly heterogeneous orebody requires control and minimization of blast-induced rock movement to reduce ore-loss and dilution. The objective of this study is to characterize the influence of rock mass properties on blast-induced rock movement and fragmentation. Statistical analysis of rock mass geological and geomechanical data as well as multi-year blasting data collected from Detour Lake mine, indicate that both intact rock strength and RQD can influence blast-induced rock fragmentation, however, blast-induced rock movement is only influenced by the intact rock strength. Using predictive analytics the blast-induced outcomes (fragmentation and movement) were modeled by incorporating rock mass properties and blasting parameters. Decision trees were developed which can help to achieve the desired blast-outcomes by changing the blasting parameters.
Successive Cancellation List-Based Latency and Computational Complexity Reduction for Polar Codes
Keywords: bit skipping
hybrid decoding
list decoding
polar codes
successive-cancellation decoding

Polar codes provide a promising new direction in channel coding that is expected to play a vital role in 5G wireless cellular communication systems. Successive cancellation list (SCL) decoding, as a widely adopted decoding scheme for polar codes, sacrifices decoding complexity and latency to improve error performance. To address the shortcomings of SCL, a decoding complexity and latency reduction technique, denoted bit skipping and verified to be applicable for most list decoders, is proposed in this thesis. By bypassing unnecessary sorting operations, bit skipping reduced the decoding complexity, for a half rate code, by 27.2% while increasing throughput by 19.1%. A hybrid decoder for decoding complexity reduction was also proposed and was shown to reduce the decoding complexity by up to 97.8% under favorable channel conditions.
Nicotinamide Mononucleotide in the Context of Elevated Plasma Levels of Free Fatty Acids Improves Glucose Tolerance by Decreasing Insulin Clearance
Keywords: beta cell dysfunction
insulin clearance
lipotoxicity
nicotinamide mononucleotide
SIRT
type 2 diabetes

The NAD-dependent deacetylase SIRT1 has been shown to be beneficial to beta cell function. Nicotinamide Mononucleotide (NMN), the product of the rate-limiting enzyme in NAD synthesis, has recently been shown to have positive effects on glucose tolerance in mice fed a high fat diet. This is the first study to examine the effects of NMN on insulin clearance and FFA-induced beta cell dysfunction. NMN was i.v. infused, with or without oleate, in C57BL/6 mice over 48h in order to elevate intracellular NAD levels and consequently increase SIRT1 activity. We demonstrated that administration of NMN in the context of elevated plasma FFA levels results in a significant decrease in insulin clearance as well as partial protection against FFA-induced beta cell dysfunction in vivo. This culminated in a large improvement in glucose tolerance. In summary, NMN may have a therapeutic potential to improve glucose tolerance in conditions of increased plasma FFA levels, which is typical in patients with type 2 diabetes mellitus.
Once Daily Aminoglycoside Pharmacokinetics and Optimal Tobramycin Dosing in the Burn Population: A Prospective Study
Keywords: burn
once daily aminoglycoside
pharmacokinetic
tobramycin

Background. Once-daily aminoglycoside (ODA) dosing is not commonly recommended in burn patients due to altered pharmacokinetics (PK). The objective was to determine the ability of ODA dosing to achieve target concentrations in burn patients. Methods. A single dose of tobramycin 10 mg/kg was given to patients with a total burn surface area (TBSA)
The Impact of Adult Heatlh Care Model (Academic versus Community) on Emergent Health Resource Utilization in Patients with Pediatric-onset Inflammatory Bowel Disease
Keywords: Health Resource Utilization
Inflammatory Bowel Disease
Transition

Background: Patients diagnosed with Inflammatory Bowel Disease (IBD) during childhood require transfer to an adult gastroenterologist. Purpose: The purpose of this study was to determine the impact of post-transfer health care setting (academic vs. community) on emergent health resource utilization. Methods: This was a population-based retrospective cohort study using health care administrative data from Ontario, Canada. Patients with PO-IBD were identified and health resource utilization during a 2-year pre-transfer period, transfer of care period and 2-year post-transfer period was analyzed. Comparator groups included academic vs. community vs. loss-to-follow-up. The primary outcome comprised Emergency Department (ED) utilization. Secondary outcomes included hospitalizations, surgeries, ambulatory visits, endoscopic and radiological investigations. Results: There were no significant differences found in ED use, ambulatory care visits (aside from the lost to follow-up group), hospitalizations, endoscopic or radiological procedures. Conclusion: Post-transfer healthcare setting does not impact emergent health resource utilization in the post-transfer period..
The Development and Characterization of VX-770 Molecular Probes
Keywords: CFTR
cystic fibrosis
potentiator

Cystic fibrosis is the most common genetic disease affecting the Canadian population. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, and there is currently no cure. In 2012, VX-770 became the first FDA approved drug targeting the genetic defects of CF; its binding site and mechanism of action are currently unknown. In the present study, we studied the structure-function relationship of VX-770. We determined the structural components that are critical for activity and identified a position on the structure that could be modified without compromising its effects. These findings led to the generation of VX-770-Biotin and VX-770-Rhodamine. Subsequent testing of the two molecular probes suggests that they both retain properties of the parental drug VX-770. Hence, VX-770-Biotin and VX-770-Rhodamine may be used to provide further insight into the VX-770 binding site and mechanism of action, enabling the design of more effective drugs for CF therapy.
Design & Validation of a Hybrid-capture Next-generation Sequencing-based T-cell Clonality Assay
Keywords: bioinformatics
clonality
gene rearrangement
lymphoma
t-cell receptor
validation

This project details the development of a novel NGS-based T-cell clonality assay, incorporating all four TcR loci. The assay was both analytically and clinically validated. For the former, a series of idealized specimens was used, with combined PCR/Electrophoresis and Sanger Sequencing to confirm NGS-data. The latter validation compared NGS results to the current gold standard for clinical T-cell clonality testing (i.e. the BIOMED primer PCR-based method) on an appropriately-sized minimally-biased sample of hematopathology specimens. In the latter dataset, the patterns of T-cell clonality were also correlated with clinical, pathologic, and outcome data.
Integrated Asymmetric Hybrid Plasmonic Waveguides and Devices
Keywords: Integrated circuits
Nanofabrication
Optoelectronics
Photonics
Plasmonics
Semiconductors

Long-range hybrid plasmonic modes with optimal loss-confinement trade-off are enabled in asymmetric waveguides irrespective of material or structural symmetry by engineering conditions for electric field matching. A field-symmetric superposition of coupled hybrid and SPP modes enable the design of asymmetric hybrid-SPP plasmonic waveguides with 0.021dB/Îźm propagation losses and 0.15Îźm^2 mode area confinement across telecom-wavelength range. Moreover, a highly efficient junction coupling of 71% between hybrid-SPP waveguides and silicon nanowires allows integration of compact plasmonic devices such as microring resonators and photodetectors into conventional silicon technologies. The performance for these passive devices are experimentally verified in samples that can be reproducibly fabricated thanks to improvements in the latest nanofabrication techniques. The unique properties of the coupling mechanism asymmetry between hybrid and SPP modes allow the potential to explore the design of both low loss optical circuits, as well as enhanced absorption for photodetection on the same platform.
Survival, Treatment Patterns, and Identifying Predictors of Receipt of Adjuvant Therapy and Survival for Curative-intent Pancreatic Adenocarcinoma: A Population-based Analysis
Keywords: Adjuvant treatment
Marginalization
Outcomes
Pancreatic cancer
Population

Introduction: Pancreatic adenocarcinoma (PC) is a leading cause of cancer-related mortality in North America. Methods: This study was conducted as a retrospective observational cohort trial of patients undergoing resection of PC in the province of Ontario, Canada between 2005-2010. The study involved linkage of administrative datasets, and abstraction of resection specimen pathology reports. Overall survival (OS) and receipt of adjuvant treatment were the primary outcomes in this study. Adjuvant treatment was classified as chemotherapy (CT) or chemoradiation therapy (CRT). Results: While adjuvant CT or CRT were not associated with improved OS, those with node-negative disease benefited from adjuvant CT. Histopathologic factors were the strongest prognostic factors. Substantial variation in the likelihood of receiving adjuvant treatment between different institutions treating PC was identified. Residential instability, material deprivation, rurality, and median income were associated with receipt of surgery among PC patients. Conclusions: Outcomes following resection are primarily determined by tumour biology.
Expression of Clostridium acidurici 9a Glycine Cleavage System in Escherichia coli for Formatotrophic Growth via Reductive Glycine Pathway
Keywords: Biofuel
Escherichia coli
Formate
Glycine Cleavage System

There has been a marked increase in carbon dioxide levels in the atmosphere over the years, presenting countries with the task of reducing the emissions. This drives the motivation of discovering methods to fix carbon dioxide into valuable commodities. Microorganisms can be engineered to express pathways that do not exist naturally, and more efficient at providing high yields and titre of a particular product. This principle serves as the basis for this research project. A computationally designed carbon fixation pathway for growth on formate, known as the reductive glycine pathway, can theoretically produce pyruvate, a central to E. coli metabolites, through the expression of recombinant genes. The goal of the project is to test the expression of a bidirectional glycine cleavage system that has been cloned from C. acidurici 9a in E. coli, which is predicted to be a major pathway expression challenge for the reductive glycine pathway.
Characterizing the Immuno-genomic Landscape of High-grade Serous Ovarian Cancer Patients with Exceptional Long- and Short-term Survival
Keywords: BRCA1/BRCA2
Cancer Genomics
Ovarian Cancer
Survival

Despite poor overall survival (OS) for patients diagnosed with high-grade serous ovarian cancer (HGSOC), a subset experience long-term (LT) survival (â Ľ 10 years, vs. 1.7 years median OS). In this study, we compared clinical, genomic, and transcriptomic characteristics of 41 treatment-naive tumour specimens from HGSOC LT (n=20) and short-term (ST,
Frequency Detection for Reference-less Baud-rate Clock and Data Recovery in 28nm CMOS
Keywords: baud-rate
CDR
CTLE
DFE
frequency detectors
wireline transceivers

This thesis presents the analysis, design, simulation, and measurements of a frequency detection method for a reference-less baud-rate clock data recovery (CDR) circuit. This CDR was designed with a continuous-time linear equalizer (CTLE) and a 1-tap decision feedback equalizer (DFE) to implement a high-speed wireline receiver in a 28nm CMOS process and packaged in a 40-pin Quad-Flat No-leads (QFN) package. The frequency detection method automatically controls an adjustable baud-rate phase detector to correct frequency error between the incoming data and the recovered clock without a separate frequency acquisition loop in the CDR. To characterize the performance of this method, PRBS-31 data ranging from 22.5Gb/s to 32Gb/s was transmitted across a Tyco 5-inch channel with -10.1dB to -14.8dB channel loss at Nyquist. The frequency detection method was measured to achieve a capture range of 34%. The entire receiver achieved a power eciency ranging from 2.9pJ/bit to 3.2pJ/bit.
Global and CMV-specific Immune Assays to Predict Clinical Outcomes and Inform Clinical Practice in Solid Organ Transplant Recipients
Keywords: Cell-mediated Immunity
CMV
Immunosuppressive medication
Infectious Disease
Transplantation

Solid organ transplantation is an effective procedure for the treatment of end-stage organ failure. However, transplantation can be limited by imprecise immunosuppression and thereby, susceptibility to infections. Assays that measure immune function by quantifying release of cytokines following stimulation of immune cells have shown some predicative value for the development of infections in immunocompromised individuals. This thesis investigates the predictive value, feasibility and clinical benefit of using immune assays in the context of solid organ transplantation. We demonstrated that a newly developed global (innate and adaptive) cell-mediated immune assay called QuantiFERON-Monitor had the ability to quantify the degree of immunosuppression and predict susceptibility of transplant recipients for developing infections. Furthermore, we showed that a cytomegalovirus(CMV)-specific immune assay called QuantiFERON-CMV could predict which patients were susceptible for developing recurrent CMV infections. Finally, we demonstrated that CMV-specific cell-mediated immunity as measured by QuantiFERON-CMV was both feasible and useful in personalizing CMV prophylaxis.
The Effect of Folic Acid Supplementation on Chemosensitivity of Human Breast Cancer Cells in an in vitro Model
Keywords: 5-fluorouracil
breast cancer
chemosensitivity
folate
folic acid

In North America, blood folate levels have dramatically increased due to mandatory folic acid (FA) fortification and widespread supplement use. Breast cancer patients report highest FA containing supplement use. 5-fluorouracil (5-FU) is the cornerstone of breast cancer chemotherapy, mechanisms of action which are based in part on interruption of folate metabolism. Concerns have been raised whether increased folate status may interfere with 5-FU chemotherapy for breast cancer. This study investigated whether FA supplementation can affect chemosensitivity of human breast cancer cells to 5-FU in 3 distinct human breast cancer cell lines. FA supplementation significantly decreased 5-FU chemosensitivity in MDA-MB 231 cells, significantly increased 5-FU chemosensitivity in HCC1937 cells and induced an inverted U shape response in MCF-7 cells. Given the high FA intake in breast cancer patients, the results from this study are concerning and future studies are warranted to clarify the effect of FA supplementation on 5-FU chemosensitivity.
The Activism of First Generation Somali Canadian Women within a Neoliberal Multicultural State
Keywords: Activism
Anti-Black Racism
Immigration
Intersectionality
Multiculturalism
Somali Women

This thesis aims to explore the activism of first generation Somali Canadian Women (FGSCWA). It specifically asks 1) how do Somali women activists engage, contest and modify existing social relations within their community and mainstream society to foster anti-racist, anti-Islamaphobic feminist spaces; 2) in what ways does their activism challenge the systematic racism and Islamaphobia that is explicitly and implicitly imbedded in Canadian institutions and social relations and; 3) how has their activism and advocacy challenged the normative discourse of neoliberal multiculturalism, while simultaneously contesting gender norms and cultural dogma within the Somali community. This study combines two theoretical approaches to understand issues of citizenship, boundaries of Blackness and Muslim identity, power, representation and knowledge production in relation to Somali women activists. Working within a post-colonial and Black feminist framework, this research paper utilizes the in-depth interviews I conducted with eight Somali women activists, narrating their perspectives and lived experiences.
Addressing the Effects of Distractors in a Brain-computer Interface
Keywords: brain-computer interface
cognitive load
distractor
electroencephalography
motor imagery

This thesis investigated the effects of transient, visual task-irrelevant distractors on a brain-computer interface (BCI). In the first study, a motor imagery BCI was developed using electroencephalography (EEG) to measure brain signals. The performance of this system was validated in both an offline and online setting. The second study examined the effect of distractors on motor imagery-related brain patterns and on the classification accuracy of the developed BCI system. While distractors appeared to attenuate motor imagery-specific brain activity, BCI performance did not differ significantly amid distractors, indicating that the BCI system was fairly robust to distractor effects. In the third study, distractors were found to significantly increase a physiological index of cognitive load. This thesis demonstrated that it is important to address the effects of distractors in BCIs, particularly on cognitive load, to allow for the eventual translation of BCIs from the lab to the home.
Development of a Receptor Internalization Assay for Measuring and Analysing RGS9-2 and Palmitoyl-CoA Transferase Activity in HEK Cells
Keywords: D2R
DHHC5
Internalization
R7BP
RGS9-2

Regulator of G-protein signalling 9-2 (RGS9-2) complex inhibits agonist-dependent dopamine receptor D2R activity and internalization, and plays a protective role against the development of neuro-reward circuit dysfunction. R7 binding protein (R7BP) is necessary for RGS9-2 protein stability and trafficking. Preliminary work from our group has shown the palmitoyl-CoA transferase, DHHC5, can facilitate R7BP trafficking, however this function can also enhance RGS9-2 trafficking and function. The aim of this work is to establish an in vitro assay to verify the effects of DHHC5 and R7BP on the internalization of D2R in HEK cells. We established a modified ELISA protocol that consistently showed ~20% internalization of surface D2R, which is not ideal, possibly due to the poor internalization properties of D2R in HEK cells. Future efforts, therefore, will require the development of other functional assays to examine the role of DHHC5, R7BP and RGS9- 2 as a regulator of D2R signalling and function
Anti-RBC Antibody Mediated Erythrocyte Phagocytosis and its Therapeutic Role in Immune Thrombocytopenia (ITP)
Keywords: Anti-D
anti- erythrocyte antibodies
Immune Thrombocytopenia
platelets

Immune thrombocytopenia (ITP) is a platelet autoimmune disorder diagnosed by an isolated low platelet count and the absence of other causes of thrombocytopenia. Rh immune globulin (anti-D) is a first line therapy for ITP which targets the RhD antigen on erythrocytes. Monoclonal antibodies are desirable alternatives to anti-D for various reasons. Here, nine erythrocyte-specific antibodies were evaluated for their ability to opsonize RBCs for phagocytosis and prevent platelet destruction in vitro using these opsonized RBCs. Only three (34-3C, TER119 and M1/69) effectively induced phagocytosis of RBCs. Antibodies that were able to opsonize RBCs for phagocytosis also inhibited platelet phagocytosis. TER119, 34-3C and M1/69 are the only antibodies tested that ameliorate ITP in a passive mouse model. These data suggest that the ability of an antibody to prevent platelet phagocytosis in vitro could be indicative of its ability to ameliorate ITP. We speculate that a future screening tool to test the therapeutic ability of monoclonal antibodies in ITP may be possible using these methods.
Galectin-9 Regulates B Cell Receptor Signaling
Keywords: B cell activation
BCR signaling
Galectin-9
Glycan-galectin-9 lattices

B cells are an essential component of the adaptive immune system, which secrete soluble antibody against pathogen (antigen). Given that glycan-galectin lattices have been shown to regulate cell surface glycoprotein organization and signaling, one of these galectins is Galectin-9 (Gal-9); a secreted lectin with two carbohydrate recognition domains linked by a flexible peptide. Here, we show that Gal-9 is expressed at the cell surface of primary B cells, organized into discrete puncta. Gal-9 deficiency enhanced BCR microcluster formation and increased BCR signaling. Moreover, treatment of wild-type B cells with exogenous Gal-9 is sufficient to inhibit cell signaling upon BCR stimulation, suggesting that Gal-9 is a negative regulator of B cell activation. We identified CD45 and IgM as ligands for Gal-9 to which they colocalized with Gal-9 lattices. Taken together, our data suggests that Gal-9-glycan interactions at the surface of B cells plays an important role in regulating B cell signaling.
Metabolic Engineering of Escherichia coli for Production of Adipic Acid through 2-Hexenedioate Pathway
Keywords: 2-hexenedioate
adipic acid
alpha-ketoadipate
alpha-ketoglutarate
Escherichia coli
metabolic engineering

Adipic acid is one of the most important platform chemicals in industry. Bio-based production of adipic acid is a promising alternative to the current petrochemical production routes which cause environment and energy concerns. This work describes efforts to construct a platform strain of Escherichia coli for production of adipic acid. First, we constructed an E. coli strain harbouring part of the α-aminoadipate pathway from Saccharomyces cerevisiae. Through fed-batch fermentation, the strain showed its capability of producing α-ketoadipate, a precursor of adipic acid, from its native metabolite α-ketoglutarate. Second, we constructed an E. coli strain harbouring a pathway converting α-ketoadipate to adipic acid. Through various studies, we were able to illustrate that all enzymes of the pathway are active in vivo. This work demonstrates the capability of E. coli for production of α-ketoadipate and paves the way for further studies on conversion of α-ketoadipate to adipic acid.
Childhood Maltreatment and Parenting Alliance: Can We Get Along if You Regulate My Emotions?
Keywords: childhood maltreatment
emotion co-regulation
parenting alliance

This study investigated the effect of childhood maltreatment history on parenting alliance and examined whether emotion regulation mediates this link. I further examined whether emotion co-regulation could buffer individuals with childhood abuse history and their co-parenting partner against poor parenting alliance. This model was tested using mothers and fathers recruited from the community and from intervention programs addressing family violence. Consistent with my predictions, child maltreatment history was negatively associated with self-reported and partner-reported parenting alliance. However, contrary to my hypotheses emotion regulation abilities did not mediate this relationship. Furthermore, perceived partner emotion co-regulation abilities did not act as a buffer for maltreated individuals, as perceived partner co-regulation predicted better parenting alliance regardless of maltreatment severity. These findings highlight the associations between child maltreatment and subsequent co-parenting outcomes, and suggest that clinicians consider the positive influence of emotion co-regulation on co-parenting functioning for maltreated individuals and their co-parenting partners.