VictorJuiz/thesis huggingface dataset:
Digital Labcoat: An Active Learning Tool for Teaching the Scientific Method in the Social Sciences
Keywords: Digital Labcoat
eLearning
online learning
scientific literacy

Active learning methods have established themselves as the "gold standard" of teaching, and are recommended as part of good teaching practice. In high-enrollment university courses, incorporating active learning activities can be difficult, as they are often a resource-intensive undertaking, requiring large time commitments on the part of the instructor. By turning to online technologies, it may be possible to introduce low-cost implementations of active learning activities. To this end, we have created a web application called Digital Labcoat -- a tool for introductory social sciences courses that implements active learning methodology to engage students in the scientific method and improve scientific literacy. The present study examines the use the Digital Labcoat software in large university courses, and assesses its success at achieving its educational goals. The results establish Digital Labcoat as a feasible assessment tool that is associated with increased student understanding of the scientific method.
lprof: A Non-intrusive Request Flow Profiler for Distributed Systems
Keywords: Distributed system
Performance
Profiling
Static analysis
System logging

Applications implementing cloud services, such as HDFS, Hadoop YARN, Cassandra, and HBase, are mostly built as distributed systems designed to scale. In order to analyze and debug the performance of these systems efficiently, it is essential to understand the performance behavior of system requests, both in aggregate and individually. lprof is a profiling tool that automatically reconstructs the execution flow of each request in a distributed application. It infers the execution-flow from logs and binary code and thus does not require any modifications to the application. lprof first statically analyzes an application’s binary code to infer how logs can be parsed so that the dispersed and intertwined log entries can be stitched and associated to specific individual requests. We evaluate lprof on the four widely used distributed services mentioned above. The result shows that lprof ’s precision in request extraction is 90%, and lprof is helpful in diagnosing 65% of the random sampled real-world performance anomalies.
Innate Immune Responses to Infection with the Lyme Disease Pathogen in Diet-induced Obesity
Keywords: Borrelia burgdorferi
Diet-induced obesity
Immune
Innate
Macrophage
Neutrophil

This thesis reports the effects of high-fat diet (HFD)-induced obesity (DIO) on infection the Lyme disease pathogen Borreali burgdorferi. Male and female mice were fed a HFD or normal diet (ND) and infected with B. burgdorferi. Bacterial burden, pathology, systemic leukocyte and cytokine responses, basal and Borrelia-elicited macrophage cytokine production, and neutrophil and macrophage and leukocyte bacterial uptake assays were performed. DIO was associated with increased bacterial DNA burden and Lyme carditis pathology, which were associated with attenuated Borrelia uptake and cytokine production by neutrophils and macrophages in infected mice. DIO-dependent increases in burden were most pronounced in TLR4-expressing mice and females. Unexpectedly, Borrelia infection alone caused weight gain in ND mice at a rate similar to HFD. Together, these results suggested that obesity may be a risk factor for and affect outcomes of Lyme disease in humans.
Microsimulating Active Transportation Mode Choice using Smartphone-based Travel Survey and Transportation Tomorrow Survey Data
Keywords: active transportation
bicycle
built environment
mode choice
smartphone-based travel survey
walk

Using a new smartphone-based travel survey and a traditional travel survey, the Toronto Tomorrow Survey (TTS), a probit active transportation mode choice model is built and integrated into the GTAModel V4.0, an agent-based regional travel demand model for the Greater Toronto and Hamilton Area (GTHA). The model incorporates a set of traffic analysis zone (TAZ)-based built environment measures that can reflect the environment pedestrians experience, including land-use mix, pedestrian infrastructure, street safety factors, the presence of barriers, average elevation difference, and the presence of recreational space. The results show that pedestrian infrastructure and street speed have the most impact on the choosing walk and bicycle modes, while the impact of degree of land use mix is moderate. The model calibrated using TTS showed an acceptable degree of improvement, especially in walk mode choices. The smartphone-based travel survey has potential but needs to be more robust for further improvements.
Modeling and Analysis of User-centric and Disjoint Cooperation in Network MIMO Systems
Keywords: Beamforming
cooperative coomunications
coordinated multi-point (CoMP)
network MIMO
stochastic geometry

This thesis provides an analytical performance characterization of user-centric and disjoint cooperation for both uplink (UL) and downlink (DL) network multiple-input multipleoutput (MIMO) systems, where base-stations (BSs) form clusters to jointly transmit information to and receive information from multiple mobile users. We specically focus on the user-centric BS clustering strategy in which cooperating cluster of neighboring BSs is formed for each user individually and the clusters for dierent users may overlap. We consider the random topology where the BSs and users form Poisson point processes to facilitate analysis. This thesis shows that as compared to with disjoint BS clusters, the eect of user-centric clustering is that it improves signal strength in both UL and DL, while reducing cluster-edge interference in the DL. As a result, user-centric clustering has larger ergodic rate gain in the UL than DL, while it has signicant rate gain for cluster-edge users in the DL.
Effects of Orthodontic Appliances on Diagnostic Quality of MR Images of the Head
Keywords: artifact
brackets
diagnostic quality
MRI
orthodontic appliances
retainers

Introduction: The influence of four common fixed orthodontic appliances on artifact formation and diagnostic quality of head MR images produced by a 3 Tesla MR scanner was studied. Methods: Stainless steel brackets, ceramic brackets, combination of ceramic brackets and steel molar tubes, and multistranded steel mandibular lingual retainers were embedded into custom made Essix® trays for each of 10 adult subjects. Head MR scans of nine regions were acquired for each subject wearing these trays. Sagittal T1-weighted, axial T2-weighted, axial gradient-recalled, axial diffusion-weighted, non-contrast axial MR angiography and axial fluid-attenuated inversion recovery MR sequences were included. Two neuroradiologists evaluated image distortions and diagnostic qualities of the 13860 acquired images. Results: Images were affected by appliance, head region and MR sequence. Conclusions: Head MR images are differentially affected by the presence of orthodontic appliances. The appliance, region imaged and MR sequence need consideration before imaging patients wearing different fixed orthodontic appliances.
Interaction and Secrecy in Gaussian Diamond Relay Networks
Keywords: diamond relay network
fundamental limits
information theory
physical layer security
secure degrees of freedom
wiretap channel

In this thesis, the physical layer secrecy for several Gaussian network models are studied. We first establish the secure degrees of freedom (d.o.f.)~of helper-assisted Gaussian wiretap channel with shared keys between the transmitter and the helpers. As a natural extension, we next consider the Gaussian diamond wiretap channel where the relays can obtain common randomness from the source node. Secure d.o.f.~for the diamond wiretap channel is established and upper and lower bounds for the multi-relay case are also provided. We then study the diamond channel with conferencing links and investigate the effects of the conferencing links under Gaussian channel as well as binary adder MAC channel. Finally we discuss the artificial noise transmission for secrecy with constant-amplitude constraint for the beamforming vector. The effects of such constraint are examined and algorithms to solve for the beamforming vector are given.
Development of Water-soluble Mn(III) Porphyrin as Extracellular MRI Contrast Agents: Optimizing Relaxivity at High Magnetic Field
Keywords: Contrast Medium
Magnetic Resonance Imaging
Metalloporphyrins

In magnetic resonance imaging (MRI), contrast agent (CA) plays a significant role in modulating signal intensity and enhancing tissue contrast. Gadolinium-based CAs (GBCAs) are routinely applied in clinical settings for detecting diseases involving disrupted vascularity, such as tumors and stroke. Despite their clinical success, the applications are constrained by their suboptimal contrast enhancement efficiency (relaxivity) at high clinical field and their associated Gd-toxicity. To overcome these limitations, we focus on the development of Gd-free CAs based on manganese(III) porphyrin (MnP). MnTCP was developed as the first MnP-based ECF agents with superior properties.. In the thesis, three different chemical approaches have been explored to further optimize MnTCP. Approaches of improving relaxivity by dimerization (Chapter 2), incorporating biocompatible polyhydroxyl amide (Chapter 3) and tuning electronic properties in porphyrin ligand (Chapter 4) are investigated. Among all novel MnTCP derivatives, MnTrCP2 showed the most promising results. Preliminary studies on relaxivity optimization have yielded encouraging results.
Adverse Cardiac Events Among Older Patients on Venlafaxine: A Population-based Study
Keywords: Adverse Drug Safety
Cardiovascular
Venlafaxine

Background: It is unknown whether the common antidepressant, venlafaxine, is associated with increased cardiovascular risk. Objective: To examine the cardiac safety of venlafaxine in older individuals. Methods: A population-based retrospective cohort study (Ontario, Canada) compared patients aged >=66 years who commenced treatment with venlafaxine, sertraline or citalopram between 2000 and 2009. The primary outcome was a composite of death or hospitalization for myocardial infarction or heart failure within the first year of therapy. Results: Following inverse probability of treatment weighting with the propensity score, we found no difference in the primary outcome with venlafaxine relative to sertraline (hazard ratio (HR) 0.97; 95% confidence interval (CI) 0.93 to 1.02). When compared to citalopram, however, an increased risk was observed (HR 1.39; 95% CI 1.19 to 1.62). Conclusions: As compared with sertraline, venlafaxine was not associated with an increased risk of adverse cardiac events. The increased risk observed in the venlafaxine -citalopram comparison warrants further study.
Preliminary Study Integrating CACNA1C RS1006737, Hippocampal and Amygdala Volumes, and Peripheral Endothelial Function in Youth with Bipolar Disorder
Keywords: Amygdala
CACNA1C
Hippocampus
Imaging
Reactive Hyperemia Index
Youth Bipolar Disorder

Multiple genome wide association studies have identified a bipolar disorder (BD) - risk allele polymorphism (CACNA1C rs1006737). rs1006737 is implicated in neurostructural differences in non-BD carriers. As CACNA1C codes for a protein subunit responsible for endothelial function, we predicted it might serve as a genetic underpinning for both the cardiovascular and neurological phenotypes seen in BD. Fifty adolescents (25 healthy controls, 25 BD) completed genotyping, structural scans, and an endothelial function test [reactive hyperemia index (RHI)]. No gene effects were observed in the amygdala or hippocampus, however healthy carriers of the risk allele showed trending reduced volume in the bilateral hippocampus and amygdala when compared to healthy non-carriers. Furthermore, RHI was non-significantly negatively correlated with left hippocampus volume in HC non-carriers, and a significant gene-RHI interaction was observed in the hippocampus of HC. These findings suggest CACNA1C rs1006737 warrants further study as a potential bridge between BD and vascular dysfunction.
Cost-­effective Care Delivery Models in Ambulatory Surgery: Expedited Discharge and Virtual Care
Keywords: ambulatory surgery
cost-effectiveness
delivery of health care
health services research
health technology assessment
quality of health care

My Master’s thesis applies the Value Agenda framework to the ambulatory breast reconstruction population. The first study uses patient level quality of recovery (QoR) data to determine if autologous breast reconstruction is suitably performed in an ambulatory facility. We found that QoR scores approach baseline by postoperative day 7; and are comparable to other ambulatory surgery patient populations1. In keeping with the Value Agenda, this study uses patient outcome data to support autologous breast reconstruction in more cost-effective, ambulatory facilities. The second study models the cost-effectiveness of replacing in-person follow-up care with mobile app follow-up care during the first month following ambulatory breast reconstruction. We found a societal incremental net benefit of $245 CAD between mobile app and in-person follow-up care. Mobile app follow-up care expands the geographical reach of breast reconstruction by reducing the burden of physical patient travel and its associated costs after surgery.
Renewable Energy Technology and the Hotel Sector of Small Island Developing States (SIDS): Managing Sustainability Transitions on the Island of Barbados
Keywords: Barbados
Governance
Hotels
Renewable Energy
Small Island Developing States
Transition Management

This thesis examines the barriers to renewable energy technology within the hotel sector of Barbados. The topic is approached using the theoretical perspective of transition management. An economic analysis of renewable energy technologies applicable to Barbados is coupled with the insights of stakeholder interviews. Consequently, the space created for hotels to implement innovations in renewable energy technology is discussed. In particular, identified barriers are used to characterize the existing energy regime on the island. The categories of barriers identified are: institutional, market, economic, technical and socio-cultural. Despite favorable levelized costs of electricity for renewable energy technologies there must be new governance activities and market-based approaches to facilitate an energy transition within island hotels.
Multi-modal Heart-Beat Estimation on an iPhone
Keywords: Heart Rate
iOS application
Machine Learning
Signal Processing

Current generation smartphone video cameras and microphones enable photoplethysmography (PPG) and phonocardiography (PCG) acquisition. In this thesis, I utilized the iPhone microphone and camera to measure heart rate. We developed a heart rate measurement system using triple sensing mechanisms (finger and face color changes and heart sound measurement) all on the iPhone. The three proposed measurement systems each provide an independent heart rate estimate, as well as a combined estimation based on the fusion of the individual sensors.The proposed algorithm estimates the heart rate by (1) heart pulse analysis to compute the heart rate of the user using our version of the EMD algorithm which is used in advanced biomedical signal processing, (2) assessing the quality of the PPG and PCG waveforms using the Support Vector Machine (SVM) classifier,(3) concisely combining heart rate information from the three different modalities based on the assessed quality of the waveforms.
Role of Adiponectin in Monocytic Microparticle-Induced Endothelial Dysfunction
Keywords: Adiponectin
AMPK
inflammation
Microparticles
microvesicles

Monocyte-derived microparticles (MPs) have been suggested to link cardiovascular risk factors to vascular injury. We hypothesized that adiponectin, an anti-inflammatory and vasculoprotective adipokine, limits the production and/or action of monocytic MPs on endothelial cells. Adiponectin attenuated MP release from untreated THP-1 monocytes and lipopolysaccharide (LPS)-treated conditions. Furthermore, peritoneal monocytes from Adipoq−/− mice generated significantly greater MPs than those from Adipoq+/+ littermates in the absence and presence of LPS. LPS-induced MP expression of NLRP3 inflammasome and its principal components, namely cleaved ASC, caspase-1, and IL-1β (pro- and cleaved), were all markedly attenuated by adiponectin treatment. HUVECs incubated with MPs from LPS-treated THP-1 cells exhibited an increase in the expression of VCAM-1; adiponectin inhibited this effect. The effects of adiponectin on MP release and molecular signaling occurred at least in part through modulation of the AMPK-Akt and NFκB pathways. The findings highlight another pleiotropic effect of adiponectin in limiting endothelial activation.
Novel Synthesis of Phosphonamidated Carbohydrates Designed as Transition-State Analog Inhibitors of CE4 De-N-acetylases
Keywords: antimicrobial
Biofilm
De-N-acetylase
PgaB
Phosphonamidate
SpPgdA

Carbohydrate Esterase Family 4 enzymes include de-N-acetylases that are essential bacterial virulence factors. They include enzymes that deacetylate PNAG, a glycan composed of repeating units of beta-1,6 linked N-acetylglucosamine residues, to form polysaccharide intercellular adhesion (PIA or dPNAG), which is an essential component of the biofilm matrix of many pathogens. They also include de-N-acetylases that act on beta-1,4 linked N-acetylglucosamine residues present in bacterial peptidoglycan, which allows evasion of innate immune defenses. To target these enzymes for development of antimicrobial agents, transition-state analog inhibitors containing a phosphonamidate moiety and various specificity groups around a central glucose scaffold were synthesized using a novel direct Staudinger-phosphonite reaction. The inhibitors were tested via in vitro inhibition assays with purified PgaB, the PNAG de-N-acetylase from Escherichia coli, and SpPgdA, the peptidoglycan de-N-acetylase from streptococcus pneumonia. This resulted in identification of the most potent inhibitor of peptidoglycan de-N-acetylases reported to date, with an inhibition constant of 80 µM.
On the Catalytic Gasification of a Municipal Solid Waste Residue, using Alkali and Alkaline Earth Carbonate Catalysts
Keywords: catalytic gasification
drop tube furnace steam gasification
Municipal solid waste
municipal solid waste residue
Oxygen gasifying agent
thermogravimetric analysis oxygen gasification

Catalysis in gasification has been known since 1921. At that time the primary substrate was coal. New substrates have since been processed and include biomasses, sludges, and recently the carbonaceous portion of municipal solid waste (MSW). An analogue of the residue of the last substrate is natural graphite, as under severe (+550 celcius) pyrolysis conditions, carbon tends to graphitize. This material tends to accumulate in processes such as downdraft steam gasifiers,leading to low carbon efficiencies. To improve these inefficiencies, graphite is investigated under oxygen gasifying conditions, using a potassium carbonate catalyst in a thermogravimetric apparatus (TGA). The goal is to obtain intrinsic rate information by correcting for the diffusional limitations inherent in the device. Doing so gives a close correlation with literature in terms of activation energy and rates. Finally, as the expense incurred by not recycling valuable catalyst can be uneconomical, retention and displacement of valuable catalysts was also investigated.
Validation of a Health-related Quality of Life Measure based on the Minimum Data Set by Mapping and Regression
Keywords: Health-related quality of life
HUI2
Long-term care
MDS-HSI
Quality of life

This study is the first to directly compare the Minimum Data Set- Health Status Index (MDS-HSI) based prediction of health-related quality of life (HRQOL) using the Resident Assessment Instrument- Minimum Data Set (RAI-MDS) with the actual resident-ratings of HRQOL based on the Health Utilities Index-2 (HUI2). This study involved secondary analysis of HUI2 survey response data from long-term care residents in Ontario. At the individual level, there was poor correlation between MDS-HSI and HUI2 multi-attribute and single health attribute scores. The Self-care attribute was the most discrepant health attribute and had the largest impact on the poor overall ICC between the MDS-HSI and the HUI2 scores. At the group level, the MDS-HSI and HUI2 findings showed mixed results. The results suggest that the source of HRQOL information is an important factors to consider when conducting HRQOL research in long-term care settings.
Dissecting Shared and Unique Neural Circuitry Underlying Negative Symptoms, Social Cognition, and Functional Outcome in Schizophrenia
Keywords: Diffusion Tensor Imaging
Functional Outcome
Negative Symptoms
Schizophrenia
Social Cognition
White Matter

Schizophrenia is a devastating illness with significant disability and poor long-term clinical and functional outcome. Negative symptoms and social cognitive impairments are two key symptom domains that affect functional outcome in schizophrenia. This thesis explores the shared and unique neural circuitry related to negative symptoms, social cognition, and functional outcome in schizophrenia. In study one, the relationship between white matter fractional anisotropy, negative symptoms, and functional outcome in schizophrenia participants was investigated. Study two includes a broad sample of patient and healthy control populations, which is in line with the RDoC methodology. In this study, the relationship between white matter tracts implicated in functional outcome and social cognitive domains was investigated in a sample of schizophrenia, bipolar disorder, and healthy control participants on a continuum of social cognitive performance. Taken together, these studies elucidate circuitry that may be impaired in schizophrenia, and may represent neurobiological correlates of negative symptoms, social cognition, and functional outcome.
The Anticonvulsant Effects of Progesterone, its Metabolites, and 5α-Dihydroprogesterone Novel Analogs in Amygdala-kindled Seizures in Rats
Keywords: 5α- DHP novel analogs
5α-dihydroprogesterone
complex partial seizure
dose-response study
progesterone
rat-amygdala kindling

Introduction: Complex partial epilepsy is the most common type of drug-resistant epilepsy in adults. The present study was designed to test the anticonvulsant activity of 5α-dihydroprogesterone (5α-DHP) novel analogs in an animal model of human complex partial epilepsy − the rat amygdala-kindling model. Methods: Confirmatory replication studies were carried out on progesterone and its metabolites. Subsequently, nine 5α-DHP novel analogs were screened for anticonvulsant potential. Finally, emerging lead compounds, MC008 and MC009, were examined in dose-response studies, time-response studies, and Lӧscher's ataxia toxicity studies. Results: Progesterone and its metabolites were generally anticonvulsant. Analogs MC008 and MC009 were effective against both the focal and the generalized kindled seizures. Toxic side-effects (ataxia), however, accompanied focal seizure suppression. Conclusion: MC008 and MC009 do not seem to be ideal candidates for the treating human complex partial seizures due to potential toxicity. Other 5α-DHP analogs have been synthesized and will be tested in future experiments.