VictorJuiz/thesis huggingface dataset:
Architectural Analysis for Supervisory Control of Discrete-Event Systems

Using probabilistic automata (PA) within the Ramadge and Wonham (RW) framework, the model of discrete-event systems (DES) is extended to include probabilistic information. The extended model can provide useful numerical results for performance analysis of DES by exploiting Markov Chain properties, as well as allowing the use of logical synthesis techniques. Using the extended model, performance evaluation and pros and cons analysis of centralized and decentralized architectures are provided for two typical DES, Small Factory and Transfer Line. Given estimated cost and profit data, the centralized and decentralized architectures are evaluated in these two examples, and various summary rules as to which architecture to implement are obtained. For the Transfer Line example, â material feedbackâ in the loop and only partial knowledge of the global system state in the decentralized architecture can result in blocking. Blocking removal strategies are introduced and compared.

Keywords: architectural analysis
discrete-event systems
probabilistic automaton
Advisor: Kwong, Raymond H
Wonham, Walter M
RESOURCE OPTIMIZATION ACROSS GEOGRAPHICALLY DISTRIBUTED DATACENTERS

Cloud computing provides users and enterprises shared pools of resources to store and process their data. To provide quality-of-service guarantees for customers and reduce resource wastage, how to manage resources becomes a crucial problem for cloud providers. In this thesis, we propose and implement different approaches for resource optimization with various objectives. Resource optimization algorithms used by cloud providers have a significant impact on the performance of virtual machines (VMs) that users rent for computation as well as the ability for datacenters to accommodate user requests. We propose a multi-dimensional online VM placement algorithm that can balance the usage of resources along multiple dimensions and improve VM performance effectively. There are also some applications like geo-replication that need to transfer data across datacenters within a time period. We propose and implement an efficient solution that maximizes throughput for multiple concurrent inter-datacenter multicast transfers while meeting their deadlines.

Keywords: Datacenter
Resource optimization
Routing
Virtual machine
Advisor: Li, Baochun
Alpha-Dystroglycan Plays Functional Roles in Platelet Aggregation and Thrombus Growth

Fibrinogen (Fg) and von Willebrand factor (VWF) have been considered essential for platelet adhesion and aggregation. However, platelet aggregation still occurs in mice lacking Fg and/or VWF but not β3 integrin, suggesting other, unidentified αIIbβ3 integrin ligand(s) mediate platelet aggregation. Through screening published platelet proteomics data, we identified a candidate, alpha-dystroglycan (α-DG). Using Western blot and flow cytometry, I found α-DG is expressed on platelets. Using aggregometry, I observed that antibodies against α-DG or its N-terminal Laminin-binding site, decreased platelet aggregation induced by various platelet agonists in both platelet-rich plasma and gel-filtered platelets. These antibodies also decreased platelet adhesion/aggregation in perfusion chambers independent of α-DG-Laminin interaction. Using laser injury intravital microscopy and carotid artery thrombosis models, we further found that these anti-α-DG antibodies decreased thrombus growth in vivo. Our results showed that α-DG may form an α-DG-fibronectin complex that binds to αIIbβ3 integrin, contributing to platelet adhesion/aggregation, and thrombus growth.

Keywords: Blood
Hemostasis
Integrins
Platelets
Thrombosis
Advisor: Ni, Heyu
Chasing the Dream: Canadian Track and Field Student-Athlete Migration to the NCAA Division I

While there is interest in understanding the motivations and experiences of student-athletes who migrate to the NCAA, there is a lack of data quantifying migration to the NCAA. Specifically, in the case of track and field, the last quantitative effort to identify Canadian student-athlete migration to the NCAA was published in the early 1990â s by John Bale. Using descriptive research methods, this thesis defines the population of Canadian track and field student-athletes who migrated to the NCAA DI between the 2005/06 and 2012/13 academic years. Results indicate that during this eight year period, 562 Canadian student-athletes migrated to the NCAA Division I to participate in track and field. Canadian track and field student-athletes who migrate to the NCAA Division I comprise more than half of the athletes competing internationally for the Canadian National Track and Field Team.

Keywords: athletics
Canadian
migration
NCAA
student-athlete
track and field
Advisor: Donnelly, Peter
Towards Practical Driver Cognitive Load Detection Based on Visual Attention Information

With growing popularities of intelligent in-vehicle technologies, monitoring of driver cognitive load is becoming more important for both safety and comfort concerns. This task is recognized to be challenging due to limited prior knowledge. This thesis explores the feasibility of classifying driver cognitive load levels based on visual attention features. First, we contribute a dataset collected from 37 experienced drivers. The collection process focuses on eliciting three levels of cognitive load effectively. The resulting dataset consists a total of eight measurements, gathered from visual, vehicular, physiological sensors and subjective-questionnaires. Next, we focus on the eye-tracking modality and propose meta-features for capturing variations in visual attention intensity and direction. Then, five machine learning algorithms are applied for subject-independent classification. Issues arose from the machine learning workflow, such as evaluation bias, are examined. The most promising algorithm (Random Forest) achieves 70.3% accuracy on classifying between high and low cognitive load.

Keywords: cognitive load
driver monitoring
machine learning
Advisor: Plataniotis, Konstantinos N.
Temporal and Spatial Variations of PM2.5, surface O3, and Smog in Ontario, Canada

This study focuses on seasonal and interannual variations of PM2.5, surface O3, and smog from 2003 to 2015 in six Ontarian cities, including Sarnia, Hamilton, and Toronto in the south, and North Bay, Sudbury, and Sault Ste. Marie in the north. All cities had the highest PM2.5 and smog events in summer and the highest O3 in spring. PM2.5 and smog events were greater in the southern cities than in the northern ones; the pattern is the opposite for surface O3. For most cities, the annual PM2.5 decreased insignificantly while surface O3 increased significantly. The diurnal variation of surface O3 altered by rains in an Ontarian city, Mississauga, is also investigated for the warm seasons of 2014 and 2015. At daytimes, surface OÂŹÂŹ3 during rain decreased by 7 ppb, resulting from less photochemical production. At night, O3 during rain increased by 6 ppb, attributing to the chemical reduction of NO.

Keywords: air pollution
Ontario
PM2.5
rain
smog
surface ozone
Advisor: Liu, Jane
Role of Notch Signaling in Development of IL4-producing Innate T cells in Neonates

Notch signaling is required for early stages of intrathymic T cell development and for antigen-induced peripheral differentiation of Type 2 CD4+ T helper cells, in part through induction of GATA3, an obligate transcription factor for IL4 expression. Therefore, we asked if Notch signaling also regulates production of innate-like natural killer T (NKT) and TCR cells that develop as â pre-activatedâ innate effector T (IET) cells. We bred mice in which CD4Cre induced or inactivated RBPJ-dependent Notch signaling in CD4+ T cell precursors, and used flow cytometry to characterize innate T cell development. Interestingly, CD4Cre-induced Notch1 activation dramatically increased CD4+/- oligoclonal TCR and TCR IL4-producing IET cells selectively in neonatal mice, whereas Notch inactivation greatly decreased their neonatal production. By adolescence, mice with overactive Notch1 signaling exhibited high levels of serum IL4, IgE, and eosinophilia. Thus, intrathymic Notch signaling regulates development of innate-like cell lineages, and must be restrained during the neonatal period to avoid systemic inflammation.

Keywords: neonatal
NKT cell
Notch
V6
Advisor: Guidos, Cynthia J
FISH: Linux System Calls for FPGA Accelerators

This work presents the FISH (FPGA-Initiated Software-Handled) framework which allows FPGA accelerators to make system calls to the Linux operating system in CPU-FPGA systems. A special FISH Linux kernel module running on the CPU provides a system call interface for FPGA accelerators, much like the ABI which exists for software programs. The work presents the proposed framework that facilitates the FPGA to Linux kernel system call interface. The work also presents a proof-of-concept implementation of the framework running on an Intel Cyclone V SoC device. The FISH framework could be especially useful for high-level synthesis (HLS) by making it possible to synthesize software code that contains system calls. This would expand the subset of code that is currently synthesizable, and allow behavior in accelerators that was previously not possible.

Advisor: Brown, Stephen
A Quantitative Study of Ozone Deposition Velocity over a Mixed Temperate-Boreal Forest

Rising tropospheric ozone is an alarming environmental problem. The impact of forests on ozone deposition, a process to remove tropospheric ozone, is rarely investigated. This study aims to address this issue by quantifying ozone deposition velocity over a temperate-boreal forest at Borden, Canada, for multiple years. Results show that deposition is much stronger over this forest than a non-forested area during summer. Mean summer canopy deposition velocity (Gc) is approximately 8 mm/s, and is roughly 4 times larger during the day than at night. The stomatal pathway dominates during dry daytime conditions, while the non-stomatal pathway dominates at night and during wet conditions. Temperature, radiation, and leaf-area index (LAI) strongly influence Gst at the yearly scale, while humidity, precipitation, and soil moisture strongly influence Gst and Gns during the summer. In addition, precipitation, soil moisture, and LAI are found to be important factors explaining interannual variations in ozone deposition velocities.

Keywords: Canopy
Environmental factors
Mixed forest
Non-stomatal
Ozone deposition velocity
Stomatal
Advisor: Liu, Jane
Environmental Robustness in Populations Adapted to Constant Environments and Heterogeneous Environments

Environmental robustness is the reduction of phenotypic variation under environmental perturbation and is essential for populations to persist in stressful conditions, but few empirical studies have examined the conditions under which robustness evolve. Here we consider two hypotheses, robustness evolves via environmental heterogeneity or as a by-product of adaption to specific constant environments. We assessed environmental robustness in juvenile viability of 20 D. melanogaster populations evolving under constant or heterogeneous environments. Contrary to prediction, in the original selective environments, populations from heterogeneous regimes were not the most robust ones. In the novel environments, populations from the constant salt regime were more robust than populations from the constant cadmium regime. Populations from heterogeneous regimes had intermediate level of robustness. Our results suggest that environmental robustness is an indirect product of adaptation to specific environments and environmental heterogeneity plays a relative less important role in inducing robustness than the details of adaptation.

Keywords: Environmental Heterogeneity
Plasticity
Robustness
Advisor: Agrawal, Aneil F.
Are Vascular Function and Oxygen Uptake Kinetics Related in People with Type 1 Diabetes?

Measures of aerobic fitness (VO2 peak), vascular function, and oxygen uptake kinetics (VO2 kinetics) were collected in people with type 1 diabetes (T1D) and controls to determine the relationship between calf blood flow and oxygen uptake kinetics. Outcomes were measured over two days, where calf blood flow was measured by strain gauge plethysmography and oxygen uptake kinetics was determined by 3 minute alternating square wave test at 80% of their predetermined ventilatory threshold. There were no significant differences between the two groups in measures of fitness, vascular function, or VO2 kinetics (P > 0.05), and the relationship between VO2 kinetics and maximal blood flow was not significant in this cohort (P > 0.05). With proper exercise and adequate glucose control, people with T1D may maintain vascular health and VO2 kinetics similar to people without T1D.

Keywords: Blood Flow
Exercise
Oxygen Uptake Kinetics
Type 1 Diabetes
Vascular Function
VO2 Kinetics
Advisor: Thomas, Scott G
Mercury Methylation in Riparian Areas Across Minnesota

Five rivers in Minnesota have been identified to have particularly elevated mercury concentrations in fish despite relatively low total mercury concentrations in water and sediment. One hypothesis is that methylmercury production in riparian areas and hydrological connectivity of riparian areas to streams are important contributors to river methylmercury loads and bioaccumulation. We conducted methylation (Kmeth) assays, using enriched mercury isotopes, across two geomorphically distinct riparian zones in each of five Minnesota watersheds and across seasons from 2015 through 2016. Kmeth was generally higher in-stream and lower with increasing distance away from the stream. Results show that although methylation does occur in riparian areas, it is not likely that these areas are the primary source of MeHg found in fish due to hydrological flow patterns observed at these sites. More research is needed to determine the source of elevated MeHg concentrations found in the fish of these â high-5â watersheds.

Advisor: Mitchell, Carl PJ
From discrete to continuous online limb-target regulation processes: A matter of time?

A pseudo-continuous model of online sensorimotor control suggests that visual information is gathered from peak acceleration until movement end (Elliott et al., 2010). Although seminal evidence for the model employed relatively slow movements, Tremblay et al. (2013; 2017) have provided evidence for optimal online visual information utilization during early stages of fast reaching movements (i.e., ~350 ms). The current study examined the generalizability of these results to faster and slower reaching movements (i.e., 350 ms or 700 ms). During reaching movement participants were provided with a 20 ms window of visual information (i.e., at 35%, 60% or, 85% of PV) and a target-jump manipulation. Overall, the strategy to implement a single correction was supported for faster movements, whereas the pseudo-continuous model (Elliott et al., 2010) was supported for slower movements. Theoretically, online visual uptake strategies could be merely dependent on the time available for utilization and implementation of amendments.

Keywords: Online control
Reaching
Target jump
Vision
Advisor: Tremblay, Luc
The acute physiological response to high-intensity interval exercise in patients with coronary artery disease

High-intensity interval exercise (HIIE) elicits quicker and more substantial improvements in aerobic capacity compared to moderate-intensity continuous exercise (MICE), but the protocol that optimizes the physiological stimulus and patient preference is undetermined. Fifteen patients with coronary artery disease (CAD) underwent physiological assessment during 3 different HIIE protocols and MICE. The 4x4 protocol elicited a greater physiological stimulus, as indicated by heart rate (HR), oxygen uptake (VO2), rating of perceived exertion (RPE), and blood pressure responses, but was the least preferred HIIE protocol. The 10x1 protocol was most preferred, it was comparable to MICE, and should be considered a timesaving alternative. TRIP proved to be a strong physiological stimulus and may be a viable choice opposed to long duration intervals, for its similar HR response and RPE at a higher VO2 compared to MICE. These results indicate that HIIE is an efficient and well-tolerated exercise prescription for CAD patients.

Keywords: acute exercise
coronary artery disease
high-intensity
interval
Advisor: Goodman, Jack M
Deep learning models for RNA-protein binding

RNA binding proteins(RBPs) are crucial bio-molecules that fine-tune gene expression in cells. Each RBP prefers to bind to a specific RNA sub-sequence, like a key fitting a lock. Understanding the specific binding preferences of RBPs is an important step to understanding the various steps of gene expression in cells and in solving several genetic disorders. There are thousands of RBPs in humans and only a small fraction of them are well understood. In this work, we develop deep neural network models that allow us to learn binding preferences for a large number of RBPs from high-throughput data, without requiring any specific domain knowledge or feature engineering. Deep learning has improved state of the art in several fields such as image classification, speech recognition, and even genomics. Deep learning approaches obviate the need for careful feature engineering by learning useful representations directly from the data. We propose two deep architectures and use them to predict RNA-protein binding. Based on recent findings that show the importance of RNA secondary structure in RBP binding, we incorporate computationally predicted secondary structure features as input to our models and show its effectiveness in boosting prediction performance. We demonstrate that our models achieve significantly higher correlations on held out in vitro testing data compared to previous approaches. We show that our model can generalize well to in-vivo CLIP-SEQ data and achieve higher median AUCs than other approaches. We demonstrate that our models discover known preferences for proteins such as CPO and VTS1 as well as report other proteins for which we find secondary structure playing an important role in binding. We demonstrate the strengths of our model compared to other approaches such as the ability to combine information from long distances along the sequence input.

Keywords: Deep learning
Genomics
Machine learning
RBP
RNA
Advisor: Frey, Brendan J
Duvenaud, David K
Right Heart and Pulmonary Hemodynamic Response to Prolonged Exercise in Middle-Aged Endurance Athletes

Chronic endurance exercise has shown to contribute to disproportionate right ventricular (RV) remodeling in athletes, and prolonged strenuous exercise has been associated with acute changes in RV function post-exercise, which are transient. RV function has been closely coupled to pulmonary arterial (PA) hemodynamics, and PA pressures appear to increase progressively with exercise intensity. There is however a paucity of directly-measured pulmonary hemodynamic data to support this observation. We characterized the PA hemodynamic and RV functional responses to acute, step-incremental (n=16) and sustained steady-state aerobic exercise (n=5) in healthy, middle-aged endurance athletes. All subjects underwent simultaneous right heart catheterization and echocardiography. PA pressures increased after initiation of exercise, then stabilized, without further change during acute and prolonged exercise. Accordingly, indices of RV function did not decline during prolonged exercise, altogether arguing against the notion that sustained elevations in pulmonary pressures may compromise RV systolic performance during prolonged aerobic exercise.

Keywords: Endurance Athlete
Exercise
Heart Catheterization
Pulmonary Artery Pressure
Pulmonary Hemodynamics
Right Ventricle
Advisor: Goodman, Jack M
The Association of Anemia with Cardiopulmonary Exercise Capacity and Adverse Patient Outcomes in Noncardiac Surgery

Cardiorespiratory impairment and preoperative anemia are associated with postoperative adverse events. Since hemoglobin concentration contributes to oxygen delivery, the association of anemia with outcomes may be due to patient inability to meet postoperative metabolic demands. This thesis examined the association of hemoglobin concentration with two measures of cardiorespiratory reserve, VO2 peak and AT. In patients undergoing major elective surgery, hemoglobin concentration explained 4.9% of the variation in VO2 peak and AT. Each 10 g/L increase in hemoglobin was associated with decreased postoperative complications in a multivariable model adjusted for VO2 peak [aOR 0.86 (95% CI, 0.77-0.96), p=0.007] and AT [aOR 0.86 (95% CI, 0.77-0.97), p=0.01], but not a composite endpoint reflecting end-organ impairment due to decreased systemic oxygen delivery. The magnitude of increased risk for postoperative adverse events associated with anemia is likely small. Interventions mitigating modifiable risk factors, of which anemia is just one, could lead to outcome improvements.

Keywords: Anemia
Exercise Capacity
Exercise Tolerance
Perioperative
Risk
Surgery
Advisor: Wijeysundera, Duminda N
Characterizing the Putative Disperser Morph in Naked Mole-Rats

Naked mole-rats are eusocial mammals; their hierarchy consists of one breeding female, 1 to 3 male consorts, and their reproductively suppressed siblings and offspring. A potential â disperserâ subcaste has been suggested. The purpose of the current study was to better characterize the putative disperser morph. I hypothesized that dispersers and workers would exhibit different in-colony and out-colony behaviors, colony characteristics would affect the presence of dispersers, and dispersers would reproduce quicker than workers. The results found that naked mole-rats of both sexes consistently dispersed. Male dispersers and workers had minimal differences in in-colony behaviors and both preferred familiar colony odor. Queen aggression increased presence of female dispersers only. Dispersers were heavier and fatter than workers. Dispersers and workers produced litters at a similar rate to each other. These results suggest that dispersers may not be a separate subcaste, but rather a subset of the existing workers with increased exploratory behavior.

Keywords: Behavior
Disperser Morph
Naked mole-rat
Subcastes
Advisor: Holmes, Melissa M
An Investigation of Temperate Region Lake Ice in Central Ontario

This study investigates ice formation for three lakes in central Ontario, detailing the climatological influences on the ice phenology for two seasons. This study also presents an investigation of the use of the Canadian Lake Ice Model (CLIMo) for simulating ice and snow cover for two of the study lakes during the 2015-2016 and 2016-2017 ice season. Field-based measurements combined with data collected from an on-shore automatic weather station, camera imagery during both seasons, as well as the addition of ice thickness from a Shallow Water Ice Profiler (SWIP) for the 2016-2017 ice year, form the basis of the results presented in this thesis. Snow cover, lake ice and climate interactions at lower latitudes have rarely been studied and the results of this thesis form the basis for further exploration of these interactions as lakes ice impacts climate, regional energy and water budgets, aquatic productivity, and socioeconomic activities.

Keywords: Central Ontario
Ice Thickness
Lake Ice
Lake Ice Modeling
Snow Cover
Snow Ice
Advisor: Brown, Laura C