VictorJuiz/thesis huggingface dataset:
Low Order Solutions to the Perfect Regulation Problem with Bounded Peaking

High gain control is an intrinsic aspect of high performance systems. The perfect regulation problem with bounded peaking refers to regulating a system arbitrarily fast, while maintaining boundedness at the output. In this thesis, we construct a family of controllers of low dynamic order parameterized by a gain parameter which solves this problem for multivariable, linear time-invariant systems which are invertible and minimum phase. In particular we obtain a lower bound on the order of the controller which is only a function of a structural property of the system known as the orders of infinite zeros. A further development shows how, under certain conditions, the techniques developed can be used to design decentralized controllers which also solve the perfect regulation problem with bounded peaking.

Keywords: Control systems
High gain control
High performance systems
Linear systems
Stability of linear systems
Advisor: Davison, Edward J
Kwong, Raymond H
TASK Channels on Basal Forebrain Cholinergic Neurons Modulate Electrocortical Signatures of Arousal by Histamine

Activation of basal forebrain cholinergic neurons by histamine elicits cortical arousal. TWIK-like acid sensitive K+ (TASK) channels modulate neuronal excitability, but the role of TASK channels in the histamine-basal forebrain arousal circuit is unknown. I studied the role of TASK channels in modulating electrocortical activity in vivo using freely-behaving wild-type and ChAT-Cre:TASKf/f mice, the latter lacking TASK-1/3 channels on cholinergic neurons. TASK channel deletion altered endogenous electroencephalogram oscillations in multiple frequency bands. TASK channel deletion also affected electrocortical activity during microperfusion of histamine into the basal forebrain. In NREM sleep, TASK channel deletion attenuated the histamine-induced increase in 30-50Hz activity. During active wakefulness, histamine increased 30-50Hz activity in ChAT-Cre:TASKf/f but not wild-type mice, showing that the histamine response depended upon the prevailing cortical arousal state. Summarizing, I identified that TASK channels on cholinergic neurons modulate endogenous electroencephalogram oscillations and the electrocortical response to histamine at the basal forebrain in vivo.

Keywords: Basal Forebrain
Histamine
Sleep
TASK Channels
Wakefulness
Advisor: Horner, Richard L
Evaluating the Correspondence between Genetic Interactions and Gene Order of Action in S. cerevisiae

Although a molecular function has been revealed for over 80% of Saccharomyces cerevisiae genes, the specific position of genes within ordered biological pathways remains elusive. Much of the information we have about connectivity and directionality of genes within pathways comes from genetic interaction analysis. Positive interactions, defined by double mutant phenotypes that are less extreme than expected, suggest that genes work in the same pathway or in series. Masking and suppression relationships are important subtypes of positive genetic interactions that can sometimes indicate gene order of action1,2,3,4,5,6,7,8. Here I describe studies of the relationship between genetic interactions and functional gene order by extracting genetic interaction information of gene pairs with known order from large-scale Synthetic Genetic Array (SGA) data7 and small-scale DNA repair related genetic interaction data8. This represents the first systematic evaluation of the applicability of quantitative epistasis analysis to reveal gene order.

Keywords: Epistasis
Gene order
Advisor: Roth, Frederick P
Falls Post-stroke: A Setback on the Road to Recovery?

Accidental falls are common among individuals with stroke. Falls can have significant physical and psychosocial consequences, including injury, fear of falling, and reduced activity. The impact of falls on post-stroke recovery is not clear. The current work is comprised of two studies. The first study aimed to investigate how falls during in-patient stroke rehabilitation affected length of stay, functional status, and discharge destination. Individuals who fell had a longer length of stay compared to those who did not fall; however, both groups achieved similar functional levels, and were discharged home. The second study aimed to determine how falls among community-dwelling stroke survivors affected outcomes of stroke recovery after six months post-discharge from hospital. Performance in balance and motor recovery were compromised among individuals who fell compared to those who did not fall. The results of both studies suggest that falls may delay post-stroke recovery.

Keywords: accidental falls
recovery
rehabilitation
stroke
Advisor: Mansfield, Avril
Brooks, Dina
Framing the Mental Timeline: Egocentric and Allocentric Contributions to Space-time Compatibility Effects

Temporal concepts are often thought to be implicitly associated with a spatial feature- within a spatial frame of reference- described as a mental timeline. Consequently, conceptual processing of temporal cues can modulate spatial responses in a left-to-right representation. However, empirical support for this view is limited to paradigms where attention operates along a strictly dichotomous, viewer-centered frame of reference (e.g., left vs. right). The present thesis investigates the nature of this spatial bias in (a) more complex spatial layouts consisting of more than two possible locations and (b) in frames of reference that are anchored to the stimulus rather than the viewer. Our results reveal that time-based attentional biases are able to extend to stimulus-centered frame of reference, but are mediated by the canonical arrangement of the visual targets. Results are discussed in light of the cognitive flexibility and specificity in the construction of a mental timeline.

Keywords: embodied cognition
mental timeline
metaphorical mapping
spatial attention
time-space compatibility
Advisor: Ferber, Susanne
Positive and Negative Emotion Vulnerability Following a Positive Mood Induction in the Context of Borderline Personality Disorder

Studies to date have demonstrated that greater borderline personality disorder (BPD) symptom severity is related to greater negative emotional experience, and that depression, trait negative affect, and difficulties regulating emotion each play a role in this relationship. Additional research is necessary, however, to determine if positive emotional experience may be similarly affected by BPD features. In the current study, data was collected from 120 undergraduate students pertaining to baseline intensity, reactivity, and post-induction stability for both positive and negative emotion in the context of three discrete positive mood inductions. Measures of BPD and depression symptom severity, trait negative affect, and maladaptive emotion regulation were administered at baseline. It was found that greater BPD symptom severity predicted greater concurrent negative reactivity and less positive emotion decay at 3-minute follow-up. These findings may portend to intervention strategies designed to foster healthier positive emotional experience for those with BPD.

Keywords: Borderline Personality Disorder
Emotion
Emotion Regulation
Emotion Vulnerability
Positive Emotion
Advisor: Uliaszek, Amanda A
Variability in ECG Biometrics: State of the Art and Subspace Methods

This work addresses the challenges of evaluating electrocardiogram (ECG) biometric recognition systems. While ECG has attracted significant interest, most of the prior art have approached it from the perspective of a typical biometric modality and have neglected the physiological factors that affect the respective systems. This work presents the UofT ECG Database (UofTDB) and offers a comprehensive analysis of the underlying inter-individual variability under a number of conditions such as body posture, physical activity and time-lapse. The performance of various methodologies is reported under the above mentioned conditions and a method based on template fusion is proposed to address these shortcomings. Furthermore this work proposes a ECG-based posture-detection algorithm and state-detection verification method to overcome the problem of verification under uncontrolled posture settings. Finally we evaluate different subspace methodologies for ECG recognition under different ECG variability to establish a baseline performance for future works.

Advisor: Hatzinakos, Dimitrios
HMGB-1 Release and the CD8+ T Cell Response Elicited by Radiation Treatment in Malignant Pleural Mesothelioma

Malignant pleural mesothelioma (MPM) is a cancer of the pleura that is associated with the inhalation of asbestos. Treatments, such as radiation therapy, have direct cytotoxic effects on cancer cells in addition to immune activating effects through the release of pro-inflammatory molecules associated with cancer cell death. The goal of this project was to investigate the role of High Mobility Group Box 1 (HMGB-1), a typical Danger Associated Molecular Pattern (DAMP) protein released after radiation treatment, in CD8+ T Cell mediated tumor killing and in patient survival. Radiated tumor cells release HMGB-1 in vitro. Furthermore, radiation treatment leads to HMGB-1 release and correlates with higher survival in vivo. This thesis demonstrates that radiation leads to HMGB-1 release which is correlated to MPM cell death and increased survival in vivo. The findings of this project could be used to develop new therapies in combination with radiation.

Keywords: Cancer
Immunology
Immunotherapy
Radiation
Treatment
Advisor: de Perrot, Marc
Vitamin B12 and Choline Status in a Cohort of Canadian Pregnant Women and their Newborn Infants

This study determined maternal and cord blood concentrations of vitamin B12, choline and their metabolites as well as their association with maternal diet and fetal genetic variants. Dietary intakes of vitamin B12 and choline were assessed in 368 Canadian pregnant women. Concentrations of vitamin B12, choline and their metabolites were measured in maternal blood at recruitment and at delivery, and in the cord blood. Fetal DNA was genotyped for twenty genetic variants in vitamin B12 and choline metabolism. Maternal vitamin B12 and choline metabolite concentrations were the strongest predictors of corresponding cord concentrations. Maternal and cord nutrient and metabolite concentrations were not significantly altered by maternal diet or fetal genetic variants. Our data underscore the importance of maternal vitamin B12 and choline concentrations during pregnancy in fetal development as they are the primary predictors of cord blood concentrations of these nutrients.

Keywords: choline
fetal genotype
maternal diet
pregnancy
vitamin B12
Advisor: Kim, Young-In
O'Connor, Deborah L
Analysis and Design of Multiple-input Multiple-output Synthetic Aperture Sonar Systems

A synthetic aperture sonar (SAS) system is a sophisticated invention which forms high resolution images of the seafloor. The main issue of a SAS system is its low platform speed. This is due to the need to accurately estimate the position of the sonar transducers in real-time. Using a single transmitter, multiple receiver (SIMO) system reduces this problem. In an attempt to further augment the traveling speed, we propose a SAS system with multiple transmitting elements placed along the cross-range direction, and colocated with some of the receiving elements. The transmitters emit a set of orthogonal (or nearly orthogonal) waveforms. We analyze the pros and the cons of this multiple input multiple output (MIMO) design with a simulator that is built during this project, and look into ways to resolve some of the complications. Specifically, we show that the MIMO configuration does allow for faster platform speed. Further, the MIMO configuration can improve the near field cross-range resolution. Finally, we show that these gains are possible if any cross-talk between the transmitted waveforms is suppressed.

Advisor: Adve, Raviraj S.
Impedance Spectroscopy of Single Cells Using Embedded AgPDMS Electrodes

This thesis presents a microfluidic device with wide channels and embedded AgPDMS electrodes for measuring the electrical properties of single cells. The work demonstrates the feasibility of using a large channel design and embedded electrodes for impedance spectroscopy to circumvent issues such as channel clogging and limited device re-usability. AgPDMS electrodes were formed on channel sidewalls for impedance detection and cell characterization. Equivalent circuit models were used to interpret multi-frequency impedance data to quantify the cytoplasm conductivity and specific membrane capacitance of each cell. T24 cells were tested to validate the microfluidic system and modeling results. Comparisons were then made by measuring two leukemia cell lines (AML-2 and HL-60) which were found to have different cytoplasm conductivity values (0.29 ± 0.15 S/m vs. 0.47 ± 0.20 S/m) and specific membrane capacitance values (41 ± 25 mF/m2 vs. 55 ± 26 mF/m2).

Keywords: Cells
Impedance spectroscopy
Microfluidics
Advisor: Sun, Yu
Senescent Carcinoma Associated Fibroblasts Up-regulate Interleukin 8 to Enhance Pancreatic Cancer Progression

Carcinoma associated fibroblasts (CAFs) represent a significant component of pancreatic cancer stroma. Within the stroma exists a subpopulation of CAFs which have ceased proliferation and undergone cellular senescence. These senescent CAFs possess an altered secretory phenotype that can influence cancer progression. Induction of senescence in primary cultured CAFs resulted in up-regulation of interleukin 8 (IL-8). Senescent CAFs increased cancer invasion and metastasis in in vitro and in vivo models. Addition of recombinant IL-8 also enhanced cancer invasion while inhibition of IL-8 receptors mitigated the pro-invasive effects of senescent CAFs. The proportion of senescent fibroblasts in pancreatic cancer tissue correlated with survival in cases without lymph node involvement. Cytokine pathways modulated by senescent fibroblasts are a potential therapeutic target in pancreatic cancer.

Keywords: CAF
Fibroblasts
Interleukin 8
Pancreatic cancer
Senescence
Advisor: Tsao, Ming-Sound
Setting the Balance of Care for Sexually Diverse Seniors: The Social Exclusion of LGBT Seniors in Home and Community Care

The central aim of this dissertation is: to identify how past experiences of social exclusion have influenced the current cohort of lesbian, gay, bisexual, and transgender (LGBT) seniors and health care providers in Toronto, Ontario regarding accessing and using home and community care (H) services, and to consider what can be done. To do this, I conducted a case study on LGBT seniors’ use of H services in Toronto, Ontario. My findings suggest that past experiences of social exclusion impact on LGBT seniors’ access and use of H services. H providers acknowledge an overall lack of H for LGBT seniors, but differ in their approaches to providing culturally appropriate H I conclude with recommendations regarding remedies to the social exclusion of LGBT seniors within H, and policy options for reducing social exclusion more broadly.

Advisor: Williams, A. Paul
Interpolative Hyperbolic Realizable Moment Closures for Non-equilibrium Flows with Heat Transfer

The predictive capabilities of a novel, 14-moment, maximum-entropy-based, interpolative closure are explored for multi-dimensional non-equilibrium flows of a monatomic gas with heat transfer. Unlike the maximum-entropy closure on which it is based, the interpolative closure provides closed-form expressions for the closing fluxes while retaining a large region of hyperbolicity. Properties of the moment system are explored via a dispersion analysis and an implicit finite-volume solution procedure is proposed. Multi-dimensional applications of the closure are then examined for several canonical non-equilibrium flow problems in order to provide an assessment of its capabilities. The predictive capabilities of the closure were found to surpass those of the 10-moment Gaussian closure. It was also found to predict interesting non-equilibrium phenomena, such as counter-gradient heat flux. The proposed implicit solver showed improved computational performance compared to the previously studied semi-implicit technique.

Keywords: Computational fluid dynamics
Kinetic theory
Moment closure
Non-equilibrium gases
Advisor: Groth, Clinton P.T.
McDonald, James G.
Anxiety in Chronic Moderate to Severe Traumatic Brain Injury: Measurement and Relation to Hippocampal Volume Loss

Moderate to severe traumatic brain injury (TBI) can result in chronic and progressive atrophy of the hippocampus (HPC), a bilateral brain structure housed in the medial temporal lobes. As demonstrated in a recent study of individuals with amnestic Mild Cognitive Impairment and early Alzheimer’s disease, anxiety is a candidate mechanism underlying atrophy of the medial temporal lobes in neurological populations. This thesis investigates (1) the validity of the Beck Anxiety Inventory (BAI) for measuring anxiety in chronic TBI and (2) the role of anxiety in HPC volume loss in this population. First, evidence for the validity of the BAI in chronic TBI is provided. Second, it is shown that higher anxiety on the BAI at 5 and 12 months post-injury predicts subsequent atrophy of the right HPC complex, particularly of the right HPC head.

Advisor: Green, Robin EA
Comparing and Contrasting Two Clients in Emotion-focused Therapy for Generalized Anxiety Disorder across and within Four (4) Dimensions of: Negative Treatment-of-Self, Positive Treatment-of-self, Negative Emotions, and Positive Emotions

The current research paper presents a good-outcome and a poor-outcome case, individuals who were treated with Emotion-Focused Therapy, drawn from the Generalized Anxiety Disorder Pilot study. EFT is an evidence-based treatment for depression, couple distress and trauma and has shown promise for anxiety disorders, interpersonal problems, and eating disorder (Greenberg Watson, 2006; Paivio Nieuwenhivs, 2001; Greenberg Dolhanty, 2009; Mennin, 2004). The purpose of this research study was to track clients’ patterns of emotional change across treatment and within each therapy sessions, and to describe and examine how emotion changes for GAD clients in EFT. Using the individual case comparison methodology (Watson, Goldman, Greenberg, 2007) and implementing Plutchik’s wheel-of-emotion this study tracks the process of change between these two clients, across the four dimension of: Negative treatment-of-self, positive treatment-of-self, negative emotions, and positive emotions. The results represent certain factors that are specific to good and poor outcome clients.

Keywords: Case Comparison
Case study
EFT
Emotion Focused Therapy
GAD
Generalized anxiety disorder
Advisor: Watson, Jeanne
Optimized Decentralized Control of Large Dynamic Structures

This thesis has proposed a new optimal decentralized controller design method for solving the tracking and disturbance rejection problems for the class of large scale LTI systems, using only low order decentralized controllers. The objective of the controller is to reject system constant disturbances and track constant reference signals by using an optimal decentralized control procedure. The proposed controller also has the property that if a sensor actuator failure occurs, thereby producing an unstable pole at the origin, that there is time for a repair to be carried out before massive destruction occurs. The proposed optimal controller also has the property that it is strongly robust as compared to the standard centralized LQR-Observer. In particular, the proposed controller can have the property of being some 5 orders of magnitude more robust than the standard LQR-Observer controller.

Keywords: Large Scale System
Optimization
PID Control
System Control
Advisor: Davison, Edward J.
CMOS VCSEL Driver Circuit for 25+Gbps/channel Short-reach Parallel Optical Links

This thesis proposes a new CMOS driver for Vertical Cavity Surface Emitting LASER (VCSEL) diode arrays. A VCSEL is a promising light source for optical communication. However, its threshold voltage (1.5V for a 850-nm VCSEL) exceeds the rated supply voltage of nanoscale CMOS technologies. This makes difficult designing a driver sourcing a modulated current to a VCSEL’s anode directly, an arrangement suitable for low-cost parallel optical links. To overcome this problem, a combination of analog circuit techniques is proposed including a novel pad shield driving technique. A prototype fabricated in a 65-nm CMOS technology achieved 26-Gb/s bit-rate and 1.80-pJ/b power efficiency with an optical modulation amplitude (OMA) of +1.8dBm and 3.1ps-rms jitter when driving a 850-nm 14Gb/s commercial VCSEL. This is the highest-speed anode-driving CMOS VCSEL driver reported to date. Also it has the best power efficiency and the smallest area (0.024mm2) amongst anode-driving drivers in any process technology.

Advisor: Chan Carusone, Anthony
Investigating βPix as a Novel Upstream Regulator of the Hippo Pathway

The Hippo pathway regulates cell growth and organ size and dysregulation of the pathway leads to cancer. In mammals, the core Hippo pathway consists of Mst/Lats kinases, which phosphorylate and inhibit transcriptional co-activators, Yap and Taz, by promoting cytoplasmic sequestration. Here, we identify the guanine nucleotide exchange factor (GEF), Arhgef7, or βPix, as a positive Hippo pathway regulator. Upon upstream Hippo signals emanating from cell-cell contact and actin cytoskeletal rearrangements, βPix functions to regulate Yap/Taz localization and activity in a GEF-independent manner. βPix interacts with Yap via the C-terminal KER domain and this physical interaction plays a key role in βPix-mediated Yap/Taz regulation. In normal mammary epithelial cells, Lats kinases are required for βPix function while Mst kinases are not required for Hippo signalling. In breast cancer cells, ectopic expression of βPIX is sufficient to re-couple the Hippo kinase cassette to Yap/Taz, suggesting a possible role as a tumour suppressor.

Keywords: Arfgef7
Hippo
Lats
Mst
Yap/Taz
Advisor: Attisano, Liliana
Network Calculus Analysis of Feedback Systems with Random Service

Feedback systems are deployed in many network related applications and various analytical approaches have tried to evaluate the performance of these systems. Network calculus is one such approach that uses (min,plus)-algebra for the analysis of networks. Although network calculus has successfully analyzed feedback systems under deterministic assumptions, the analysis of random feedback systems remains an open problem. In this thesis, we use network calculus to extend the deterministic analysis of feedback systems to stochastic settings. We provide statistical service bounds for the service function of a feedback system modelled by a window flow control scheme. We find an exact characterization for the stochastic service of special cases in window flow control and provide the upper and lower bounds for the service function of the feedback system. We also derive backlog bounds based on our analysis and compare these bounds with the simulated experiments.

Keywords: Computer Networks
Feedback Analysis
Network Calculus
Advisor: Liebeherr, Jorg