VictorJuiz/thesis huggingface dataset:
Sensitivity and Stability Analysis for Inverse Optimization with Applications in Intensity-modulated Radiation Therapy
Keywords: IMRT
Inverse optimization
Sensitivity
Stability

Inverse optimization aims to use observed data to understand the dynamics of a system by estimating the parameters of the underlying optimization problem. In this dissertation, we first develop an inverse model and investigate its properties for the cases where single and multiple observed data points are available. Next, we study the sensitivity and stability of the inverse model with respect to changes in the model parameters and perturbations in data. In particular, we illustrate the sensitivity of the inverse model with respect to the type of penalty functions used in the objective. Furthermore, we show that perturbations in the observed data can dramatically alter the outcome of the inverse model. We subsequently generalize our model to improve its stability with respect to perturbations in the input. Finally, we perform extensive simulations on synthetic and Intensity-Modulated Radiation Therapy (IMRT) data to validate the effectiveness of the generalized inverse model.
Glycosyl Methanesulfonates in Regio- and Stereoselective Glycosylations Catalyzed by Borinic Acids
Keywords: Borinic Acid
Carbohydrate
Glycosylation
Regioselective
Stereoselective
Sulfonate

Stoichiometric and catalytic activation of unprotected glycosyl acceptors toward reaction with glycosyl donors represent a growing breadth of methodologies recently developed with the goal of simplifying the synthesis of important carbohydrate targets. Most of these methods rely on glycosyl halides, a class of donor which has been essentially deprecated in recent literature by the advent of more convenient and versatile species. This report describes the development and use of glycosyl methanesulfonates in borinic acid-catalyzed glycosylations of partially protected acceptors. Good to high yields and selectivities for 1,2-trans-linked disaccharides are obtained without the need for a participating group. Studies of glycosylations with variously protected and configured donors and acceptors suggest wide applicability of the method to the preparation of important classes of linkages and protecting group patterns. Finally, mechanistic insights from NMR observation of the intermediate methanesulfonates are reported and discussed to develop a rationale for the observed catalyst-controlled stereoselectivity.
How does Genetic Burden Determine Disease Onset of Systemic Lupus Erythematosus?
Keywords: age of onset
genetic
lupus
risk
scores
SLE

Systemic Lupus Erythematosus (SLE) is a chronic, multisystem autoimmune disease product of the interaction between genetic and environmental factors. Although patients with pediatric-onset SLE (pSLE) and adult-onset SLE (aSLE) differ in disease presentation, activity and outcomes, all studies to date have not found any set of genes specific to pSLE as compared to aSLE. However, some studies found that early-onset SLE patients exhibited higher polygenetic risk scores. The present study included a large, multi-ethnic pSLE and aSLE cohort to identify how non-HLA and HLA genetic risk scores are associated with age of SLE onset. Samples were genotyped using Immunochip, scores were calculated based on validated SLE SNPs, analyzed in the total population and in each ancestry separately. We found that HLA and non-HLA alleles had different associations with SLE onset; the higher the non-HLA score the younger the patient, whereas the higher the HLA scores the older the SLE patient.
Recovery of Skeletal Muscle Microvascular Myogenic Reactivity After Smooth Muscle Cell-TNF Knockout
Keywords: Ca2+ sensitivity
compensation
resistance artery
sphingosine-1-phosphate
tumor necrosis factor
vascular smooth muscle

Resistance arteries possess an intrinsic ability, termed the myogenic response, which enables them to adapt to changes in blood pressure, allowing for the regulation of total peripheral resistance and thus blood flow. Tumor necrosis factor (TNF) is a master regulator of the myogenic response, as pharmacological inhibition and inducible smooth muscle cell-knockout of TNF specifically abrogated the myogenic response and accordingly lowers blood pressure. Surprisingly, the attenuated myogenic responsiveness following smooth muscle cell TNF knockout completely recovered within 7 days, independent of enhanced transcription of TNF and its receptors. Interestingly, the recovered myogenic response still depended completely on TNF signaling. Furthermore, the recovered myogenic response was much stronger at physiological pressures. This was associated with a significantly higher reliance on Ca2+-independent myogenic signaling. These findings advance the idea of a redundantly organized myogenic response that is required for the essential maintenance of hemodynamic homeostasis.
Dental Sedation and General Anaesthesia in Manitoba: A Survey of Need, Demand, and Perceptions
Keywords: Anxiety
Avoidance
Conscious sedation
General anaesthesia
Manitoba
Sedation

Background: Dental anxiety is a major reason why patients seek sedation/general anaesthesia (SGA) for dental treatment. Objective: To investigate patients’ reported and perceived dental anxiety and provision of SGA services in Manitoba dental practices. Methods: A paper-based survey was distributed to Manitoba dentists registered to provide intravenous sedation and a sample of their patients. Results: 21 dentists (53% response) and 505 patients participated. Dentists overestimated patients’ dental anxiety (Dental Fear/Avoidance Scale, p = 0.01; Index Dental Anxiety/Fear, p = 0.02), and underestimated patient interest for SGA. Patients also reported a preference for SGA services (ie., 2.5-fold demand for restorations) more often than they received SGA services (ie., 11.1-fold increase for implant surgery.) Conclusion: Dentists overestimate their patients’ anxiety levels but underestimate their interest in SGA services. Use of validated dental anxiety scales would aid in more accurate assessment of patient anxiety, and better alignment with patients SGA needs and demands.
The Effects of Multiple Mutualisms in the Tropical Perennial Plant, Turnera
Keywords: ant-plant interactions
extrafloral nectar
floral nectar
myrmecochory
pollination
trade-off

Many species interact with multiple mutualists, yet most studies investigate mutualisms as pairwise interactions between partners, potentially obscuring the benefits of multiple mutualists that interact synergistically or the costs of multiple mutualists that conflict. To examine costs of associating with multiple mutualists, I manipulated floral and extrafloral nectar (EFN) production and found that the two nectars trade off. This trade-off negatively affected ant defense and pollination mutualisms in the field. I then tested if EFN plays a role in seed removal, in addition to defense. Plants with active extrafloral nectaries had increased seed removal, demonstrating a novel role of EFN and an example of ecological pleiotropy. To explore how focal species avoid negative interactions between partners, I measured ant preference for EFN versus floral nectar using baits and a CAFE assay. Ants consumed similar volumes, but recruited more to EFN, suggesting that the rewards are tailored to the specific mutualist.
The Fibroblast Specific α11β1 Integrin is Important for Postnatal Cardiomyocyte Growth, Alignment and Function
Keywords: Cardiac Development
Extracellular Matrix
Heart Structure and Function
Integrins

Integrins are transmembrane adhesion and signaling receptors that interact with the extracellular matrix to mediate diverse cellular and developmental processes. Recent work has demonstrated cardiac fibroblasts mediate cardiomyocyte development through integrins. However, the predominant integrins involved and the role of integrins in cardiac development is poorly defined. Thus, we investigated the contribution of the α11β1 integrin (α11), which is expressed by fibroblasts and binds preferentially to type I collagen fibers, in mediating postnatal cardiomyocyte development and function. Utilizing a germline mutation of the α11 gene in mice, we found that deletion resulted in growth and structural abnormalities in cardiomyocyte development and reductions in myocardial collagen, which was associated with impairments in both active and passive diastolic function. These results suggest that the α11 integrin is a key component of the cardiac fibroblast that is required for the normal development of cardiomyocytes and maintenance of cardiac function.
Quadrotor Control in the Presence of Unknown Mass Properties
Keywords: Control Systems
L1 Adaptive Control
Quadrotor Dynamics

Quadrotor UAVs are popular due to their mechanical simplicity, as well as their capability to hover and vertically take-off and land. As applications diversify, quadrotors are increasingly required to operate under unknown mass properties, for example as a multirole sensor platform or for package delivery operations. The work presented here consists of the derivation of a generalized quadrotor dynamic model without the typical simplifying assumptions on the first and second moments of mass. The maximum payload capacity of a quadrotor in hover, and the observability of the unknown mass properties are discussed. A brief introduction of L1 adaptive control is provided, and three different L1 adaptive controllers were designed for the Parrot AR.Drone quadrotor. Their tracking and disturbance rejection performance was compared to the baseline nonlinear controller in experiments. Finally, the results of the combination of L1 adaptive control with iterative learning control are presented, showing high performance trajectory tracking under uncertainty.
Investigating the use of Reliability-calibrated Partial Factors in Tunnel Design
Keywords: Limit state design
Probabilistic design
Reliability based design
Tunnel design

Variability is prevalent in rock engineering conditions. This renders commonly used deterministic design approaches with empirical factors of safety unsuitable for objectively quantifying safety. Instead, probabilistic reliability based design (RBD) can objectively do so with probabilities of failure. However, due to the unfamiliarity of RBD to practicing engineers, 'partial factors' are calibrated which allow deterministic analyses to achieve designs of predefined probabilities of failure. This dissertation investigates the application of calibrated partial factors in tunnel liner design, and its possible inclusion in a coherent design code format. The dissertation concludes that partial factors calibrated from RBD can be applied in design of tunnel liners. However, due to the lack of data collected in rock engineering, development of a design code cannot be currently undertaken. In addition, it is only realistically feasible for simple tunnel construction and support sequences, suggesting that the application of RBD is best done on case-by-case basis.
Excitation of Molecular Systems by Incoherent Light
Keywords: Coherences
Incoherent Light
Open Quantum Systems
Photosynthesis
Quantum Dynamics

The excitation of molecular systems by incoherent light is studied primarily using a V-system model in the Partial Secular Bloch-Redfield formalism. First, the dynamical regimes are characterized for a system irradiated by suddenly turned on light and the relevant timescales are defined in terms of system parameters. Then excitation by slowly turned-on light is studied, showing a decay in the magnitude of noise-induced coherences with increasing turn-on times, leading to their disapearance in the very slow turn-on limit relevant to many natural systems.
Shift of Argument Subalgebras and Gelfand-Tsetlin Bases
Keywords: Gelfand-Tsetlin

There is a famous construction of a maximal commutative subalebgra in U(gln) called the Gelfand-Tsetlin algebra, with the special property that its eigenvectors are precisely the Gelfand-Tsetlin basis for gln and each eigenspace has dimension 1. We aim to find a replacement for the Gelfand-Tsetlin subalgebra in types B, C, and D by using shift of argument subalgebras, which are a family of commutative subalgebras in U(g) parametrized by elements of h. We compute generators of shift of argument subalgebras in the cases of so4 and sp4, and in the case of sp4 we also check these generators against the Gelfand-Tsetlin basis of sp4.
Reward Processing following Mindfulness-based Cognitive Therapy and Cognitive-behavioral Therapy for Wellbeing
Keywords: Cognitive behavioral therapy
Mindfulness
Mindfulness based cognitive therapy
Neuroimaging
Reward
Wellbeing

The aim of this study was to examine: (a) treatment-related changes in the reward system following two interventions designed to prevent the recurrence of depression, Mindfulness-Based Cognitive Therapy (MBCT) and Cognitive Behavioral Therapy with Wellbeing focus (CBT-WB); (b) changes following treatment that relate to relapse status at a two-year follow-up. Previously depressed patients were randomly assigned to 8-week MBCT (N=43) or CBT-WB (N=34) and scanned using fMRI while completing a card gambling task before and after treatment. Whole-brain analyses found that an increased neural sensitivity in the reward system following treatment to winning trials (outcome phase) and reduced sensitivity to the anticipation of a win were associated with relapse status. Differences between interventions were found for the anticipatory phases of winning. Overall, these findings suggest that maintenance interventions may derive their therapeutic effects from preserving baseline responses, rather than heightening reward sensitivity to outcome.
Evaluating the Relationship between Ceramides and Depressive Symptoms in Coronary Artery Disease Patients
Keywords: Ceramides
Coronary Artery Disease
Depression
Depressive Symptoms
Sphingolipids

Depression is highly prevalent in individuals with coronary artery disease (CAD), and increases risk of mortality. Ceramides, a family of sphingolipid species, have been implicated in the pathophysiology of both CAD and depression due to their pro-inflammatory and pro-apoptotic characteristics. This study assessed the relationship between ceramides and depression in a CAD population. Linear regression models were used to assess the association between plasma ceramide concentrations and depressive symptoms, as measured by the Center for Epidemiological Studies Depression Scale (CESD). High performance liquid chromatography coupled electrospray ionization tandem mass spectrometry was used to measure ceramide species. Higher plasma concentrations of the ceramide species C16:0 (β=0.195, p=0.039) and C22:1 (β=0.199, p=0.039) were significantly associated with greater depressive symptoms. Plasma concentrations of C18:0 (β =0.108, p=0.257) and C20:0 (β=0.167, p=0.078) were not significantly associated with depressive symptoms. Findings suggest a potential role of specific ceramides in the pathophysiology of depression in CAD.
Joint Power Control and User Association in Downlink Heterogeneous Networks
Keywords: 5G
Communications
Heterogeneous
Mobile
Networking
Wireless

As 5G aims to provide 1000-fold network capacity to mobile networks, heterogeneous networks (HetNet) have become a promising technology to deliver this goal. This thesis proposes a novel algorithm to maximize network utility of a downlink SISO HetNet jointly over user association and BS power control. The proposed problem formulation allows for investigation of a trade-off between network utility and network power consumption in the HetNet. Through finding the appropriate balance in the trade-off, the proposed algorithm forms a non-greedy heuristic to determine the appropriate activation of BSs under arbitrary total network consumption constraints. Greedy heuristics as motivated by those in literature are further used to compare with the proposed heuristic. Furthermore, this thesis considers the division of the downlink spectrum into multiple sub-bands and optimizes user association and BS powers independently over each sub-band. This provides an interesting alternative to the existing "soft frequency reuse" (SFR) scheme widely employed to maintain high network capacity while ensuring coverage for cell-edge users. Rate performances under various sub-band divisions are compared with the SFR scheme to examine the impact on user rates by considering a two-tier HetNet in a regular hexagonal deployment, where pico BSs are placed at known locations near the edges of macro-cells.
Opportunistic Scheduling in Cluster Computing
Keywords: cluster computing
Distributed systems

Distributed computing frameworks have become popular in recent years because of their ability to easily scale computation to thousands of machines. Previous studies show that the popularity of data on these systems is highly skewed. A small set of files are responsible for a significant number of accesses. This data reuse should typically lead to performance improvements, but we find that cluster computing systems are unable to fully take advantage of this sharing. This is due to the fact that distributed systems schedule their work with no consideration of what is cached in the cluster. We have designed a system called Quartet that is aware of the data cached in memory and uses this information to opportunistically schedule work where the input data is cached. Our experimental results show that when workloads reuse data, Quartet can significantly increase the cluster cache hit rate and reduce the run times.
The Impact of Mindfulness-based Cognitive Therapy on Neural Processing of Sadness Provocation and Depressive Relapse in a High-risk Sample
Keywords: depressive relapse
fMRI
major depressive disorder
MBCT
mindfulness
therapy

The current study sought to investigate the neural mechanisms underlying Mindfulness-based Cognitive Therapy (MBCT). Eighty-one remitted patients with a lifetime history of depression were recruited and randomly assigned to either MBCT or Cognitive Behavioral Wellbeing Therapy. Participants underwent functional MRI while completing a sadness provocation task at pre- and post-treatment. MBCT participants evinced lower activation of the posterior insula, a region implicated in body awareness, whereas MBCT relapsers evinced further MPFC deactivation, a region implicated in ruminative thinking. Moreover, it appeared non-relapsers exhibited stable brain responsiveness across time points, whereas relapsers tended to fluctuate. Findings indicate MBCTâ s emphasis on stabilizing behavioral symptoms extends to functional brain profiles, and the activation pattern in relapsers may reflect dissociation from current sensory experiences when confronted by dysphoric cues. Implications pertain to clinical practice in terms of the importance of regularly monitoring client progress throughout treatment and addressing the misapplication of mindfulness skills.
Identification of Novel Compounds That Inhibit HIV-1 Gene Expression by Targeting Viral RNA Processing
Keywords: anti-viral therapy
HIV
RNA processing
splicing

Novel strategies targeting different stages of the HIV lifecycle are vital for continued success in combating viral infection. Since HIV gene expression is dependent upon controlled splicing of the viral transcript, small molecule modulators of RNA processing hold tremendous promise as novel drugs. To this end, we screened splicing modulators for their effect on HIV-1 gene expression. We identified four compounds, 191, 791, 833 and 892, that strongly suppressed accumulation of HIV-1 incompletely spliced RNA and expression of viral structural/regulatory proteins. Furthermore, compound treatment had limited effects on alternative splicing of host RNA splicing events. Subsequent studies confirmed anti-HIV activity of two compounds in the context of peripheral blood mononuclear cells. The distinct effects of these compounds from previously characterized HIV-1 RNA processing inhibitors validate targeting this stage of the virus lifecycle. Elucidating the mechanism by which these compounds alter HIV-1 gene expression holds key insights for novel therapeutic strategies.
Analysis of Yolk Cell Microtubule Network Dynamics and Organization during Zebrafish Epiboly
Keywords: Danio rerio
Epiboly
Microtubules
Yolk cell
Zebrafish

Epiboly, the first morphogenetic event in zebrafish development, is a coordinated process of the blastoderm and yolk syncytial layer spreading over the yolk cell. In the yolk cell, microtubule arrays extend longitudinally and their dynamics have been suggested to be important for normal epiboly. Despite these findings, the function of the yolk cell microtubules remains unclear. Live imaging of EB3-GFP, a microtubule plus-end tracking protein, revealed a change from active microtubule growth during early epiboly to a non-growing state during late epiboly. Antibody staining for tyrosinated and detyrosinated tubulin, markers of dynamic and stabilized microtubules respectively, revealed the presence of stable microtubules during late epiboly but not during early epiboly. The yolk microtubule network also appeared to be more resistant to the microtubule depolymerizing agent nocodazole at late epiboly stages. For the first time, I report a change in microtubule dynamics and suggest different roles of microtubules throughout epiboly phases.
Hollow Core Bragg Waveguide Design and Fabrication for Enhanced Raman Spectroscopy
Keywords: Bragg
Hollow core
Hollow core waveguide
Raman
Spectroscopy

Raman spectroscopy is a widely used technique to unambiguously ascertain the chemical composition of a sample. The caveat with this technique is its extremely weak optical cross-section, making it difficult to measure Raman signal with standard optical setups. In this thesis, a novel hollow core Bragg Reflection Waveguide was designed to simultaneously increase the generation and collection of Raman scattered photons. A robust fabrication process of this waveguide was developed employing flip-chip bonding methods to securely seal the hollow core channel. The waveguide air-core propagation loss was experimentally measured to be 0.17 dB/cm, and the Raman sensitivity limit was measured to be 3 mmol/L for glycerol solution. The waveguide was also shown to enhance Raman modes of standard household aerosols that could not be seen with other devices.
Model Order Reduction and Stability Enforcement of Finite-difference Time-domain Equations Beyond the CFL Limit
Keywords: CFL Extension
FDTD Sub-gridding
Finite-Difference Time Domain
Model Order Reduction
Stability Enforcement

The Finite-Difference Time Domain (FDTD) method is a versatile and popular method for solving Maxwell's equations. As a consequence of the explicit time integration, the maximum stable time-step of FDTD is constrained by the Courant-Friedrichs-Lewy (CFL) limit. This thesis focuses on two interdependent topics: model order reduction (MOR) of explicit FDTD equations and stability enforcement above the CFL limit. The combination of these two topics leads to the proposed CFL extension technique which has been demonstrated for 2D and 3D simulations. In addition, the proposed method has also been applied to the FDTD sub-gridding application. Comparisons have been made with existing implicit and explicit CFL extension techniques with respect to versatility, computational efficiency, and numerical dispersion errors. While there exist computation and memory limitations, the proposed method has demonstrated excellent versatility and accuracy for all test cases while having significant speed-ups over standard FDTD.