VictorJuiz/thesis huggingface dataset:
Task Scheduling on Parallel Processors: Semi-Online Settings and Job Placement Constraints

Scheduling tasks/jobs on parallel processors/machines is a classical scheduling problem that is well studied in the literature due to its applicability in parallel computing systems and operations research. Even though it is a well studied problem, new scheduling models that consider the emerging aspects in the continuously evolving parallel computing systems are required to analyze and improve their performance. In this thesis we initially study scheduling on parallel processors under three new semi-online paradigms with motivations from computational offloading systems (e.g. mobile cloud computing, mobile edge computing, hybrid cloud, etc.), where only partial information about the tasks is available. First, we study makespan minimization on a set of local processors and a set of remote processors under the semi-online setting where the task processing times on the local processors are known a priori, but are unknown on the remote processors. Second, considering that each offloaded task incurs a cost, we study makespan-plus-weighted-offloading-cost minimization when the task processing times are not known a priori, but their offloading costs are known. Third, we consider the scenario where offloaded task incurs non-negligible communication overhead and study makespan minimization under the semi-online setting where task communication overheads are known a priori, but their processing times are not known. For each of the above problems we propose efficient algorithms, analyze their performance in the worst case, by deriving competitive ratios, and study their average performance using simulation. Finally, we identity a new job model in scheduling on parallel processors, where a job has placement constraints and multi-processor requirement. Under the job placement constraints we solve a problem of assigning identical jobs to machines. We establish novel results for this problem under generalized objective functions. We propose a new algorithm and analyze its runtime complexity. Further, using benchmark input instances we show that the proposed algorithm has orders of magnitude lower runtime than the existing algorithms.

Keywords: competitive-ratio
Computational offloading
makespan
scheduling
semi-matching
Semi-online
Advisor: Liang, Ben
The Dynamic Interaction of Mantle Compositional Heterogeneities at the Surface and the Core-Mantle Boundary

The Earth's D'' layer, the lowermost 200-300 km of the mantle, is perhaps as rich in chemical, phase and structural heterogeneity as the lithosphere. For instance, tomography studies show the existence of Large Low Shear Velocity Provinces (LLSVPs) extending through D'' beneath Africa and the Pacific that may be compositionally distinct. Of particular interest is the potential interaction between compositional heterogeneity in D'' and the mobility of tectonic plates. This is explored using the convection code MC3D featuring compositional variations, dynamically evolving tectonic plates and continents. To model compositional variations, the tracer ratio method was programmed into MC3D and benchmarked. Plates are modeled using a force-balance method. Also, subroutines were programmed into MC3D that allow tracers to track plate and continent boundary positions. A suite of approximately 40 calculations is used to analyze the effect of introducing a compositionally dense layer into a vigorously convecting mantle initially characterized by mobile-lid tectonics. Subsequent to the introduction of the dense layer, surface mobility is monitored. It was found that upwelling vigor tends to decrease as either the enriched material volume or density is increased, which is accompanied by a reduced rate of surface rupturing. Consequently, long-term surface mobility ceases if either the volume or density of the enriched material is increased beyond a threshold. Another suite of models is used to analyze the effect of introducing a compositionally dense layer into the D'' region of a mantle featuring mobile-lid convection with continents. Subsequently, the supercontinent cycle frequency is monitored for a range of oceanic and continental yield strengths. In calculations featuring a uniform D'' composition, upwelling positions can remain fixed in position over billions of years. However, calculations featuring enriched material exhibited upwellings with substantial lateral movement. It was found that supercontinent aggregation was hindered by the presence of fixed upwellings. Consequently, supercontinent cycle frequency increased in the presence of enriched material. In addition, it was found that the compositionally dense material formed into one or two large provinces for the majority of the time in all calculations featuring compositional variations, similar to the present-day structure of Earth's LLSVPs.

Keywords: Large Low Shear Velocity Province (LLSVP)
Mantle Composition
Supercontinent Cycle
Tectonic Plates
Thermochemical Convection
Tracer Method
Advisor: Lowman, Julian P
Pricing and Matching in the Sharing Economy

We study operational problems related to the sharing economy. Sharing economy platforms such as Uber offer the crowdsourced suppliers a wage for providing services/goods, and charge the customers a price for using them. In Chapter 2, we study the fixed commission rate contract practiced by many sharing economy platforms. We show that by using the optimal flat-commission contract, the platform achieves at least 75% of the optimal profit of the first-best benchmark, in which the platform freely chooses the price and wage under various market conditions. In Chapter 3, we consider a platform's problem of dynamically matching random demand and supply of heterogeneous types in a periodic-review fashion. The platform decides the optimal matching policy to maximize the total discounted rewards minus costs. We provide sufficient and robustly necessary conditions only on matching rewards such that the optimal matching policy follows a priority hierarchy among possible matching pairs. In Chapter 4, we study the dynamic matching problem in Chapter 3 under two specific forms of reward structures. First, we consider the problem with horizontally differentiated supply and demand types. In that problem, supply and demand types locate on a unidirectional circle. The unit matching reward between a supply type j and a demand type i is a decreasing function with respect to the unidirectional distance from the location of j to that of i on the circle. We then study the problem with vertically differentiated supply and demand types, for which we impose a reward structure in which types have â qualityâ differences. For both cases, we apply the results in Chapter 3 to characterize the optimal matching policy. In Chapter 5, we study the pricing behaviors of two agents under incentives generated from social comparison. We demonstrate how opposite-directional social comparisons interact with demand variability to change competitive behaviors. In particular, we show that the stronger the behind aversion behavior, the more intense the price competition, and that there is a threshold on the market variability above which price competition is more alleviated and below which price competition is more intensified, when the agents exhibit stronger ahead-seeking behavior.

Keywords: Matching
Pricing
Sharing economy
Advisor: Hu, Ming
The Effects of Social Context on Physiological Covariation

Physiological covariation – shared patterns of autonomic physiology between people – has been documented within all social relationships and predicts a variety of interpersonal outcomes. At a basic level, however, there remains uncertainty about how much “social experience” is needed for physiological covariation to occur. The present research addressed this issue by manipulating various facets common to social experiences. Study 1 manipulated social versus nonsocial engagement during cooperative and competitive tasks and examined whether physiological covariation predicts measures of affiliation. Across social contexts, partners exhibited physiological covariation in the sympathetic (SNS) and the parasympathetic (PNS) branches of the autonomic nervous system (ANS). However, whether partners exhibited shared increases versus decreases in autonomic activity differed by social context. Moreover, SNS covariation predicted measures of affiliation and appeared to be predominantly influenced by social processes. Conversely, PNS covariation did not predict measures of affiliation and occurred due to the procedural influences of the task. Studies 2 and 3 addressed, for the first time, what happens when the minimum requirement of two people is exceeded. Specifically, in a quasi-experimental field study (Study 2) and in an experimental paradigm (Study 3), I examined whether group size predicts physiological covariation during a group-based meditation comprised of a guided meditation followed by a silent meditation. I also explored the relationship between physiological covariation and familiarity. Across studies, group size predicted physiological covariation in SNS and PNS activity over time. How group size exerted its influence, however, depended on the branch of the ANS and the period of the meditation in which physiological covariation was observed. Among experienced meditators, large groups exhibited SNS covariation during the guided meditation, whereas small groups displayed PNS covariation. Among inexperienced meditators, both large and small groups displayed physiological covariation across the ANS. However, large groups exhibited shared decreases in PNS activity whereas small groups displayed shared increases. During silent meditation, the patterns of physiological covariation exhibited by large and small groups were also inconsistent across studies. Furthermore, familiarity predicted physiological covariation, but only in Study 3. The implications for physiological covariation research, the development of social relationships, and group dynamics are discussed.

Keywords: affiliation
autonomic nervous system
meditation
physiological covariation
Advisor: Page-Gould, Elizabeth
Selective Transformations of Unprotected Carbohydrates Using Organoboron Compounds to Modulate Hydroxyl Reactivity

Regioselective glycosylation of unprotected glycoside substrates has emerged as an attractive strategy for streamlining the synthesis of oligosaccharide targets. However, differentiation of multiple potentially reactive hydroxyl (OH) groups is not always straightforward. The use of small organic molecules to enforce regiocontrol in glycosylation reactions by enhancing the differences in reactivity of carbohydrate OH groups or by altering the innate regioselectivity of the substrate is a useful strategy. The work presented in this thesis describes how the interactions between carbohydrates and organoboron compounds can be used to promote selective transformations of unprotected glycosyl acceptors. Chapter 1 describes how organoboron-promoted regioselective glycosylation reactions can be used to streamline the synthesis of oligosaccharide targets by minimizing protection/deprotection steps. An initial regioselective glycosylation allows differentiation of the remaining OH groups of the disaccharide-derived diols, enabling further selective transformations through substrate controlled processes. Chapter 2 describes the development of a protocol for the regioselective protection of carbohydrate derivatives using boronic acids as temporary blocking groups which can be recovered/recycled. Boronic ester formation with carbohydrate-derived diols attenuates the nucleophilicity of the boron-bound alkoxides, permitting selective functionalization of free OH groups. Chapter 3 describes a novel boronic acid-mediated sequential functionalization protocol. Exploitation of the complementary reactivity of tricoordinate (protecting group) and tetracoordinate (activating group) boronate complexes allows multiple bond-forming reactions to be carried out without the need to isolate intermediate compounds. This allows the production of highly functionalized glycoside products directly from unprotected starting materials. In Chapter 4, strategies for the selective activation of 1,2- or 1,3-cis-diol groups are presented. The interaction between the glycosyl acceptor and the boronic- or borinic acid enables selective activation of one of the two diol groups. This chapter also describes how tuning the properties of a borinic acid catalyst can alter the regiochemical outcome of glycosylation reactions.

Keywords: activation
borinic acids
boronic acids
carbohydrates
protection
regioselective
Advisor: Taylor, Mark S
Solid-Phase Resonance Energy Transfer Based Bioassays Using Immobilized Upconverting Nanoparticles as Donors and Quantum Dots as Acceptors

The work herein describes the development of interfacial bioassays for the detection of biomolecules on glass and paper substrates. Monodisperse water soluble upconverting nanoparticles (UCNPs) were covalently immobilized on modified cover slips and cellulose paper for the development of bioassays. Investigations included examination of the effectiveness of luminescence resonance energy transfer (LRET) for optical signal generation. This work presents the first account of covalent immobilization of UCNPs for use as energy donors. The functionality and stability of the immobilized UCNPs as donors was demonstrated by use of quantum dots (QDs) as energy acceptors in configurations suitable for LRET. A monolayer of densely packed UCNPs was achieved on glass cover slips and was used for the detection of thrombin using selective aptamers. On paper, a sandwich assay for the detection of unlabeled oligonucleotide targets offered a limit of detection in the femtomole range and a dynamic range spanning nearly 3 orders of magnitude. The use of QDs provided improved sensitivity, limit of detection, dynamic range and selectivity compared to similar assays that have used molecular fluorophores as acceptors. The selectivity of the assay was enhanced by the decoration of the QDs with polyethylene glycol to eliminate non-specific adsorption. The assay was extended to the simultaneous detection of three targets using a single form of UCNP as donor and three different color emitting QDs as acceptors. The intensity of emission from each nanoparticle was determined using an epifluorescence microscope and an optical band-pass filter without the need for spectral deconvolution. An instrument with luminescence lifetime measurement capabilities was assembled to investigate the efficiency of resonance energy transfer. The work presented in this thesis describes the essential elements required to assemble a LRET-based assay for the sensitive and selective multiplexed detection of nucleic acids on paper using UCNPs as energy donors.

Advisor: Krull, Ulrich J
Novel Oncogenic Roles of Neuropilin-1 in Pancreatic Adenocarcinoma and its Relevance as a Therapeutic Target

Pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer, is a prominent cause of cancer mortality in Canada, with the lowest five-year survival rate. Recent evidence suggests that cellular processes such as endothelial-to-mesenchymal transition (EndMT), epithelial-to-mesenchymal transition (EMT), and autophagy when aberrantly upregulated, are unifying mechanisms of chemoresistance in PDAC. Apart from being involved in numerous cancer-initiating and promoting events, angiogenic co-receptor neuropilin-1 (NRP-1) is a mediator of TGFβ signaling, which remains the primary signaling mechanism regulating EndMT, EMT and autophagy. Overexpression of NRP-1 and transforming growth factor β (TGFβ) signaling is well-documented in PDAC. We investigated the role of NRP-1 in regulating EndMT, EMT and autophagy in pancreatic cancer. We observed a significant association between NRP-1 levels, EndMT, EMT and autophagy markers’ expression in human PDAC tissue obtained from a clinically relevant orthotopic model of PDAC in athymic rats. Knockdown of NRP-1 inhibited, while overexpression of NRP-1 promoted EndMT and associated fibrosis, respectively, through modulation of TGFβ signaling and Slug expression in endothelial cells. Moreover, in human pancreatic cancer cell lines and their chemoresistant forms, knockdown of NRP-1 inhibited, while overexpression of NRP-1 promoted EMT and associated invasiveness, respectively, via modulation of TGFβ signaling and SNAIL expression. Finally, NRP-1 knockdown inhibited autophagy, while NRP-1 overexpression activated autophagy by repressing mTOR activation in human pancreatic cancer cell lines. NRP-1 was also able to regulate autophagy induced by nutrient starvation and chemotherapy stress and subsequently, affect cancer cell survival. Together, these results suggest that anti-NRP-1 therapy could potentially overcome chemoresistance in PDAC and may emerge as an adjuvant therapy to existing chemotherapy strategies.

Keywords: Chemoresistance
Neuropilin
Pancreatic cancer
Advisor: Leong-Poi, Howard
Human Optic Nerve Head Glial Cell Activation Following Biomechanical Compression

Glaucoma is the most prevalent neurodegenerative disease and the worldâ s second leading cause of blindness resulting from the slow and painless neuropathy of the optic nerve head, and death of the retinal ganglion cells. While very little is known about the onset and pathology of the disease, activated astrocytes are found in the optic nerve heads of early glaucoma patients. Activation of glial cells, including astrocytes, is known to be associated with several neurodegenerative diseases and believed to contribute to their pathophysiology. Glial cell activation has successfully been induced using biomechanical stretch, which was predicted to be experienced by the lamina cribrosa under elevated intra ocular pressure conditions. However, biomechanical compression was also predicted to be even more prevalent, although no good models existed to replicate this condition in vitro. It is for this reason that I have developed a novel model for replicating cellular compression by compressing the medium to which cells adhere in an equi-axial manner. Through careful calibration this model uses a device that is capable of generating specific and consistent amounts of compression by pre-stretching a sylastic membrane upon which cells are then seeded and cultured. The membranes are then removed from the device allowing them to return to their un-stretched state and compressing all cells that are attached. In this research I show how the model was designed and calibrated as well as its usefulness as an in vitro model for glial cell activation using biomechanical compression on human astrocytes and lamina cribrosa glial cells. Using advanced proteomic techniques, nearly 350 unique proteins of interest were observed to be regulated as a result of activation giving us significant insight into the pathways and networks involved in this process. Of particular interest are PEA15, RhoA, IL6, MMP2, HSP90, and FLNB. This model was also successfully used to target and block the actin stress fibre formation pathway, which is normally present in activated astrocytes. The results presented in this research give a powerful new model for examining the effects of cellular compression. It also provides insight into the networks and pathways associated with glial cell activation allowing us to better understand its role in the pathophysiology of glaucoma. This information will assist in efforts to understand the disease and develop better methods for detection, treatment and potential cure for this debilitating disease.

Keywords: Astrocyte
Compression
Glaucoma
Lamina Cribrosa
Neurodegeneration
Reactive Glial Cells
Advisor: Flanagan, John G
Aging and the Early Visual Pathways

The role of aging on cognitive decline has been looked at with a great deal of interest over the past few decades. To a large extent, the aging literature has focused heavily on the impact of aging on memory and cognitive resources, and one area of literature that remains underdeveloped has been the role on how aging affects the cognitive processes of vision. More specifically â does aging change the activity and mutually inhibitory processes of the magnocellular (M) and parvocellular (P) pathways? In order to test how aging affects these two visual pathways, I implemented techniques known to hinder or bolster the M-pathway in younger adults with older adults. In Experiment 1, I tested if the inhibition of the M-pathway with a pulsed pedestal design also occurs with older adults. In this task, I had younger and older adults perceive low and high spatial frequency Gabors with either a pulsed or steady visual pedestal. In Experiment 2, I examined if the connection between the M-pathway and action processing found in younger adults changes with age. In Experiment 3, I examined the connection between object-based attention and the two visual pathways. Across the first three experiments, older adults showed a greater deficit to the M-pathway in the pulsed pedestal condition than younger adults. In Experiment 4, I examined if placing the hands proximal to visual images, which facilitates M-pathway processing in younger adults, also occurs in older adults. Here I found that older adults showed the opposite effect; greater advantage for low spatial frequency Gabors compared to younger adults when the hands were proximal. The data across all four experiments suggest that older adults may have noisier visual pathways, with larger deficits when the M-pathway is inhibited and larger benefits when the M-pathway is bolstered.

Keywords: Aging
Perception
Vision
Visual Pathways
Advisor: Pratt, Jay
Nonlinear Dynamics of the Cosmic Neutrino Background

At least two of the three neutrino species are known to be massive, but their exact masses are currently unknown. Cosmic neutrinos decoupled from the rest of the primordial plasma early on when the Universe was over a billion times hotter than it is today. These relic particles, which have cooled and are now non-relativistic, constitute the Cosmic Neutrino Background and permeate the Universe. While they are not observable directly, their presence can be inferred by measuring the suppression of the matter power spectrum. This suppression is a linear effect caused by the large thermal velocities of neutrinos, which prevent them from collapsing gravitationally on small scales. Unfortunately, it is difficult to measure because of degeneracies with other cosmological parameters and biases arising from the fact that we typically observe point-like galaxies rather than a continous matter field. It is therefore important to look for new effects beyond linear suppression that may be more sensitive to neutrinos. This thesis contributes to the understanding of the nonlinear dynamics of the cosmological neutrino background in the following ways: (i) the development of a new injection scheme for neutrinos in cosmological N-body simulations which circumvents many issues associated with simulating neutrinos at large redshifts, (ii) the numerical study of the relative velocity field between cold dark matter and neutrinos including its reconstruction from density fields, (iii) the theoretical description of neutrinos as a dispersive fluid and its use in modelling the nonlinear evolution of the neutrino density power spectrum, (iv) the derivation of the dipole correlation function using linear response which allows for the Fermi-Dirac velocity distribution to be properly included, and (v) the numerical study and detection of the dipole correlation function in the TianNu simulation. In totality, this thesis is a comprehensive study of neutrino density and velocity fields that may lead to a new technique for constraining neutrino properties via the dipole correlation function.

Keywords: Cosmology
Neutrinos
Advisor: Pen, Ue-Li