VictorJuiz/thesis huggingface dataset:
Exploring the αvβ3/β5 Integrin Gated Proliferation of Hippocampal Neural Progenitor Cells
Keywords:  Department of Biology
Biology
Developmental Neurobiology
Adult Neurogenesis
Thesis

Neural progenitor cell (NPC) proliferation and differentiation is influenced by factors like local cell-to-cell interactions, soluble mitogens and extracellular matrix (ECM) molecules. These factors have been shown to maintain NPC pools and restrict the production of new neurons to neurogenic zones in the adult brain. Previous research has not yet addressed whether the interaction between ECM molecules localized to the subgranular zone, and the NPCs via the αvβ3/β5 integrin receptor could enable the maintenance of the stem cell pool and the production of neurons. Thus, we investigated the gating effects of various (Arg-Gly-Asp) RGD-motif ECM molecules through the αvβ3/β5 integrin receptor on growth factor mediated NPC proliferation. Using hippocampal mouse-derived NPCs that express or lack the integrin αvβ3/β5, we investigated the difference in endogenous proliferation rates, and then tested the gating effect of various ECM substrates via the integrin αvβ3/β5 on Shh, VEGF, and IGF-1 mediated NPC proliferation. Here, we show that NPCs with the αvβ3/β5 integrin have increased NPC proliferation compared to those that lack the integrin αvβ3/β5 when plated on the ECM substrates vitronectin, fibronectin, and collagen. Next, we show that IGF-1 yields a greater increase in proliferation in NPCs that express the integrin αvβ3/β5 compared to those that lack the integrin αvβ3/β5 when plated on vitronectin, fibronectin, laminin, and MFG-E8. This work improves our understanding of the interaction between NPCs and the local microenvironment of the adult brain as we seek to develop the tools to understand and artificially manipulate NPC proliferation and differentiation.
An ex-situ study of retained structural changes and densification in oxide glasses recovered from high pressure and temperature using NMR spectroscopy [electronic resource]
Keywords: Geological and Environmental Sciences.

This study attempts to understand the pressure effects on the structure and density of glasses recovered from 1-3 GPa pressure using 27Al, 11B, 29Si and 23Na MAS NMR spectroscopy. A quantitative spectroscopic study of the pressure-induced structural changes and densification is conducted on aluminosilicate and aluminoborosilicate glass compositions. We have demonstrated that high-pressure experiments in solid media pressure apparatus conducted at high-pressure and near the glass transition temperature retain much of the pressure-induced structural changes and densification compared to high-pressure experiments above the melting temperature. Our study of Na, Ca and Mg aluminosilicate glasses show that the role of non-bridging oxygen (NBO) in pressure-induced structural changes varies systematically upon changing modifier from Na to Ca to Mg. The network cation coordination (Al) increase are larger for the NBO-rich composition compared to NBO-poor composition in Na aluminosilicate glasses, while both NBO-rich and poor Mg aluminosilicate glasses showed no apparent difference in aluminum coordination increase. In Ca aluminoborosilicate glasses with varying B/Si ratio, we observe both aluminum and boron coordination to rise with pressure. However, the average aluminum coordination and densification increases were larger for the high boron composition compared to that of low boron. In this thesis, we propose a mechanism that describe such interaction between boron and aluminum network cations. We also look at aluminoborosilicate glasses with varying modifier from Ca2+ to La3+ to Y3+ studying the effect of modifier field strength on network cation coordination increases with pressure. Our results show that network cation coordination increases (B and Al) are dramatically larger for smaller and highly charged modifier cations (La and Y) compared to Ca.
Fast, distributed computations in the cloud [electronic resource]
Keywords: Electrical Engineering.

Control planes of cloud frameworks trade off between scheduling granularity and performance. Centralized systems schedule at task granularity, but only schedule a few thousand tasks per second. Distributed systems schedule hundreds of thousands of tasks per second but changing the schedule is costly. This dissertation presents a new, third strategy, called execution templates. Execution templates leverage a program's repetitive control flow to cache control plane decisions in templates. A template is a parametrisable block of tasks: it caches some information (e.g., task dependencies) but instantiation requires some parameters (e.g., task identifiers). Executing the cached tasks in a template requires sending a single message that loads the new parameters. Large-scale scheduling changes install new templates, while small changes apply edits to existing templates. Execution templates are not bound to a static control flow and efficiently capture nested loops and data dependent branches. Evaluation of execution templates in Nimbus, a cloud computing framework, shows that they provide the fine-grained scheduling flexibility of centralized control planes while matching the performance of the distributed ones. Execution templates in Nimbus support not only the traditional data analytics, but also complex, scientific applications such as hybrid graphical simulations.
Fast linear algebra algorithms and applications to computational flow physics [electronic resource]
Keywords: Mechanical Engineering.

This is an interdisciplinary study on fast linear algebra algorithms and high performance computing methods with applications in flow physics. Fast linear algebra algorithms are the essence of most high performance scientific calculations. In this thesis we study various novel fast linear algebra techniques, including adaptive fast multipole method and fast sparse linear solvers using low-rank approximation and extended sparsification. We also discuss numerical and computational methods developed for high fidelity simulation of heated particle-laden flows, which is followed by review of new physics discovered. We show heated particles can modify spectral properties of the background turbulence. The effect of particle preferential concentration in particle-to-gas heat transfer is studied. In addition, we use the developed computational physics framework to benchmark our proposed novel sparse matrix linear solver.
Fate, Belief, and Consolation: Fortunetelling and Divination in South Korea
Keywords:  Department of Anthropology
fortunetelling
divination
South Korea
Department of Anthropology
Thesis

This thesis investigates the popularity of fortunetelling in South Korea, which has today situated itself as a leisurely activity, and one that also generates sociality. Patrons hardly sit across from fortunetellers expecting an accurate peak into the future; the pleasure of dwelling
where excitement and eerie fright cross, the hazy zone of belief and non-belief, and stories embellished with inexplicable, but fascinating experiences, sustain the
relish and popularity of fortunetelling. By constituting and contending "truths" of the session together, fortunetelling also opens up possibility for therapeutic efficacy. Fortunetelling is understood as an opportunity to untangle perplexing emotional problems at hand through a meticulous naming of the past, present, and the future, as well as through the reinstatement of hope that practitioners are invested in offering their patrons. By shedding light on a uniquely Korean emotion, dapdapham, and the recently burgeoning trend towards hɪlɪŋ, a search for consolation and encouragement, that drive these visits to the fortunetellers, I argue that patrons in particular seek a way to make heard burdensome stories, whether those be pestering problems of the everyday or much weightier ones. Fortunetelling, through this lens, is not merely an extension of the tradition it is steeped in; it is also a thoroughly modern response to the hectic rhythm and values that leave little room for attention to individual accounts of affliction.
Fatigue of metallic alloys at sub-millimeter sizes [electronic resource]
Keywords: Mechanical Engineering.

This thesis reviews fatigue data available in the literature for smaller size scales, focusing on metallic alloys. Then, it summarizes different testing approaches that have been developed to perform fatigue testing of small specimens. With that background, we set out to build a machine that would allow for very simple, precise, and efficient testing of fatigue properties of engineering materials at a sub-millimeter size scale. We determined that using rotating wire as the method of testing fatigue was the simplest way to ensure that fatigue would happen where we predicted in a specimen (wire). It also avoided the need to manufacture tiny specimens, which can be challenging. It allowed for a high cyclic frequency and precise determination of stress, based on the geometry of the bend of a wire. The machine needed to maintain the length of the wire very precisely in order to maintain the desired stress levels. Using a motor mounted to a translation stage, and bushings set at fixed intervals, we were able to control the geometry and create a precise rotating wire machine. Analyses supporting the design of the test machine are provided, as well as a detailed description of the design.
Feature-conditioned neural network pre-training for skin cancer classification
Keywords: Ben Wegbreit Prize for Best Undergraduate Honors Thesis
Artificial Intelligence
Computer Science
Thesis

Despite tremendous advances in image recognition using convolutional neural networks over the past few years, the performance of deep learning based models on supervised classification is typically benchmarked using enormous labeled datasets comprising millions of images. Realistically, for many highly impactful classification tasks, such as medical image analysis, obtaining sufficient labeled data may be prohibitively expensive, time-consuming, or even impossible. However, it is often easier to obtain unlabeled image datasets, along with con-textual information that is related to the true desired labels. In this work, we propose two separate pre-training algorithms to leverage these datasets a GAN-based pre-training algorithm, and a purely CNN-based algorithm and evaluate their performance specifically for binary classification of skin lesions as either benign moles or cancerous melanomas. When tested against traditional model pre-training using the ImageNet dataset, both pre-training algorithms boost performance on the classification task, especially when smaller labeled datasets of only 5,000-10,000 images are available for training. Additionally, using the feature conditioned CNN-based pre-training algorithm, subsequent model performance exceeds both dermatologist and previous state-of-the-art results when evaluated on a test set of dermoscopic skin lesion images.
Feedback regulation of steady-state epithelial turnover and organ size [electronic resource]
Keywords: Molecular and Cellular Physiology.

Continual cell turnover is crucial for the long‐term maintenance of healthy organs, but to avoid pathological consequences, new cells must be produced at the precise rate that old cells are lost. Here we identify the signaling basis of feedback inhibition that equalizes cell production and loss during stem cell‐driven turnover of the Drosophila intestinal epithelium. E‐cadherin at the cortex of mature enterocytes inhibits EGF‐dependent stem cell divisions by repressing the EGF maturation factor rhomboid. Single, apoptotic enterocytes disrupt this inhibitory relay by degrading E‐cadherin, which de‐ represses rhomboid to activate EGFR and promote divisions of nearby stem cells. Ectopic loss of E‐cadherin in non‐apoptotic cells upregulates rhomboid, causing EGFR hyperactivation and excessive divisions. In contrast, blocking apoptosis precludes EGFR activation and slows down divisions to keep total cells constant. Thus, stem cell divisions require enterocyte apoptosis to relieve proliferative inhibition, ensuring equal rates of cell production and loss.
A Fermi liquid perspective on the high field ground state of the cuprate superconductors [electronic resource]
Keywords: Physics.

The nature of the parent metallic state from which high temperature superconductivity emerges has remained fiercely controversial in the three decades since the discovery of the cuprate superconductors. Surprisingly, recent experiments in magnetic fields high enough to quench superconductivity have revealed a metallic state whose properties are remarkably conventional, and well explained within the context of Fermi liquid theory. Yet, even within this paradigm, these experiments have raised several fundamental theoretical questions. This thesis focuses on a few such experimentally motivated matters of theoretical principle. The primary themes involve issues surrounding quantum oscillations, as well as the recent discovery of charge density waves (CDWs) in the underdoped cuprates. I begin with a discussion of how charge density waves in YBCO can be related to earlier discovered stripes in the `214' family of cuprates, and also consider the experimental consequences of the resulting vestigial orders which break discrete rotational and/or mirror symmetries. I show that X-ray scattering measurements of seemingly biaxial CDW order, can in fact originate from a three dimensional `crisscrossed' pattern of stripes. This three dimensional pattern breaks mirror symmetries, leading to sharp consequences for quantum oscillation spectra, possible detection in elastoresistance experiments, and each of these topics form chapters of this thesis. The discussion of quantum oscillations starts by considering whether they are even possible in the presence of incommensurate CDWs that formally destroy translation symmetry, rendering the concept of a Fermi surface approximate at best. Using exact dualities, I show that quantum oscillations are no longer periodic in 1/B, and even disappear for sufficiently strong incommensurate CDWs. In a subsequent chapter, I use similar dualities to constrain the form of the Fermi surface that is possible in YBCO, and discuss the strong evidence for both mirror symmetry breaking and significant quasiparticle renormalization. Finally, I examine the behavior of the Hall number of a metal when nematicity results in a Lifshitz transition where the Fermi surface topology evolves from a closed pocket to open sheets. I provide analytic expressions for the critical behavior of the Hall number, and also relate these results to recent experiments in the cuprates. I conclude this thesis by synthesizing these ideas into a proposed doping evolution for the Fermi surface of an idealized cuprate.
Field theory for cosmology [electronic resource] : an effective approach
Keywords: Physics.

Effective field theory (EFT) is our most successful tool to date for exploring the fundamental processes of particle physics: it has been able to describe all know particle interactions in the lab to astonishing accuracy. We are now entering an era of precision cosmology, where we can use the power of EFT, a tool that has only recently been applied to the field of cosmology, to fully make use of cosmological observations. This thesis comprises recent work applying effective field theory in the context of early-universe cosmology and large-scale structure (LSS).
Financial markets and trading networks [electronic resource]
Keywords: Statistics.

In this doctoral dissertation, I study the market structure and efficiency of over-the-counter (OTC) financial markets. Specifically, I model how financial trading networks endogenously form, and how trading networks and trade protocols affect pricing, trading behavior, liquidity, and efficiency. This dissertation consists of two chapters. The first chapter addresses the endogenous structure of financial networks. Here, I model how core-periphery trading networks arise endogenously in over-the-counter markets as an equilibrium balance between trade competition and inventory efficiency. A small number of firms emerge as core dealers to intermediate trades among a large number of peripheral firms. The equilibrium number of dealers depends on two countervailing forces: (i) competition among dealers in their pricing of immediacy to peripheral firms, and (ii) the benefits of concentrated intermediation for lowering dealer inventory risk through dealers' ability to quickly net purchases against sales. For an asset with a lower frequency of trade demand, intermediation is concentrated among fewer dealers, and interdealer trades account for a greater fraction of total trade volume. I show, party in separate work, that these two predictions are strongly supported by evidence from the markets for German sovereign bonds and U.S. corporate bonds. From a welfare viewpoint, I show that there are too few dealers for assets with frequent trade demands, and too many dealers for assets with infrequent trade demands. The second chapter models bargaining in over-the-counter network markets over the terms and prices of contracts. Of concern is whether bilateral non-cooperative bargaining is sufficient to achieve efficiency in this multilateral setting. For example, will market participants assign insolvency-based seniority in a socially efficient manner, or should bankruptcy laws override contractual terms with an automatic stay? The model provides conditions under which bilateral bargaining over contingent contracts is efficient for a network of market participants. Examples include seniority assignment, close-out netting and collateral rights, secured debt liens, and leverage-based covenants. Given the ability to use covenants and other contingent contract terms, central market participants efficiently internalize the costs and benefits of their counterparties through the pricing of contracts. We provide counterexamples to efficiency for less contingent forms of bargaining coordination.
Fingerpad skin deformation for sensory substitution of force in teleoperation and virtual reality [electronic resource]
Keywords: Mechanical Engineering.

During real-world physical interaction, haptic information provides people with important information about environment properties and interaction forces. While world-grounded kinesthetic devices have traditionally been used to provide multi-degree-of-freedom haptic feedback to the users of teleoperation and virtual reality systems, another option is skin deformation feedback, where a device stimulates mechanoreceptors within the skin. Skin deformation can be used to convey force information similar to that provided by kinesthetic devices, but does not necessitate external grounding, meaning that it could potentially function in much larger workspaces. This thesis presents the development and evaluation of novel skin deformation devices for sensory substitution of force in teleoperation and virtual reality applications. With a new lateral skin deformation device capable of deforming skin on the fingerpads during teleoperation of a robot manipulator, we showed that user stiffness discrimination was as good with skin deformation feedback as with kinesthetic force feedback. The usefulness of this device and feedback method were validated in a teleoperated palpation experiment, during which participants performed just as well as with kinesthetic feedback and better than with previously investigated sensory substitutes, without the risk of feedback-induced instability. Next, we designed and validated a new fingertip-wearable skin deformation device for use in virtual reality systems. Users were able to perform virtual palpation and surface friction discrimination with feedback from this device. By using two of these devices on the index finger and thumb, we showed that naive users were able to determine virtual object physical properties such as mass, stiffness, and friction with no prior experience or training. Finally, we integrated haptic rendering with pseudohaptic graphical scaling to extend the range of virtual mass rendering and determine how mass perception is affected by the haptic and visual channels when using skin deformation feedback. These results show that skin deformation feedback is an effective substitute for kinesthetic force feedback in both teleoperation and virtual reality scenarios. With minimal training, users of systems with skin deformation feedback are able to perform nearly as well as with true force feedback, while avoiding many of the issues traditionally associated with kinesthetic feedback systems.
Flexible bandwidth allocation framework [electronic resource]
Keywords: Electrical Engineering.

We present NUMFabric, a novel transport design that provides flexible and fast bandwidth allocation control. NUMFabric is flexible: it enables operators to specify how bandwidth is allocated amongst contending flows to optimize for different service-level objectives such as weighted fairness, minimizing flow completion times, multipath resource pooling, prioritized bandwidth functions, etc. NUMFabric is also very fast: it converges to the specified allocation 2.3 times faster than prior schemes. Underlying NUMFabric is a novel distributed algorithm for solving network utility maximization problems that exploits weighted fair queueing packet scheduling in the network to converge quickly. We evaluate NUMFabric using realistic data center topologies and highly dynamic workloads and show that it is able to provide flexibility and fast convergence in such stressful environments.
Flexible Weinstein structures and applications to symplectic and contact topology [electronic resource]
Keywords: Mathematics.

This thesis has three parts. In the first part, we introduce the notions of regular and flexible Lagrangian manifolds with Legendrian boundary in Weinstein domains. We show that flexible Lagrangians satisfy an existence and uniqueness h-principle (up to ambient symplectomorphism) and give many examples of flexible Lagrangians in the standard symplectic ball. In the second part, we show that all flexible Weinstein fillings of a given contact manifold have isomorphic integral cohomology, generalizing similar results in the subcritical Weinstein case. We also prove relative analogs of our results for flexible Lagrangian fillings of Legendrians. As an application, we show that any closed exact, Maslov zero Lagrangian in a cotangent bundle that intersects a cotangent fiber exactly once has the same cohomology as the zero-section. In the third part, we construct many new exotic symplectic and contact structures. For instance, we show that many closed n-manifolds of dimension at least three can be realized as exact Lagrangian submanifolds of the cotangent bundle of the n-sphere with possibly an exotic symplectic structure. We also show that in dimensions at least five any almost contact class that has an almost Weinstein filling has infinitely many different contact structures. We also construct the first known infinite family of almost symplectomorphic Weinstein domains whose contact boundaries are not contactomorphic.