VictorJuiz/thesis huggingface dataset:
Novel MRI tools for focused ultrasound surgery [electronic resource]
Keywords: Electrical Engineering

Magnetic resonance imaging (MRI) guided focused ultrasound (MRgFUS) is a promising non-invasive and non-ionizing therapy in which the acoustic energy penetrates to the target through the intact surrounding tissue without causing any significant bioeffects and without any incisions. At the target, ultrasound energy is converted to heat, causing tissue coagulation and necrosis. MRI guidance is used with FUS to provide high quality tumor margin definition as well as the ability to monitor the temperature of the tissue and assess the treatment. Among the MRgFUS applications are treatments of tumors in the prostate, breast, uterine fibroids, liver and brain. To make these applications widely acceptable and available to patients, improvement of image guidance is essential. The goal of this work was to develop novel MRI tools for visualization of the focal spot and for adaptive focusing of ultrasound. Visualization of the ultrasound focus is performed to con rm that the beam's focus is placed on the target anatomy. Currently, it is achieved by producing a small temperature rise in a test spot, which is detected using MRI temperature monitoring techniques. Focus localization often relies on multiple applications of ultrasound, the cumulative effects of which can lead to potentially irreversible changes in healthy tissue. In addition, visualization of the temperature rise with MRI is problematic in tissue with high fat content such as breast. The thesis addresses the challenges of focus visualization by introducing novel imaging methods, that image displacement of tissue due to acoustic radiation force: 2D Fourier Transform (2DFT) spin-echo and single-shot echo planar imaging (EPI) MR guided acoustic radiation force imaging (MR-ARFI). The new pulse sequences are demonstrated ex vivo and optimized for in vivo brain applications. One of the challenges of using FUS to treat brain pathology is overcoming the phase aberrations of ultrasound caused by heterogeneous acoustic properties of the skull bone. These aberrations result in partial or complete destruction of the focal spot, and therefore prevent the delivery of sufficient energy to the targeted volume, and cause heating where it was not intended. The current correction method estimates the aberrations from the thickness and density of the skull bone obtained from pre-operative computerized tomography (CT) images of the patient's head. Recently introduced alternative methods use adaptive focusing approach combined with MR-ARFI. The transducer elements' emissions are manipulated until the acoustic intensity, which is proportional to tissue displacement, is maximized. Promising, but very time consuming, these methods do not o er a practical solution. In this work, it is shown how using Zernike polynomials, actively utilized in optics, can increase the efficiency of MR-ARFI-based adaptive focusing, making it a more suitable technique for clinical applications.
Numerical approaches to theory of spectroscopy in correlated materials [electronic resource]
Keywords: Physics

Strongly correlated systems exhibit novel phenomena such as superconductivity and magnetism that arise from the interplay between many intertwined degrees of freedom. In this dissertation I discuss my work using state-of-the-art exact diagonalization simulations in attempts to understand the physics of correlated materials via their response to various experimental probes. I first discuss simulating x-ray absorption spectra to extract crucial information regarding correlation effects in iron-based superconductors and the pressure-induced phase transitions in hematite. I then discuss modeling resonant inelastic x-ray scattering spectra of the cuprate superconductors and studying the orbital characters of the excitation profiles. Following the discussion of photon-based spectroscopies, I then shift the focus to magnetic properties of iron-based superconductors. I will discuss a possible orbital ordering scenario in connection with the orthorhombic anisotropies observed in neutron scattering, transport, and other spectroscopic experiments performed on these materials. At the end of the dissertation, I examine the role of magnetic frustration and demonstrate how the response of antiferromagnets to non-magnetic impurities and magnetic Raman scattering can reveal the degree of frustration and help narrow the possible models for the iron-pnictide materials.
Offloading Critical Security Operations to the GPU
Keywords: Computer Science.
Graphics processing units
Data encryption > Computer science
Thesis

General computing with Graphics Processing Units (GPUs) has taken off the last few years because of their unique ability to perform parallel calculations very efficiently.
More developers have started to take advantage of this processor to improve software performance. Similarly, security developers have considered using the GPU to offload calculations as a way to improve the speed and robustness of security software. In this thesis, I outline reasons why this process might not necessarily be secure and provide experiments I have performed to find security flaws in GPU offloading.
On a free boundary problem for embedded minimal surfaces and instability theorems for manifolds with positive isotropic curvature [electronic resource]
Keywords: Mathematics

In this thesis, we describe a min-max construction of embedded minimal surfaces satisfying the free boundary condition in any compact 3-manifolds with boundary. We also prove the instability of minimal surfaces of certain conformal type in 4- manifolds with positive isotropic curvature. Given a compact 3-manifold M with boundary [d̳]M, consider the problem of find- ing an embedded minimal surface [Sigma] which meets [d̳]M orthogonally along [d̳][Sigma]. These surfaces are critical points to the area functional with respect to variations preserving [delta]M. We will use a min-max construction to construct such a free boundary solution and prove the regularity of such solution up to the free boundary. An interesting point is that no convexity assumption on [d̳]M is required. We also discuss some geometric properties, genus bounds for example, for these free boundary solutions. Just as positive sectional curvature tends to make geodesics unstable, positive isotropic curvature tends to make minimal surfaces unstable. In the second part of this thesis, we prove a similar instability result in dimension 4. Given a compact 4- manifold M with positive isotropic curvature, we show that any complete immersed minimal surface [Sigma] in M which is uniformly conformally equivalent to the complex plane is unstable. The same conclusion holds in higher dimensions as well if we assume that the manifold has uniformly positive complex sectional curvature. The proof uses the H ̈ormander's weighted L^2 method and the stability inequality to derive a contradiction.
On asymptotically optimal source coding and simulation of stationary sources [electronic resource]
Keywords: Electrical Engineering

Source coding or lossy data compression has been extensively studied ever since Shan- non formally described the problem more than half of a century ago. Yet source coding schemes approaching the theoretical Shannon limit even on simple stationary sources such as IID Gaussian or IID uniform sources remain elusive. In this dissertation, both source coding and the related rate-constrained simulation problem are studied. Four necessary conditions for asymptotically optimal sliding-block or stationary codes for source coding and rate-constrained simulation are derived. The first two necessary conditions are proved for stationary ergodic sources while the remaining two necessary conditions are proved for IID sources. A new code design algorithm which attempts to satisfy all four necessary conditions is presented. The code structure has intuitive similarities to classic random coding arguments as well as to "fake process" methods and alphabet-constrained methods. Experimental results show that the new coding design algorithm provides comparable or superior performance with respect to previously published methods on common IID and autoregressive examples, often by significant margins. In many cases, such as IID Gaussian, IID uniform and discrete IID binary sources, the performance approaches the theoretical Shannon limit.
On latent systemic effects in multiple hypotheses [electronic resource]
Keywords: Statistics

This dissertation deals with two closely related topics of latent systemic effect in multiple hypothesis testing in addition to supplying an overview of the growing literature in the field. The first part aims at searching for associations with a primary variable among a great many candidate variables in high throughput settings. High throughput hypothesis testing can be made difficult by the presence of systemic effects and other latent variables. Dependencies can change the relative ordering of significance levels among hypotheses. We propose a two stage analysis to counter the effects of latent variables on the ranking of hypotheses. Our method, called LEAPP, statistically isolates the latent variables from the primary one. In simulations it gives better ordering of hypotheses than competing methods such as SVA and EIGENSTRAT. For an illustration, we turn to data from the AGEMAP study relating gene expression to age for 16 tissues in the mouse. LEAPP generates rankings with greater consistency across tissues than the rankings attained by the other methods. The second part studies the detection of DNA copy number variation (CNV) across samples. Experimental artifacts, such as local trends, if not carefully removed, may be misconstrued as significant recurrent regions. We develop an alternating algorithm to adjust the effects of latent variables on the detection of recurring CNVs. Our method, called CNVlatent, improves accuracy in detecting CNVs for simulated data compared to methods without adjustments for latent effects. We resort to two data sets for illustration. One is from the chromosome 9p region in 44 pediatric leukemia samples and the other is from a region on cytoband 11 on the q-arm of chromosome 22. CNVlatent successfully detects visible copy number changes and adjusts for the latent effects. There are many studies regarding segmentation of CNVs, but incorporating copy number information into association tests remains an open problem for lack of accuracy of copy number genotyping. We proposed a statistical framework for genotyping CNVs on a detected genomic region encompassing the putative CNVs in the analysis of both inherited and somatic copy number variants. To pool information across SNPs, we take into account the different response rates and noise properties of each SNP. We carry out the model calibration with an Expectation-Maximization (EM) based algorithm. Our method achieves higher estimation precision in synthetic data and generate estimators with greater consistency across a data set with replicate samples than existing methods such as CNVtools.
On redemption, the value of putting bad things to good use [electronic resource]
Keywords: Philosophy

This dissertation offers a theory of a solution to the problem of lost meaning in life due to regrettable, past events. Each of us wishes for a meaningful life, but each of us, too, is vulnerable to threats to the meaning in life. The dissertation argues that a phenomenon called redemption can restore lost meaningfulness, and increase the value of our lives, overall. The first step in the argument is to demonstrate the need for a new model of redemption. The next step is to argue that redemption is a matter of transforming the meaning of events in our lives from bad to good in a thick, eudaimonistic sense related to a person's well-being. Finally, I show that this transformation not only increases a person's well-being but, more importantly, changes the relationship a person has with his past; By satisfying conditions for meaningfulness—a special value a life can have, distinct from its moral goodness or happiness—redemption renders the past more meaningful that it would have otherwise been. Because of this, redemption can solve the problem articulated in the beginning of the dissertation—the problem of lost meaning in life due to bad, past events.
Open trade, closed borders [electronic resource] : immigration policy in the era of globalization
Keywords: Political Science.

This thesis argues that immigration policy cannot be studied in the absence of trade and capital policy. Trade is a substitute for immigration for both policymakers and firms. Opening trade forces firms to become more productive, move overseas, or close their doors; all three choices reduce firms' incentives to push for open immigration and allows policymakers to move immigration policy closer to the ideal policy of the rest of their constituents by restricting immigration. Opening capital reinforces this effect by increasing the probability that firms will move overseas in response to trade openness instead of remaining at home. The thesis tests this theory on two new datasets, one on the immigration policy of 19 states from the late 18th century through the early 21st century and one on the voting behavior of US Senators on immigration from 1865-2008. In both datasets, there is a powerful, robust and enduring relationship between trade and immigration. Trade openness leads to greater immigration restrictions and this relationship is made stronger when we examine capital openness as well.
Optogenetic studies of brain disease [electronic resource] : engineering light delivery into biological tissue
Keywords: Bioengineering.

Optogenetic neuromodulation is giving scientists an unprecedented ability to modulate neural circuits, providing specificity with regards to location, cell type, as well as neuromodulatory effect. On the other hand, electrical stimulation and lesions, methods commonly used to study neural circuits, are lacking in specificity, often affecting both local cells and passing axons, as well as multiple cell types. Our laboratory has been at the forefront of the field of optogenetics, having developed, for use in mammalian systems, Channelrhodopsin-2 (ChR2), an algal light-activated cation channel that depolarizes neurons in response to blue light, and Natronomonas pharaonis halorhodopsin (eNpHR), a chloride pump that hyperpolarizes neurons in response to amber light. These proteins can control neuronal activity with millisecond timescale precision, and through promoters, they can be targeted to specific cell-types in heterogeneous tissue. Along with its specificity, light stimulation with optogenetic tools often allows the recording of neural activity without the artifact that obfuscates recordings with electrical stimulation. The advantages provided by optogenetics allowed us to make a breakthrough in determining the therapeutic mechanism of deep brain stimulation, a robust treatment for Parkinson's disease in which stimulating electrodes are implanted deep in the brain. Using optogenetics, we replicated the effect of deep brain stimulation by modulating cortical inputs into the region where the stimulating electrode is normally placed. Combined with other corroborating publications, a hypothesis is emerging that electrical stimulation deep in the brain actually produces its effect by modulating cortical projections to the deep brain region. Based on this concept, several clinical studies are being done to better understand the cortical role in Parkinson's disease and determine whether cortical stimulation (potentially non-invasive), could be an alternative to the invasive implants currently used. In order to perform these experiments, we studied the transmission of visible light in brain tissue to estimate the volume of activation produced by optogenetic stimulation and developed a device to measure fluorescence in awake, behaving animals, allowing the quantification of virally transfected gene expression over time, as well as the localization of expression along axon bundles. The knowledge gained from these experiments will have a significant impact on future experiments in the broader field of optogenetics.
Organic transistors for flexible electronics [electronic resource] : fabrication and device physics
Keywords: Electrical Engineering

Organic semiconductors have shown promising potentials in flexible electronics. Because the materials can be directly fabricated on flexible plastic substrates at low temperatures, researchers envision development of novel flexible applications, such as flexible displays, flexible circuits, and conformal sensors. In order to develop these practical devices, organic transistor technologies should provide reliable fabrication processes and mature techniques to control the electrical characteristics of each device. In this dissertation, I will discuss several methods to overcome these issues. First, I have demonstrated high-capacitance gate dielectric using atomic layer deposition. This low-temperature process was used to fabricate low-voltage and high-performance flexible organic transistors and inverters. I will also present controlling current-voltage characteristics of organic transistors from the device physics point of view.
Orientability of moduli spaces and open Gromov-Witten invariants [electronic resource]
Keywords: Mathematics

We show that the local system of orientations on the moduli space of J-holomorphic maps from a bordered Riemann surface is isomorphic to the pull-back of a local system defined on the product of the Lagrangian and its free loop space. The latter is defined using only the first and second Stiefel-Whitney classes of the Lagrangian. In the presence of an anti-symplectic involution, whose fixed locus is a relatively spin Lagrangian, we define open Gromov-Witten type invariants in genus zero.
Pade-legendre method for uncertainty quantification with fluid dynamics applications [electronic resource]
Keywords: Mechanical Engineering

Abstract: The Pade-Legendre (PL) method, a novel approach for uncertainty quantification is introduced. The proposed method uses a rational function expansion and is designed to effectively characterize uncertainties in strongly non-linear or discontinuous systems. The discontinuities can be either in the underlying functions (inherent discontinuities) or from lack of sufficient data resolution (multi-scale discontinuities). In the former case, PL method can produce an accurate response surface without spurious oscillations and does not require prior knowledge of the discontinuities. For the latter type of discontinuities, the PL method can help reduce the number of deterministic simulations required to accurately represent the response surface. If sufficient data resolution is achieved, the PL method degenerates to standard polynomial reconstruction. The present approach is illustrated in a number of applications as an uncertainty propagation technique. Moreover, the method is applied to an inference problem in which a sharp discontinuity in the system input is present. The PL method shows a considerable improvement over the traditional approach when discontinuities are present. In addition, an ongoing effort called the UQ Experiment in which we used the PL method to help design the experimental setup is discussed.
Part I, unnatural thymidine analogs and shape mimics as substrates for human thymidine kinases; Part II, fluorescent size-expanded DNA analogs as efficient substrates for a template-independent DNA polymerase. [electronic resource]
Keywords: Chemistry

This thesis is composed of two separate studies involving unnatural nucleoside (DNA) analogs in two different types of enzymes: human thymidine kinases 1 and 2 and terminal deoxynucleotidyl transferase (TdT). The ability of two types of unnatural DNA analogs, nonpolar nucleoside analogs and expanded nucleoside analogs, to act as efficient substrates in enzymes will be described. Nonpolar nucleoside analogs lacking the ability to hydrogen bond were synthesized to systematically vary in size and shape, and then used to probe the ability of two types of human thymidine kinases (TK1 and TK2) to recognize and phosphorylate these analogs. The results establish that nucleoside recognition mechanisms for these two classes of thymidine kinase are very different. On the basis of this data, nonpolar nucleosides are likely to be active in the nucleotide salvage pathway in human cells, suggesting new designs for bioactive molecules. Another class of nucleoside analogs, expanded nucleoside (xDNA) analogs, maintain the ability to hydrogen-bond to their respective natural bases, but have enhanced pi-stacking due to their larger size, allowing the molecule to have greater stability in a DNA duplex, and unique fluorescent properties. It was found that terminal deoxynucleotidyl transferase (TdT), a template-independent DNA polymerase, can accept multiple xDNA nucleotide analogs as substrates with efficiencies close to that of natural nucleotides. In addition, the expanded adenine (xA) and cytosine (xC) analogs show a visible and spectral change in fluorescence when TdT incorporates multiple analogs. The ease of enzymatic synthesis of these analogs and their inherent fluorescence suggest their use in nucleic acid labeling and hybridization studies. The comparable efficiencies which nonpolar nucleoside analogs and xDNA nucleotide analogs have to natural bases in thymidine kinases and TdT give new information about the steric and electronic requirements of these enzymes, and will be useful for potential therapeutic and biotechnological applications.
Path-policy compliant networking and a platform for heterogeneous IaaS management [electronic resource]
Keywords: Electrical Engineering

The dissertation is divided into two parts, each of which can stand independently of the other: ICING and Expedient. The ICING project aims to build a network architecture that empowers the end-points of a communication by giving them control over the path used for the communication. The challenge is providing this control without violating the policies of the providers carrying the communication's traffic and ensuring that the path is followed. ICING consists of a number of sub-projects: ICING-PVM, ICING-ON, and ICING-L3. Expedient is an answer to the following question: How can users manage resources across a federated set of Infrastructure-as-a-Service (IaaS) providers? These resources may be heterogeneous, consisting of different types of network, compute, or other resources, they may be sliced, virtualized, or fully delegated, and they may cross trust boundaries. Expedient provides a platform that gives users access to all resources using one set of credentials, does not require infrastructure developers to change their systems, and allows infrastructure providers to enforce their policies concerning the use of their resources. This dissertation discusses Expedient in the context of GENI, a federated set of IaaS providers with the goal of providing resources for experimental network research.