VictorJuiz/thesis huggingface dataset:
Magnetic resonance imaging of human articular cartilage of the knee in vivo [electronic resource]

Osteoarthritis (OA) is a degenerative joint disease that affects over 80% of the population of the U.S. by age 65. However, there is currently no disease-modifying treatment for OA. In order to develop and evaluate potential treatments, it is necessary to assess cartilage health over the course of the disease. Here, an MRI method is presented to obtain sodium images of tissue that pushes the current state of the art of sodium MRI and can provide new information about cartilage. The method presented here enables sodium imaging at high resolution and with lower noise levels than previously reported. This technique uses custom-made radio-frequency (RF) coils and a 3D-cones k-space trajectory and is well suited to imaging at high field strengths like 3 T and 7 T. A second novel method is presented for generating high-resolution, 3D T2 and ADC maps of the human knee in vivo. The maps are derived from diagnostic-quality morphological MR images. This method is based on a new variation of the 3D double echo steady-state (DESS) sequence and solves many of the current challenges of traditional imaging techniques. Finally, a third method is presented allowing independent excitation of two or more volumes with a short RF pulse for MRI. This method enables different volumes to be excited with different RF pulse parameters, including flip angle, slice profile or thickness, phase modulation, etc., increasing the flexibility of the excitation. In summary, the techniques presented here generate measurements of sodium, T2, and ADC in cartilage, all biomarkers of interest for this tissue. These measurements are either less noisy or more efficiently obtained than with previous methods. The methods presented in this dissertation also improve the efficiency of diagnostic image acquisition for the knee.

Keywords: Electrical Engineering
Advisor: Hargreaves Brian Andrew primary advisor. Thesis advisor
Gold Garry E.
Pauly John (John M.) advisor. Thesis advisor
Magnetic resonance imaging of magnetic fields from radiofrequency ablation at 64 megahertz [electronic resource]

Radiofrequency ablation (RFA) is an effective minimally invasive treatment for tumors, using RF currents to deposit energy and create local heating. MRI has been proposed to monitor RFA due to its ability to acquire images of heating. If the ablation is performed at 64 MHz (the Larmor frequency of a 1.5 Tesla MRI system) instead of the typical 460-500 kHz, the magnetic fields associated with the RF currents can be used as the MR excitation. RF field mapping techniques can then be used to image those magnetic fields, providing information about the underlying current density. The current distribution will change during the course of ablation due to changes in the complex conductivity of the treated tissue. Knowledge of the magnetic fields could be used to steer currents into a more efficient ablation pattern as well as evaluate the process of the ablation by monitoring changes in the electrical properties of the tissue. In this thesis, I show results from performing RFA at 64 MHz and discuss improvements to MRI RF field mapping techniques for imaging the fields from the ablation currents. I have optimized the Actual Flip-Angle (AFI) RF field mapping sequence to achieve the best SNR of the field maps within a given scan time by considering noise propagation, errors from T1 relaxation and incomplete spoiling of transverse magnetization. I have then designed an adiabatic partial passage pulse that, when used in the AFI sequence, captures a much larger dynamic range, up to 16:1. Finally, I have performed RFA at 64 MHz and imaged the RF magnetic fields.

Keywords: Electrical Engineering
Advisor: Pauly John (John M.) primary advisor. Thesis advisor
Nishimura Dwight George advisor. Thesis advisor
Scott Greig Cameron
Making belief [electronic resource] : religion and the state in Korea, 1392-1960

This dissertation investigates the relationship between religion and the state in the formation of a new belief about modern Korea. It examines how religion has shaped the idea of nation, an ostensibly novel way of imagining the collective. I argue that two types of religion have been central to that imagination: the state religion of the Chosŏn and the imported notion of religion as a category for legitimate belief. In the first chapter, I consider the way in which the Chosŏn used religion to present itself as a divinely mandated polity located outside the Ming's sphere of influence. By utilizing official chronicles, astrological literature, ceremonial manuals, and private writings of the elites, I demonstrate that official religion under the Choson dynasty served to instill a sense of collective belonging before the advent of nationalism. In the second chapter, I examine the creation of a new national identity by Koreans who denied that Japan and State Shinto were the only roads into the light of civilization and modern nationhood. In the third chapter I focus on the definition of superstition by the colonial state and how colonial Korean identity became grounded in that definition in the run up to the official campaign to promote State Shinto. In the final chapter I discuss how Korean Buddhism became the vehicle for claiming a new national identity by the nascent Republic of Korea, which inherited both the religious policies of the colonial state and ideas about religion and nation harbored by Koreans thinkers of the past.

Keywords: Religious Studies
Advisor: Bielefeldt Carl primary advisor. Thesis advisor
Faure Bernard primary advisor. Thesis advisor
Moon Yumi advisor. Thesis advisor
Manipulating light with nanostructured metals [electronic resource]

Plasmonics has emerged as a technology that enables the creation of a wide range of miniaturized photonic devices. Nanostructured metals provide numerous new opportunities for manipulating light at a deep-subwavelength scale. This dissertation covers our work on exploiting nanostructured metals to create new and improved optical functionality. We provided the first experimental demonstration of far-field lensing using an aperiodic plasmonic slit array. This approach offers large design freedom, since these structures derive their behavior from local geometry. We illustrated this flexibility through simulations of efficient and compact planar nanoslit lenses that compensate for various angles of incidence. We further demonstrated the ability to perform phase front design in two dimensions by varying the local geometry in metallic nanoscale pillar arrays. We also considered aperiodic arrays of coupled metallic waveguides and numerically demonstrated that, for an incident plane wave, a focus of as small as one-hundredth of a wavelength can be achieved for a focal distance that is much longer than the wavelength. Moreover, the focusing behavior can be controlled by changing either the incident wavelength or the angle of incidence. We showed that this behavior can be understood using Hamiltonian optics ray tracing. Lastly, we developed the coupled-mode theory for resonant apertures. Such apertures are of fundamental interest, and form the basic building blocks for many applications in subwavelength optics and optoelectronics. We showed that the maximum transmission and absorption cross sections for subwavelength resonant apertures are only related to the wavelength of the incident light and the directivity of the aperture's radiation pattern and explained the spectral behavior of structures that support multiple resonances.

Keywords: Electrical Engineering
Advisor: Fan Shanhui
Brongersma Mark L. advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
Mass participation under autocratic rule [electronic resource]

This dissertation utilizes game theoretic modeling and statistical analysis tools to examine the role that citizens play in contemporary authoritarian politics, and more specifically, their role in overthrowing predatory regimes. I show both theoretically and empirically that contrary to the common view in the literature that focuses mostly on elite politics, the political economy of mass participation influences the survival chances of contemporary autocrats and shapes authoritarian politics.

Keywords: Political Science
Advisor: Fearon James D. primary advisor. Thesis advisor
Magaloni Beatriz primary advisor. Thesis advisor
Cohen Joshua
Tomz Michael advisor. Thesis advisor
Meaningful engagement in educational activity and purposes for learning [electronic resource]

The American political culture that encourages competition on standardized tests, epitomized by the policy of Race to the Top, oversimplifies students' motivation for learning. This dissertation argues that educational research on student learning and activity engagement should consider motives beyond the pursuit of good grades in the classroom, prestigious college credentials, and going to school because it is what students are supposed to do. In particular, the studies highlight the moral inspirations and cultural habits behind students' engagement in life activities, and how inspiration and habits help to direct learning in life. A case study of an ordinary high school senior articulates a common motive to enroll in college to achieve success in life. Comparative case studies contrast emotional experiences with social responsibilities in order to articulate purposes for learning beyond standardized achievement. Findings suggest that volunteer community service, engagements with family, involvement in religious activities, and working for pay could provide inspiration for students to engage in learning in life.

Keywords: Education.
Advisor: Damon William
Antonio Anthony Lising
Krumboltz John D. advisor. Thesis advisor
Labaree David F.
Measurement of hadronic event shapes and jet substructure in proton-proton collisions at 7.0 TeV center-of-mass energy with the ATLAS detector at the large hadron collider [electronic resource]

This thesis presents the first measurement of 6 hadronic event shapes in proton-proton collisions at a center-of-mass energy of 7.0 TeV using the ATLAS detector at the Large Hadron Collider. Results are presented at the particle-level, permitting comparisons to multiple Monte Carlo event generator tools. Numerous tools and techniques that enable detailed analysis of the hadronic final state at high luminosity are described. The approaches presented utilize the dual strengths of the ATLAS calorimeter and tracking systems to provide high resolution and robust measurements of the hadronic jets that constitute both a background and a signal throughout ATLAS physics analyses. The study of the hadronic final state is then extended to jet substructure, where the energy flow and topology within individual jets is studied at the detector level and techniques for estimating systematic uncertainties for such measurements are commissioned in the first data. These first substructure measurements in ATLAS include the jet mass and sub-jet multiplicity as well as those concerned with multi-body hadronic decays and color flow within jets. Finally, the first boosted hadronic object observed at the LHC -- the decay of the top quark to a single jet -- is presented.

Keywords: Physics
Advisor: Su Dong
Jaros John
Peskin Michael Edward
Measurement of the D_s leptonic decay constant f_{D_s} and observation of new resonances decaying to D^(*)pi [electronic resource]

The absolute branching fractions for the decays $D^-_s\rightarrow\ell^-\bar{\nu}_{\ell}$ ($\ell=e$, $\mu$, or $\tau$) are measured using a data sample corresponding to an integrated luminosity of 521 fb$^{-1}$ collected at center of mass energies near 10.58 GeV with the BABAR detector at the PEP-II ^+e^-$ collider at SLAC. The number of $D_s^-$ mesons is determined by reconstructing the recoiling system $DKX\gamma$ in events of the type ^+e^-{\rightarrow}DKXD^{*-}_s$, where $D^{*-}_s\rightarrow D^-_s\gamma$ and $X$ represents additional pions from fragmentation. The $D^-_s\rightarrow\ell^-\nu_{\ell}$ events are detected by full or partial reconstruction of the recoiling system $DKX\gamma\ell$. The following results are obtained: $B(D^-_s \to \mu^- \nu) = (6.02 \pm 0.38 \pm 0.34) \times 10^{-3}$, $B(D^-_s \to \tau^- \nu) = (5.00 \pm 0.35 \pm 0.49) \times 10^{-2}$, and $B(D^-_s \to e^- \nu) < 2.8 \times 10^{-4} at 90% C.L.$, where the first uncertainty is statistical and the second is systematic. The branching fraction measurements are combined to determine the $D^-_s$ decay constant _{D_s} = (258.6 \pm 6.4 \pm 7.5)$ MeV. In addition, a study has been performed of the $D^+\pi^-$, $D^0\pi^+$, and $D^{*+}\pi^-$ systems in inclusive ^+e^- \rightarrow c\bar{c}$ interactions in a search for excited $D$ meson states. The dataset used consists of $\sim 54 fb$^{-1}$. The mass spectra for these systems show, for the first time, candidates for the radial excitations of the $D^0$, $D^{*0}$, and $D^{*+}$, as well as the $L=2$ excited states of the $D^0$ and $D^+$, where $L$ is the orbital angular momentum of the quarks. Finally, a prototype of a next generation Detector of Internally Reflected Cherenkov radiation (Focusing DIRC) has been tested using a 10 GeV electron beam at SLAC. The Focusing DIRC is based on the DIRC which was used in the BABAR detector, but has new pixel photon detectors which improve the resolution on the single photon time of propagation by about an order of magnitude allowing, for the first time, to correct the chromatic smearing in the Cherenkov angle. The Focusing DIRC may be used in a future Super-B factory.

Keywords: Physics
Advisor: Leith David W. G. S. primary advisor. Thesis advisor
Peskin Michael Edward
Roodman Aaron J. (Aaron Jay)
Measurements of a three-dimensional shock-boundary layer interaction [electronic resource]

A series of measurements were taken of the shock-boundary layer interaction (SBLI) in a Mach 2.1 continuously operated wind tunnel. The SBLI was generated by a small (~1.1mm tall) 20° wedge located on the top wall, and data were taken both in the region near the compression wedge and in the area where this shock impinged on the bottom wall. PIV was the primary measurement tool in both locations, though pressure data were also acquired near the compression wedge. Data were acquired at 4 spanwise locations to study the three-dimensionality of the flow. Both interactions were found to be highly 3-D, with a stronger interaction observed near the channel centerline. Evidence of a corner vortical structure in the compression corner was observed, and substantiated by CFD. Intermittent flow reversal was seen in the reflected shock interaction near the channel centerline, though not in the corners. The data suggest the presence of vortical structures generated near the channel centerline and pushed towards the sidewalls. Following the characterization of the base case, a Monte Carlo experiment was performed in which geometric perturbations were installed along the bottom wall of the wind tunnel and their effect on the flow was studied. The Monte Carlo device was designed and installed at the location predicted to be most sensitive by CFD. The majority of the locations initially tested displayed minimal sensitivity, with only the largest and most upstream quasi-2D cases showing significant effects on the flow at the corner. The perturbation device was redesigned and moved upstream, and additional quasi-2D cases were tested. It was found that some configurations accelerated the flow and strengthened the primary shock, while others slowed the flow and weakened the shock. Overall, the flow was observed to be very sensitive to some perturbations, but only to those located within a limited range of streamwise positions, and with a wide variety of system responses possible.

Keywords: Mechanical Engineering
Advisor: Eaton John K. primary advisor. Thesis advisor
Iaccarino Gianluca advisor. Thesis advisor
Mungal Mark Godfrey advisor. Thesis advisor
Mechanics of hysteretic adhesive elastic mechanical contact between rough surfaces [electronic resource]

In experiments that involve contact with adhesion between two surfaces, as found in atomic force microscopy or nanoindentation, two distinct contact force (P ) vs. indentation-depth (h) curves are often measured depending on whether the indenter moves towards or away from the sample. The origin of this hysteresis is not well understood and is often attributed to moisture, plasticity or viscoelasticity. We present experiments, atomistic simulations and continuum mechanics models that will show that hysteresis can exist without these effects, and that its magnitude depends on surface roughness. We explain the observed hysteresis as the result of a series of surface instabilities, where the contact area grows or recedes by a finite amount. We also demonstrate that when this is the case material properties can be estimated uniquely from contact experiments even when the measured P -h curves are not unique. The hysteresis energy loss during contact is also a measure of the adhesive toughness of the contact interface. We show experimentally that roughness can both increase and decrease the adhesive toughness of the contact interface. We show through numerical simulation of continuum adhesive contact models that the contact interface is optimally tough at conditions at which the contact region is at the cusp of the transition through which it turns form being mostly simply connected to being predominantly multiply connected.

Keywords: Mechanical Engineering
Advisor: Lew Adrian primary advisor. Thesis advisor
Barnett David M. advisor. Thesis advisor
Cai Wei
Nix William D. advisor. Thesis advisor
Mechanisms of oncogene addiction and tumor recurrence in MYC-induced lymphomas [electronic resource]

Cancers arise through the acquisition of genetic and epigenetic changes which result in the activation of growth-promoting oncogenes and the inactivation of growth-inhibitory tumor suppressor genes. Despite the accumulation of many diverse mutations, some tumors exhibit sensitivity to the targeted inhibition of single gene products, in a phenomenon known as oncogene addiction. In the Emu-tTA/tetO-MYC transgenic mouse model, overexpression of MYC results in the development of aggressive T-cell lymphoma, and subsequent inactivation of MYC results in rapid tumor regression occurring primarily via cell cycle arrest, senescence, and apoptosis. This thesis presents work investigating various aspects of oncogene addiction in MYC-induced lymphomas. We have discovered that tumor recurrence in MYC-induced lymphomas following initial MYC inactivation occurs mainly through the persistence and expansion of cells that fail to suppress MYC expression. This demonstrates that addiction to some oncogenes may be inescapable and that resistance to MYC therapy would likely occur through the restoration of MYC function. We have also discovered that activation of the Wnt/beta-catenin pathway is a common secondary event in MYC-induced lymphomagenesis. Beta-catenin was found to be frequently stabilized due to mutations that prevent its phosphorylation and subsequent degradation, including a novel splice acceptor site mutation. Inhibition of beta-catenin resulted in robust apoptosis, indicating that MYC-induced lymphomas can exhibit addiction to multiple different oncogenes.

Advisor: Felsher Dean (Dean Walton) primary advisor. Thesis advisor
Levy Ronald
Martinez Olivia
Sage Julien advisor. Thesis advisor
Mechanistic studies and biomedical applications of antimicrobial peptoids against multi-drug resistant bacterial infections [electronic resource]

The increasing prevalence of chronic, difficult-to-treat resistant bacterial infections have created a pressing need for the discovery of promising, novel pharmaceutical candidates that could replace or complement current therapies, which are becoming less reliable and effective due to a rise in bacterial resistance. Antimicrobial peptides (AMPs) are a naturally occurring, ubiquitous, and ancient class of antibiotics that offer a unique template for the development of novel antimicrobial therapies. However, in vivo therapeutic peptides have a short half-life since they are easily degraded by proteases, thus reducing their bioavailability, which renders them a less attractive choice therapeutically. Consequently, non-natural mimics of AMPs, which can emulate the favorable characteristics of AMPs are becoming significantly important. Poly-N-substituted glycines, also called "Peptoids", are structural and functional mimics of AMPs and are resistant to proteolysis. Predecessors in the Barron laboratory designed and characterized antimicrobial peptoids against free-floating, planktonic bacteria. However, almost 60% of infections are caused by bacterial biofilms. These complex communities of microorganisms are protected by an excreted matrix of adhesive biomacromolecules and are more difficult to kill with conventional antibiotics than planktonic bacteria. Furthermore, to develop peptoids as potential therapeutics, the mechanisms by which they interact with bacteria need to be understood, which are still under investigation. Here, we report that peptoids have similar or better efficacy than conventional antibiotics against biofilms of a clinical isolate of drug-resistant P. aeruginosa. We determined the effects of peptoids on bacterial biomass and cell viability, by Crystal Violet assay and bacterial plating, respectively. We also explored the efficacy of peptoids against Mycobacterium (an organism resistant to antibiotics due to the presence of a thick waxy coating) and intracellular L. monocytogenes by bioluminescent imaging. In addition, we also investigated the mechanisms of action of peptoids and peptides by biophysical techniques (Ultra-Violet Visible spectroscopy) and bioluminescent imaging. We report that peptoids are non-lytic and cause bacterial killing by aggregating the bacterial ribosomes and decreasing ATP levels inside the cell. Lastly, we present a mouse wound model, which suggests that peptoids are effective in vivo in reducing P. aeruginosa infections.

Advisor: Barron Annelise E. primary advisor. Thesis advisor
Contag Christopher H. advisor. Thesis advisor
Swartz James R. advisor. Thesis advisor
Media imagery and political choice [electronic resource] : how visual cues influence the citizen news diet

The research presented in this manuscript contrasts a text-only and graphical display of news, to assess the personal and environmental factors affecting news preferences. This research was conducted in two stages. First, an online experiment and survey of 1,000 participants assessed the effects of political attitudes, personal demographics, and visual cues on news selection behaviors. Second, an eyetracking study evaluated the ocular and cognitive behaviors associated with the processing of each news display. Analyses specifically examined which factors influence (i) an individual's preferences for hard and soft news, (ii) an individual's preferences for specific news sources, and (iii) how stable or susceptible to change these preferences are over time. Results indicate that visual design, political attitudes, and personal demographics all affect the type of news and source selected. Specifically, a graphical news layout encourages the selection of soft news categories, though this is moderated by education. A graphical layout also enables more repeat selections to the same source. Furthermore, eyetracking shows that a graphical news format produces lower levels of attention and cognitive processing. Broader implications for the future of news display and news acquisition are discussed.

Keywords: Communication
Advisor: Iyengar Shanto primary advisor. Thesis advisor
Fishkin James S. advisor. Thesis advisor
Jackman Simon
Nass Clifford Ivar advisor. Thesis advisor