VictorJuiz/thesis huggingface dataset:
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]
Keywords: Physics

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.
Measurement of the D_s leptonic decay constant f_{D_s} and observation of new resonances decaying to D^(*)pi [electronic resource]
Keywords: Physics

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.
Measurements of a three-dimensional shock-boundary layer interaction [electronic resource]
Keywords: Mechanical Engineering

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.
Mechanics of hysteretic adhesive elastic mechanical contact between rough surfaces [electronic resource]
Keywords: Mechanical Engineering

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.
Media imagery and political choice [electronic resource] : how visual cues influence the citizen news diet
Keywords: Communication

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.
Memory optimizations of embedded applications for energy efficiency [electronic resource]
Keywords: Electrical Engineering

The current embedded processors often do not satisfy increasingly demanding computation requirements of embedded applications within acceptable energy efficiency, whereas application-specific integrated circuits require excessive design costs. In the Stanford Elm project, it was identified that instruction and data delivery, not computation, dominate the energy consumption of embedded processors. Consequently, the energy efficiency of delivering instructions and data must be sufficiently improved to close the efficiency gap between application-specific integrated circuits and programmable embedded processors. This dissertation demonstrates that the compiler and run-time system can play a crucial role in improving the energy efficiency of delivering instructions and data. Regarding instruction delivery, I present a compiler algorithm that manages L0 instruction scratch-pad memories that reside between processor cores and L1 caches. Despite the lack of tags, the scratch-pad memories with our algorithm can achieve lower miss rates than caches with the same capacities, saving significant instruction delivery energy. Regarding data delivery, I present methods that minimize memory-space requirements for parallelizing stream applications, applications that are commonly found in the embedded domain. When stream applications are parallelized in pipelining, large enough buffers are required between pipeline stages to sustain the throughput (e.g., double buffering). For static stream applications where production and consumption rates of stages are close to compile-time constants, a compiler analysis is presented, which computes the minimum buffer capacity that maximizes the throughput. Based on this analysis, a new static streamscheduling algorithm is developed, which yields considerable speed-up and data delivery energy saving compared to a previous algorithm. For dynamic stream applications, I present a dynamically-sized array-based queue design that achieves speed-up and data delivery energy saving compared to a linked-list based queue design.
Mercury reaction chemistry in combustion flue gases from experiments and theory [electronic resource]
Keywords: Energy Resources Engineering

Emissions from coal combustion processes constitute a significant amount of the elemental mercury released into the atmosphere today. Coal-fired power plants in the United States, with the capacity of just over 300GW, are the greatest anthropogenic source of mercury emissions. Mercury exists in coal combustion flue gas in a variety of forms depending on the coal type and combustion conditions; i.e., elemental, oxidized and particulate. Particulate mercury in the flue gas can be removed using air pollution control devices such as electrostatic precipitators and fabric filters. Oxidized mercury is easily captured by wet flue gas desulfurization scrubbers, while gaseous elemental mercury passes through the scrubbers readily. Activated carbon, when injected into the gas stream of coal-fired boilers, is effective in capturing both elemental and oxidized mercury through adsorption processes. However, the mechanism by which mercury adsorbs on activated carbon is not exactly known and its understanding is crucial to the design and fabrication of effective capture technologies for mercury. The objective of the current study is to apply theoretical-based cluster modeling to examine the possible binding mechanism of mercury on activated carbon. The effects of activated carbon's different surface functional groups and halogens on elemental mercury adsorption have been examined. Also, a thermodynamic approach is followed to examine the binding mechanism of mercury and its oxidized species such as HgCl and HgCl2 on a simulated carbon surface with and without Cl. Energies of different possible surface complexes and possible products are compared and dominant pathways are determined relatively. Since different methods are employed to capture varying forms of mercury, understanding mercury speciation during combustion and how the transformations occur between different forms is essential to developing an effective control mechanism for removing mercury from flue gas. In this study, homogeneous oxidation of mercury via chlorine is examined experimentally in a simulated flue gas environment. Mercury and chlorine are introduced into a laminar premixed methane-air flame. Cooled flue gas is sampled and sent to a custom-built electron ionization quadrupole mass spectrometer specially designed for mercury measurement on the order of parts per billion (ppb) in flue gas. The use of a mass spectrometer allows for distinguishing between the different forms of oxidized mercury (Hg+, Hg+2). By directly measuring mercury species accurately, one can determine the actual extent of mercury oxidation in the flue gas, which will aid in further developing mercury control technologies.
Mesh adaption strategies for vortex-dominated flows [electronic resource]
Keywords: Aeronautics and Astronautics

A new adaptive mesh refinement strategy that is based on a coupled feature-detection and error-estimation approach is developed. The overall goal is to apply the proper degree of refinement to key vortical features in aircraft and rotorcraft wakes. The refinement paradigm is based on a two-stage process wherein the vortical regions are initially identified for refinement using feature-detection, and then the appropriate resolution is determined by the local solution error. The feature-detection scheme uses a local normalization procedure that allows it to automatically identify regions for refinement with threshold values that are not dependent upon the convective scales of the problem. An error estimator, based on the Richardson Extrapolation method, then supplies the identified features with appropriate levels of refinement. The estimator is shown to be well-behaved for steady-state and time-accurate aerodynamic flows. The above strategy is implemented within the Helios code, which features a dual-mesh paradigm of unstructured grids in the near-body domain, and adaptive Cartesian grids in the off-body domain. A main objective of this work is to control the adaption process so that high fidelity wake resolution is obtained in the off-body domain. The approach is tested on several theoretical and practical vortex-dominated flow-fields in an attempt to resolve wingtip vortices and rotor wakes. Accuracy improvements to rotorcraft performance metrics and increased wake resolution are simultaneously documented.
Methods and applications for position-specific evolutionary features in clinical genomics [electronic resource]
Keywords: Biomedical Informatics.

One of the grand challenges in genomic medicine is to translate fundamental scientific discoveries regarding the structure, variation, and function of the genomes of individuals and populations towards improved health outcomes. The main hypothesis of this thesis is that all forms of human genetic variation contributing to the etiology and pathophysiology of modern human diseases have distinct and quantifiable evolutionary histories, which can be computed for every position in the human genome independent of human population characteristics, and used as informative quantitative priors in the discovery and assessment of variants of clinical importance in modern human populations. To enable robust evaluation of the specific questions posed by this thesis, I first explore the necessary properties and theoretical basis for a null evolutionary hypothesis for Evolutionary Genomic Medicine, and conclude that the well-established Neutral Theory of Molecular Evolution provides a sound theoretical and methodological basis for evaluating alternative hypothesis in Evolutionary Genomic Medicine. Due to advances in multiplex genotyping technologies, genome-wide associations studies (GWAS), have emerged as the premier modality for discovery and assessment clinical genomic variation. Although these efforts have been successful in revealing thousands variants robustly associated with a broad spectrum of clinical phenotypes, the variants established by the GWAS approach have so far failed to explain large proportions of the known genetic variance associated with important clinical traits such as Type 2 Diabetes and Hypertension. Because disease-associated variation is linked with genomic loci of functional importance which have undergone evolutionary selection, and even the proxy loci (e.g. tagging SNPs) used to probe for disease associated loci themselves have quantifiable evolutionary histories, I evaluate a compendium of disease-associated variants to evaluate the effect of long-term evolutionary histories on the discovery of disease-associated variants. Through this work I demonstrate that disease-associated variants have distinct evolutionary properties, and that evolutionary features of positions can be incorporated as priors to improve discovery of disease-associated variants. A similar approach is applied to evaluate pharmacogenomics variants associated with warfarin, demonstrating that evolutionary features of genomic positions improve clinical assessment of pharmacogenomics variation. Through the findings and insights gained from efforts in pursuit of my thesis which are reported here, my collaborators and I clearly demonstrate that quantitative evolutionary features can be estimated for each position in the human genome across species, and then applied to modern human population data to improve discovery and assessment of genomic variation associated with clinical phenotypes.
Methods of study integration in multiplex molecular medicine [electronic resource]
Keywords: Biomedical Informatics.

The acquisition of biomedical research data is continually expanding, both in the number of variables measured in any single experiment and the number of experiments being done. To bring the fruits of all this labor into medical practice, we need to develop techniques for integrating high dimensional assays across experimental studies. In this thesis, I develop and demonstrate several approaches to multiplex meta-analysis, the synthesis multiple of high dimensional studies. I discuss the development of an overall expression map, examining the properties of gene expression dynamics across thousands of studies. I use this analysis of gene expression dynamics to develop methods of integrating highly parallelized gene expression studies to both identify new biomarkers of disease process, and to prioritize genes likely to contribute to disease risk. Finally, I demonstrate a method for clinical genomics, integrating disease linked genetic variants across an entire genome for translation into medical practice.
Methylation of the retinoblastoma tumor suppressor by SMYD2 and functional interactions between retinoblastoma and C-MYC in a mouse model of hepatocellular carcinoma [electronic resource]
Keywords: Cancer Biology.

The retinoblastoma tumor suppressor RB is a central cell cycle regulator. Here we demonstrate that RB can be methylated by SMYD2 at lysine 860, a highly conserved and novel site of modification. This methylation event occurs in vitro and in cells and is regulated during cell cycle progression, cellular differentiation, and in response to DNA damage. Furthermore, we show that RB mono-methylation at lysine 860 provides a direct binding site for the methyl-binding domain of the transcriptional repressor L3MBTL1. This modification may be crucial for regulating the function of RB as a tumor suppressor. Inactivation of RB and activation of the MYC family of oncogenes are frequent events in a large spectrum of human cancers. Here, we sought to also test whether loss of RB function would affect cancer development in a mouse model of c-MYC-induced hepatocellular carcinoma (HCC). We found that RB inactivation has minimal effects on the cell cycle, cell death, and differentiation features of liver tumors driven by increased levels of c-MYC. However, combined loss of RB and activation of c-MYC led to an increase in polyploidy in mature hepatocytes before the development of tumors and a trend for decreased survival after cancer initiation.
Mixed equation-simulation circuit optimization [electronic resource]
Keywords: Electrical Engineering

One of the main challenges in designing analog circuits today is to cope with the complex behaviors of modern devices. For example, the drain current of a deep- submicron MOSFET device can no longer be predicted by the long-channel models, due to various effects including carrier velocity saturation, vertical-field induced mobility degradation, drain-induced barrier lowering (DIBL), and narrow channel effects, to name only a few. In addition, the characteristics of each individual device can be further affected by random variability and proximity effects. As a result, it is extremely difficult to design an optimal circuit at the presence of these complex phenomena without relying on computational aids, e.g. circuit optimizers. However, many circuit optimizers based on global optimization techniques such as simulated annealing or evolutionary algorithms may also have difficulties unless they are provided with good initial guesses. This research focuses on building a circuit optimizer that leverages designer's intent to help the simulation-based optimizers find solutions quickly. The technique is inspired by continuation techniques in numerical analysis where a difficult problem is solved by constructing an easier problem first and gradually refining its solution to that of the hard problem. In a circuit optimization context, the designer's simplified equations for the circuit serve as the easier problem. These simplified design equations are easy to write as they need not be completely accurate and have solutions that are easy to reason about. While these design equations may not generate a good initial design for optimizing real circuits directly, they can help guide the optimizer towards an optimal solution by constructing and solving a series of intermediate problems that gradually change from the initial problem based on design equations to the real circuit problem with accurate device models. Assuming that the solutions to these intermediate problems change only gradually along this path, each problem can be solved very efficiently via local optimization methods, using the solution to the previous problem as a starting point. Although more problems have to be solved, since each is solved very efficiently, the overall computational costs can be lower than that of solving the final problem directly. We apply our circuit optimization approach to several design examples and investigate the importance of the initial designer's equations by comparing our optimizer's performances against those of a local optimizer and a generic continuation- based optimizer. We extend this basic idea to leverage hierarchy to help optimize large circuits, and demonstrate this technique with a PLL design example. Besides the runtime benefit, performing optimization hierarchically is also intuitive and more in line with how a circuit designer would approach designing a large circuit problem like the PLL.