VictorJuiz/thesis huggingface dataset:
Image reconstruction for high-resolution PET [electronic resource] : GPU-accelerated strategies for improving image quality and accuracy

Molecular imaging can interrogate subtle molecular disease signatures non-invasively in living subjects. Positron emission tomography (PET), one particular molecular imaging modality, is able to sense molecular signals deep within tissue. Although PET is well suited for imaging signals associated with cancerous lesions in humans, it is still unable to resolve very small (< 2 mm) structures. Improving the spatial resolution of PET is an active area of research driven by many potential applications. However, the new generation of high-resolution PET systems raise new challenges for image reconstruction. In this dissertation, several strategies and algorithms are proposed to enable accurate and practical image reconstruction for high-resolution PET. Reconstruction is performed directly from the list-mode data via maximum-likelihood estimation. A shift-varying model of the imaging process is incorporated in the reconstruction. For fast reconstruction, the calculations are implemented using highly-parallel graphics processing units (GPU). A Bayesian sequence reconstruction algorithm is also used to position the annihilation photons that deposit energy in multiple detection elements. We show that the reconstruction provides near-uniform spatial resolution throughout the field-of-view, enhanced trade-off between noise and contrast, and better image quantitative accuracy. Furthermore, thanks to the computing power of graphics hardware, reconstruction times are practical for clinical applications.

Keywords: Electrical Engineering
Advisor: Levin Craig primary advisor. Thesis advisor
Hanrahan P. M. (Patrick Matthew) advisor. Thesis advisor
Pauly John (John M.) advisor. Thesis advisor
Implementable schemes for lossy compression [electronic resource]

In spite of all the achievements of information theory in the last 60 years, some of its basic questions, specially in the area of source coding, have not found satisfying solutions yet. Finding an implementable scheme for universal lossy compression, that is part of the focus of this work, serves as a good example. Unlike universal lossless compression, for which there are several well-known practical algorithms, e.g., the famous work published in 1978 by Lempel and Ziv which its modified versions are used even today, for the universal lossy compression, the situation is not so positive. We propose two new paradigms for universal lossy compression. One of them takes advantage of Markov chain Monte Carlo combined with simulated annealing, and the other one has Viterbi algorithm at its core. Both algorithms try to approximate the solution of a universal exhaustive search scheme which has enormous computational complexity. The performance of both algorithms, theoretically, gets as close as desired to the solution of the original algorithm, but we do not have a bound on the required computations versus the desired precision. However, we show through our simulations on memoryless binary, and first-order binary Markov sources that the performance of both algorithms gets close to the rate-distortion curve for a number of computations linear in the block size. We also consider the Wyner-Ziv (WZ) problem of lossy compression where the decompressor observes a noisy version of the source, whose statistics are unknown. A new family of WZ coding algorithms is proposed and their universal optimality is proven. Compression consists of sliding-window processing followed by Lempel-Ziv (LZ) compression, while the decompressor is based on a modification of the discrete universal denoiser DUDE algorithm to take advantage of side information. The new algorithms not only universally attain the fundamental limits, but also suggest a paradigm for practical WZ coding. The effectiveness of our approach is illustrated with experiments on binary images, and English text using a low complexity algorithm motivated by our class of universally optimal WZ codes. Finally, we investigate the problem of Multiple Description MD coding of discrete ergodic processes. We introduce the notion of MD stationary coding, and characterize its relationship to the conventional block MD coding. In stationary coding, in addition to the two rate constraints normally considered in the MD problem, we consider another rate constraint which reflects the conditional entropy of the process generated by the third decoder given the reconstructions of the two other decoders. The relationship that we establish between stationary and block MD coding enables us to devise a universal algorithm for MD coding of discrete ergodic sources, based on simulated annealing ideas that were recently proven useful for the standard rate distortion problem.

Keywords: Electrical Engineering
Advisor: Weissman Tsachy primary advisor. Thesis advisor
Cover T. M.
Montanari Andrea advisor. Thesis advisor
Influence of magnetic field on dielectric susceptibility of amorphous solids at ultra low temperature [electronic resource]

The dielectric response of some amorphous solids below 100 mK is known to be sensitive to an applied magnetic field. This work presents new experimental data on the behavior of BK7, Aluminum-Barium-Silicate, Suprasil, Corning® microscope cover glass and Mylar® film (amorphous Polyethylene Terephthalate) samples in the temperature range from 2 mK to 100 mK in presence of a slowly varying magnetic field. We studied the dielectric constant by means of continuous wave AC capacitance measurements at 1 kHz. We observed hysteresis in the dielectric response to a magnetic field varying in a saw-like pattern with field strengths up to 2 milliTesla. The pattern of the response differs depending on the glass composition. The results presented in this work are consistent with previously made observations that nuclear spins greater than 1/2 play a crucial role in the observed magnetic field dependence.

Keywords: Physics.
Advisor: Osheroff Douglas D. primary advisor. Thesis advisor
Cabrera Blas advisor. Thesis advisor
Lipa John A. advisor. Thesis advisor
Insights into the Evolution of a Coastal Barrier System Using Ground-Penetrating Radar: Bay of Plenty, New Zealand

The internal structure of a prograding barrier ridge system within the coastline of the Bay of Plenty, New Zealand, was investigated using ground-penetrating radar (GPR). This technique allowed analysis of the evolution of the barrier, which is affected by tectonism, volcanism, and human influences. Sedimentary facies interpreted from the GPR include: prograding shoreface (including nearshore, shoreface, and eolian dune facies), truncated progradation and cut-and-fill, infill, and alluvial bank. The relationships of these structures suggest development that has varied over the barrier's history (approximately 8,000 years).

Keywords:  Department of Geological and Environmental Sciences
School of Earth Energy &amp; Environmental Sciences
coastlines
New Zealand
Thesis
Advisor: Graham Stephan
Ingle James
Interface and stress engineering in germanium metal-oxide-semiconductor field-effect-transistors for high performance application [electronic resource]

Germanium has been attracting great interests as a high mobility channel material for MOSFETs to replace silicon in LSI chips. Germanium also has advantages over any other high mobility material, such as high compatibility to Silicon LSI technologies, low temperature process which enable 3DIC integration with low thermal budget. In order to realize high performance Ge MOS integration in future technology nodes, device and process issues have to be thoroughly addressed and investigated. In this work, first, the property of metal/Ge contact was studied. Since Ge suffers from very strong Fermi-level pinning near its valence band, n-type metal/Ge contact causes high contact resistance whatever workfunction metal is used. New technique, which is insertion of ultrathin insulator between metal and Ge, was proposed and Fermi-level depinning was experimentally demonstrated. In the second part, radical oxidation was investigated for GeO2 growth for highly reliable interface gate dielectric in high-k/Ge gate stack. Although Ge does not have chemically stable native oxide unlike Si, GeO2 has been regarded as a promising interface gate dielectric with high-k dielectric capping. High density radical oxidation enables very low temperature oxidation and provides high quality GeO2 with low interface states. In the third part, the effects of stress in Ge NMOSFETs were studied. Stress engineering has been playing a key role in the current high performance Si LSI technologies and it can also enhance device performance of Ge MOSFETs. Mobility enhancement was experimentally achieved by applying uniaxial stress to Ge NMOSFETs and performance limit of Ge NMOSFET with uniaxial stress was also theoretically examined. It is clarified that stress engineering is effective in future technology nodes.

Keywords: Electrical Engineering
Advisor: Nishi Yoshio
Saraswat Krishna advisor. Thesis advisor
Wong Hon-Sum Philip
Interface-engineered Ge MOSFETs for future high performance CMOS applications [electronic resource]

As the semiconductor industry approaches the limits of traditional silicon CMOS scaling, introduction of performance boosters like novel materials and innovative device structures has become necessary for the future of CMOS. High mobility materials are being considered to replace Si in the channel to achieve higher drive currents and switching speeds. Ge has particularly become of great interest as a channel material, owing to its high bulk hole and electron mobilities. However, replacement of Si channel by Ge requires several critical issues to be addressed in Ge MOS technology. High quality gate dielectric for surface passivation, low parasitic source/drain resistance and performance improvement in Ge NMOS are among the major challenges in realizing Ge CMOS. Detailed characterization of gate dielectric/channel interface and a deeper understanding of mobility degradation mechanisms are needed to address the Ge NMOS performance problem and to improve PMOS performance. In the first part of this dissertation, the electrical characterization results on Ge NMOS and PMOS devices fabricated with GeON gate dielectric are presented. Carrier scattering mechanisms are studied through low temperature mobility measurements. For the first time, the effect of substrate crystallographic orientation on inversion electron and hole mobilities is investigated. Direct formation of a high-k dielectric on Ge has not given good results in the past. A good quality interface layer is required before the deposition of a high-K dielectric. In the second part of this dissertation, ozone-oxidation process is introduced to engineer Ge/insulator interface. Electrical and structural characterizations and stability analysis are carried out and high quality Ge/dielectric interface with low interface trap density is demonstrated. Detailed extraction of interface trap density distribution across the bandgap and close to band edges of Ge, using low temperature conductance and capacitance measurements is presented. Ge N-MOSFETs have exhibited poor drive currents and low mobility, as reported by several different research groups worldwide. In spite of the increasing interest in Ge, the major mechanisms behind poor Ge NMOS performance have not been completely understood yet. In the last part of this dissertation, the results on Ge NMOS devices fabricated with the ozone-oxidation and the low temperature source/drain activation processes are discussed. These devices achieve the highest electron mobility to-date, about 1.5 times the universal Si mobility. Detailed interface characterizations, trapping analyses and gated Hall device measurements are performed to identify the mechanisms behind poor Ge NMOS performance in the past.

Keywords: Electrical Engineering
Advisor: Saraswat Krishna primary advisor. Thesis advisor
Krishnamohan Tejas
Wong Hon-Sum Philip
Is Enrollment into Graduate School Affected by the Business Cycle?

In the current economic climate, reports of increased enrollment at graduate school programs frequently appear in the media. This increased enrollment is generally attributed to the declining opportunity cost of education during times of economic weakness, and thus increased investments in education as opposed to employment. Another potential effect of economic weakness on educational attainment, often overlooked, is a decline in the ability to fund education, or the credit constraints effect. Evidence in the current economic literature documents the existence of both the opposing opportunity cost and credit constraints effects of the business cycle on educational attainment. However, the empirical relationship between educational attainment and the business cycle has been primarily studied only at the level of college and high school education. This study seeks to answer the question: Is enrollment into graduate school affected by the business cycle? Specifically, I use a modified Human Capital Theory Model, and enrollment data from 1976-2005, to examine the effects of key economic indicators (the unemployment rate, employment growth, GDP growth, personal income growth, and personal disposable income growth) on changes in graduate enrollment in the United States.

Keywords:  Department of Economics
Stanford Department of Economics
postgraduate education
graduate school
recession
human capital theory
graduate programs
unemployment
labor market
educational attainment
business cycle
Thesis
Advisor: Hoxby Caroline
Laser-based diagnostics for hydrocarbon fuels in the liquid and vapor phases [electronic resource]

Laser-absorption measurements of fuel concentration are widely used in engine development and for studying the combustion chemistry of hydrocarbon fuels. Direct injection of liquid fuel is common in many combustion technologies (e.g. internal combustion engines and gas turbine engines), however, these multiphase (gas and liquid) environments present significant challenges to laser-absorption measurements. These challenges include optical scattering from liquid fuel droplets and strong optical absorption from liquid fuel films. This thesis describes the development of two novel multi-phase diagnostics. Developing these diagnostics required quantitative measurements of the previously unknown refractive index spectra of several liquid hydrocarbons (n-decane, n-dodecane, and several gasoline samples). These measurements are presented, revealing important characteristics of liquid fuels. The first diagnostic developed uses three laser wavelengths for measuring fuel-vapor mole fraction and temperature in evaporating aerosols. Demonstration measurements were made over a large range of temperatures and fuel loadings in an aerosol shock tube, providing the first known laser-absorption measurements of vapor concentration and temperature in an evaporating fuel spray. The second diagnostic uses two laser wavelengths for measurements of fuel-vapor mole fraction and liquid fuel film thickness. The first known laser-absorption measurements of fuel vapor and liquid film thickness were demonstrated in the laboratory. These diagnostic techniques have been incorporated into a commercial sensor for engine development.

Keywords: Mechanical Engineering
Advisor: Hanson Ronald primary advisor. Thesis advisor
Bowman Craig T. (Craig Thomas)
Jeffries Jay Barker advisor. Thesis advisor
A microfluidic biochip based on magnetoresistive detection of nanoparticles [electronic resource]

The detection of magnetic nanoparticle (MNP) labels is a promising alternative to optical detection of fluorescent labels in biomolecular assays, in part because MNPs are not susceptible to pH, bleaching, or autofluorescence, but especially because microscopic quantities of MNPs can be detected with simple and inexpensive magnetoresistive sensors such as spin valves. The goal of this dissertation was to develop and demonstrate a biochip based on this detection principle. The particular novelty of this work is the extensive demonstration of magnetic biochips in real assays, the establishment of a compatible microfluidic fabrication process, and the development of a simple mathematical model which explains the experimentally observed signal scaling trends.

Keywords: Materials Science and Engineering
Advisor: Wang Shan X. primary advisor. Thesis advisor
Melosh Nicholas A. advisor. Thesis advisor
White Robert L. (Robert Lee)
Modeling the martian surface using bistatic radar at high incidence angles [electronic resource]

A bistatic radar system uses a transmitter and receiver in two separate locations to measure electromagnetic wave reflections at a distance. Such systems have been used since the 1960s to probe planetary surfaces, yielding information on their physical and electrical properties. Here we report the first successful uplink-geometry planetary bistatic radar observations. In 2005, the planet Mars was illuminated 56 times for 20 minutes each by an unmodulated 75-cm wavelength circularly polarized wave transmitted from the SRI International 46-m antenna in the Stanford foothills. The direct signal and a Martian surface echo, separated by differential Doppler frequency shifts, were received simultaneously by the one-bit receiver on board the Mars Odyssey orbiter. The surface echoes exhibit both fluctuating amplitude and varying spectral width, which are responses to surface reflectivity and roughness variations along the surface track. We analyze the echo data using quasi-specular scattering theory and exploit high-resolution Mars Orbiter Laser Altimeter topographic maps to better model the scattering surface in three dimensions at positions along the specular track of the echo. Assuming a two-scale classical scattering model, we infer surface roughness in the form of rms surface slopes. The results are important for evaluating landing safety for Mars exploration spacecraft, because the radar is sensitive to slopes on the order of a wavelength in size and larger. Most recently our results were used by NASA for the 2007 Phoenix Mars Lander landing site selection.

Keywords: Electrical Engineering.
Advisor: Linscott Ivan primary advisor. Thesis advisor
Zebker Howard A. primary advisor. Thesis advisor
Fraser-Smith A. C. (Antony C.) advisor. Thesis advisor
Moving Towards Full Renewability: The Potential Impacts of a Renewable Hydrogen Economy on California’s Water Resource

California would be exposing its energy sector to drought risk and locked-in energy losses were it to make major investments in electrolysis-based hydrogen systems. Though a renewable electrolysis-based hydrogen economy could assure dispatchability and energy storage capacity while limiting harmful emissions, many of its benefits are associated with the challenge of patching renewable energy supply into the aging legacy of the current grid system. Faced with the opportunity to redesign energy delivery systems as the grid infrastructure comes to the end of its lifetime, California must recognize that an energy system fundamentally designed around hydrogen rather than electricity as the main energy carrier does not make sense. Not only are significant conversion losses associated with converting electricity into hydrogen and back, but electrolysis demands a substantial amount of very high quality water that is not realistically
available in California. Given California's high growth rate, threatened water supply. ecosystems, and delivery infrastructure, and demonstrated need to use scarce energy as efficiently as possible, the combined problems of high losses and water dependence that a hydrogen economy presents assure that long-term hydrogen-dependent infrastructural investments would be, at best, an inefficient use of resources.

Keywords: Hydrogen as fuel
Sustainable energy
Water-supply > California
Water use > California
Thesis
Advisor: Freyberg David L.
Stanford University. Department of Civil and Environmental Engineering.
Multisite phosphorylation generates ultrasensitivity in the regulation of Cdc25C by Cdk1. [electronic resource]

Multisite Phosphorylation generates ultrasensitivity in the regulation of Cdc25C by Cdk1 abstract. The mitotic phosphatase Cdc25C opposes the inhibitory activity of the mitotic kinases Wee1 and Myt1 as part of a double feedback loop system that gates entry into mitosis. The substrate for both Cdc25C and Wee1 is the kinase Cdk1, which activates Cdc25C and inhibits Wee1 via hyperphosphorylation of both proteins' N-terminal regulatory regions. This work characterizes the structure, or lack thereof, of the N-terminal regulatory domain of Cdc25C through biochemical assays and NMR analysis. Furthermore, while previous evidence has shown that the response of Wee1 phosphorylation is ultrasensitive with respect to Cdk1 activity, this work demonstrates that Cdc25C is similarly hyperphosphorylated in an ultrasensitive fashion in Xenopus extract. The ultrasensitive hyperphosphorylation of Cdc25C does not depend on competition from other Cdk1 substrates and is unchanged in a diluted extract system. The response function of Cdc25C in a simplified in vitro system remains ultrasensitive, although to a lesser extent. This mild ultrasensitive response becomes Michaelian as phosphosites are mutated, indicating that some fraction of Cdc25C's ultrasensitivity is the result of multisite phosphorylation by Cdk1. However, a significant remaining fraction of the response cannot be explained by intrinsic ultrasensitivity, and appears to be due to extract-specific factors.

Advisor: Ferrell James Ellsworth primary advisor. Thesis advisor
Bogyo Matthew
Cimprich Karlene advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor