VictorJuiz/thesis huggingface dataset:
Acoustic detection of ultra-high energy neutrinos [electronic resource]
Keywords: Applied Physics

Understanding the origin and evolution of cosmic accelerators by measuring ultra-high energy cosmic rays is one of the main goals of astroparticle physics. UHE neutrinos are thought to be better indicators of cosmic accelerators since they travel from their source undeflected by magnetic fields and unimpeded by interactions with the cosmic microwave background. Both cosmic rays and neutrinos have extremely low fluxes at these energies, which makes measurements difficult. Neutrino measurements have the added challenge of a longer interaction length that makes the atmosphere not suitable as a target. Here, we present the Study of Acoustic Ultra-high energy Neutrino Detection (SAUND) which uses an underwater acoustic sensor array spanning 1500 cubic kilometers to search for UHE neutrinos interacting in the ocean. A description of the data acquisition system, results of the background noise study, and an analysis based on an integrated 130 days of data are presented here. Two events are found to have properties compatible with UHE-neutrino-induced particle showers. Since our understanding of transient backgrounds is limited, a flux upper limit is set providing the most sensitive limit to date on UHE neutrinos using the acoustic technique.
Adaptive distributed source coding [electronic resource]
Keywords: Electrical Engineering

Distributed source coding, the separate encoding and joint decoding of statistically dependent sources, has many potential applications ranging from lower complexity capsule endoscopy to higher throughput satellite imaging. This dissertation improves distributed source coding algorithms and the analysis of their coding performance to handle uncertainty in the statistical dependence among sources. We construct sequences of rate-adaptive low-density parity-check (LDPC) codes that enable encoders to switch flexibly among coding rates in order to adapt to arbitrary degrees of statistical dependence. These code sequences operate close to the Slepian-Wolf bound at all rates. Rate-adaptive LDPC codes with well-designed source degree distributions outperform commonly used rate-adaptive turbo codes. We then consider distributed source coding in the presence of hidden variables that parameterize the statistical dependence among sources. We derive performance bounds for binary and multilevel models of this problem and devise coding algorithms for both cases. Each encoder sends some portion of its source to the decoder uncoded as doping bits. The decoder uses the sum-product algorithm to simultaneously recover the source and the hidden statistical dependence variables. This system performs close to the derived bounds when an appropriate doping rate is selected. We concurrently develop techniques based on density evolution to analyze our coding algorithms. Experiments show that our models closely approximate empirical coding performance. This property allows us to efficiently optimize parameters of the algorithms, such as source degree distributions and doping rates. We finally demonstrate the application of these adaptive distributed source coding techniques to reduced-reference video quality monitoring, multiview coding and low-complexity video encoding.
Adhesion and degradation of hard transparent coatings [electronic resource]
Keywords: Materials Science and Engineering

Hard transparent coatings are an essential component of structures involving polymer surfaces. An important application is airplane passenger windows, which are subject to large variations in pressure, temperature and humidity as well as UV exposure and abrasive conditions. The coatings suitable for such extreme environments must have high hardness, resistance to UV degradation and excellent adhesion to the polymer substrate. Measuring the adhesion of a hard coating on a compliant substrate is not trivial; hence, qualitative cross-cut tape tests have been the standard for automotive and aerospace industries. In this dissertation we address the quantitative assessment of adhesion of hard transparent coatings on polymer substrates. An asymmetric double cantilever beam specimen was employed to sample the interface without contribution from crazing in the substrate. Fracture energies of coatings that had passed standard tests were found to vary from 1.4 J/m2 to 22 J/m2. Significant subcritical crack growth was observed in coatings on windows with interfacial fracture energy of 7 J/m2. Cracks were found to continue to grow at driving forces below 2 J/m2 due to viscoelastic deformation at the crack tip. Simulated outdoor weathering decreased the adhesion energy and led to cracking and delamination. Driving force for cracking and delamination was correlated to UV cross-linking of the coating; FTIR evidence showed that the ratio of network forming Si—O—Si bonds increased with outdoor exposure. The effect of surface pre-treatments on adhesion was assessed. Mechanical polishing and UV-Ozone treatment were found to increase adhesion significantly. The effect of UV absorbers on stress generation in coatings exposed to UV was investigated. A cyanoacrylate absorber was found to perform better than a benzophenone absorber at high concentrations. However, both absorbers seemed to change the molecular structure of the coating and did not increase the lifetime of the coating significantly. Atmospheric plasma deposition was employed as a solvent-free and wasteless alternative to sol-gel processing of hybrid coatings. We focused on molecularly bridged hybrid coatings for improved cohesion and resistance to water assisted crack growth. A high temperature precursor delivery system was designed and constructed for deposition of molecularly bridged hybrid silica coatings. Bridged precursors with very low vapor pressure were deposited on silicon and polycarbonate substrates. The effects of precursor flow rate, temperature and other plasma parameters on deposition rate were investigated. Bridged precursor coatings developed significantly higher growth stresses than curing stresses in sol-gel coatings, but the former were comparable to atmospheric plasma coatings deposited using conventional silanes.
Advances in breast MRI [electronic resource]
Keywords: Biophysics.

Breast magnetic resonance imaging (MRI) is becoming an increasingly valuable technology for breast cancer detection, especially for women at high risk for the disease. Stanford Hospital alone performed approximately 1,000 breast MRIs last year. This demand and need to increase specificity of breast MRI motivates improving current breast MR protocols, as well as exploring new applications of MR technology to breast imaging. Most clinical breast MR exams are performed at a 1.5T field strength. 3T scanners, however, are becoming more prevalent in the clinical setting and thus the breast MR protocol needs to be tuned accordingly. The first project includes measurements of T1 and T2 of breast fat and glandular tissue at 1.5T and 3T and the corresponding recommendation for altering the TR and TE for 3T breast imaging. The beating heart posterior to the breast often produces artifacts in breast MR images. The second project is a cylindrical saturation method that reduces unwanted signal from the heart while avoiding signal loss from the breast tissue of interest. Detecting tumor oxygenation non-invasively may give insight on tumor differentiation, predict susceptibility to antiangiogenic therapeutics, and monitor chemotherapeutics. The third project introduces the application of BOLD contrast imaging, a technique usually applied in functional brain MR imaging for characterizing tumor oxygenation in the breast.
Advection of Crust through a Restraining Bend at Mass Flux Steady State in the Santa Cruz Mountains, CA, Inferred from Cosmogenic Radionuclide Denudation Rates and Topographic Analysis
Keywords:  Department of Geological and Environmental Sciences
School of Earth Energy &amp; Environmental Sciences
topography
Santa Cruz Mountains
Thesis

The asymmetric topography of the Santa Cruz Mountains, CA has been ascribed to the advection of material southwest of the right-lateral San Andreas Fault through a restraining bend, while material northeast of the fault remains trapped in the zone of contraction resulting from the fault's restraining geometry. This model predicts a rapid decrease in rock uplift rates with distance along the fault from the restraining bend, which is observed in rock uplift recorded by marine terraces along the Santa Cruz and San Mateo County coast. Here, I present eighteen cosmogenic radionuclide (CRN) denudation rates from basins southwest of the fault, which decrease systematically from 0.60 to 0.15 mm/yr with distance north of the bend. These rates capture the expected spatial distribution of rock uplift rates associated with the advection model, and their magnitude falls in the same range as those recorded by coastal marine terraces.
Algorithmic reconstruction methods in diffraction microscopy using a priori information [electronic resource]
Keywords: Electrical Engineering

Recent technological and algorithmic advances have enabled lensless imaging techniques, paving the way for high resolution three dimensional analysis. In these methods, a coherent x-ray source illuminates a sample and the amplitude of the far-field diffraction pattern is recorded. Reconstruction of the sample object requires recovery of the missing phase information by exploiting additional side information in conjunction with a computational reconstruction algorithm. Two different sources of additional information are considered. First, the phase recovery problem is formulated as an optimization problem where knowledge of the form of the object (smoothness, positivity, particular material characteristics) are included as part of the objective or enforced as constraints. This problem is then approximated as a convex problem and solved using existing methods. The second approach assumes that the prior knowledge is in the form of a low resolution image of the sample and uses the wavelet domain to express this information. Experimental limitations include coherence, noise and missing data as well as algorithmic limitations such as data centering, support determination and complex valued reconstructions. Reconstruction results include those of optical equivalent experiments and of both soft and hard x-ray experiments. In all three settings the two proposed sources of information are successfully used to obtain reconstructions for a variety of objects. For the application of non-destructively examining the buried metallization pattern of integrated circuits, we employed a coherent beam of 0.17nm X-rays to image a 100 nm metal pattern. The metal layer was fabricated on a 100 micron silicon substrate and buried beneath one micron of siliocn dioxide. From the diffraction pattern were able to successfully reconstruct the image of the metal pattern.
Algorithms for the equilibration of matrices and their application to limited-memory quasi-newton methods [electronic resource]
Keywords: Computational and Mathematical Engineering.

Diagonally scaling a matrix can reduce its condition number. Equilibration scales a matrix so that the row and column norms are equal. We review the existence and uniqueness theory for exact equilibration. Then we introduce a formalization of approximate equilibration and develop its existence and uniqueness theory. Next we develop approximate equilibration algorithms that access a matrix only by matrix-vector products. We address both the nonsymmetric and symmetric cases. Limited-memory quasi-Newton methods may be thought of as changing the metric so that the steepest-descent method works effectively on the problem. Quasi-Newton methods construct a matrix using vectors of two types involving the iterates and gradients. The vectors are related by an approximate matrix-vector product. Using our approximate matrix-free symmetric equilibration method, we develop a limited-memory quasi-Newton method in which one part of the quasi-Newton matrix approximately equilibrates the Hessian. Often a differential equation is solved by discretizing it on a sequence of increasingly fine meshes. This technique can be used when solving differential-equation-constrained optimization problems. We describe a method to interpolate our limited-memory quasi-Newton matrix from a coarse to a fine mesh.
Alignment of cryo-electron tomography images using Markov Random Fields [electronic resource]
Keywords: Electrical Engineering

Cryo-Electron tomography (CET) is the only imaging technology capable of visualizing the 3D organization of intact bacterial whole cells at nanometer resolution in situ. However, quantitative image analysis of CET datasets is extremely challenging due to very low signal to noise ratio (well below 0dB), missing data and heterogeneity of biological structures. In this thesis, we present a probabilistic framework to align CET images in order to improve resolution and create structural models of different biological structures. The alignment problem of 2D and 3D CET images is cast as a Markov Random Field (MRF), where each node in the graph represents a landmark in the image. We connect pairs of nodes based on local spatial correlations and we find the "best'' correspondence between the two graphs. In this correspondence problem, the "best'' solution maximizes the probability score in the MRF. This probability is the product of singleton potentials that measure image similarity between nodes and the pairwise potentials that measure deformations between edges. Well-known approximate inference algorithms such as Loopy Belief Propagation (LBP) are used to obtain the "best'' solution. We present results in two specific applications: automatic alignment of tilt series using fiducial markers and subtomogram alignment. In the first case we present RAPTOR, which is being used in several labs to enable real high-throughput tomography. In the second case our approach is able to reach the contrast transfer function limit in low SNR samples from whole cells as well as revealing atomic resolution details invisible to the naked eye through nanogold labeling.
Alternate exons in Caenorhabditis elegans slo-1 diversify BK channel calcium dependence [electronic resource]
Keywords: Molecular and Cellular Physiology.

Ion channels coordinate the movement of ions across biological membranes in response to a diversity of cellular signals to regulate most if not all aspects of physiology. The large-conductance Ca2+- and voltage-activated potassium (BK) channel is widely expressed across tissues and functions to repolarize action potentials, regulate smooth muscle tone and endocrine function, and tune auditory hair cells. In all tissues, BK channels provide a functional link between cytosolic Ca2+ and membrane excitation. Extensive alternate splicing of the slo-1 gene, encoding the BK channel, significantly diversifies channel function. We identified all twelve predicted BK channel splice variants expressed by the nematode Caenorhabditis elegans, and measured the Ca2+ and voltage dependence for each. Alternate exons encode portions of two regions of the cytoplasmic tail: the RCK domain, important for Ca2+ coordination, and an unstructured region, termed the C-linker. Using the patch clamp technique, we determined that alternate splicing across multiple sites diversifies activation kinetics and Ca2+ sensitivity by manipulating the functional interaction between the RCK domain and C-linker. We recovered two slo-1 alleles (pg34 and pg52) that contain point-mutations near an alternative splice site in the C-linker from a mutant screen. Using real-time PCR, we determined that both mutations change slo-1 splice variant expression profiles. The pg34 mutation encodes an A698T substitution, and the pg52 mutation is located in an intron. When heterologously expressed, the A698T mutation changes BK channel Ca2+ sensitivity in specific splice variant backgrounds by disrupting the functional connection between the C-linker and the RCK domain. Using in vivo electrophysiology, we determined that the pg34 mutation reduces but does not abolish BK channel function in C. elegans neurons. These results suggest that alternate splicing of slo-1 modulates the functional connection between the RCK domain and the C-linker of the BK channel to establish a proper balance between intracellular Ca2+ and membrane excitation in a variety of cell type and physiological conditions.
Alternative splicing analysis using RNA-seq data [electronic resource]
Keywords: Statistics

A single gene may produce multiple variants of a protein called isoforms. This process is mediated by alternative splicing of the mRNA transcript. We discuss some of the challenges inherent in the tasks of isoform quantification and novel isoform discovery on a given sample, and steps we have taken to address these challenges. In particular, in the first portion of this thesis we discuss the isoform quantification problem and give a technical condition describing under what conditions it is identifiable. In the second half of this thesis, we present a mathematical formulation of a novel approach to solving the isoform discovery problem. We show that our approach performs well on simulated data under both uniform read sampling and significantly biased sampling, and that it also returns a reasonable result on several test genes taken from an actual RNA-seq data set.
Amplitude and phase modulation of single photons and biphotons [electronic resource]
Keywords: Applied Physics

Single photons and entangled photons are valuable resources in quantum information science. We describe, in this dissertation, the generation of time-frequency entangled pairs of photons with narrow linewidths and coherence times that are about six orders of magnitude longer than those of photons produced via spontaneous parametric downconversion in nonlinear crystals. These photons are produced using the mechanism of electromagnetically induced transparency and the associated slow light effect. Using existing detectors it is possible to temporally resolve the structure of these narrowband photons and commercial electro-optic modulators may be used to manipulate their amplitude and phase. In this context, we discuss three recent experiments. In the first, we demonstrated amplitude modulation, with arbitrary shapes, of heralded single photons. In the second, we demonstrated a Fourier technique to measure the shapes of biphoton wavepackets using fast amplitude modulators and slow detectors. The third experiment is a demonstration of spread spectrum techniques at the single photon level.
Amyloid-beta inhibits E-S plasticity and LTP through inhibition of cannabinoid receptor 1-dependent synaptic disinhibition [electronic resource]
Keywords: Molecular and Cellular Physiology.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder affecting the elderly that is characterized by loss of short-term memory and cognitive decline. Studies in both human patients and animal models of AD point to over-accumulation of soluble oligomers of amyloid-beta peptide (Abeta) as a mediator of learning and memory impairments early in the disease (Rowan, Klyubin et al. 2005; Selkoe 2008). Support for Abeta's role in learning deficits comes from studies demonstrating impaired plasticity of synaptic inputs to neurons, as measured in the paradigm of long-term potentiation (LTP) of synaptic strength in hippocampal slices (Chen, Kagan et al. 2000; Freir, Holscher et al. 2001; Walsh, Klyubin et al. 2002; Wang, Pasternak et al. 2002; Townsend, Shankar et al. 2006), the prime candidate for the neuronal substrate of learning and memory behavior (Bliss and Collingridge 1993). Induced concurrently with synaptic LTP is an increase in the electrical coupling between the dendritic synaptic inputs and the soma, such that a greater proportion of the EPSP survives at the spike trigger zone, resulting in greater action potential output for a given EPSP. This potentiation of EPSP-spike coupling (E-S coupling) provides an additional boost to the efficacy of the EPSP on top of the potentiation (LTP) that occurs at the synapse (Bliss and Lomo 1973). While LTP of synaptic strength is an essential component of memory storage, in all models of learning, memory recall occurs only when spikes are evoked in the neurons participating in a representation. Thus E-S potentiation exerts control over the essential substrate of memory retrieval. Although LTP and E-S potentiation are mechanistically distinct processes, several features during the induction phase are shared. Studies have shown that Abeta impairs the induction, but not maintenance of LTP (Wang, Walsh et al. 2004; Townsend, Shankar et al. 2006), leaving the possibility that Abeta-mediated impairment to memory is not specific to LTP. Nevertheless, focus has centered on pathways central to LTP, while impairment to other forms of plasticity have not been explored. Here we show a mechanism by which Abeta peptides impairs post-tetanic suppression of inhibition, thereby inhibiting E-S potentiation. This impairment to E-S potentiation was occluded by GABAA-receptor, Cannabinoid 1 receptor (CB1R), and muscarinic acetylcholine receptor (mAChR), but not mGluR block. This suggests that the impairment is mediated by mAChR-initiated endocannbinoid signaling. Together, the results provide a mechanism to explain learning and memory impairments in early Alzheimer's disease.
An Analysis of the Timing of Fertility in Rural India
Keywords:  Department of Economics
Stanford Department of Economics
fertility
India
birth spacing
survival analysis
Thesis

Fertility has long been modeled as the household supply and demand for children. However, very little empirical work has been done on understanding the timing of fertility in the developing country setting. Assuming that households are utility maximizing, it is expected that they choose when to begin reproduction, when to have the next child and when to cease reproduction. This paper looks at how the timing of fertility decisions is affected by household wealth and parental education across maternal cohorts. Modeling births in a survival analysis function framework, this paper finds that education delays all births and wealth delays the first birth but accelerates subsequent births. Lastly, cohort effects play a significant role in the time to the first birth but not the latter births, suggesting that only the preference of when to have the first child has changed over time.
An Implementation of Quad-fragment Merging for Micropolygon Rendering
Keywords: Computer Science.
Computer Graphics
Geometry > Data processing
Thesis

Current graphics cards (GPUs) shade small polygons inefficiently. When surfaces are represented using micropolygons of less than a pixel in size, many shading computations performed by a GPU are redundant. Since shading is typically the most expensive operation in a graphics pipeline, this leads to poor rendering performance.
This thesis presents a prototype implementation of quad-fragment merging, which reduces redundant shading work by buffering and selectively merging rasterized fragments prior to shading. The prototype quad-fragment merger is described in detail, and evidence is presented that it is amenable to implementation in fixed-function hardware. Performance results indicate that our implementation decreases shader executions by a factor of eight when rendering micropolygons, and effectively makes use of a number of optimizations to yield high performance. Finally, an early prototype of a corollary technique that shades scenes with motion blur is described, and preliminary results are presented.