Physical Sciences and Mathematics Commons^™

Improving Error Discovery Using Guided Model Checking, Neha Shyam Rungta

Theses and Dissertations

State exploration in directed software model checking is guided using a heuristic function to move states near errors to the front of the search queue. Distance heuristic functions rank states based on the number of transitions needed to move the current program state into an error location. Lack of calling context information causes the heuristic function to underestimate the true distance to the error; however, inlining functions at call sites in the control flow graph to capture calling context leads to exponential growth in the computation. This paper presents a new algorithm that implicitly inlines functions at call sites to …

Jigsaw: Solving The Puzzle Of Enterprise 802.11 Analysis, Yu-Chung Cheng, John M. Bellardo, Péter Benkö, Alex C. Snoeren, Geoffrey M. Voelker, Stefan Savage

Computer Science and Software Engineering

The combination of unlicensed spectrum, cheap wireless interfaces and the inherent convenience of untethered computing have made 802.11 based networks ubiquitous in the enterprise. Modern universities, corporate campuses and government offices routinely de-ploy scores of access points to blanket their sites with wireless Internet access. However, while the fine-grained behavior of the 802.11 protocol itself has been well studied, our understanding of how large 802.11 networks behave in their full empirical complex-ity is surprisingly limited. In this paper, we present a system called Jigsaw that uses multiple monitors to provide a single unified view of all physical, link, network and …

Diagnosing Bias In The Inverse Probability Of Treatment Weighted Estimator Resulting From Violation Of Experimental Treatment Assignment, Yue Wang, Maya L. Petersen, David Bangsberg, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Inverse probability of treatment weighting (IPTW) is frequently used to estimate the causal effects of treatments and interventions. The consistency of the IPTW estimator relies not only on the well-recognized assumption of no unmeasured confounders (Sequential Randomization Assumption or SRA), but also on the assumption of experimentation in the assignment of treatment (Experimental Treatment Assignment or ETA). In finite samples, violations in the ETA assumption can occur due simply to chance; certain treatments become rare or non-existent for certain strata of the population. Such practical violations of the ETA assumption occur frequently in real data, and can result in significant …

Extending Marginal Structural Models Through Local, Penalized, And Additive Learning, Daniel Rubin, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Marginal structural models (MSMs) allow one to form causal inferences from data, by specifying a relationship between a treatment and the marginal distribution of a corresponding counterfactual outcome. Following their introduction in Robins (1997), MSMs have typically been fit after assuming a semiparametric model, and then estimating a finite dimensional parameter. van der Laan and Dudoit (2003) proposed to instead view MSM fitting not as a task of semiparametric parameter estimation, but of nonparametric function approximation. They introduced a class of causal effect estimators based on mapping loss functions suitable for the unavailable counterfactual data to those suitable for the …

A Minimal Critical Set Of A Class Of Youden Squares, L. Fitina, Ken Russell, Jennifer Seberry

Faculty of Informatics - Papers (Archive)

We consider the Youden square formed by deleting one row of a v x v back-circulant Latin square and establish a critical set that contains a number of elements which is equal to v2/4 (v even) or (v2 — 1)/4 (v odd). We show that this critical set is minimal, for v even.

A Hand-Held Neutron Detection Sensor Systems, K. Osberg, N. Schemm, S. Balkir, Jennifer I. Brand, M. Susan Hallbeck, Peter A. Dowben

Peter Dowben Publications

In this paper, a hand-held neutron radiation sensor application is described. The sensor system utilizes a new class of boron-carbide diode that interacts with incoming neutrons. To interface with the boron-carbide diode an integrated front-end is designed in a 1.5/spl mu/m standard CMOS technology. With the diode and front-end microchip, a hand-held neutron detection system was realized with an embedded microcontroller for realtime processing. The hand-held detector operation was then tested with a plutonium-beryllium neutron source. Testing results confirm the validity of the approach and the functionality of the design.

Nonextensivity In Magnetic Nanoparticle Ensembles, Christian Binek, Srinivas Polisetty, Xi He, Tathagata Mukherjee, Rajasekaran Rajesh, Jody G. Redepenning

Department of Physics and Astronomy: Faculty Publications

A superconducting quantum interference device and Faraday rotation technique are used to study dipolar interacting nanoparticles embedded in a polystyrene matrix. Magnetization isotherms are measured for three cylindrically shaped samples of constant diameter but various heights. Detailed analysis of the isotherms supports Tsallis' conjecture of a magnetic equation of state that involves temperature and magnetic field variables scaled by the logarithm of the number of magnetic nanoparticles. This unusual scaling of thermodynamic variables, which are conventionally considered to be intensive, originates from the nonextensivity of the Gibbs free energy in three-dimensional dipolar interacting particle ensembles. Our experimental evidence for nonextensivity …

Algorithms For Computational Genetics Epidemiology, Jingwu He

Computer Science Dissertations

The most intriguing problems in genetics epidemiology are to predict genetic disease susceptibility and to associate single nucleotide polymorphisms (SNPs) with diseases. In such these studies, it is necessary to resolve the ambiguities in genetic data. The primary obstacle for ambiguity resolution is that the physical methods for separating two haplotypes from an individual genotype (phasing) are too expensive. Although computational haplotype inference is a well-explored problem, high error rates continue to deteriorate association accuracy. Secondly, it is essential to use a small subset of informative SNPs (tag SNPs) accurately representing the rest of the SNPs (tagging). Tagging can achieve …

Adaptive Online Program Analysis: Concepts, Infrastructure, And Applications, Matthew B. Dwyer, Alex Kinneer, Sebastian Elbaum

CSE Technical Reports

Dynamic analysis of state-based properties is being applied to problems such as validation, intrusion detection, and program steering and reconfiguration. Dynamic analysis of such properties, however, is used rarely in practice due to its associated run-time overhead that causes multiple orders of magnitude slowdown of program execution. In this paper, we present an approach for exploiting the state-fullness of specifications to reduce the cost of dynamic program analysis. With our approach, the results of the analysis are guaranteed to be identical to those of the traditional, expensive dynamic analyses, yet with overheads between 23% and 33% relative to the un-instrumented …

Novel Mesoscale Defect Structure On Nio(1 0 0) Surfaces By Atomic Force Microscopy, S. C. Petitto, Cindy L. Berrie, Marjorie Langell

Marjorie A. Langell Publications

Cleaved NiO(1 0 0) surfaces were imaged with atomic force microscopy (AFM) to determine defect concentrations and morphology. Random (0 1 0) and (0 0 1) oriented steps, which have been previously characterized, were the most common defect observed on the cleaved surface and formed with step heights in multiples of 2.1 Å, the Ni–O nearest-neighbor distance, and terrace widths in the range of 25–100 nm. In addition, the surface showed novel mesoscale (~0.5–2 μm) square pyramidal defects with the pyramid base oriented along (1 0 0) symmetry related directions. Upon etching, the pyramidal defects converted to more stable cubic …

Conditional Likelihood Methods For Haplotype-Based Association Analysis Using Matched Case-Control Data, Jinbo Chen, Carmen Rodriguez

UPenn Biostatistics Working Papers

Genetic epidemiologists routinely assess disease susceptibility in relation to haplotypes, i.e., combinations of alleles on a single chromosome. We study statistical methods for inferring haplotype-related disease risk using SNP genotype data from matched case-control studies, where controls are individually matched to cases on some selected factors. Assuming a logistic regression model for haplotype-disease association, we propose two conditional likelihood approaches that address the issue that haplotypes cannot be inferred with certainty from SNP genotype data (phase ambiquity). One approach is based on the likelihood of disease status conditioned on the total number of cases, genotypes, and other covariates within each …

Absorption Properties Of A Porous Organic Crystalline Apohost Formed By A Self-Assembled Bis-Urea Macrocycle, Mahender B. Dewal, Michael W. Lufaso, Andrew D. Hughes, Stevan A. Samuel, Perry J. Pellechia, Linda S. Shimizu

Faculty Publications

We report herein the characterization and binding properties of a microporous crystalline host formed by the self assembly of a bis-urea macrocycle 1. Bis-urea macrocycle 1 has been designed to crystallize into stacked hollow columns. The self-assembly process is guided primarily by hydrogen bonding and aromatic stacking interactions that yield crystals of filled host 1âacetic acid (AcOH). The AcOH guests are bound in the cylindrical cavities of the crystal. The guest AcOH can be removed by heating to form a stable crystalline apohost 1. Apohost 1 displays a type I gas adsorption isotherm with CO₂ that is consistent with …

The Maintenance Of High Affinity Plasminogen Binding By Group A Streptococcal Plasminogen-Binding M-Like Protein Is Mediated By Arginine And Histidine Residues Within The A1 And A2 Repeat Domains., Martina L. Sanderson-Smith, Mark J. Walker, Marie Ranson

Faculty of Science - Papers (Archive)

Subversion of the plasminogen activation system is implicated in the virulence of group A streptococci (GAS). GAS displays receptors for the human zymogen plasminogen on the cell surface, one of which is the plasminogen-binding group A streptococcal M-like protein (PAM). The plasminogen binding domain of PAM is highly variable, and this variation has been linked to host selective immune pressure. Site-directed mutagenesis of full-length PAM protein from an invasive GAS isolate was undertaken to assess the contribution of residues in the a1 and a2 repeat domains to plasminogen binding function. Mutagenesis to alanine of key plasminogen binding lysine residues in …

Community Engagement, Education & Research, Public Lands Institute

Presentations (PLI)

The Public Lands Institute is dedicated to strengthening the national fabric that is essential for the protection, conservation, and management of public lands.

Sequences, Series, And Function Approximation, Lawrence Stout

Lawrence N. Stout

Sequences are important in approximation: the usual representation of real numbers using decimals is in fact the process of giving a sequence of rational numbers approximation the real number in question successively better as more decimal places are given. These decimal approximation sequences are actually rather special: successive decimal approximations never get smaller (so the sequence is monotone nondecreasing) and two approximations which agree to the kth decimal place differ by at most 10-k (so the sequence is a Cauchy sequence: to make two values in the sequence close to each other all you need to do is take them …

Generalized Confidence Intervals For The Ratio Or Difference Of Two Means For Lognormal Populations With Zeros, Yea-Hung Chen, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

We discuss in this article methods for analyzing lognormal data that may include zeros. Specifically, we are interested in interval estimation for the ratio or difference of the population means. We propose here two generalized pivotal (GP) approaches: a ``true'' GP method and an ``approximate'' GP method. Additionally, we propose two likelihood-based approaches: a signed log-likelihood ratio (SLLR) method and a modified SLLR method. Our simulation studies suggest that the approximate generalized pivotal approach outperforms all other known methods; it results in highly accurate coverage frequencies and fairly low bias, even in small sample settings.

Multiple Imputation - Review Of Theory, Implementation And Software, Ofer Harel, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

Missing data is a common complication in data analysis. In many medical settings missing data can cause difficulties in estimation, precision and inference. Multiple imputation (MI) \cite{Rubin87} is a simulation based approach to deal with incomplete data. Although there are many different methods to deal with incomplete data, MI has become one of the leading methods. Since the late 80's we observed a constant increase in the use and publication of MI related research. This tutorial does not attempt to cover all the material concerning MI, but rather provides an overview and combines together the theory behind MI, the implementation …

Multiple Imputation For The Comparison Of Two Screening Tests In Two-Phase Alzheimer Studies, Ofer Harel, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

Two-phase designs are common in epidemiological studies of dementia, and especially in Alzheimer research. In the first phase, all subjects are screened using a common screening test(s), while in the second phase, only a subset of these subjects is tested using a more definitive verification assessment, i.e. golden standard test. When comparing the accuracy of two screening tests in a two-phase study of dementia, inferences are commonly made using only the verified sample. It is well documented that in that case, there is a risk for bias, called verification bias. When the two screening tests have only two values (e.g. …

Entanglement Evolution In The Presence Of Decoherence, Jin Wang, Herman Batelaan, Jeremy Podany, Anthony F. Starace

Anthony F. Starace Publications

The entanglement of two qubits, each defined as an effective two-level, spin 1/2 system, is investigated for the case that the qubits interact via a Heisenberg XY interaction and are subject to decoherence due to population relaxation and thermal effects. For zero temperature, the time dependent concurrence is studied analytically and numerically for some typical initial states, including a separable (unentangled) initial state. An analytical formula for non-zero steady state concurrence is found for any initial state, and optimal parameter values for maximizing steady state concurrence are given. The steady state concurrence is found analytically to remain non-zero for low, …

Reflections On Wallace, Charles H. Smith

DLPS Faculty Publications

An unpublished paper has recently come to light, which shows that even at an early age, Alfred Russel Wallace was bold enough to approach the scientific establishment with his ideas.

Reflections On Wallace, Charles H. Smith

Charles Kay Smith

2006 Fall Engr333 Project Assignment, Matthew K. Heun

ENGR 333

In the Fall 2006 semester, I challenged the ENGR333 students to “construct a realistic plan to make a significant impact on the Calvin College campus with electrical power generated from wind resources.”

Customer

The customer for this project was Calvin’s VP for finance Henry DeVries.

Bear River Resource Conservation And Development Council Area Plan, United States Department Of Agriculture, Natural Conservation Service, Bear River Resource Conservation And Development Council

All U.S. Government Documents (Utah Regional Depository)

This five-year Area Plan is the guiding document for the Bear River RC&D Council, Inc. It identifies needs and opportunities and goals and objectives which lead the RC&D Council in its work.

Slow Light With Large Fractional Delays By Spectral Hole-Burning In Rubidium Vapor, Ryan M. Camacho, Michael V. Pack, John C. Howell

Mathematics, Physics, and Computer Science Faculty Articles and Research

We report on the experimental realization of large fractional pulse delays in a hot, Doppler-broadened rubidium vapor. A pump laser burns a deep spectral hole in the inhomogeneously broadened vapor. The delay is shown to be widely tunable by both power broadening the resonance and frequency modulating the pump laser. The simplicity of the scheme opens up the possibility for practical optical delays and buffers.

Tau-Tubulin Kinase 1 (Ttbk1), A Neuron-Specific Tau Kinase Candidate, Is Involved In Tau Phosphorylation And Aggregation, Shinji Sato, Ronald Cerny, James L. Buescher, Tsuneya Ikezu

Ronald Cerny Publications

Neurofibrillary tangles, which are major pathological hallmarks of Alzheimer’s disease (AD), are composed of paired helical filaments (PHFs) containing hyperphosphorylated tau. Specific kinases regulate tau phosphorylation and are closely linked to the pathogenesis of AD. We have characterized a human tau-tubulin kinase 1 (TTBK1) gene located on chromosome 6p21.1. TTBK1 is a serine/threonine/tyrosine kinase that is conserved among species and belongs to the casein kinase 1 superfamily. It is specifically expressed in the brain, especially in the cytoplasm of cortical and hippocampal neurons. TTBK1 phosphorylates tau proteins in both a Mg²⁺- and a Mn²⁺-dependent manner. Phosphopeptide …

Expressing Business Process Model As Owl-S Ontologies, M. A. Aslam, S. Auer, J. Shen, M. Herrmann

Faculty of Informatics - Papers (Archive)

BPEL4WS is a well-established business process standard that can be used to orchestrate service-based workflows. However, the rapid growth and automation demands of e-business and grid applications require BPEL4WS to provide enhanced semantic annotations to achieve the goal of business processes automation. Here, OWL-S (OWL for Web Services) is designed to represent such kind of semantic information. Furthermore, there exists a similarity in the conceptual model of OWL-S and BPEL4WS that can be employed to overcome the lack of semantics in BPEL4WS by mapping the BPEL4WS process model to the OWL-S suite of ontologies. The mapped OWL-S service can be …

Good Benchmarks Are Hard To Find: Toward The Benchmark For Information Retrieval Applications In Software Engineering, Alex Dekhtyar, Jane Huffman Hayes

Computer Science and Software Engineering

Seven to eight years ago, the number of applications of Information Retrieval (IR) methods in Software Engineering was close to zero. These days, IR and text mining methods are accepted approaches to analysis of textual artifacts generated during the software lifcycle. The incentive to try IR methods in such analysis is strong: the field comes with a reputation for proven industrial and academic success, and some important Software Engineering problems related to textual artifacts, can be translated into an instance of a standard IR problem in a reasonably straightforward manner.

In this position paper, we observe that part of the …

Optical Image Blending For Underwater Mosaics, Fan Gu, Yuri Rzhanov

Center for Coastal and Ocean Mapping

Typical problems for creation of consistent underwater mosaic are misalignment and inhomogeneous illumination of the image frames, which causes visible seams and consequently complicates post-processing of the mosaics such as object recognition and shape extraction. Two recently developed image blending methods were explored in the literature: "gradient domain stitching" and "graph-cut" method, and they allow for improvement of illumination inconsistency and "ghosting" effects, respectively. However, due to the specifics of underwater imagery, these two methods cannot be used within a straightforward manner. In this paper, a new improved blending algorithm is proposed based on these two methods. By comparing with …

Calving Giant Icebergs: Old Principles, New Applications, James P. Kenneally, Terence J. Huges

Earth Science Faculty Scholarship

Earth-orbiting satellites can now monitor calving of large icebergs from ice shelves bordering the marine West Antarctic Ice Sheet, and recent calving events have stimulated interest in calving mechanisms. To advance this interest pioneering work in brittle and ductile fracture mechanics is reviewed, leading to a new application to calving of giant icebergs from Antarctic ice shelves. The aim is to view iceberg calving as more than terminal events for Antarctic ice when glaciologists lose interest. Instead calving launches Antarctic ice into the larger dynamic system of Earth's climate machine. This encourages a holistic approach to glaciology.

Phytoplankton In The Damariscotta River Estuary, Brian Thompson, Mary Jane Perry, Christopher V. Davis

Maine Sea Grant Publications

This research project examined the distribution of phytoplankton in the Damariscotta River, as well as environmental factors, such as nutrients, light, and physical conditions, in order to assess the estuary’s ability to sustain additional farms.