Digital Commons Network^™

Computational Promoter Analysis Of Mouse, Rat, And Human Antimicrobial Peptide-Coding Genes, Chin-Yo Lin, Manisha Brahmachary, Christian Schonbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S. P. T. Krishnan, David A. Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic

Faculty Publications

Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect the expression of AMP-coding genes (AMPcgs). For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized. Results- Based upon the RIKEN full-length cDNA and public sequence data derived from human, mouse and rat, we identified 178 candidate AMP transcripts derived from 61 genes belonging to 29 AMP families. However, only for 31 mouse genes belonging to 22 AMP families we …

Getting Langue Winded How The European Union Language Policy Came To Be, Clinton R. Long

Student Works

While many people remember hearing about the French Revolution slogan of libert, galit et fraternit ringing through the streets of Paris in the eighteenth century, fewer people remember hearing about similar ideals ringing through the streets of Brussels, Bonn, and other European capitals in the 1950s with regard to the language policy of a united Europe. Even those familiar with the language policy of the European Union (EU) and its predecessors only talk about how the EU language policy is langue winded (langue means language in French) due to its inefficiencies without considering that these ideals-equality in particular-shaped the very …

A Bayesian Perspective On Estimating Mean, Variance, And Standard-Deviation From Data, Travis E. Oliphant

Faculty Publications

This article shows how to compute confidence intervals for mean, standard-deviation, and variance using Bayesian methods. The method is implemented in SciPy as scipy.stats.bayes_mvs After reviewing some classical estimators for mean, variance, and standard-deviation and showing that un-biased estimates are not usually desirable, a Bayesian perspective is employed to determine what is known about mean, variance, and standard deviation given only that a data set in-fact has a common mean and variance. Maximum-entropy is used to argue that the likelihood function in this situation should be the same as if the data were independent and identically distributed Gaussian. A non-informative …

A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron J. Adams, U. Gozel, K. B. Nguyen, R. N. Inserra, R. M. Giblin-Davis

Faculty Publications

The D2-D3 and ITS regions of rDNA from 33 Florida populations of Belonolaimus spp. were sequenced and subjected to phylogenetic analysis. Our objective was to derive a theoretical evolutionary framework for interpreting phenotypic differences as they relate to the taxonomy of the genus. The most striking aspect of the phylogenetic analysis is that none of the three nominal species (B. longicaudatus, B. euthychilus, and B. gracilis) are monophyletic. Additionally, two taxa appear to have discordant ITS and LSU sequences. Three major clades of B. longicaudatus exhibited discernible, overlapping, geographic foci from east to west across the peninsula. Morphological character states …

The Smith-Mundt Act's Ban On Domestic Propaganda: An Analysis Of The Cold War Statute Limiting Access To Public Diplomacy, Edward L. Carter, Allen W. Palmer

Faculty Publications

For more than fifty years, the U.S. Code has authorized the federal government to disseminate messages about America to international audiences. For at least thirty years, federal law has also prohibited those international propaganda messages from being disseminated within the United States. Given the realities of the acceleration and dispersion of information flow across international borders in the twenty-first century, a ban on dissemination of information that is tied to geographic boundaries raises both practical and policy issues. The domestic dissemination ban may have outlived its usefulness and relevance. Further, futile enforcement of the statute contradicts general U.S. policy promoting …

Slovakia's Surge: The New System's Impact On Fiscal Decentralization, Phillip J. Bryson, Gary C. Cornia

Faculty Publications

Slovakia's transition history long paralleled that of the Czech Republic, but the former adopted bold new reforms early in tis decade. This paper is a comparative treatment of fiscal decentralization since 1993 and more recent reforms of public administration, the two efforts representing the foundation of the New System. Czech experience is invoked simply to provide an appropriate benchmark for the evaluation of Slovakia's New System introduced in 2004, including the 19% "flat tax" and other striking measures in local public finance. The second focus of the paper is on the macro-economic impact of the New System. It is too …

Vision-Based Target Geo-Location Using A Fixed-Wing Miniature Air Vehicle, D. Blake Barber, Joshua D. Redding, Timothy W. Mclain, Randal W. Beard, Clark N. Taylor

Faculty Publications

This paper presents a method for determining the GPS location of a ground-based object when imaged from a fixed-wing miniature air vehicle (MAV). Using the pixel location of the target in an image, with measurements of MAV position and attitude, and camera pose angles, the target is localized in world coordinates. The main contribution of this paper is to present four techniques for reducing the localization error. In particular, we discuss RLS filtering, bias estimation, flight path selection, and wind estimation. The localization method has been implemented and flight tested on BYU’s MAV testbed and experimental results are presented demonstrating …

Information Infrastructure For Integrated Ecohydraulic And Water Resources Modeling And Assessment, R. Wallace, K. Pathak, M. Fife, Norman L. Jones, J. P. Holland, D. Stuart, J. Harris, C. Butler, D. R. Richards

Faculty Publications

Watershed management increasingly requires ecohydraulic modeling and assessment within a regional context, rather than on a project-by-project basis. Such holistic modeling and assessment require evaluation capabilities across multiple temporal and spatial scales. Thus, modeling and assessment tools must be integrated in a scientifically and computationally effective infrastructure. The US Army Engineer Research and Development Center, in concert with the Hydrologic Engineering Center and its academic partners, including Brigham Young University, is establishing a comprehensive set of hydroinformatics modeling and assessment tools for ecohydraulic and water resources management applications, all linked based on a common data and information infrastructure. This paper …

Recognizing, Digitizing, Advertising: Gnarp Efforts With Unique German Studies Materials, Richard Hacken

Faculty Publications

Presented in the Winter 2005-2006 issue of the Global Resources Newsletter, the German-North American Resources Partnership issue. GNARP's Digital Libraries Working Group (DLWG) is tooling up to act as a sounding board and clearinghouse for collaborative projects that provide access, and add value, to materials sought by scholars. The spectrum of the group's activities can be summed up in the three verbs: recognizing, digitizing, advertising.

Culturally Adapted Mental Health Interventions: A Meta-Analytic Review, Timothy B. Smith, Derek Griner

Faculty Publications

There is a pressing need to enhance the availability and quality of mental health services provided to persons from historically disadvantaged racial and ethnic groups. Many previous authors have advocated that traditional mental health treatments be modified to better match clients? cultural contexts. Numerous studies evaluating culturally adapted interventions have appeared, and the present study used meta-analytic methodology to summarize these data. Across 76 studies the resulting random effects weighted average effect size was d = .45, indicating a moderately strong benefit of culturally adapted interventions. Interventions targeted to a specific cultural group were four times more effective than interventions …

Predicting On-Orbit Static Single Event Upset Rates In Xilinx Virtex Fpgas, Joshua Engel, Keith S. Morgan, Michael J. Wirthlin, Paul S. Graham

Faculty Publications

Sponsorship: Department of Energy, Los Alamos National Laboratory. This document describes the methodology used to predict single-event upset rates for Xilinx Virtex FPGAs based on the CREME96 orbit modeling tool. Using this methodology, SEU upset rates are obtained for several Xilinx Virtex FPGAs including Virtex, Virtex-II, and Virtex-4. Further, SEU upset rates are obtained for a variety of orbits for each of these FPGAs.

Simulation Of A Carbon Nanotube-Based Compliant Parallel-Guiding Mechanism: A Nanomechanical Building Block, Martin L. Culpepper, Christopher M. Dibiasio, Robert M. Panas, Spencer P. Magleby, Larry L. Howell

Faculty Publications

The authors report the behavior of a nanoscale parallel-guiding mechanism wherein the compliant components are single-walled carbon nanotubes. Parallel-guiding mechanisms are often the building blocks of macro- and microscale mechanical systems. The authors present results that provide insight into the performance of a parallel-guiding mechanism for nanoscale devices. The device exhibits a range over 75% of the device size, i.e., 5.5 nm, when actuated with 6.4 nN. Below 3.6 nN, displacements are due to bulk elastic bending of the nanotubes. Above 5.2 nN, displacements are governed by the hingelike bending of kinks in the nanotubes. van der Waals forces are …

Eliminating Redundant And Less-Informative Rss News Articles Based On Word Similarity And A Fuzzy Equivalence Relation, Ian Garcia, Yiu-Kai D. Ng

Faculty Publications

The Internet has marked this era as the information age. There is no precedent in the amazing amount of information, especially network news, that can be accessed by Internet users these days. As a result, the problem of seeking information in online news articles is not the lack of them but being overwhelmed by them. This brings huge challenges in processing online news feeds, e.g., how to determine which news article is important, how to determine the quality of each news article, and how to filter irrelevant and redundant information. In this paper, we propose a method for filtering redundant …

Developing A Campus Copyright Education Program: Conquering The Challenge, Susie Quartey

Faculty Publications

Developing a copyright educational program at a University can be a daunting task. Many professors do not want to hear the word in connection with their teaching or academic pursuits. It can strike fear in the hearts of many educators who have hidden behind the mask of ignorance for years. With the complex nature of copyright law and budget restrictions, few institutions have the luxury of on-site copyright experts. A well-planned, conscientiously formulated copyright education campaign can ease the anxieties of the ignorant; empower the helpless; and fuel the passion of those striving to enlighten others about copyright compliance at …

Anisotropic High Aspect Ratio Etch Development For Fluorinated Polymers With Stress Relief Technique, S. Kim, Gregory P. Nordin, N. Rahmanian

Faculty Publications

The authors have developed an anisotropic, high aspect ratio (18:1) etch for perfluorocyclobutyl (PFCB) polymers with trenches as narrow as 800 nm using a CO/O2 etch chemistry in an inductively coupled plasma reactive ion etcher. Anisotropy is achieved by carbon sidewall passivation. The motivation for this etch development is to use the air trenches as very compact waveguide splitters [S. Kim et al., Opt. Eng. 45, 054602 (2006)] The authors report a new trench widening mechanism due to tensile stress of the PFCB films and a method of avoiding this widening through the use of additional stress relief trenches on …

Omega-3 Fatty Acid Consumption In The Reduction Of Sudden Cardiac Death: A Critical Appraisal, Katie J. Walker, A. Elaine Bond, Renea L. Beckstrand, Mary Williams

Faculty Publications

This article examines the effects of omega-3 fatty acid consumption in reducing sudden cardiac death risk, and provides useful dosing recommendations for patients–with or without a history of coronary heart disease–in a primary care practice.

The Effects Of The Strong Kids Curriculum On Students At-Risk For Internalizing Behavior Disorders, Marenda Brown, Michelle Marchant, Paul Caldarella, Hilda Sabbah, Michael Adams

Faculty Publications

Advantage of Deveoping Social/Emotional Skills in Schools: School is a context that is accessible to children and youth. Schools provide an environment rich in opportunities for social and emotional development (Miller et al., 1998). Classroom experiences are made up of social and emotional interactions (Elksnin & Elksnin, 2006). Children typically feel comfortable in the school setting (Roeser, 2001).

Positive Behavior Support And Perceptions Of School Quality: An Empirical Study, Hilda Sabbah, Lynnette Christensen, Paul Caldarella, Michael Richardson, Adrian Juchau, Michelle Marchant, K. Richard Young

Faculty Publications

Purpose of the BYU-Positive Behavior Support Initiative…to contribute to the knowledge and understanding of the issues that facilitate, sustain and nurture the emotional, social and moral development of youth by designing, implementing and evaluating school-wide positive behavior support.

Time-Varying Mimo Channels: Measurement, Analysis, And Modeling, Michael A. Jensen, Jon W. Wallace

Faculty Publications

communication nodes is analyzed. A wide-band 8 times 8 sounder is employed to measure the response of indoor and outdoor channels at 2.55 and 5.2 GHz. The rate of channel temporal variation is then quantified in terms of information theoretic metrics that indicate the loss in channel quality as transmit and receive channel state information becomes increasingly outdated. Finally, these metrics are used to investigate the ability of two different modeling strategies-a random matrix model and a physical time-varying cluster model-to capture the channel temporal variation.

An Improved Distance Heuristic Function For Directed Software Model Checking, Eric G. Mercer, Neha Rungta

Faculty Publications

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 an exponential growth in the computation. This paper presents a new algorithm that implicitly inlines functions at call sites …

Ordering Tendencies In The Binary Alloys Of Rh, Pd, Ir, And Pt: Density Functional Calculations, Gus L. W. Hart, Brian Kolb, Stefan Müller, David B. Botts

Faculty Publications

The binary alloys of Rh, Pd, Ir, and Pt are important because of their high catalytic potential. We report in this paper that the Rh1-xIrx and Rh1-xPtx systems, long thought to phase separate at low temperatures, actually exhibit miscibility over the entire concentration and temperature range. We find low critical ordering temperatures, indicating that long-range order is unlikely to be observed experimentally. These results are compared with previous theoretical predications for the other binary alloys of Rh, Pd, Ir, and Pt and with calculations performed here on the Pt1-xIrx and Pd1-xIrx systems. We discuss these results and investigate the mechanisms …

Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson

Faculty Publications

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N–1)]^1/2, and the ratio of average collision energy to average kinetic energy is …

Potential Energy Surfaces For Small Alcohol Dimers I: Methanol And Ethanol, Richard L. Rowley, Tapani A. Pakkanen, Christopher M. Tracy

Faculty Publications

Potential energy landscapes for homogeneous dimers of methanol and ethanol were calculated using counterpoise (CP) corrected energies at the MP2/6-311+G(2df,2pd) level. The landscapes were sampled at approximately 15 dimer separation distances for different relative monomer geometries, or routes, given in terms of a relative monomer yaw, pitch, and roll and the spherical angles between the monomer centers (taken as the C atom attached to the O). The 19 different routes studied for methanol and the 22 routes examined for ethanol include 607 CP corrected energies. Both landscapes can be adequately represented by site-site, pairwise-additive models, suitable for use in molecular …

Emergency Nurses' Perceptions Of Obstacles And Supportive Behaviors In End-Of-Life Care, Sondra Heaston, Renea L. Beckstrand, A. Elaine Bond, Sheri P. Palmer

Faculty Publications

Introduction: Little is known about emergency nurses' perceptions of either obstacles or supportive behaviors for providing end-of life (EOL) care to dying patients. The purpose of this study was to determine the perceived obstacles and supportive behaviors in providing EOL care to dying patients in emergency departments.

Methods: In this survey research, a 73-item questionnaire regarding EOL care was mailed to a geographically dispersed national random sample of 300 members of the Emergency Nurses Association. Descriptive statistics were calculated for the 54 Likert-type items and demographic items. Two open-ended questions were analyzed using content analysis.

Results: Returns after 3 mailings …

Optical Emission Study Of Nonthermal Plasma Confirms Reaction Mechanisms Involving Neutral Rather Than Charged Species, Morris D. Argyle, Gui-Bing Zhao, Maciej Radosz

Faculty Publications

Charge transfer reactions are commonly used to explain NOX conversion in nonthermal plasma. An analysis of optical emission spectra induced by pulsed corona discharge in NOX-containing argon suggests that, in fact, the contribution of charge transfer reactions to NOX conversion in nonthermal plasma is negligible. During electrical discharge in such gas mixtures, NO(B), an electronic excited state of NO formed due to the dissociative recombination reactions of NO2+ and N2O+ and the optical emission of NO(B) could be a proof that cations are responsible for NOX conversion. However, the optical emission of NO(B) is not observed, leading to the conclusion …

Warming Up With An Ice Vest: Core Body Temperature Before And After Cross-Country Racing, J. Ty Hopkins, Iain Hunter, Douglas J. Casa

Faculty Publications

Context: Athletes running in a hot, humid environment may have an increased risk of heat illness. In the 2004 Olympic Games, American and Australian athletes were provided with ice vests designed to cool their bodies before performance. The vest appeared to be effective in keeping body temperatures down and improving the performance of the marathoners. However, body temperatures have not been reported when the vest was used before an actual competition. Objective: To determine if wearing the Nike Ice-Vest decreased core temperature (Tc) before and during athletic performance in warm (26°C to 27°C), humid (relative humidity = 50% to 75%) …

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

Open Source, Openness, And Higher Education, David Wiley

Faculty Publications

With the growth of open source software and other related trends, a culture of openness is advancing from the edges of society to the core of academic culture. In this article I provide an overview of how the expansion of open source software in culture at large has affected the world of education, describe how the greater use of open source software in education has unfolded hand-in-hand with the development of open course content and open access research, and argue that this more comprehensive shift towards "openness" in academic practice is not only a positive trend, but a necessary one …

Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell

Faculty Publications

DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that …

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor

Faculty Publications

Each year people suffer from complications of adverse drug reactions, but with pharmacogenomics there is hope to prevent thousands of these people from suffering or dying needlessly. The CYP2D6 gene is responsible for metabolizing a large portion of these drugs. Because of the gene’s importance, various approaches have been taken to analyze CYP2D6 and single nucleotide polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyze the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each nonsynonymous substitution using the program TreeSAAP. We apply this technique to SNPs found in the …