Physical Sciences and Mathematics Commons^™

Modeling Correlated Main-Chain Motions In Proteins For Flexible Molecular Recognition., Maria Zavodsky, Ming Lei, M. Thorpe, Anthony Day, Leslie Kuhn

Anthony Roy Day

We describe a new method for modeling protein and ligand main-chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large-scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystallography or NMR. A secondary goal is to assess the degree of flexibility consistent with protein–ligand recognition. Flexibility analysis of the target protein is performed using the graph-theoretic algorithm FIRST, which also identifies coupled networks of covalent and noncovalent bonds within the …

An Approach To Facilitate Reliability Testing Of Web Services Components, Jia Zhang

Jia Zhang

No abstract provided.

Modelling The Turbulent Mixing Noise Associated With Coanda Jets, Caroline Lubert

Caroline P Lubert

No abstract provided.

Evaluation Of Extent And Bioavailability Of Chromium Contamination Near An Abandoned Strip Mine, C. Appel, J. Stuckey, A. Cosley, R. Donald, C. Griffith, S. Lager, M. Perry, T. Ray, P. Smith

Earth and Soil Sciences

Chromium is a potentially toxic element to plants and animals commonly associated with serpentine and anthropogenic sources. An abandoned Cr strip-mine at US National Guard Camp SLO, CA containing serpentinitic parent material was tested for total and bioavailable Cr in the soil and overlying vegetation via US EPA Methods 3050a (Total Cr) and 1311 (Total Characteristic Leaching Procedure, TCLP) (US EPA, 1995), respectively. The analysis of total and bioavailable Cr was used to assess the risk of nearby surface and groundwater contamination and to evaluate the site’s need for remediation. In addition, trends in soil Cr levels with respect to …

Bayesian Hierarchical Distributed Lag Models For Summer Ozone Exposure And Cardio-Respiratory Mortality, Yi Huang, Francesca Dominici, Michelle L. Bell

Johns Hopkins University, Dept. of Biostatistics Working Papers

In this paper, we develop Bayesian hierarchical distributed lag models for estimating associations between daily variations in summer ozone levels and daily variations in cardiovascular and respiratory (CVDRESP) mortality counts for 19 U.S. large cities included in the National Morbidity Mortality Air Pollution Study (NMMAPS) for the period 1987 - 1994.

At the first stage, we define a semi-parametric distributed lag Poisson regression model to estimate city-specific relative rates of CVDRESP associated with short-term exposure to summer ozone. At the second stage, we specify a class of distributions for the true city-specific relative rates to estimate an overall effect by …

Weighted Segmented Digital Watermarking, Glen Wheeler, R. Safavi-Naini, N. P. Sheppard

Faculty of Informatics - Papers (Archive)

We introduce the notion of weighted watermarking for proof-of-ownership watermark protection of multimedia works that are the product of more than one author and where each author is considered to be of different importance relative to the other authors. We specifically examine weighted segmented watermarking for still images and generalise previous work on performance measurement of watermark embedding patterns in the presence of cropping attacks.

The White Dwarf Luminosity Function: The Shape Of Things To Come, Ted Von Hippel, M. Kilie, J. Munn, K. Williams, J. Libert, D. E. Winget, T. S. Metcalfe, Et Al.

Publications

We describe a new survey for cool white dwarfs that supplements Sloan Digital Sky Survey photometry with USNO proper motions and followup spectroscopy. To date we have discovered and spectroscopically confirmed 80 new moderate temperature and cool white dwarfs. We have also found a handful of high-velocity white dwarfs and we expect a sizable fraction of these to be thick disk or possibly halo objects. Our survey is designed to find 104 new white dwarfs, although only 60 will be among the faintest white dwarfs (MV 16), where most of the age-sensitivity resides. We discuss an extension of our survey …

Cmg Training In Spatio-Temporal Statistical Analysis Of Multi-Platform Ocean Optical Observations, Mary Jane Perry

University of Maine Office of Research Administration: Grant Reports

This project will be a five-week summer school on the topic of spatio-temporal statistical analysis and its application to multi-platform, multi-sensor bio-optical oceanic data. The summer school seeks to address some of the analysis challenges anticipated as the Integrated Ocean Observing System is established. These are associated with the very diverse range of spatial and temporal sampling afforded by the different components of such a system and contemporaneous process experiments. Statistical experts in spatial information engineering with experience in collaboration with ocean scientists will discuss some of the modern tools for statistical analysis of such data and associated challenges, while …

Problems With The Dartmouth Wireless Snmp Data Collection, Tristan Henderson, David Kotz

Computer Science Technical Reports

The original Dartmouth wireless network study used SNMP to query the college's Cisco 802.11b access points. The perl scripts that performed the SNMP queries suffered from some problems, in that they queried inappropriate SNMP values, or misunderstood the meaning of other values. This data was also used in a subsequent analysis. The same scripts were used to collect data for a subsequent study of another wireless network. This document outlines these problems and indicates which of the data collected by the original scripts may be invalid.

Nanoscale Hydrophobic Interaction And Nanobubble Nucleation, T. Koishi, S. Yoo, K. Yasuoka, Xiao Cheng Zeng, T. Narumi, R. Susukita, A. Kawai, H. Furusawa, A. Suenaga, N. Okimoto, N. Futatsugi, T. Ebisuzaki

Xiao Cheng Zeng Publications

We report large-scale atomistic simulation of midrange nanoscale hydrophobic interaction, manifested by the nucleation of nanobubble between nanometer-sized hydrophobes at constrained equilibrium. When the length scale of the hydrophobes is greater than 2 nm, the nanobubble formation shows hysteresis behavior resembling the first-order transition. Calculation of the potential of mean force versus interhydrophobe distance provides a quantitative measure of the strength of the nanoscale hydrophobic interaction.

2004 Scholars And Artists Bibliography, Michael Schwartz Library, Cleveland State University, Friends Of The Michael Schwartz Library

Scholars and Artists Bibliographies

This bibliography was created for the annual Friends of the Michael Schwartz Library Scholars and Artists Reception, recognizing scholarly and creative achievements of Cleveland State University faculty, staff and emeriti

The Next Edition Of Iho-S-57 (4.0): A Primer, Lee Alexander

Center for Coastal and Ocean Mapping

The International Hydrographic Organization (IHO) is an intergovernmental consultative and technical organization that was established in 1921 to support the safety of navigation and the protection of the marine environment. IHO Special Publication 57 (IHO S-57) is the IHO Transfer Standard for Digital Hydrographic Data. It is the standard to be used for the exchange of digital hydrographic data between hydrographic offices (HOs), and for the distribution of hydrographic data to manufacturers, mariners and other data users (e.g., GIS). It was developed so that the transfer all forms of hydrographic data would take place in a consistent and uniform manner. …

Ship-Based Nitric Acid Measurements In The Gulf Of Maine During New England Air Quality Study 2002, Jack E. Dibb, Eric Scheuer, Sallie I. Whitlow, Marcy Vozzella, Eric Williams, Brian M. Lerner

Earth Sciences

Gas phase nitric acid (HNO₃) was measured at 5-min resolution on board the National Oceanographic and Atmospheric Administration (NOAA) research vessel Ronald H. Brown during the second leg (29 July to 10 August) of the New England Air Quality Study (NEAQS) 2002 cruise. A primary objective of the cruise was to improve understanding of the oxidation of NO_x in, and removal of the oxidation products from, the polluted marine boundary layer east of northeastern North America. For the first 9 days of this leg the ship remained north of Cape Cod, and the cruise track did not …

2004 Forage Spokesperson Contestants, James Chestnut, Jimmy May, Steve Meredith, Bill Payne

Kentucky Grazing Conference

No abstract provided.

Strategies For Reducing Stored Feed Requirements, Don Ball

Kentucky Grazing Conference

A basic, desirable goal for virtually any livestock producer is to minimize stored feed requirements. It is less expensive to have livestock harvest forage for themselves by grazing than to harvest it for them; therefore, the greater the extent to which pasture can be used to provide nutrition, the more profitable a livestock operation will generally be. Thus, it is worthwhile to consider all options that might be available for reducing stored feed needs.

Stocking Decisions: They Make Or Break You, Glen E. Aiken

Kentucky Grazing Conference

Decisions on species and variety of forage to plant and manage are economically critical because it establishes the potential to meet a particular production goal. However, the stocking rate used to graze these forages is more critical because it ultimately determines if a targeted level of production is reached. Most cattlemen aim for a stocking rate that provides maximum economic return, but it should be emphasized that an economically optimum stocking rate is one that potentially provides sustained economic return. It is obvious that dollar return is not maximized if excessive heavy grazing results in costly pasture renovation, ranging from …

Grazing: Getting From Where You Are To Where You Want To Be, Gary Bates

Kentucky Grazing Conference

When trying to design a forage and grazing program, producers often try to consider so many factors that it becomes mind-boggling. If basic plant physiology, how and when a forage plant grows is considered, improving a forage program will usually become easier, especially in developing a controlled grazing system. The purpose of a controlled grazing system should be to improve the utilization of the high quality forage produced on the farm. In order to improve this utilization, it is helpful to understand plant growth and quality, and the factors that affect them.

Will Improved Grazing Pay For Extra Fencing And Water Cost?, Ken Johnson

Kentucky Grazing Conference

Expectation is founded on faith, and in faith lays opportunities. I suppose as we look at most farming operations most changes occur from force not by choice. What I propose today and hope to convince most of you; is that here is an opportunity to make more profit, if you’re willing to change and have faith that it will work. Most of us have heard of, if not practiced rotation grazing for a long time. The question many ask, is it worthwhile. Does better grazing management make me any more money? I hope to at least provide some insight as …

Present And Future Tall Fescue Varieties, Timothy D. Phillips

Kentucky Grazing Conference

Tall fescue has played a key role in forage production over the past century in the USA. It has other uses besides forage applications, such as turf, mine reclamation, and highway rights-of-way, but in this presentation we will focus on forage varieties. Several hundred turf-type tall fescue varieties have been developed over the past 30 years, mainly by private seed companies using material from Reed Funk at Rutgers University in New Jersey. Forage varieties aren’t as numerous. I will discuss some of the older and current forage tall fescue varieties, and finish by discussing the newest varieties, and those that …

Fertilizing Pastures For Profit, Byron Sleugh

Kentucky Grazing Conference

It has been known for centuries that providing certain nutrients to plants is critical for high productivity. The nutrient source and manner in which it is applied may vary, but the desired outcome is the same: high crop yield and quality. Fertilization is the most practical means that producers have to ensure that crops receive the nutrients they need. While increasing fertilizer application and managing pH by liming can lead to increase forage production, your investment should be measured against the potential return. Also, over application of nutrients can potentially cause environmental problems.

Role Of Legumes In Pasture Systems, Garry D. Lacefield

Kentucky Grazing Conference

Successful livestock programs are dependent on forage programs which supply large quantities of adequate quality, homegrown feed. A major percentage of the feed units for beef (83%) and dairy (61%) cattle come from forages. In addition, forages supply an estimated 91%, 72%, 15% and 99% of the nutrients consumed by sheep and goats, horses, swine and ruminant wildlife, respectively. These values can be put in perspective when we consider that 63% of Kentucky's Agricultural Cash Receipts are from livestock and livestock products. Cash hay accounts for approximately 28% of the total crop value. Hay ranks second only to tobacco in …

Foreword And Kfgc Award Winners [2004], Garry D. Lacefield, Christi L. Forsythe

Kentucky Grazing Conference

No abstract provided.

Multiple Testing And Data Adaptive Regression: An Application To Hiv-1 Sequence Data, Merrill D. Birkner, Sandra E. Sinisi, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Analysis of viral strand sequence data and viral replication capacity could potentially lead to biological insights regarding the replication ability of HIV-1. Determining specific target codons on the viral strand will facilitate the manufacturing of target specific antiretrovirals. Various algorithmic and analysis techniques can be applied to this application. We propose using multiple testing to find codons which have significant univariate associations with replication capacity of the virus. We also propose using a data adaptive multiple regression algorithm to obtain multiple predictions of viral replication capacity based on an entire mutant/non-mutant sequence profile. The data set to which these techniques …

Surface Structure Of Ultrathin Copolymer Films Of Ferroelectric Vinylidene Fluoride (70%) With Trifluoroethylene (30%) On Graphite, Lei Cai, Hongwei Qu, Chenxi Lu, Stephen Ducharme, Peter A. Dowben, Jiandi Zhang

Department of Physics and Astronomy: Faculty Publications

The structure and local structural distortions, through the polarization manipulation, of crystalline films of ferroelectric vinylidene fluoride (70%) with trifluoroethylene (30%) [P(VDF-TrFE)] copolymer on graphite were studied by scanning tunneling microscopy (STM). A quasispiral twist in C[Single Bond]C bonds with rotations about the polymer chain axis was observed by high-resolution STM, indicating a surface relaxation of the strained copolymer films. Such a relaxation behavior appears to be linked to the observed local dipole rotations accompanied by the reversal of the local polarization with biasing the STM tip. A structure model is proposed based upon the observations

Ultra-Fast Formation Of Stable Nanoparticle Film Assemblies, Dan Sheibley, Renee Szymanik, Michael C. Leopold

Chemistry Faculty Publications

Novel assembled films of monolayer-protected clusters (MPCs) can be grown on gold and glass substrates with a 20-fold higher efficiency than established procedures. Thick MPC films grown using this new method, which can easily be scaled up or automated, are extremely stable and have properties identical to traditionally formed nanoparticle films, including unique quantized double layer charging effects. This new procedure for growing nanoparticle films shares the versatility of the traditional method but exhibits accelerated growth attributed to highly efficient sorption and mobility of metal ion linkers within swelled films and improved mass transfer of nanoparticles to assembly sites. Concentration …

Evaluation And Management Of Chronic Wasting Disease Transmission, Kurt C. Vercauteren

United States Department of Agriculture Wildlife Services: Staff Publications

National Wildlife Research Center Scientists Assess the Potential for Chronic Wasting Disease (CWD) Transmission Between Wild and Domestic Cervids and Develop Methods to Reduce/Manage the Disease

Wildlife Services’ (WS) National Wildlife Research Center (NWRC) is the only Federal research organization devoted exclusively to resolving conflicts between people and wildlife through the development of effective, selective, and acceptable methods, tools, and techniques. As increased urbanization leads to a loss of traditional wildlife habitat, the potential for conflicts between people and wildlife increases. Such conflicts can take many forms, but recently the potential for the transmission of diseases among wildlife, livestock, and …

Gllamm Manual, Sophia Rabe-Hesketh, Anders Skrondal, Andrew Pickles

U.C. Berkeley Division of Biostatistics Working Paper Series

This manual describes a Stata program gllamm that can estimate Generalized Linear Latent and Mixed Models (GLLAMMs). GLLAMMs are a class of multilevel latent variable models for (multivariate) responses of mixed type including continuous responses, counts, duration/survival data, dichotomous, ordered and unordered categorical responses and rankings. The latent variables (common factors or random effects) can be assumed to be discrete or to have a multivariate normal distribution. Examples of models in this class are multilevel generalized linear models or generalized linear mixed models, multilevel factor or latent trait models, item response models, latent class models and multilevel structural equation models. …

Import/Export In Digital Rights Management, R. Safavi-Naini, N. P. Sheppard, Takeyuki Uehara

Faculty of Informatics - Papers (Archive)

The inherently controlled nature of digital rights management systems does little to promote inter-operability of systems provided by different vendors. In this paper, we consider import and export functionality by which multimedia protected by one digital rights management regime can be made available to a multimedia device that supports a different digital rights management regime, without compromising the protection afforded to the content under the original regime. We first identify specific issues to be addressed by developers of digital rights management import/export regimes and outline a variety of methods by which these regimes may be implemented. We then apply our …

Assessment Of Engineering Mechanics Instructional Multimedia In A Variety Of Instructional Settings, Richard H. Hall, Nancy Hubing, Timothy A. Philpot, Ralph E. Flori, Vikas Yellamraju

Business and Information Technology Faculty Research & Creative Works

Students from Ten Schools, Representing Seven Countries, Used Interactive Multimedia as a Part of their Engineering Statics Classes. the Software Consisted of Four Modules, Which Focused On: Mohr's Circle; Centroid and Moment of Inertia; Stress Transformation; and Structural Analysis. the Students Completed On-Line Surveys About their Experience with the Software. Analysis of the Results Indicated that Students Rated their Knowledge of the Subject Matter Covered in the Software as Increasing Significantly as a Consequence of using the Software. However, This Increase Was Substantially More Pronounced for Students in U.S. Schools. Students Rated the Software as Significantly More Effective Than their …

Development Of A High Performance Liquid Chromatography/Mass Spectroscopy Method For The Determination Of Strychnine Concentrations In Insects Used To Assess Potential Risks To Insectivores, Randal S. Stahl, Wendy M. Arjo, Kim K. Wagner, Carol Furcolow, Dale L. Nolte, John J. Johnston

United States Department of Agriculture Wildlife Services: Staff Publications

A high performance liquid chromatography/mass spectrometry (HPLC/MS) method was developed in support of a study to assess potential tertiary risks posed to insectivores by strychnine baited pocket gophers (Thomomys sp.). Necropholous insects are primary consumers of pocket gopher carcasses. A field study was conducted to collect insects from strychnine-baited and control pocket gopher carcasses. The majority of the insects collected were from the orders Diptera (flies, assayed separately as adults and larvae), Coleoptera (beetles), and Hymenoptera (ants and wasps, assayed separately). Samples (0.5 g) were extracted in acetic acid (2%) and analyzed with the mass spectrometer configured for tandem …