Physical Sciences and Mathematics Commons^™

An Informatics Search For The Low-Molecular Weight Chromium-Binding Peptide, Deendayal Dinakarpandian, Vincent Morrissette, Shveta Chaudhary, Kambiz Amini, Brian Bennett, J David Van Horn

Physics Faculty Research and Publications

Background

The amino acid composition of a low molecular weight chromium binding peptide (LMWCr), isolated from bovine liver, is reportedly E:G:C:D::4:2:2:2, though its sequence has not been discovered. There is some controversy surrounding the exact biochemical forms and the action of Cr(III) in biological systems; the topic has been the subject of many experimental reports and continues to be investigated. Clarification of Cr-protein interactions will further understanding Cr(III) biochemistry and provide a basis for novel therapies based on metallocomplexes or small molecules.

Results

A genomic search of the non-redundant database for all possible decapeptides of the reported composition yields three …

Changes In The Photochemical Environment Of The Temperate North Pacific Troposphere In Response To Increased Asian Emissions, D. D. Parrish, E. J. Dunlea, E. L. Atlas, S. Schauffler, Stephen G. Donnelly Ph.D., V. Stroud, A. H. Goldstein, D. B. Millet, M. Mckay, D. A. Jaffe, H. U. Price, P. G. Hess, F. Flocke, J. M. Roberts

Chemistry Faculty Publications

Measurements during the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2K2) field study characterized the springtime, eastern Pacific ozone distribution at two ground sites, from the National Oceanic and Atmospheric Administration WP-3D aircraft, and from a light aircraft operated by the University of Washington. D. Jaffe and colleagues compared the 2002 ozone distribution with measurements made in the region over the two previous decades and show that average ozone levels over the eastern midlatitude Pacific have systematically increased by ∼10 ppbv in the last two decades. Here we provide substantial evidence that a marked change in the photochemical environment in …

Multiscale Simulations Of Tropospheric Chemistry In The Eastern Pacific And On The U.S. West Coast During Spring 2002, Youhua Tang, Gregory R. Carmichael, Larry W. Horowitz, Itsushi Uno, Jung Hun Woo, David G. Streets, Donald Dabdub, Gakuji Kurata, Adrian Sandu, James Allan, Elliot Atlas, Frank Flocke, Lewis Gregory Huey, Roger O. Jakoubek, Dylan B. Millet, Patricia K. Quinn, James M. Roberts, Douglas R. Worsnop, Allen Goldstein, Stephen G. Donnelly Ph.D., Sue Schauffler, Verity Stroud, Kristen Johnson, Melody A. Avery, Hanwant B. Singh, Eric C. Apel

Chemistry Faculty Publications

Regional modeling analysis for the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2K2) experiment over the eastern Pacific and U.S. West Coast is performed using a multiscale modeling system, including the regional tracer model Chemical Weather Forecasting System (CFORS), the Sulfur Transport and Emissions Model 2003 (STEM-2K3) regional chemical transport model, and an off-line coupling with the Model of Ozone and Related Chemical Tracers (MOZART) global chemical transport model. CO regional tracers calculated online in the CFORS model are used to identify aircraft measurement periods with Asian influences. Asian-influenced air masses measured by the National Oceanic and Atmospheric Administration (NOAA) …

Chemical Composition Of Air Masses Transported From Asia To The U.S. West Coast During Itct 2k2: Fossil Fuel Combustion Versus Biomass-Burning Signatures, J. A. De Gouw, O. R. Cooper, C. Warneke, P. K. Hudson, F. C. Fehsenfeld, J. S. Holloway, G. Hübler, Jr K. Nicks, J. B. Nowak, D. D. Parrish, T. B. Ryerson, E. L. Atlas, Stephen G. Donnelly Ph.D., S. M. Schauffler, V. Stroud, K. Johnson, G. R. Carmichael, D. G. Streets

Chemistry Faculty Publications

As part of the Intercontinental Transport and Chemical Transformation experiment in 2002 (ITCT 2K2), a National Oceanic and Atmospheric Administration (NOAA) WP-3D research aircraft was used to study the long-range transport of Asian air masses toward the west coast of North America. During research flights on 5 and 17 May, strong enhancements of carbon monoxide (CO) and other species were observed in air masses that had been transported from Asia. The hydrocarbon composition of the air masses indicated that the highest CO levels were related to fossil fuel use. During the flights on 5 and 17 May and other days, …

Multiple Testing Procedures For Controlling Tail Probability Error Rates, Sandrine Dudoit, Mark J. Van Der Laan, Merrill D. Birkner

U.C. Berkeley Division of Biostatistics Working Paper Series

The present article discusses and compares multiple testing procedures (MTP) for controlling Type I error rates defined as tail probabilities for the number (gFWER) and proportion (TPPFP) of false positives among the rejected hypotheses. Specifically, we consider the gFWER- and TPPFP-controlling MTPs proposed recently by Lehmann & Romano (2004) and in a series of four articles by Dudoit et al. (2004), van der Laan et al. (2004b,a), and Pollard & van der Laan (2004). The former Lehmann & Romano (2004) procedures are marginal, in the sense that they are based solely on the marginal distributions of the test statistics, i.e., …

Azimuthal Anisotropy And Correlations At Large Transverse Momenta In P+P And Au+Au Collisions At √SNn=200 Gev, Star Collaboration, T.D. Gutierrez

Physics

Results on high transverse momentum charged particle emission with respect to the reaction plane are presented for Au+Au collisions at √s_NN=200  GeV. Two- and four-particle correlations results are presented as well as a comparison of azimuthal correlations in Au+Au collisions to those in p+p at the same energy. The elliptic anisotropy v₂ is found to reach its maximum at pt∼3  GeV/c, then decrease slowly and remain significant up to p_t≈7–10  GeV/c. Stronger suppression is found in the back-to-back high-p_t particle correlations for particles emitted out of plane compared to those emitted in plane. The …

Chemical Analyses In Support Of Yucca Mountain Studies, Jeanette Daniels, Klaus J. Stetzenbach, Drew Coleman, Amy J. Smiecinski, Raymond E. Keeler

Publications (YM)

The objective of this task “Chemical Analyses in Support of Yucca Mountain Studies” is to provide the Department of Energy (DOE) with data and reports from comprehensive chemical analyses of waters sampled from the wells of the Nye County Early Warning Drilling Program (NCEWDP), the Inyo County’s Drilling Program, and the Nye county Tracer Test. In addition, this task will be used to provide other laboratory support needs as they arise within the Yucca Mountain Project. This support is provided by the Harry Reid Center for Environmental Studies (HRC) at University of Nevada, Las Vegas (UNLV), which is part of …

Optimal Cooling Strategies For Magnetically Trapped Atomic Fermi-Bose Mixtures, Michael Brown-Hayes, Roberto Onofrio

Dartmouth Scholarship

We discuss cooling efficiency for different-species Fermi-Bose mixtures in magnetic traps. A better heat capacity matching between the two atomic species is achieved by a proper choice of the Bose cooler and the magnetically trappable hyperfine states of the mixture. When a partial spatial overlap between the two species is also taken into account, the deepest Fermi degeneracy is obtained for an optimal value of the trapping frequency ratio between the two species. This can be achieved by assisting the magnetic trap with a deconfining light beam, as shown in the case of fermionic 6Li mixed with 23Na, 87Rb, and …

Technical Memorandum: Taunton River Assessment, Massachusetts Riverways Program

Reference Documents

No abstract provided.

Ranking Usrds Provider-Specific Smrs From 1998-2001, Rongheng Lin, Thomas A. Louis, Susan M. Paddock, Greg Ridgeway

Johns Hopkins University, Dept. of Biostatistics Working Papers

Provider profiling (ranking, "league tables") is prevalent in health services research. Similarly, comparing educational institutions and identifying differentially expressed genes depend on ranking. Effective ranking procedures must be structured by a hierarchical (Bayesian) model and guided by a ranking-specific loss function, however even optimal methods can perform poorly and estimates must be accompanied by uncertainty assessments. We use the 1998-2001 Standardized Mortality Ratio (SMR) data from United States Renal Data System (USRDS) as a platform to identify issues and approaches. Our analyses extend Liu et al. (2004) by combining evidence over multiple years via an AR(1) model; by considering estimates …

Referent Selection Strategies In Case-Crossover Analyses Of Air Pollution Exposure Data: Implications For Bias, Holly Janes, Lianne Sheppard, Thomas Lumley

UW Biostatistics Working Paper Series

The case-crossover design has been widely used to study the association between short term air pollution exposure and the risk of an acute adverse health event. The design uses cases only, and, for each individual, compares exposure just prior to the event with exposure at other control, or “referent” times. By making within-subject comparisons, time invariant confounders are controlled by design. Even more important in the air pollution setting is that, by matching referents to the index time, time varying confounders can also be controlled by design. Yet, the referent selection strategy is important for reasons other than control of …

Comparisons Of Long-Term Trends And Variability In The Middle Atmosphere, Troy Wynn, Joshua P. Herron, Vincent B. Wickwar

Posters

The USU Rayleigh Lidar (41.74°N 111.81°W) has been regularly used to measure temperatures in the middle atmosphere from 45 to 90 km. It is well suited for nightly observation; provides excellent vertical temperature resolution; and does not need external calibration. It began operation in August 1993 and a dataset spanning more than ten years has been collected. The analysis here includes 593 nightly temperature profiles from September 1993 through July 2003.

With many sources of variation in the atmosphere, all temperature effects cannot be easily detected. The largest source of temperature variation, and the easiest to measure, is the annual …

Certalert: Deer Hazard To Aircraft And Deer Fencing

Other Bird Strike and Aviation Materials

Elevated deer populations in the United States represent an increasingly serious threat to both Commercial and General Aviation Aircraft. It is currently estimated that there over 26 million deer in the United States. Because of increasing urbanization and rapidly expanding deer populations, deer are adapting to human environments, especially around airports, where they often find food and shelter. From 1990 to 2004, over 650 deer-aircraft collisions were reported to the Federal Aviation Administration (FAA). Of these reports, over 500 indicated the aircraft was damaged as a result of the collision.

In light of recent incidents where a Learjet landing at …

The Strange Physics Of Low Frequency Mirror Mode Turbulence In The High Temperature Plasma Of The Magnetosheath, R. A. Treumann, C. H. Jaroschek, O. D. Constantinescu, R. Nakamura

Dartmouth Scholarship

Mirror mode turbulence is the lowest frequency perpendicular magnetic excitation in magnetized plasma proposed already about half a century ago by Rudakov and Sagdeev (1958) and Chandrasekhar et al. (1958) from fluid theory. Its experimental verification required a relatively long time. It was early recognized that mirror modes for being excited require a transverse pressure (or temperature) anisotropy. In principle mirror modes are some version of slow mode waves. Fluid theory, however, does not give a correct physical picture of the mirror mode. The linear infinitesimally small amplitude physics is described correctly only by including the full kinetic theory and …

Medical Image Processing Using Transient Fourier Holography In Bacteriorhodopsin Films, Sri-Rajasekhar Kothapalli, Pengfei Wu, Chandra S. Yelleswarapu, D.V.G.L.N. Rao

Physics Faculty Publications

Real time image processing is demonstrated by recording and reconstructing the transient photoisomerizative grating formed in the bR film using Fourier holography. Desired spatial frequencies including both high and low band in the object beam are reconstructed by controlling the reference beam intensity. The results are in agreement with a theoretical model based on photoisomerization grating. We exploit this technique to process mammograms in real-time for identification of microcalcifications buried in the soft tissue for early detection of breast cancer. A feature of the technique is the ability to transient display of selected spatial frequencies in the reconstructing process which …

Sm2Nairo6, A Monoclinically Distorted Double Perovskite, Samuel J. Mugavero Iii, Irina V. Puzdrjakova, Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

Single crystals of the lanthanide-containing iridate, disamarium sodium iridium hexaoxide, Sm₂NaIrO₆, were prepared via high-temperature flux growth and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/n and is a double perovskite, consisting of a 1:1 ordered rock-salt-type lattice of corner-shared NaO₆ and IrO₆ distorted octahedra. Samarium occupies the eightfold coordination site generated by the connectivity of the octahedra.

Atmospheric Circulation And Cyclone Frequency Variations Linked To The Primary Modes Of Greenland Snow Accumulation, Jeffrey C. Rogers, Deborah J. Bathke, Ellen Mosley-Thompson, Sheng-Hung Wang

School of Natural Resources: Faculty Publications

Data from 34 Greenland firn cores, extending from 1982 to 1996, are used to identify spatial accumulation variability patterns and their associated atmospheric circulation and cyclone frequencies. The first principal component, representing west-central Greenland accumulation, is correlated to NAO variability, having increased southwesterly (northeasterly) flow over that area during high (low) accumulation winters. The flow is linked to a relative increase in cyclone activity on the west central region of the ice sheet during high accumulation periods. The second principal component represents accumulation over southeastern Greenland where strong westerly flow leads to high accumulation and an increase in lee cyclones …

A Neptune-Mass Planet Orbiting The Nearby M Dwarf Gj 436, R. Paul Butler, Steve S. Vogt, Geoffrey W. Marcy, Debra A. Fischer, Jason T. Wright, Gregory W. Henry, Gregory Laughlin, Jack J. Lissauer

Information Systems and Engineering Management Research Publications

We report precise Doppler measurements of GJ 436 (M2.5 V) obtained at Keck Observatory. The velocities reveal a planetary companion with orbital period of 2.644 days, eccentricity of 0.12 (consistent with zero), and velocity semiamplitude of K = 18.1 m s-1. The minimum mass (M sin i) for the planet is 0.067MJup = 1.2MNep = 21MEarth, making it the lowest mass exoplanet yet found around a main-sequence star and the first candidate in the Neptune-mass domain. GJ 436 (mass = 0.41 M☉) is only the second M dwarf found to harbor a planet, joining the two-planet system around GJ 876. …

The Initial-Final Mass Relationship: Spectroscopy Of White Dwarfs In Ngc 2099 (M37), Jasonjot Singh Kalirai, Ted Von Hippel, Et Al.

Publications

We present new observations of very faint white dwarfs (WDs) in the rich open star cluster NGC 2099 (M37). Following deep, wide-field imaging of the cluster using the Canada-France-Hawaii Telescope, we have now obtained spectroscopic observations of candidate WDs using both the Gemini Multi-Object Spectrograph on Gemini North and the Low-Resolution Imaging Spectrometer on Keck. Of our 24 WD candidates (all fainter than V = 22.4), 21 are spectroscopically confirmed to be bona fide WDs, four or five of which are most likely field objects. Fitting 18 of the 21 WD spectra with model atmospheres, we find that most WDs …

Multiple Testing Procedures: R Multtest Package And Applications To Genomics, Katherine S. Pollard, Sandrine Dudoit, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics. The current version of multtest provides MTPs for tests concerning means, differences in means, and regression parameters in linear and Cox proportional hazards models. Procedures are provided to control Type I error rates defined as tail probabilities for arbitrary functions of the numbers of false positives and rejected hypotheses. These error rates include tail probabilities …

Semiparametric Regression In Capture-Recapture Modelling, O. Gimenez, C. Barbraud, Ciprian M. Crainiceanu, S. Jenouvrier, B.T. Morgan

Johns Hopkins University, Dept. of Biostatistics Working Papers

Capture-recapture models were developed to estimate survival using data arising from marking and monitoring wild animals over time. Variation in the survival process may be explained by incorporating relevant covariates. We develop nonparametric and semiparametric regression models for estimating survival in capture-recapture models. A fully Bayesian approach using MCMC simulations was employed to estimate the model parameters. The work is illustrated by a study of Snow petrels, in which survival probabilities are expressed as nonlinear functions of a climate covariate, using data from a 40-year study on marked individuals, nesting at Petrels Island, Terre Adelie.

Quantum Entanglement Of Anisotropic Magnetic Nanodots, Ralph Skomski, Andrei Y. Istomin, Anthony F. Starace, David J. Sellmyer

Department of Physics and Astronomy: Faculty Publications

Anisotropic magnetic nanodots are promising physical realizations of qubits for quantum computing at finite temperature owing to their well-separated low-lying energy levels and scalability. The entanglement of two interacting magnetic nanodots is investigated and shown both analytically and numerically to be resonantly dependent on their interaction strength and on differences in their properties. These results provide criteria for fabricating and coupling magnetic nanodots so that their low-lying eigenstates can be significantly entangled.

Anchoring The Potential Energy Surface Of The Cyclic Water Trimer, Julie A. Andersen, Kelly Crager, Lisa Fedoroff, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

Six cyclic stationary points on the water trimer potential energy surface have been fully optimized at the MP2 level with the aug-cc-pVQZ basis set. In agreement with previous work, harmonic vibrational frequencies indicate that two structures are minima, three are transition states connecting minima on the surface while the remaining stationary point is a higher-order saddle point. The 1-and n-particle limits of the electronic energies of each of these six structures were estimated by systematically varying both the basis sets and theoretical methods. The former limit was approached with the cc-pVXZ and aug-cc-pVXZ families of basis sets (X=2-7) while MP2, …

Atomic Force Microscope Conductivity Measurements Of Single Ferritin Molecules, Degao Xu

Theses and Dissertations

Conductive Atomic Force Microscope (c-AFM) was used to measure the conductivity of single horse spleen ferritin (HoSF) and azotobacter vinelandii bacterial ferritin (AvBF) molecules deposited on flat gold surfaces. A 500 micron diameter gold ball was also used as a contact probe to measure the conductivity of a thin film of ferritin molecules. The average current measured for holo HoSF was 13 and 5 times larger than that measured for apo HoSF as measured by c-AFM at 1V and gold ball at 2V and respectively, which indicates that the core of ferritin is more conductive than the protein shell and …

Probabilistic Risk Assessment For Snails, Slugs, And Endangered Honeycreepers In Diphacinone Rodenticide Baited Areas On Hawaii. Usa, John J. Johnston, William C. Pitt, Robert T. Sugihara, John D. Eisemann, Thomas M. Primus, Melvin J. Holmes, Joe Crocker, Andy Hart

United States Department of Agriculture Wildlife Services: Staff Publications

Three probabilistic models were developed for characterizing the risk of mortality and subacute coagulopathy to Poouli, an endangered nontarget avian species, in broadcast diphacinone-baited areas on Hawaii, USA. For single-day exposure, the risk of Poouli mortality approaches 0. For 5-d exposure, the mean probability of mortality increased to 3% for adult and 8% for juvenile Poouli populations. For Poouli that consume snails containing diphacinone residues for 14 d, the model predicted increased levels of coagulopathy for 0.42 and 11% of adult and juvenile Poouli populations, respectively. Worst-case deterministic risk characterizations predicted acceptable levels of risk for nonthreatened or endangered species …

Semi-Parametric Single-Index Two-Part Regression Models, Xiao-Hua Zhou, Hua Liang

UW Biostatistics Working Paper Series

In this paper, we proposed a semi-parametric single-index two-part regression model to weaken assumptions in parametric regression methods that were frequently used in the analysis of skewed data with additional zero values. The estimation procedure for the parameters of interest in the model was easily implemented. The proposed estimators were shown to be consistent and asymptotically normal. Through a simulation study, we showed that the proposed estimators have reasonable finite-sample performance. We illustrated the application of the proposed method in one real study on the analysis of health care costs.

Femtosecond Laser-Induced Formation Of Submicrometer Spikes On Silicon In Water, M. Y. Shen, Catherine Hirshfeld Crouch, J. E. Carey, E. Mazur

Physics & Astronomy Faculty Works

We fabricate submicrometer silicon spikes by irradiating a siliconsurface that is submerged in water with 400 nm, 100 fs laser pulses. These spikes are less than a micrometer tall and about 200 nm wide—one to two orders of magnitude smaller than the microspikes formed by laser irradiation of silicon in gases or vacuum. Scanning electron micrographs of the surface show that the formation of the spikes involves a combination of capillary waves on the molten siliconsurface and laser-induced etching of silicon. Chemical analysis and scanning electron microscopy of the spikes show that they are composed of silicon with a 20-nm-thick …

Parallel Writing On Zirconium Nitride Thin Films By Local Oxidation Nanolithography, N. Farkas, J. R. Comer, G. Zhang, Edward A. Evans, R. D. Ramsier, S. Wight, J. A. Dagata

Chemical, Biomolecular, and Corrosion Engineering Faculty Research

Parallel pattern transfer of submicrometer-scale oxide features onto zirconium nitride thin films is reported. The oxidation reaction was verified by Auger microprobe analysis and secondary ion mass spectrometry. Oxide features of similar to70 nm in height can be formed and selectively etched in a dilute aqueous hydrogen fluoride solution. This provides an interesting route to potential new applications for high-melting point, biocompatible surfaces that possess small feature sizes with controlled geometries. (C) 2004 American Institute of Physics.

Hyperbolic Sets That Are Not Locally Maximal, Todd L. Fisher

Faculty Publications

This paper addresses the following topics relating to the structure of hyperbolic sets: First, hyperbolic sets that are not contained in locally maximal hyperbolic sets. Second, the existence of a Markov partition for a hyperbolic set. We construct new examples of hyperbolic sets which are not contained in locally maximal hyperbolic sets. The first example is robust under perturbations and can be constructed on any compact manifold of dimension greater than one. The second example is robust, topologically transitive, and constructed on a 4-dimensional manifold. The third example is volume preserving and constructed on R4. We show that every hyperbolic …

Damage Reduction Estimates And Benefit-Cost Ratios For Feral Swine Control From The Last Remnant Of A Basin Marsh System In Florida, Richard M. Engeman, Henry T. Smith, Robert Severson, Mary Ann Severson, John Woolard, Stephanie A. Shwiff, Bernice Constantin, Daniel Griffin

United States Department of Agriculture Wildlife Services: Staff Publications

The introduction of swine (Sus scrofa) has adversely affected the environment of many natural habitats throughout the world. Basin marshes are dwindling ecosystems in Florida that are especially vulnerable to damage by feral swine. In January 2003, the estimated amount of swine damage to the exposed portion of the last remnant of a basin marsh system in Savannas Preserve State Park (SPSP) was 19% (an area of 5 ha). Economic valuations for the swine damage were based on the monetary amounts that wetland regulators have allowed permit applicants to spend in mitigation attempts to replace lost wetland resources. …