Index Catalog // ScholarsArchive@OSU

Quantifying predator dependence in the functional response of generalist predators

Creator:: Novak, Mark, Wolf, Christopher, Coblentz, Kyle E., and Shepard, Isaac D.
Abstract:: A long-standing debate concerns how functional responses are best described. Theory suggests that ratio dependence is consistent with many food web patterns left unexplained by the simplest prey-dependent models. However, for logistical reasons, ratio dependence and predator dependence more generally have seen infrequent empirical evaluation and then only so in...
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Full Text:: predators Mark Novak,1* Christopher Wolf,2 Kyle E. Coblentz1 and Isaac D. Shepard1† Abstract A long

Influence of sediment characteristics on the composition of soft-sediment intertidal communities in the northern Gulf of Mexico

Creator:: Coblentz, Kyle E., Henkel, Jessica R., Sigel, Bryan J., and Taylor, Caz M.
Abstract:: Benthic infaunal communities are important components of coastal ecosystems. Understanding the relationships between the structure of these communities and characteristics of the habitat in which they live is becoming progressively more important as coastal systems face increasing stress from anthropogenic impacts and changes in climate. To examine how sediment characteristics...
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Counterflow ignition of n-butanol at atmospheric and elevated pressures

Creator:: Brady, Kyle B., Hui, Xin, Sung, Chih-Jen, and Niemeyer, Kyle E.
Abstract:: Critical to the development of predictive combustion models is a robust understanding of the coupled effects of chemical kinetics and convective-diffusive transport at both atmospheric and elevated pressures. The present study describes a new variable-pressure non-premixed counterflow ignition experiment designed to address the need for well-characterized reference data to validate...
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Recent progress and challenges in exploiting graphics processors in computational fluid dynamics

Creator:: Niemeyer, Kyle E. and Sung, Chih-Jen
Abstract:: The progress made in accelerating simulations of fluid flow using GPUs, and the challenges that remain, are surveyed. The review first provides an introduction to GPU computing and programming, and discusses various considerations for improved performance. Case studies comparing the performance of CPU- and GPUbased solvers for the Laplace and...
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Full Text:: fluid dynamics Kyle E. Niemeyer · Chih-Jen Sung Received: date / Accepted: date Abstract The progress

Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs

Creator:: Niemeyer, Kyle E. and Sung, Chih-Jen
Abstract:: The chemical kinetics ODEs arising from operator-split reactive-flow simulations were solved on GPUs using explicit integration algorithms. Nonstiff chemical kinetics of a hydrogen oxidation mechanism (9 species and 38 irreversible reactions) were computed using the explicit fifth-order Runge–Kutta–Cash–Karp method, and the GPU-accelerated version performed faster than single- and six-core CPU...
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Full Text:: simulations using GPUs Kyle E. Niemeyera,b,1,∗, Chih-Jen Sungb aDepartment of Mechanical and Aerospace

Accelerating solutions of one-dimensional unsteady PDEs with GPU-based swept time-space decomposition

Creator:: Magee, Daniel J. and Niemeyer, Kyle E.
Abstract:: The expedient design of precision components in aerospace and other high-tech industries requires simulations of physical phenomena often described by partial differential equations (PDEs) without exact solutions. Modern design problems require simulations with a level of resolution difficult to achieve in reasonable amounts of time-even in effectively parallelized solvers. Though...
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Full Text:: with GPU-based swept time-space decomposition Daniel J. Mageea, Kyle E. Niemeyera,∗ aSchool of

Reduced Chemistry for a Gasoline Surrogate Valid at Engine-Relevant Conditions

Creator:: Niemeyer, Kyle E. and Sung, Chih-Jen
Abstract:: A detailed mechanism for the four-component RD387 gasoline surrogate developed by Lawrence Livermore National Laboratory has shown good agreement with experiments in engine-relevant conditions. However, with 1388 species and 5933 reversible reactions, this detailed mechanism is far too large to use in practical engine simulations. Therefore, reduction of the detailed...
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Full Text:: Reduced chemistry for a gasoline surrogate valid at engine-relevant conditions Kyle E. Niemeyer∗,† and

Mechanism reduction for multicomponent surrogates: A case study using toluene reference fuels

Creator:: Niemeyer, Kyle E. and Sung, Chih-Jen
Abstract:: Strategies and recommendations for performing skeletal reductions of multicomponent surrogate fuels are presented, through the generation and validation of skeletal mechanisms for a three-component toluene reference fuel. Using the directed relation graph with error propagation and sensitivity analysis method followed by a further unimportant reaction elimination stage, skeletal mechanisms valid...
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Transmission Eigenvalues and Thermoacoustic Tomography

Creator:: Finch, David and Hickmann, Kyle S.
Abstract:: The spectrum of the interior transmission problem is related to the unique determination of the acoustic properties of a body in thermoacoustic imaging. Under a non-trapping hypothesis, we show that sparsity of the interior transmission spectrum implies a range separation condition for the thermoacoustic operator. In odd dimensions greater than...
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Full Text:: Transmission Eigenvalues and Thermoacoustic Tomography David Finch ∗ Kyle S. Hickmann † June 23, 2013

Measurement-induced decoherence and information in double-slit interference

Creator:: Kincaid, Joshua, McLelland, Kyle, and Zwolak, Michael
Abstract:: The double slit experiment provides a classic example of both interference and the effect of observation in quantum physics. When particles are sent individually through a pair of slits, a wave-like interference pattern develops, but no such interference is found when one observes which “path” the particles take. We present...
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Full Text:: Joshua Kincaida) and Kyle McLelland Department of Physics, Oregon State University, Corvallis, Oregon

Computational upscaling of inertia effects from porescale to mesoscale

Creator:: Peszynska, Malgorzata, Trykozko, Anna, and Augustson, Kyle
Abstract:: This paper is included in the Proceedings, Part 1, of the International Conference on Computational Science 2009 (ICCS 2009) held in Baton Rouge, LA, USA, May 25-27, 2009.
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Full Text:: porescale to mesoscale Ma lgorzata Peszyńska1, Anna Trykozko2, and Kyle Augustson3 1 Oregon State

Evaluation of Heat and Mass Transfer Models for Sizing Low-Temperature Kalina Cycle Microchannel Condensers

Creator:: Fronk, Brian M. and Zada, Kyle R.
Abstract:: Waste heat driven ammonia/water Kalina cycles have shown promise for improving the efficiency of electricity production from low-temperature reservoirs (T < 150 °C). However, there has been limited application of these systems to utilize widely available, disperse, waste heat streams for smaller scale power production (1–10 kWe). Factors limiting increased deployment of these...
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Full Text:: Kalina Cycle Microchannel Heat Exchanger Condensers Authors: Brian M. Fronk and Kyle R

Post-fire logging produces minimal persistent impacts on understory vegetation in northeastern Oregon, USA

Creator:: Peterson, David W. and Dodson, Erich Kyle
Abstract:: Post-fire forest management commonly requires accepting some negative ecological impacts from management activities in order to achieve management objectives. Managers need to know, however, whether ecological impacts from post-fire management activities are transient or cause long-term ecosystem degradation. We studied the long-term response of understory vegetation to two post-fire logging...
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Full Text:: Elsevier B.V. ⇑ Corresponding author at: 1133 North Western Avenue, Wenatchee, WA 98801, USA. E-mail

Behavior of cross-laminated timber diaphragm connections with self-tapping screws

Creator:: Sullivan, Kyle, Miller, Thomas H., and Gupta, Rakesh
Abstract:: Monotonic and cyclic tests were carried out to determine strength and stiffness characteristics of 2.44 m (8 ft) long shear connections with 8 mm and 10 mm diameter self-tapping screws. The goal of this research is to compare test values of cross-laminated timber (CLT) diaphragm connections in seismic force-resisting systems...
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Full Text:: connections with self-tapping screws Kyle Sullivana,⁎, Thomas H. Millerb,⁎, Rakesh Guptac a StructureCraft

Investigation of the LTC fuel performance index for oxygenated reference fuel blends

Creator:: Niemeyer, Kyle E., Daly, Shane R., Cannella, William J., and Hagen, Christopher L.
Abstract:: A new metric for ranking the suitability of fuels in LTC engines was recently introduced, based on the fraction of potential fuel savings achieved in the FTP-75 light-duty vehicle driving cycle. In the current study, this LTC fuel performance index was calculated computationally and analyzed for a number of fuel...
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Full Text:: blends Kyle E. Niemeyera,∗, Shane R. Dalya, William J. Cannellab, Christopher L. Hagenc aSchool of

Predicting fuel research octane number using Fourier-transform infrared absorption spectra of neat hydrocarbons

Creator:: Daly, Shane R., Niemeyer, Kyle E., Cannella, William J., and Hagen, Christopher L.
Abstract:: Liquid transportation fuels require costly and time-consuming tests to characterize metrics, such as Research Octane Number (RON) for gasoline. If fuel sale restrictions requiring use of standard Cooperative Fuel Research (CFR) testing procedures do not apply, these tests may be avoided by using multivariate statistical models to predict RON and...
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Full Text:: -transform infrared absorption spectra of neat hydrocarbons Shane R. Dalya, Kyle E. Niemeyera, William J

A Novel Fuel Performance Index for Low-Temperature Combustion Engines Based on Operating Envelopes in Light-Duty Driving Cycle Simulations

Creator:: Niemeyer, Kyle E., Daly, Shane R., Cannella, William J., and Hagen, Christopher L.
Abstract:: Low-temperature combustion (LTC) engine concepts such as homogeneous charge compression ignition (HCCI) offer the potential of improved efficiency and reduced emissions of NOₓ and particulates. However, engines can only successfully operate in HCCI mode for limited operating ranges that vary depending on the fuel composition. Unfortunately, traditional ratings such as...
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Full Text:: For LTC Engines Based On Operating Envelopes In Light-Duty Driving Cycle Simulations Kyle E

Using SIMD and SIMT vectorization to evaluate sparse chemical kinetic Jacobian matrices and thermochemical source terms

Creator:: Curtis, Nicholas J., Niemeyer, Kyle E., and Sung, Chih-Jen
Abstract:: Accurately predicting key combustion phenomena in reactive-flow simulations, e.g., lean blow-out, extinction/ignition limits and pollutant formation, necessitates the use of detailed chemical kinetics. The large size and high levels of numerical stiffness typically present in chemical kinetic models relevant to transportation/power-generation applications make the efficient evaluation/factorization of the chemical kinetic...
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Full Text:: chemical kinetic Jacobian matrices and thermochemical source terms Nicholas J. Curtisa,∗, Kyle E

Effects of fuel content and density on the smoldering characteristics of cellulose and hemicellulose

Creator:: Smucker, Benjamin D., Mulky, Tejas C., Cowan, Daniel A., Niemeyer, Kyle E., and Blunck, David L.
Abstract:: Smoldering combustion in wildland fires poses hazards for both ecosystems and humans by destroying biomass, transitioning to flaming combustion, and releasing significant quantities of pollution. Understanding the parameters that control smoldering is necessary to help predict and potentially mitigate these hazards. A challenge in identifying these parameters is the wide...
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Full Text:: Characteristics of Cellulose and Hemicellulose Benjamin D. Smuckera, Tejas C. Mulkya, Daniel A. Cowana, Kyle E

Development of efficient and accurate skeletal mechanisms for hydrocarbon fuels and kerosene surrogate

Creator:: Zhong, Fengquan, Ma, Sugang, Zhang, Xinyu, Sung, Chih-Jen, and Niemeyer, Kyle E.
Abstract:: In this paper, the methodology of the directed relation graph with error propagation and sensitivity analysis (DRGEPSA), proposed by Niemeyer et al. [Combustion and Flame 157 2010) 1760–1770], and its differences to the original directed relation graph method are described. Using DRGEPSA, the detailed mechanism of ethylene containing 71 species...
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Full Text:: Kyle E. Niemeyer School of Mechanical, Industrial, and Manufacturing Engineering, Oregon State

Evaluating relocation extent versus covariate resolution in habitat selection models across spatiotemporal scales

Creator:: Nelson, Peter R., Joly, Kyle, Roland, Carl A., and McCune, Bruce
Abstract:: Many habitat selection studies have focused on the importance of spatiotemporal scales and sample size, yet often hidden within is a trade-off between using more animal locations versus more predictive covariates. Few have evaluated the outcome of choosing between these two different paths even though the trade-off can have significant...
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Full Text:: covariate resolution in habitat selection models across spatiotemporal scales Peter R. Nelson a,b,* , Kyle

Numbering-Up of Microscale Devices for Megawatt-Scale Supercritical Carbon Dioxide Concentrating Solar Power Receivers

Creator:: Zada, Kyle R., Hyder, Matthew B., Drost, M. Kevin, and Fronk, Brian M.
Abstract:: Concentrated solar power (CSP) plants have the potential to reduce the consumption of nonrenewable resources and greenhouse gas emissions in electricity production. In CSP systems, a field of heliostats focuses solar radiation on a central receiver, and energy is then transferred to a thermal power plant at high temperature. However,...
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Full Text:: Carbon Dioxide Concentrating Solar Power Receivers Authors: Kyle R. Zada, Matthew B

Fatigue Crack Growth Mechanisms for Nickel-based Superalloy Haynes 282 at 550-750° C

Creator:: Rozman, Kyle A., Kruzic, Jamie J., Sears, John S., and Hawk, Jeffrey A.
Abstract:: The fatigue crack growth rates for nickel-based superalloy Haynes 282 were measured at 550, 650, and 750 °C using compact tension specimens with a load ratio of 0.1 and cyclic loading frequencies of 25 and 0.25 Hz. The crack path was observed to be primarily transgranular for all temperatures, and...
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Full Text:: Crack Growth Mechanisms for Nickel-based Superalloy Haynes 282 at 550-750 �C Kyle A. Rozman, Jamie J

Experimental investigation of supercritical carbon dioxide in horizontal microchannels with non-uniform heat flux boundary conditions

Creator:: Jajja, Saad A., Zada, Kyle R., and Fronk, Brian M.
Abstract:: Supercritical carbon dioxide (sCO2) experiences a drastic change in its thermophysical properties near the thermodynamic critical point. A non-linear thermophysical property variation can influence the heat transfer behavior of sCO2 which is not predicted well by conventional single phase heat transfer theory. This can become a major hindrance in the...
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Full Text:: Horizontal Microchannels with Non-Uniform Heat Flux Boundary Conditions Saad A. Jajjaa, Kyle R. Zadaa

How Programmers Debug, Revisited: An Information Foraging Theory Perspective

Creator:: Lawrance, Joseph, Bogart, Christopher, Burnett, Margaret, Bellamy, Rachel, Rector, Kyle, and Fleming, Scott D.
Abstract:: Many theories of human debugging rely on complex mental constructs that offer little practical advice to builders of software engineering tools. Although hypotheses are important in debugging, a theory of navigation adds more practical value to our understanding of how programmers debug. Therefore, in this paper, we reconsider how people...
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Full Text:: !E&.(-$:$64*4&!G-3H&,%34

Bathymetry Estimation Using Drifter-Based Velocity Measurements on the Kootenai River, Idaho

Creator:: Landon, Kyle C., Wilson, Greg W., Özkan-Haller, H. Tuba, and MacMahan, Jamie H.
Abstract:: Velocity measurements from drifter GPS records are used in an ensemble-based data assimilation technique to extract the river bathymetry. The method is tested on a deep meandering reach and a shallow braided reach of the Kootenai River in Idaho. The Regional Ocean Modeling System (ROMS) is used to model numerous...
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Full Text:: the Kootenai River, Idaho Landon, Kyle C., Greg W. Wilson, H. Tuba Özkan-Haller, Jamie H. MacMahan

Phenotypic transition of microglia into astrocyte-like cells associated with disease onset in a model of inherited ALS

Creator:: Trias, Emiliano, Díaz-Amarilla, Pablo, Olivera-Bravo, Silvia, Isasi, Eugenia, Drechsel, Derek A., Lopez, Nathan, Bradford, C. Samuel, Ireton, Kyle E., Beckman, Joseph S., and Barbeito, Luis
Abstract:: Microglia and reactive astrocytes accumulate in the spinal cord of rats expressing the Amyotrophic lateral sclerosis (ALS)-linked SOD1ᴳ⁹³ᴬ mutation. We previously reported that the rapid progression of paralysis in ALS rats is associated with the appearance of prolifer- ative astrocyte-like cells that surround motor neurons. These cells, designated as Aberrant...
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Full Text:: , Derek A. Drechsel 2,3 , Nathan Lopez2,3 , C. Samuel Bradford2,3 , Kyle E. Ireton2,3,5 , Joseph S

The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii

Creator:: Lowry, David B., Hernandez, Kyle, Taylor, Samuel H., Meyer, Eli, Logan, Tierney L., Barry, Kerrie W., Chapman, Jarrod A., Rokhsar, Daniel S., Schmutz, Jeremy, and Juenger, Thomas E.
Abstract:: The process of plant speciation often involves the evolution of divergent ecotypes in response to differences in soil water availability between habitats. While the same set of traits is frequently associated with xeric/mesic ecotype divergence, it is unknown whether those traits evolve independently or if they evolve in tandem as...
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Full Text:: ecotypes of Panicum hallii Lowry, D. B., Hernandez, K., Taylor, S. H., Meyer, E., Logan, T. L., Barry, K

Life and Death Sounds of Iceberg A53a

Creator:: Dziak, Robert P., Fowler, Matthew J., Matsumoto, Haruyoshi, Bohnenstiehl, DelWayne R., Park, Minkyu, Warren, Kyle, and Lee, Won Sang
Abstract:: Atmospheric and surface ocean temperatures in the Antarctic Peninsula region have increased by a few degrees Celsius over the last few decades, and they are the most rapid changes recorded in the Southern Hemisphere during this time period (Cook et al., 2005; Meredith and King, 2005). Associated with this ongoing...
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Full Text:: Oceanography | Vol. 26, No. 210 R i p C u R R e N t | N e w s i N O C e a N O g R a p h y Atmospheric

Increase in cellular triacylglycerol content and emergence of large ER-associated lipid droplets in the absence of CDP-DG synthase function

Creator:: He, Yue, Yam, Candice, Pomraning, Kyle, Chin, Jacqueline S. R., Yew, Joanne Y., Freitag, Michael, and Oliferenko, Snezhana
Abstract:: Excess fatty acids and sterols are stored as triacylglycerols and sterol esters in specialized cellular organelles, called lipid droplets. Understanding what determines the cellular amount of neutral lipids and their packaging into lipid droplets is of fundamental and applied interest. Using two species of fission yeast, we show that cycling...
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Full Text:: function Yue Hea,b,*, Candice Yama,b,*, Kyle Pomraningc, Jacqueline S. R. China,b, Joanne Y. Yewa,b

Gender Pluralism in Problem-Solving Software

Creator:: Burnett, Margaret M., Beckwith, Laura, Wiedenbeck, Susan, Fleming, Scott D., Cao, Jill, Park, Thomas H., Grigoreanu, Valentina, and Rector, Kyle
Abstract:: Although there has been significant research into gender regarding educational and workplace practices, there has been little awareness of gender differences as they pertain to software tools, such as spreadsheet applications, that try to support end users in problem-solving tasks. Although such software tools are intended to be gender agnostic,...
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Full Text:: . Fleminga, Jill Caoa, Thomas H. Parkb, Valentina Grigoreanua,d, Kyle Rectora,e aOregon State University

Effects of Ground Failure on Bridges, Roads, and Railroads

Creator:: Ledezma, Christian, Hutchinson, Tara, Ashford, Scott A., Moss, Robb, Arduino, Pedro, Bray, Jonathan D., Olson, Scott, Hashash, Youssef M. A., Verdugo, Ramon, Frost, David, Kayen, Robert, and Rollins, Kyle
Abstract:: The long duration and strong velocity content of the motions produced by the 27 February 2010 Maule earthquake resulted in widespread liquefaction and lateral spreading in several urban and other regions of Chile. In particular, critical lifeline structures such as bridges, roadway embankments, and railroads were damaged by ground shaking...
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Full Text:: , Pedro Arduino,e) Jonathan D. Bray,f) M.EERI, Scott Olson,h) M.EERI, Youssef M.A. Hashash,h) M.EERI

Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

Creator:: Vining, Kelly, Pomraning, Kyle R., Wilhelm, Larry J., Ma, Cathleen, Pellegrini, Matteo, Di, Yanming, Mockler, Todd C., Freitag, Michael, and Strauss, Steven H.
Abstract:: Background: Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional...
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Full Text:: and regeneration of Populus trichocarpa Kelly Vining1,8*, Kyle R Pomraning2,3,8, Larry J Wilhelm4

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

Creator:: Vining, Kelly J., Pomraning, Kyle R., Wilhelm, Larry J., Priest, Henry D., Pellegrini, Matteo, Mockler, Todd C., Freitag, Michael, and Strauss, Steven H.
Abstract:: Background: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results: We surveyed DNA methylation from...
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Full Text:: -level variation and relationship to gene expression Kelly J Vining1, Kyle R Pomraning2,3, Larry J

Characterizing coal and mineral mines as a regional source of stress to stream fish assemblages

Creator:: Daniel, Wesley M., Infante, Dana M., Hughes, Robert M., Tsang, Yin-Phan, Esselman, Peter C., Wieferich, Daniel, Herreman, Kyle, Cooper, Arthur R., Wang, Lizhu, and Taylor, William W.
Abstract:: Mining impacts on stream systems have historically been studied over small spatial scales, yet investigations over large areas may be useful for characterizing mining as a regional source of stress to stream fishes. The associations between co-occurring stream fish assemblages and densities of various “classes” of mining occurring in the...
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Full Text:: , Robert M. Hughes b, Yin-Phan Tsang a, Peter C. Esselman c, Daniel Wieferich a, Kyle Herreman a, Arthur R

Bacterial Resistance to Antisense Peptide-Phosphorodiamidate Morpholino Oligomers

Creator:: Puckett, Susan E., Reese, Kaleb A., Mitev, Georgi M., Mullen, Valerie, Johnson, Rudd C., Pomraning, Kyle R., Mellbye, Brett L., Tilley, Lucas D., Iversen, Patrick L., Freitag, Michael, and Geller, Bruce L.
Abstract:: Peptide phosphorodiamidate morpholino oligomers (PPMO) are synthetic DNA mimics that bind complementary RNA and inhibit bacterial gene expression. (RFF)₃RXB- AcpP PPMO (R, arginine; F, phenylalanine; X, 6-aminohexanoic acid; B, β-alanine) is complementary to 11 bases of the essential gene acpP (encodes acyl carrier protein). The MIC of (RFF)₃RXB-AcpP was 2.5...
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Full Text:: Morpholino Oligomers 1 2 Running Title: Morpholino oligomer resistance 3 4 Susan E. Puckett1,a

Journal of Open Source Software (JOSS) : design and first-year review

Creator:: Valls Guimera, Roman, Madan, Christopher R., Ram, Karthik, Barba, Lorena A., Prins, Pjotr, Vanderplas, Jacob T., Mayes, Abigail Cabunoc, Githinji, George, Teal, Tracy K., Rokem, Ariel, Huff, Kathryn D., Niemeyer, Kyle E., Smith, Arfon M., Katz, Daniel S., Moerman, Kevin M., and Gymrek, Melissa
Abstract:: This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers...
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Full Text:: Published 12 February 2018 Corresponding authors Arfon M. Smith, arfon@stsci.edu Kyle E. Niemeyer

The role of allochrony in influencing interspecific differences in foraging distribution during the non-breeding season between two congeneric crested penguin species

Creator:: Green, Cara-Paige, Ratcliffe, Norman, Mattern, Thomas, Thompson, David, Lea, Mary-Anne, Wotherspoon, Simon, Borboroglu, Pablo Garcia, Ellenberg, Ursula, Morrison, Kyle W., Pütz, Klemens, Sagar, Paul M., Seddon, Philip J., Torres, Leigh G., and Hindell, Mark A.
Abstract:: Mechanisms promoting coexistence between closely related species are fundamental for maintaining species diversity. Mechanisms of niche differentiation include allochrony which offsets the peak timing of resource utilisation between species. Many studies focus on spatial and temporal niche partitioning during the breeding season, few have investigated the role allochrony plays in...
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Full Text:: Wotherspoon1,8, Pablo Garcia Borboroglu3,5,9, Ursula Ellenberg5,10, Kyle W. Morrison6¤, Klemens Pütz11, Paul M

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

Creator:: Slavov, Gancho T., DiFazio, Stephen P., Martin, Joel, Schackwitz, Wendy, Muchero, Wellington, Rodgers-Melnick, Eli, Lipphardt, Mindie F., Pennacchio, Christa P., Hellsten, Uffe, Pennacchio, Len A., Gunter, Lee E., Ranjan, Priya, Vining, Kelly, Pomraning, Kyle R., Wilhelm, Larry J., Pellegrini, Matteo, Mockler, Todd C., Freitag, Michael, Geraldes, Armando, El-Kassaby, Yousry A., Mansfield, Shawn D., Cronk, Quentin C. B., Douglas, Carl J., Strauss, Steven H., Rokhsar, Dan, and Tuskan, Gerald A.
Abstract:: •Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. •We resequenced 16 genomes of the model tree Populus trichocarpa...
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Full Text:: Rodgers-Melnick1, Mindie F. Lipphardt1, Christa P. Pennacchio3, Uffe Hellsten3, Len A. Pennacchio3, Lee E

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism

Creator:: Tisoncik-Go, Jennifer, Gasper, David J., Kyle, Jennifer E., Eisfeld, Amie J., Selinger, Christian, Hatta, Masato, Morrison, Juliet, Korth, Marcus J., Zink, Erika M., Kim, Young-Mo, Schepmoes, Athena A., Nicora, Carrie D., Purvine, Samuel O., Weitz, Karl K., Peng, Xinxia, Green, Richard R., Tilton, Susan C., Webb-Robertson, Bobbie-Jo, Waters, Katrina M., Metz, Thomas O., Smith, Richard D., Kawaoka, Yoshihiro, Suresh, M., Josset, Laurence, and Katze, Michael G.
Abstract:: Pandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data...
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Full Text:: Tisoncik-Go, David J. Gasper, Jennifer E. Kyle, ..., M. Suresh, Laurence Josset, Michael G. Katze

The interactive effects of excess reactive nitrogen and climate change on aquatic ecosystems and water resources of the United States

Creator:: Baron, J. S., Hall, E. K., Nolan, B. T., Finlay, J. C., Bernhardt, E. S., Harrison, J. A., Chan, F., and Boyer, E. W.
Abstract:: Nearly all freshwaters and coastal zones of the US are degraded from inputs of excess reactive nitrogen (Nr), sources of which are runoff, atmospheric N deposition, and imported food and feed. Some major adverse effects include harmful algal blooms, hypoxia of fresh and coastal waters, ocean acidification, long-term harm to...
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Full Text:: and climate change on aquatic ecosystems and water resources of the United States J. S. Baron • E. K

Comparison of Meldola’s Blue Staining and Hatching Assay with Potato Root Diffusate for Assessment of Globodera sp. Egg Viability

Creator:: Kroese, Duncan, Zasada, Inga A., and Ingham, Russell E.
Abstract:: Laboratory-based methods to test egg viability include staining with Meldola's Blue and/or juvenile (J2) hatching assays using potato root diffusate (PRD). These two methods have not been tested under identical conditions to directly compare their assessments of Globodera egg viability. Using two bioassay strategies, cysts from a Glabodera sp. population...
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Full Text:: RUSSELL E. INGHAM1 Abstract: Laboratory-based methods to test egg viability include staining with

Evidence for genes associated with the ability of Mycobacterium avium subsp hominissuis to escape apoptotic macrophages

Creator:: Bermudez, Luiz E., Danelishvili, Lia, Babrack, Lmar, and Pham, Tuan
Abstract:: Mycobacterium avium subsp. hominissuis (MAH) is an environmental bacteria that infects immunocompromised humans. MAH cases are increasing in incidence, making it crucial to gain knowledge of the pathogenic mechanisms associated with the bacterium. MAH infects macrophages and after several days the infection triggers the phagocyte apoptosis. Many of the intracellular...
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Full Text:: Bermudez, L. E., Danelishvili, L., Babrack, L., & Pham, T. (2015). Evidence for genes associated with the

Reducing Crime and Violence on Public Lands: Case Studies in the USDA Forest Service

Creator:: Chavez, Deborah J., Tynon, Joanne F., and Knap, Nancy E.
Abstract:: Studies on types and impacts of crime have indicated that crime and violent acts do occur on public lands and have negative consequences for managers of those lands and recreation visitors. It is important, then, to evaluate how to reduce or eliminate crime and violent acts on public lands. To...
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Full Text:: in the USDA Forest Service Deborah J. Chavez Joanne F. Tynon Nancy E. Knap EXECUTIVE SUMMARY

Coastal Resident Knowledge of New Marine Reserves in Oregon: The Impact of Proximity and Attachment

Creator:: Perry, Elizabeth E., Needham, Mark D., Cramer, Lori A., and Rosenberger, Randall S.
Abstract:: This article examines resident proximity and attachment to a new system of marine reserves in Oregon (USA), and the extent that these factors are related to both self-assessed and factual knowledge about these reserves. Data were from a survey of residents along the Oregon coast (n = 596). Residents reported...
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Full Text:: Oregon: The Impact of Proximity and Attachment Perry, E. E., Needham, M. D., Cramer, L. A

Abandonment of Unaweep Canyon (1.4–0.8 Ma), western Colorado: Effects of stream capture and anomalously rapid Pleistocene river incision

Creator:: Aslan, Andres, Hood, William C., Karlstrom, Karl E., Kirby, Eric, Granger, Darryl E., Kelley, Shari, Crow, Ryan, Donahue, Magdalena S., Polyak, Victor, and Asmerom, Yemane
Abstract:: Cosmogenic-burial and U-series dating, identification of fluvial terraces and lacustrine deposits, and river-profile reconstructions show that capture of the Gunnison River by the Colorado River and abandonment of Unaweep Canyon occurred between 1.4-0.8 Ma. This event led to a rapid pulse of incision unlike any documented in the Rocky Mountains....
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Full Text:: incision Aslan, A., Hood, W. C., Karlstrom, K. E., Kirby, E., Granger, D. E., Kelley, S., ... & Asmerom

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Creator:: Bruskiewich, Richard, Senger, Martin, Davenport, Guy, Ruiz, Manuel, Rouard, Mathieu, Hazekamp, Tom, Takeya, Masaru, Doi, Koji, Satoh, Kouji, Costa, Marcos, Simon, Reinhard, Balaji, Jayashree, Akintunde, Akinnola, Mauleon, Ramil, Wanchana, Samart, Shah, Trushar, Anacleto, Mylah, Portugal, Arllet, Ulat, Victor Jun, Thongjuea, Supat, Braak, Kyle, Ritter, Sebastian, Dereeper, Alexis, Skofic, Milko, Rojas, Edwin, Martins, Natalia, Pappas, Georgios, Alamban, Ryan, Almodiel, Roque, Barboza, Lord Hendrix, Detras, Jeffrey, Manansala, Kevin, Mendoza, Michael Jonathan, Morales, Jeffrey, Peralta, Barry, Valerio, Rowena, Zhang, Yi, Gregorio, Sergio, Hermocilla, Joseph, Echavez, Michael, Yap, Jan Michael, Farmer, Andrew, Schiltz, Gary, Lee, Jennifer, Casstevens, Terry, Jaiswal, Pankaj, Meintjes, Ayton, Wilkinson, Mark, Good, Benjamin, Wagner, James, Morris, Jane, Marshall, David, Collins, Anthony, Kikuchi, Shoshi, Metz, Thomas, McLaren, Graham, and van Hintum, Theo
Abstract:: The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
Resource Type:: Article
Full Text:: ,1,10 Trushar Shah,2 Mylah Anacleto,1 Arllet Portugal,1 Victor Jun Ulat,1 Supat Thongjuea,10 Kyle Braak

A resonating rainfall and evaporation recorder

Creator:: Stewart, Ryan D., Hut, Rolf, Rupp, David E., Gupta, Hoshin, and Selker, John S.
Abstract:: We propose a novel, accurate quantification of precipitation and evaporation, as needed to understand fundamental hydrologic processes. Our system uses a collection vessel placed on top of a slender rod that is securely fixed at its base. As the vessel is deflected, either by manual perturbation or ambient forcing (for...
Resource Type:: Article
Full Text:: recorder A resonating rainfall and evaporation recorder Ryan D. Stewart,1 Rolf Hut,2 David E. Rupp,3

Deep electrical resistivity structure of the Northwestern U. S. derived from 3-D inversion of USArray Magnetotelluric data

Creator:: Meqbel, Naser M., Egbert, Gary D., Wannamaker, Philip E., Kelbert, Anna, and Schultz, Adam
Abstract:: Long period (10–20,000 s) magnetotelluric (MT) data are being acquired across the continental USA on a quasi-regular grid of ∼70 km spacing as an electromagnetic component of the National Science Foundation EarthScope/USArray Program. These data are sensitive to fluids, melts, and other organic indicators, and thus provide a valuable complement...
Resource Type:: Article
Full Text:: . M., Egbert, G. D., Wannamaker, P. E., Kelbert, A., & Schultz, A. (2014). Deep electrical

Measurement Tool for Dynamics of Soil Cracks

Creator:: Stewart, Ryan D., Abou Najm, Majdi R., Rupp, David E., and Selker, John S.
Abstract:: Shrinkage cracks in soil function as a dominant control on the partitioning and distribution of moisture fluxes in the vadose zone. Their dynamics influence moisture balance and control water availability for runoff, deep infiltration, and near-surface storage. We present a new low-cost field instrument to monitor the temporal change in...
Resource Type:: Article
Full Text:: D. Stewart 1* , Majdi R. Abou Najm 1,2,3 , David E. Rupp 4,5 , John S. Selker 1 2 1

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