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Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiome?s predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.

In many situations distribution can significantly deviate from Gaussian which requires accurate treatment of IBS. Our original interest in this problem was motivated by the need to have an accurate description of beam evolution due to IBS while distribution is strongly affected by the external electron cooling force. A variety of models with various degrees of approximation were developed and implemented in BETACOOL in the past to address this topic. A more complete treatment based on the friction coefficient and full 3-D diffusion tensor was introduced in BETACOOL at the end of 2007 under the name 'local IBS model'. Such a model allowed us calculation of IBS for an arbitrary beam distribution. The numerical benchmarking of this local IBS algorithm and its comparison with other models was reported before. In this paper, after briefly describing the model and its limitations, they present its comparison with available experimental data.

Human biospecimens are subjected to collection, processing, and storage that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research that uses human tissues, it is crucial that information on the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications on biospecimen-related research and to help reassure patient contributors and the advocacy community that their contributions are valued and respected.

The RHIC polarized proton complex utilizes polarimeters in each of the Blue and Yellow beams that measure the beam polarization through the p-Carbon elastic scattering process in the Coulomb Nuclear Interference kinematic region. This along with a Polarized Hydrogen Jet Target that utilizes the proton-proton elastic scattering process to first measure the analyzing power of the reaction and using the reverse process to measure the beam polarization. The latter is used to calibrate the p-Carbon polarimeters at the desired beam energy. In Run 9 RHIC ran with beams at center-of-mass energies of 200 and 500 GeV respectively. The higher beam intensities as well as the fact that the 250 GeV beam size is much smaller than that at 100 GeV resulted in significantly higher rates seen by the polarimeters and led to observed instability. In this paper, we will discuss the problems encountered and the tests that were carried out using the AGS as a proxy in an attempt to solve the problems and the path forward we took towards the upcoming polarized proton Run11.

The Hybrid Energy Systems Testing (HYTEST) Laboratory is being established at the Idaho National Laboratory to develop and test hybrid energy systems with the principal objective to safeguard U.S. Energy Security by reducing dependence on foreign petroleum. A central component of the HYTEST is the slurry bubble column reactor (SBCR) in which the gas-to-liquid reactions will be performed to synthesize transportation fuels using the Fischer Tropsch (FT) process. SBCRs are cylindrical vessels in which gaseous reactants (for example, synthesis gas or syngas) is sparged into a slurry of liquid reaction products and finely dispersed catalyst particles. The catalyst particles are suspended in the slurry by the rising gas bubbles and serve to promote the chemical reaction that converts syngas to a spectrum of longer chain hydrocarbon products, which can be upgraded to gasoline, diesel or jet fuel. These SBCRs operate in the churn-turbulent flow regime which is characterized by complex hydrodynamics, coupled with reacting flow chemistry and heat transfer, that effect reactor performance. The purpose of this work is to develop a computational multiphase fluid dynamic (CMFD) model to aid in understanding the physico-chemical processes occurring in the SBCR. Our team is developing a robust methodology to couple reaction kinetics …

The personal dose equivalent, H{sub p}(d), is the quantity recommended by the International Commission on Radiation Units and Measurements (ICRU) to be used as an approximation of the protection quantity Effective Dose when performing personal dosemeter calibrations. The personal dose equivalent can be defined for any location and depth within the body. Typically, the location of interest is the trunk where personal dosemeters are usually worn and in this instance a suitable approximation is a 30 cm X 30 cm X 15 cm slab-type phantom. For this condition the personal dose equivalent is denoted as H{sub p,slab}(d) and the depths, d, are taken to be 0.007 cm for non-penetrating and 1 cm for penetrating radiation. In operational radiation protection a third depth, 0.3 cm, is used to approximate the dose to the lens of the eye. A number of conversion coefficients for photons are available for incident energies up to several MeV, however, data to higher energies are limited. In this work conversion coefficients up to 1 GeV have been calculated for H{sub p,slab}(10) and H{sub p,slab}(3) using both the kerma approximation and by tracking secondary charged particles. For H{sub p}(0.07) the conversion coefficients were calculated, but only to 10 …

Low-frequency analytical solutions have been obtained for phase velocities of symmetrical fluid waves within both an infinite fracture and a pipe filled with a viscous fluid. Three different fluid wave regimes can exist in such objects, depending on the various combinations of parameters, such as fluid density, fluid viscosity, walls shear modulus, channel thickness, and frequency. Equations for velocities of all these regimes have explicit forms and are verified by comparisons with the exact solutions. The dominant role of fractures in rock permeability at field scales and the strong amplitude and frequency effects of Stoneley guided waves suggest the importance of including these wave effects into poroelastic theories.

This work investigated the thermoelectric properties of thin silicon membranes that have been decorated with high density of nanoscopic holes. These ?holey silicon? (HS) structures were fabricated by either nanosphere or block-copolymer lithography, both of which are scalable for practical device application. By reducing the pitch of the hexagonal holey pattern down to 55 nm with 35percent porosity, the thermal conductivity of HS is consistently reduced by 2 orders of magnitude and approaches the amorphous limit. With a ZT value of 0.4 at room temperature, the thermoelectric performance of HS is comparable with the best value recorded in silicon nanowire system.

Two widely proposed kt-dependent gluon distributions in the small-x saturation regime are investigated using two particle back-to-back correlations in high energy scattering processes. The Weizsacker-Williams gluon distribution, interpreted as the number density of gluon inside the nucleus, is studied in the quark-antiquark jet correlation in deep inelastic scattering. On the other hand, the unintegrated gluon distribution, defined as the Fourier transform of the color-dipole cross section, is probed in the direct photon-jet correlation in pA collisions. Dijet-correlation in pA collisions depends on both gluon distributions through combination and convolution in the large Nc limit. We calculate these processes in two approaches: the transverse momentum dependent factorization approach and the color-dipole/color glass condensate formalism, and they agree with each other completely.

The construction of the Extra Low ENergy Antiprotons (ELENA) upgrade to the Antiproton Decelerator (AD) ring has been proposed at CERN to produce a greatly increased current of low-energy antiprotons for various experiments including anti-hydrogen studies. This upgrade involves the addition of a small storage ring and electrostatic beam lines. The 5.3-MeV antiproton beams from AD are decelerated down to 100 keV in the compact ring and transported to each experimental apparatus. In this paper, we describe an electrostatic beam line from the ELENA ring to the ATRAP experimental apparatus and magnetic shielding of the low-energy beam line against the ATRAP superconducting solenoid magnet. A possible rough conceptual design of this system is displayed.

The U.S. Department of Energy (DOE) designated the Advanced Test Reactor (ATR) as a National Scientific User Facility (NSUF) in April 2007. This designation allows the ATR to become a cornerstone of nuclear energy research and development (R&D) within the U.S. by making it easier for universities, the commercial power industry, other national laboratories, and international organizations to conduct nuclear energy R&D. The mission of the ATR NSUF is to provide nuclear energy researchers access to world-class facilities, thereby facilitating the advancement of nuclear science and technology within the U.S. In support of this mission, hot cell laboratories are being upgraded. These upgrades include a set of lead shielded cells that will house Irradiated Assisted Stress Corrosion Cracking (IASCC) test rigs and construction of a shielded laboratory facility. A primary function of this shielded laboratory is to provide a state of the art type laboratory facility that is functional, efficient and flexible that is dedicated to the analysis and characterization of nuclear and non-nuclear materials. The facility shall be relatively easy to reconfigure to provide laboratory scale hot cave space for housing current and future nuclear material scientific research instruments.

Waterflooding is by far the most widely used method in the world to increase oil recovery. Historically, little consideration has been given in reservoir engineering practice to the effect of injection brine composition on waterflood displacement efficiency or to the possibility of increased oil recovery through manipulation of the composition of the injected water. However, recent work has shown that oil recovery can be significantly increased by modifying the injection brine chemistry or by injecting diluted or low salinity brine. This paper reports on laboratory work done to increase the understanding of improved oil recovery by waterflooding with low salinity injection water. Porous media used in the studies included outcrop Berea sandstone (Ohio, U.S.A.) and reservoir cores from the Green River formation of the Uinta basin (Utah, U.S.A.). Crude oils used in the experimental protocols were taken from the Minnelusa formation of the Powder River basin (Wyoming, U.S.A.) and from the Green River formation, Monument Butte field in the Uinta basin. Laboratory corefloods using Berea sandstone, Minnelusa crude oil, and simulated Minnelusa formation water found a significant relationship between the temperature at which the oil- and water-saturated cores were aged and the oil recovery resulting from low salinity waterflooding. Lower …

The RHIC polarized H{sup -} ion source is being upgraded to higher intensity (5-10 mA) and polarization for use in the RHIC polarization physics program at enhanced luminosity RHIC operation. The higher beam peak intensity will allow reduction of the transverse beam emittance at injection to AGS to reduce polarization losses in AGS. There is also a planned RHIC luminosity upgrade by using the electron beam lens to compensate the beam-beam interaction at collision points. This upgrade is also essential for future BNL plans for a high-luminosity electron - proton (ion) Collider eRHIC.

The authors describe the implementation of a phase-retrieval algorithm to reconstruct phase and complex amplitude of structures on EUV lithography masks. Many native defects commonly found on EUV reticles are difficult to detect and review accurately because they have a strong phase component. Understanding the complex amplitude of mask features is essential for predictive modeling of defect printability and defect repair. Besides printing in a stepper, the most accurate way to characterize such defects is with actinic inspection, performed at the design, EUV wavelength. Phase defect and phase structures show a distinct through-focus behavior that enables qualitative evaluation of the object phase from two or more high-resolution intensity measurements. For the first time, phase of structures and defects on EUV masks were quantitatively reconstructed based on aerial image measurements, using a modified version of a phase-retrieval algorithm developed to test optical phase shifting reticles.

1. Objective: A method to determine whether beryllium (Be) components in surface swipe samples are from a natural source is needed. 2. Methods: Soil samples and surface swipes from area facilities were analyzed for marker elements to identify source pathways for beryllium (Be). To be useful, the natural marker element must be present at reasonably consistent levels across the site, must correlate with the Be concentration, and not have the potential to be present from non-natural sources. 3. Results: The research on marker elements used to identify source pathways for beryllium (Be) concentrations demonstrates a clear correlation between Be and yttrium (Y) in natural soils on the Nevada National Security Site. The Y/Be ratio is proposed as a method to characterize the source of Be in soil and surface swipe samples and to aid in recommendations for follow up actions. Swipe samples are analyzed using an ICP/MS method and compared with results from soil samples. Natural soil constituent levels and the Y/Be Ratio range is determined for the occupied and historical facilities and surrounding areas. Y/Be ratios within the statistical range established indicate the Be is from a natural source. Y/Be ratios lower than this range indicate the presence of …

Searches for the Standard Model Higgs boson at a center-of-mass energy of {radical}s = 1.96 TeV, using up to 5.4 fb{sup -1} of data collected with the CDF and D0 detectors at the Fermilab Tevatron collider in the mass range around 160 GeV/c{sup 2} are presented. As no significant excess is observed, limits on standard-model Higgs boson production are set.

The Siberian snakes are powerful tools in preserving polarization in high energy accelerators has been demonstrated at the Brookhaven Relativistic Heavy Ion Collider (RHIC). Equipped with two full Siberian snakes in each ring, polarization is preserved during acceleration from injection to 100 GeV. However, the Siberian snakes also introduce a new set of depolarization resonances, i.e. snake resonances as first discovered by Lee and Tepikian. The intrinsic spin resonances above 100 GeV are about a factor of two stronger than those below 100 GeV which raises the challenge to preserve the polarization up to 250 GeV. In 2009, polarized protons collided for the first time at the RHIC design store energy of 250 GeV. This paper presents the experimental measurements of snake resonances at RHIC. The plan for avoiding these resonances is also presented.

We develop a Bayesian model to invert surface seismic refraction data with depth constraints from boreholes for characterization of aquifer geometry and apply it to seismic and borehole datasets collected at the contaminated Oak Ridge National Laboratory site in Tennessee. Rather than the traditional approach of first inverting the seismic arrival times for seismic velocity and then using that information to aid in the spatial interpolation of wellbore data, we jointly invert seismic first arrival time data and wellbore-based information, such as depths of key lithological boundaries. We use a staggered-grid finite-difference algorithm with second order accuracy in time and fourth order accuracy in space to model seismic full waveforms and use an automated method to pick the first arrival times. We use Markov Chain Monte Carlo methods to draw many samples from the joint posterior probability distribution, on which we can estimate the key interfaces and their associated uncertainty as a function of horizontal location and depth. We test the developed method on both synthetic and field case studies. The synthetic studies show that the developed method is effective at rigorous incorporation of multiscale data and the Bayesian inversion reduces uncertainty in estimates of aquifer zonation. Applications of the …

One of the most utilized hot cell capabilities at the Idaho National Laboratory is referred to as the containment box. This is where all destructive examination samples are prepared for analysis. This one window box is contained within the much larger Hot Fuels Examination Facility which consists of a 21x10x8 meter hot cell with an inert argon atmosphere. The refurbishment of this box entailed removing of all sample preparation equipment and support systems, as well as the design and installation of new preparation equipment. The new equipment consists of low and high speed saws, grinding and polishing equipment, water recirculation systems, and sample storage units. This paper includes the details of this refurbishment.

The simulation package WARP-POSINST was recently upgraded for handling multiple bunches and modeling concurrently the electron cloud buildup and its effect on the beam, allowing for direct self-consistent simulation of bunch trains generating, and interacting with, electron clouds. We have used the WARP-POSINST package on massively parallel supercomputers to study the growth rate and frequency patterns in space-time of the electron cloud driven transverse instability for a proton bunch train in the CERN SPS accelerator. Results suggest that a positive feedback mechanism exists between the electron buildup and the e-cloud driven transverse instability, leading to a net increase in predicted electron density. Comparisons to selected experimental data are also given. Electron clouds have been shown to trigger fast growing instabilities on proton beams circulating in the SPS and other accelerators. So far, simulations of electron cloud buildup and their effects on beam dynamics have been performed separately. This is a consequence of the large computational cost of the combined calculation due to large space and time scale disparities between the two processes. We have presented the latest improvements of the simulation package WARP-POSINST for the simulation of self-consistent ecloud effects, including mesh refinement, and generation of electrons from gas ionization …

The status is presented of the commissioning of a new heavy ion preinjector at Brookhaven National Laboratory. This preinjector uses an Electron Beam Ion Source (EBIS), and an RFQ and IH Linac, both operating at 100.625 MHz, to produce 2 MeV/u ions of any species for use, after further acceleration, at the Relativistic Heavy Ion Collider (RHIC) and the NASA Space Radiation Laboratory (NSRL). Among the increased capabilities provided by this preinjector are the ability to produce ions of any species, and the ability to switch between multiple species in 1 second, to simultaneously meet the needs of both science programs. For initial setup, helium beam from EBIS was injected and circulated in the Booster synchrotron. Following this, accelerated Au{sup 32+} and Fe{sup 20+} beams were transported to the Booster injection point, fulfilling DOE requirements for project completion.

HDF5 is a cross-platform parallel I/O library that is used by a wide variety of HPC applications for the flexibility of its hierarchical object-database representation of scientific data. We describe our recent work to optimize the performance of the HDF5 and MPI-IO libraries for the Lustre parallel file system. We selected three different HPC applications to represent the diverse range of I/O requirements, and measured their performance on three different systems to demonstrate the robustness of our optimizations across different file system configurations and to validate our optimization strategy. We demonstrate that the combined optimizations improve HDF5 parallel I/O performance by up to 33 times in some cases running close to the achievable peak performance of the underlying file system and demonstrate scalable performance up to 40,960-way concurrency.

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