Article on the evolution of primary hemostasis in early vertebrates.

Article on O(N) real-space method for ab initio quantum transport calculations and application to carbon nanotube-metal contacts.

Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather than by duplication within the E. colilineage, as previously believed. In general, most neighbor regulators --regulators that are adjacent to genes that they regulate -- were acquiredby horizontal gene transfer, while most global regulators evolvedvertically within the gamma-Proteobacteria. Neighbor regulators wereoften acquired together with the adjacent operon that they regulate, sothe proximity might be maintained by repeated transfers (like "selfishoperons"). Many of the as-yet-uncharacterized (putative) regulators havealso been acquired together with adjacent genes, so we predict that theseare neighbor regulators as well. When we analyzed the histories ofregulatory interactions, we found that the evolution of regulation byduplication was rare, and surprisingly, many of the regulatoryinteractions that are shared between paralogs result from convergentevolution. Another surprise was that horizontally transferred genes aremore likely than other genes to be regulated by multiple regulators, andmost of this complex regulation probably evolved …

The balancing domain decomposition methods by constraints are extended to solving both nonsymmetric, positive definite and symmetric, indefinite linear systems. In both cases, certain nonstandard primal constraints are included in the coarse problems of BDDC algorithms to accelerate the convergence. Under the assumption that the subdomain size is small enough, a convergence rate estimate for the GMRES iteration is established that the rate is independent of the number of subdomains and depends only slightly on the subdomain problem size. Numerical experiments for several two-dimensional examples illustrate the fast convergence of the proposed algorithms.

Bruce Merrifield, trained as a biochemist, had to address three major challenges related to the development and acceptance of solid-phase peptide synthesis (SPPS). The challenges were (1) to reduce the concept of peptide synthesis on a insoluble support to practice, (2) overcome the resistance of synthetic chemists to this novel approach, and (3) establish that a biochemist had the scientific credentials to effect the proposed revolutionary change in chemical synthesis. How these challenges were met is discussed in this article.

We report results on the performance of a free-electron laser operating at a wavelength of 13.7 nm where unprecedented peak and average powers for a coherent extreme-ultraviolet radiation source have been measured. In the saturation regime, the peak energy approached 170 {micro}J for individual pulses, and the average energy per pulse reached 70 {micro}J. The pulse duration was in the region of 10 fs, and peak powers of 10 GW were achieved. At a pulse repetition frequency of 700 pulses per second, the average extreme-ultraviolet power reached 20mW. The output beam also contained a significant contribution from odd harmonics of approximately 0.6% and 0.03% for the 3rd (4.6 nm) and the 5th (2.75 nm) harmonics, respectively. At 2.75 nm the 5th harmonic of the radiation reaches deep into the water window, a wavelength range that is crucially important for the investigation of biological samples.

The influence of epitaxial strain, in the form of tetragonal distortions, on the magnetic and magnetotransport properties of La{sub 0.67}Sr{sub 0.33}MnO{sub 3} thin films was studied. The tetragonal distortion (c/a ratio) was modulated through the choice of the substrate, ranging from c/a=1.007 on (001)-oriented (LaAlO{sub 3}){sub 0.3}(Sr{sub 2}AlTaO{sub 6}){sub 0.7} substrates to 0.952 on (110)-oriented GdScO{sub 3} substrates. In agreement with previous theoretical predictions, these large values of tensile strain cause the Curie temperature and the saturation magnetization to decrease, alter the temperature dependence of the resistivity and magnetoresistance, and increase the resistivity several orders of magnitude.

This paper assesses the accuracy of the simplified frame cavity conduction/convection and radiation models presented in ISO 15099 and used in software for rating and labeling window products. Temperatures and U-factors for typical horizontal window frames with internal cavities are compared; results from Computational Fluid Dynamics (CFD) simulations with detailed radiation modeling are used as a reference. Four different frames were studied. Two were made of polyvinyl chloride (PVC) and two of aluminum. For each frame, six different simulations were performed, two with a CFD code and four with a building-component thermal-simulation tool using the Finite Element Method (FEM). This FEM tool addresses convection using correlations from ISO 15099; it addressed radiation with either correlations from ISO 15099 or with a detailed, view-factor-based radiation model. Calculations were performed using the CFD code with and without fluid flow in the window frame cavities; the calculations without fluid flow were performed to verify that the CFD code and the building-component thermal-simulation tool produced consistent results. With the FEM-code, the practice of subdividing small frame cavities was examined, in some cases not subdividing, in some cases subdividing cavities with interconnections smaller than five millimeters (mm) (ISO 15099) and in some cases subdividing cavities …

Chemical Cleaning is currently in progress for Tanks 5 and 6 at the Savannah River Site. The Chemical Cleaning process is being utilized to remove the residual waste heel remaining after completion of Mechanical Sludge Removal. This work is required to prepare the tanks for closure. Tanks 5 and 6 are 1950s vintage carbon steel waste tanks that do not meet current containment standards. These tanks are 22.9 meters (75 feet) in diameter, 7.5 meters (24.5 feet) in height, and have a capacity of 2.84E+6 liters (750,000 gallons). Chemical Cleaning adds 8 wt % oxalic acid to the carbon steel tank to dissolve the remaining sludge heel. The resulting acidic waste solution is transferred to Tank 7 where it is pH adjusted to minimize corrosion of the carbon steel tank. The Chemical Cleaning flowsheet includes multiple strikes of acid in each tank. Acid is delivered by tanker truck and is added to the tanks through a hose assembly connected to a pipe penetration through the tank top. The flowsheet also includes spray washing with acid and water. This paper includes an overview of the configuration required for Chemical Cleaning, the planned flowsheet, and an overview of technical concerns associated with …

We introduce a simple polar fluid model for the thermodynamics of dense supercritical water based on a Buckingham (exp-6) core and point dipole representation of the water molecule. The proposed exp6-polar thermodynamics, based on ideas originally applied to dipolar hard spheres, performs very well when tested against molecular dynamics simulations. Comparisons of the model predictions with experimental data available for supercritical water yield excellent agreement for the shock Hugoniot, isotherms and sound speeds, and are also quite good for the self-diffusion constant and relative dielectric constant. We expect the present approach to be also useful for other small polar molecules and their mixtures.

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We present new results of our program to systematically search for strongly lensed galaxies in the Sloan Digital Sky Survey (SDSS) imaging data. In this study six strong lens systems are presented which we have confirmed with followup spectroscopy and imaging using the 3.5m telescope at the Apache Point Observatory. Preliminary mass models indicate that the lenses are group-scale systems with velocity dispersions ranging from 466?878 km s{sup -1} at z = 0.17-0.45 which are strongly lensing source galaxies at z = 0.4-1.4. Galaxy groups are a relatively new mass scale just beginning to be probed with strong lensing. Our sample of lenses roughly doubles the confirmed number of group-scale lenses in the SDSS and complements ongoing strong lens searches in other imaging surveys such as the CFHTLS (Cabanac et al. 2007). As our arcs were discovered in the SDSS imaging data they are all bright (r {approx_equal} 22), making them ideally suited for detailed follow-up studies.

Abstract: Drained depressional wetlands are typically restored by plugging ditches or breaking drainage tiles to allow recovery of natural ponding regimes, while relying on passive recolonization from seed banks and dispersal to establish emergent vegetation. However, in restored depressions of the southeastern United States Coastal Plain, certain characteristic rhizomatous graminoid species may not recolonize because they are dispersal-limited and uncommon or absent in the seed banks of disturbed sites. We tested whether selectively planting such wetland dominants could facilitate restoration by accelerating vegetative cover development and suppressing non-wetland species. In an operational-scale project in a South Carolina forested landscape, drained depressional wetlands were restored in early 2001 by completely removing woody vegetation and plugging surface ditches. After forest removal, tillers of two rhizomatous wetland grasses (Panicum hemitomon, Leersia hexandra) were transplanted into singlespecies blocks in 12 restored depressions that otherwise were revegetating passively. Presence and cover of all plant species appearing in planted plots and unplanted control plots were recorded annually. We analyzed vegetation composition after two and four years, during a severe drought (2002) and after hydrologic recovery (2004). Most grass plantings established successfully, attaining 15%–85% cover in two years. Planted plots had fewer total species and fewer wetland …

X-ray photoelectron spectroscopy (XPS) is a quantitative, chemically specific technique with a probing depth of a few angstroms to a few nanometers. It is therefore ideally suited to investigate the chemical nature of the surfaces of catalysts. Because of the scattering of electrons by gas molecules, XPS is generally performed under vacuum conditions. However, for thermodynamic and/or kinetic reasons, the catalyst's chemical state observed under vacuum reaction conditions is not necessarily the same as that of a catalyst under realistic operating pressures. Therefore, investigations of catalysts should ideally be performed under reaction conditions, i.e., in the presence of a gas or gas mixtures. Using differentially pumped chambers separated by small apertures, XPS can operate at pressures of up to 1 Torr, and with a recently developed differentially pumped lens system, the pressure limit has been raised to about 10 Torr. Here, we describe the technical aspects of high-pressure XPS and discuss recent applications of this technique to oxidation and heterogeneous catalytic reactions on metal surfaces.

We report the results of a first-principles study of dissociative electron attachment (DEA) to H{sub 2}O. The cross sections were obtained from nuclear dynamics calculations carried out in full dimensionality within the local complex potential model by using the multi-configuration time-dependent Hartree method. The calculations employ our previously obtained global, complex-valued, potential energy surfaces for the three ({sup 2}B{sub 1}, {sup 2}A{sub 1}, and {sup 2}B{sub 2}) electronic Feshbach resonances involved in this process. These three metastable states of H{sub 2}O{sup -} undergo several degeneracies, and we incorporate both the Renner-Teller coupling between the {sup 2}B{sub 1} and {sup 2}A{sub 1} states, as well as the conical intersection between the {sup 2}A{sub 1} and {sup 2}B{sub 2} states, into our treatment. The nuclear dynamics are inherently multi-dimensional and involve branching between different final product arrangements as well as extensive excitation of the diatomic fragment. Our results successfully mirror the qualitative features of the major fragment channels observed, but are less successful in reproducing the available results for some of the minor channels. We comment on the applicability of the local complex potential model to such a complicated resonant system.

In order to reach the high peak current required for an x-ray free electron laser, two separate magnetic dipole chicanes are used in the Linac Coherent Light Source (LCLS) accelerator to compress the electron bunch length in stages. In these bunch compressors, coherent synchrotron radiation (CSR) can be emitted either by a short electron bunch or by any longitudinal density modulation that may be on the bunch. In this paper, we report detailed measurements of the CSR-induced energy loss and transverse emittance growth in these compressors. Good agreement is found between the experimental results and multi-particle tracking studies. We also describe direct observations of CSR at optical wavelengths and compare with analytical models based on beam microbunching.

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The measured physical parameters of a superconducting cavity differ from those of the designed ideal cavity. This is due to shape deviations caused by both loose machine tolerances during fabrication and by the tuning process for the accelerating mode. We present a shape determination algorithm to solve for the unknown deviations from the ideal cavity using experimentally measured cavity data. The objective is to match the results of the deformed cavity model to experimental data through least-squares minimization. The inversion variables are unknown shape deformation parameters that describe perturbations of the ideal cavity. The constraint is the Maxwell eigenvalue problem. We solve the nonlinear optimization problem using a line-search based reduced space Gauss-Newton method where we compute shape sensitivities with a discrete adjoint approach. We present two shape determination examples, one from synthetic and the other from experimental data. The results demonstrate that the proposed algorithm is very effective in determining the deformed cavity shape.

Reynolds lubrication approximation is used extensively to study flows between moving machine parts, in narrow channels, and in thin films. The solution of Reynolds equation may be thought of as the zeroth order term in an expansion of the solution of the Stokes equations in powers of the aspect ratio {var_epsilon} of the domain. In this paper, we show how to compute the terms in this expansion to arbitrary order on a two-dimensional, x-periodic domain and derive rigorous, a-priori error bounds for the difference between the exact solution and the truncated expansion solution. Unlike previous studies of this sort, the constants in our error bounds are either independent of the function h(x) describing the geometry, or depend on h and its derivatives in an explicit, intuitive way. Specifically, if the expansion is truncated at order 2k, the error is O({var_epsilon}{sup 2k+2}) and h enters into the error bound only through its first and third inverse moments {integral}{sub 0}{sup 1} h(x){sup -m} dx, m = 1,3 and via the max norms {parallel} 1/{ell}! h{sup {ell}-1}{partial_derivative}{sub x}{sup {ell}}h{parallel}{sub {infinity}}, 1 {le} {ell} {le} 2k + 2. We validate our estimates by comparing with finite element solutions and present numerical evidence that suggests …

A few observable distributions in min-bias (inelastic, non-diffractive) events which could be well constrained with early LHC data are presented, with some comments on their significance for placing constraints on theoretical models. The effects of fiducial cuts (p{perpendicular} > 0.5 GeV, |{eta}| < 2.5) and extrapolation from the Tevatron are illustrated.

Not all industrial facilities have the staff or theopportunity to perform a detailed audit of their operations. The lack ofknowledge of energy efficiency opportunities provides an importantbarrier to improving efficiency. Benchmarking programs in the U.S. andabroad have shown to improve knowledge of the energy performance ofindustrial facilities and buildings and to fuel energy managementpractices. Benchmarking provides a fair way to compare the energyintensity of plants, while accounting for structural differences (e.g.,the mix of products produced, climate conditions) between differentfacilities. In California, the winemaking industry is not only one of theeconomic pillars of the economy; it is also a large energy consumer, witha considerable potential for energy-efficiency improvement. LawrenceBerkeley National Laboratory and Fetzer Vineyards developed the firstbenchmarking tool for the California wine industry called "BEST(Benchmarking and Energy and water Savings Tool) Winery". BEST Wineryenables a winery to compare its energy efficiency to a best practicereference winery. Besides overall performance, the tool enables the userto evaluate the impact of implementing efficiency measures. The toolfacilitates strategic planning of efficiency measures, based on theestimated impact of the measures, their costs and savings. The tool willraise awareness of current energy intensities and offer an efficient wayto evaluate the impact of future efficiency measures.

A new type of global shear Alfvén Eigenmode is found in tokamak plasmas where the mode localization is in the region intersecting the Alfvén continuum. The eigenmode is formed by the coupling of two solutions from two adjacent gaps (akin to potential wells) in the shear Alfvén continuum. For tokamak plasmas with reversed magnetic shear it is shown that the toroidiciy-induced solution tunnels through the continuum to match the ellipticity-induced Alfvén eigenmode (TAE and EAE, respectively) so that the resulting solution is continuous at the point of resonance with the continuum. The existence of these Double Gap Alfvén Eigenmodes (DGAEs) allows for potentially new ways of coupling edge fields to the plasma core in conditions where the core region is conventionally considered inaccessible. Implications include new approaches to heating and current drive in fusion plasmas as well as its possible use as core diagnostic in burning plasmas.

We point out that during the reionization epoch of the cosmic history, the plasma collective effect among the ordinary matter would suppress the large scale structure formation. The imperfect Debye shielding at finite temperature would induce a residual long-range electrostatic potential which, working together with the baryon thermal pressure, would counter the gravitational collapse. As a result the effective Jean's length, {tilde {lambda}}{sub J}, is increased by a factor, {tilde {lambda}}{sub J}/{lambda}{sub J} = {radical}8/5, relative to the conventional one. For scales smaller than the effective Jean's scale the plasma would oscillate at the ion-acoustic frequency. The modes that would be influenced by this effect depend on the starting time and the initial temperature of reionization, but roughly lie in the range 0.5hMpc{sup -1} < k, which corresponds to the region of the Lyman-{alpha} forest from the inter-galactic medium. We predict that in the linear regime of density-contrast growth, the plasma suppression of the matter power spectrum would approach 1 - ({Omega}{sub dm}/{Omega}{sub m}){sup 2} {approx} 1 -(5/6){sup 2} {approx} 30%.

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