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 …

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.

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.

None

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.

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.

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.

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%.

None

The B{sub c}{sup {+-}} meson is observed through the decay B{sub c}{sup {+-}} {yields} J/{psi} {pi}{sup {+-}}, in data corresponding to an integrated luminosity of 2.4 fb{sup -1} recorded by the CDF II detector at the Fermilab Tevatron. A signal of 108 {+-} 15 candidates is observed, with a significance that exceeds 8{sigma}. The mass of the B{sub c}{sup {+-}} meson is measured to be 6275.6 {+-} 2.9(stat.) {+-} 2.5(syst.) MeV/c{sup 2}.

SciBooNE is a new experiment at FNAL which will make precision neutrino-nucleus cross section measurements in the one GeV region. These measurements are essential for the future neutrino oscillation experiments. We started data taking in the antineutrino mode on June 8, 2007, and collected 5.19 x 10{sup 19} protons on target (POT) before the accelerator shutdown in August. The first data from SciBooNE are reported in this article.

None

The Underground Test Area (UGTA) Project of the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office is in the process of assessing and developing regulatory decision options based on modeling predictions of contaminant transport from underground testing of nuclear weapons at the Nevada Test Site (NTS). The UGTA Project is attempting to develop an effective modeling strategy that addresses and quantifies multiple components of uncertainty including natural variability, parameter uncertainty, conceptual/model uncertainty, and decision uncertainty in translating model results into regulatory requirements. The modeling task presents multiple unique challenges to the hydrological sciences as a result of the complex fractured and faulted hydrostratigraphy, the distributed locations of sources, the suite of reactive and non-reactive radionuclides, and uncertainty in conceptual models. Characterization of the hydrogeologic system is difficult and expensive because of deep groundwater in the arid desert setting and the large spatial setting of the NTS. Therefore, conceptual model uncertainty is partially addressed through the development of multiple alternative conceptual models of the hydrostratigraphic framework and multiple alternative models of recharge and discharge. Uncertainty in boundary conditions is assessed through development of alternative groundwater fluxes through multiple simulations using the regional groundwater flow model. Calibration of alternative …

We present a measurement of the branching fraction and photon energy spectrum for the decay B {yields} X{sub s}{gamma} using data from the BABAR experiment. The data sample corresponds to an integrated luminosity of 210 fb{sup -1}, from which approximately 680,000 B{bar B} events are tagged by a fully reconstructed hadronic decay of one of the B mesons. In the decay of the second B meson, an isolated high-energy photon is identified. We measure {Beta}(B {yields} X{sub s}{gamma}) = (3.66 {+-} 0.85{sub stat} {+-} 0.60{sub syst}) x 10{sup -4} for photon energies E{sub {gamma}} above 1.9 GeV in the B rest frame. From the measured spectrum we calculate the first and second moments for different minimum photon energies, which are used to extract the heavy-quark parameters m{sub b} and {mu}{sub {pi}}{sup 2}. In addition, measurements of the direct CP asymmetry and isospin asymmetry are presented.

Devices become increasingly vulnerable to soft errors as their feature sizes shrink. Previously, soft errors primarily caused problems for space and high-atmospheric computing applications. Modern architectures now use features so small at sufficiently low voltages that soft errors are becoming significant even at terrestrial altitudes. The soft error vulnerability of iterative linear algebra methods, which many scientific applications use, is a critical aspect of the overall application vulnerability. These methods are often considered invulnerable to many soft errors because they converge from an imprecise solution to a precise one. However, we show that iterative methods can be vulnerable to soft errors, with a high rate of silent data corruptions. We quantify this vulnerability, with algorithms generating up to 8.5% erroneous results when subjected to a single bit-flip. Further, we show that detecting soft errors in an iterative method depends on its detailed convergence properties and requires more complex mechanisms than simply checking the residual. Finally, we explore inexpensive techniques to tolerate soft errors in these methods.

Very high energy gamma-rays are expected to be absorbed by the extragalactic background light over cosmological distances via the process of electron-positron pair production. Recent observations of cosmologically distant gamma-ray emitters by ground based gamma-ray telescopes have, however, revealed a surprising degree of transparency of the universe to very high energy photons. One possible mechanism to explain this observation is the oscillation between photons and axion-like-particles (ALPs). Here we explore this possibility further, focusing on photon-ALP conversion in the magnetic fields in and around gamma-ray sources and in the magnetic field of the Milky Way, where some fraction of the ALP flux is converted back into photons. We show that this mechanism can be efficient in allowed regions of the ALP parameter space, as well as in typical configurations of the Galactic Magnetic Field. As case examples, we consider the spectrum observed from two HESS sources: 1ES1101-232 at redshift z = 0.186 and H 2356-309 at z = 0.165. We also discuss features of this scenario which could be used to distinguish it from standard or other exotic models.

Carbonyls from gasoline powered light-duty vehicles (LDVs) and heavy-duty diesel powered vehicles (HDDVs) operated on chassis dynamometers were measured using an annular denuder-quartz filter-polyurethane foam sampler with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine derivatization and chromatography-mass spectrometry analyses. Two internal standards were utilized based on carbonyl recovery, 4-fluorobenzaldehyde for<C8 carbonyls and 6-fluoro-4-chromanone for>_C8 compounds. Gas- and particle-phase emissions for 39 aliphatic and 20 aromatic carbonyls ranged from 0.1 ? 2000 ?g/L fuel for LDVs and 1.8 - 27000 mu g/L fuel for HDDVs. Gas-phase species accounted for 81-95percent of the total carbonyls from LDVs and 86-88percent from HDDVs. Particulate carbonyls emitted from a HDDV under realistic driving conditions were similar to concentrations measured in a diesel particulate matter (PM) standard reference material. Carbonyls accounted for 19percent of particulate organic carbon (POC) emissions from low-emission LDVs and 37percent of POC emissions from three-way catalyst equipped LDVs. This identifies carbonyls as one of the largest classes of compounds in LDV PM emissions. The carbonyl fraction of HDDV POC was lower, 3.3-3.9percent depending upon operational conditions. Partitioning analysis indicates the carbonyls had not achieved equilibrium between the gas- and particle-phase under the dilution factors of 126-584 used in the current study.

This paper describes automated demand response (Auto-DR) activities, an innovative effort in California to ensure that DR programs produce effective and sustainable impacts. Through the application of automation and communication technologies coupled with well-designed incentives and DR programs such as Critical Peak Pricing (CPP) and Demand Bidding (DBP), Auto-DR is opening up the opportunity for many different types of buildings to effectively participate in DR programs. We present the results of Auto-DR implementation efforts by the three California investor-owned utilities for the Summer of 2007. The presentation emphasizes Pacific Gas and Electric Company's (PG&E) Auto-DR efforts, which represents the largest in the state. PG&E's goal was to recruit, install, test and operate 15 megawatts of Auto-DR system capability. We describe the unique delivery approaches, including optimizing the utility incentive structures designed to foster an Auto-DR service provider community. We also show how PG&E's Critical Peak Pricing (CPP) and Demand Bidding (DBP) options were called and executed under the automation platform. Finally, we show the results of the Auto-DR systems installed and operational during 2007, which surpassed PG&E's Auto-DR goals. Auto-DR is being implemented by a multi-disciplinary team including the California Investor Owned Utilities (IOUs), energy consultants, energy management control system …

In this paper we report on electron beam lifetime measurements as a function of scraper position, RF voltage and bunch fill pattern in SPEAR3. We then outline development of an empirical, macroscopic model using the beam-loss rate equation. By identifying the dependence of loss coefficients on accelerator and beam parameters, a numerically-integrating simulator can be constructed to compute beam decay with time. In a companion paper, the simulator is used to train a parametric, non-linear dynamics model for the system [1].

The International Linear Collider (ILC) is a 200-500 GeV center-of-mass high-luminosity linear electron-positron collider, based on 1.3 GHz superconducting radiofrequency (SCRF) accelerating cavities. The use of the SCRF technology was recommended by the International Technology Recommendation Panel (ITRP) in August 2004 [1], and shortly thereafter endorsed by the International Committee for Future Accelerators (ICFA). In an unprecedented milestone in high-energy physics, the many institutes around the world involved in linear collider R&D united in a common effort to produce a global design for the ILC. In November 2004, the 1st International Linear Collider Workshop was held at KEK, Tsukuba, Japan. The workshop was attended by some 200 accelerator physicists from around the world, and paved the way for the 2nd ILC Workshop in August 2005, held at Snowmass, Colorado, USA, where the ILC Global Design Effort (GDE) was officially formed. The GDE membership reflects the global nature of the collaboration, with accelerator experts from all three regions (Americas, Asia and Europe). The first major goal of the GDE was to define the basic parameters and layout of the machine--the Baseline Configuration. This was achieved at the first GDE meeting held at INFN, Frascati, Italy in December 2005 with the creation …

We present a mini-review on charm spectroscopy at the BABAR experiment. We first report on the c{bar s} meson spectrum, and present precise measurements of the D{sub s1}(2536) meson as well as the properties of the many new states discovered since 2003 (D*{sub s0}(2317), D{sub s1}(2460), D*{sub sJ}(2860), and D{sub sJ}(2700) mesons). We then discuss about charmed baryons observed recently in the BABAR experiment: {Omega}{sub c}{sup 0} and {Omega}*{sub c}{sup 0} css baryons, {Lambda}{sub c}(2940){sup +} udc baryon and the {Xi}{sub c} usc/dsc baryons.