bluuebunny/crossref_metadata_2025 huggingface dataset:
Radiative forcing by long‐lived greenhouse gases: Calculations with the AER radiative transfer models
Authors: Iacono Michael J. , Delamere Jennifer S. , Mlawer Eli J. , Shephard Mark W. , Clough Shepard A. , Collins William D.
Published: July 2008

A primary component of the observed recent climate change is the radiative forcing from increased concentrations of long‐lived greenhouse gases (LLGHGs). Effective simulation of anthropogenic climate change by general circulation models (GCMs) is strongly dependent on the accurate representation of radiative processes associated with water vapor, ozone, and LLGHGs. In the context of the increasing application of the Atmospheric and Environmental Research, Inc. (AER), radiation models within the GCM community, their capability to calculate longwave and shortwave radiative forcing for clear sky scenarios previously examined by the radiative transfer model intercomparison project (RTMIP) is presented. Forcing calculations with the AER line‐by‐line (LBL) models are very consistent with the RTMIP line‐by‐line results in the longwave and shortwave. The AER broadband models, in all but one case, calculate longwave forcings within a range of −0.20 to 0.23 W m−2 of LBL calculations and shortwave forcings within a range of −0.16 to 0.38 W m−2 of LBL results. These models also perform well at the surface, which RTMIP identified as a level at which GCM radiation models have particular difficulty reproducing LBL fluxes. Heating profile perturbations calculated by the broadband models generally reproduce high‐resolution calculations within a few hundredths K d−1 in the troposphere and within 0.15 K d−1 in the peak stratospheric heating near 1 hPa. In most cases, the AER broadband models provide radiative forcing results that are in closer agreement with high‐resolution calculations than the GCM radiation codes examined by RTMIP, which supports the application of the AER models to climate change research.
Ontology (Science)
Authors: Smith Barry
Published: July 2008

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists.
Analysis of the pseudogap-related structure in the tunnel spectra of superconducting Bi2Sr2CaCu2O8+δ revealed by break-junction technique
Authors: Ekino T. , Gabovich A. M. , Voitenko A. I.
Published: July 2008

The tunnel conductance G(V) for break junctions made of as-grown single-crystal Bi2Sr2CaCu2O8+δ samples with Tc≈86–89K is measured, and clear-cut dip–hump structures are found in the range of bias voltage V=80–120mV. A theory of tunneling in symmetric junctions between inhomogeneous charge-density-wave (CDW) superconductors, considered in the framework of the s-pairing model, is developed. It is shown that CDWs are responsible for the appearance of the dip–hump structure in the tunnel current–voltage characteristics, and a proper description of the experimental results is obtained.
Magnetic flux noise in the three-Josephson-junction superconducting ring
Authors: Il’ichev E. , Omelyanchouk A. N.
Published: July 2008

We analyze the influence of noise on magnetic properties of a superconducting loop which contains three Josephson junctions. This circuit is a classical analog of a persistent current (flux) qubit. A loop supercurrent induced by external magnetic field in the presence of thermal fluctuations is calculated. To connect with experiment, we calculate the impedance of a low-frequency tank circuit which is inductively coupled with the loop of interest. We compare the results with the results obtained in the quantum mode — when the three junction loop exhibits quantum tunneling of the magnetic flux. We demonstrate that the tank–loop impedance in the classical and quantum modes have different temperature dependence and can be easily distinguished experimentally.
Theory of stochastic saturation of ferromagnetic resonance
Authors: Ugulava A. I. , Toklikishvili Z. Z. , Chotorlishvili L. L.
Published: July 2008

One of the main models used to study problems of ferromagnetic resonance is the Landau–Lifshitz phenomenological model. According to this model, the dynamics of the magnetization in a ferromagnet is described by a nonlinear Landau–Lifshitz equation. Because of the nonlinearity of this equation the physical properties described by it are extremely diverse. Depending on the physical situation, a system is characterized by soliton or chaotic solutions. Usually it is assumed that a necessary condition for obtaining a chaotic solution is that the system be acted upon by a random field due to fluctuations of the local magnetization. It is shown here that chaotic dynamics can also be obtained in the case of a regular external force. The conditions for the appearance of Hamiltonian chaos are determined, and numerical estimates are made for concrete substances. A kinetic equation describing the dynamics of the magnetization under conditions of stochasticity is obtained. It is shown that the solution of the kinetic equation agrees well with the solutions of the Landau–Lifshitz equation, confirming the applicability of the mathematical description for chaotic dynamical systems.
Magnetoelectric states of TbMnO3 in magnetic fields of different directions
Authors: Chupis I. E.
Published: July 2008

A phenomenological analysis of the magnetoelectric diagrams of the ferroelectric antiferromagnet TbMnO3 is presented for the temperature region where the rare-earth subsystem is paramagnetic. It is shown that the behavior of the electric polarization in magnetic fields of different directions cannot be explained solely in the framework of the A configuration of the manganese spins, and the weaker G and C states must be taken into account. The magnetoelectric diagrams attest to a more complex spin structure of the “oblique cross” type. It is proved that the so-called “polarization flop” in TbMnO3 in magnetic field is not a transition like the spin flop in magnets.
Peculiarities of the spontaneous and magnetic-field-induced magnetically ordered phases in alloys of the Mn2−xFexAs0.5P0.5 system
Authors: Val’kov V. I. , Varyukhin D. V. , Golovchan A. V.
Published: July 2008

The phase diagram of the system Mn2−xFexAs0.5P0.5 is investigated experimentally and theoretically. The existence of an antiferromagnetic phase for alloys with x<0.7 is revealed. It is shown that in the region 0.5<x<0.8, ferromagnetism and antiferromagnetism can coexist in the low-temperature phase, which possesses spontaneous magnetization. This phase can be described as a canted ferromagnetic structure. The electronic structure of the alloy Mn1.5Fe0.5As0.5P0.5 is calculated in the ferromagnetic and nonmagnetic states. A comparison of the calculated and experimental values of the magnetic moment per formula unit shows that a pure ferromagnetic state is realized only in alloys with x>0.8, for which those values are in good agreement. A model is constructed that can describe correctly the main features of the spontaneous and magnetic-field-induced magnetically ordered states observed in the given system. The parameters of the model are the degree of filling of the d band, the nonmagnetic density of electronic states, and the interatomic exchange integral. Their values are estimated from the data of electronic structure calculations from first principles. The model has made it possible to predict and experimentally observe the existence of a triple point on the state diagram of these alloys.
Magnetic properties of La0.7Sr0.3MnO3 nanopowders
Authors: Kalita V. M. , Lozenko A. F. , Ryabchenko S. M. , Timopheeev A. A. , Trotsenko R. A. , Danilenko I. A. , Konstantinova T. E.
Published: July 2008

The peculiarities of the magnetization of a nanopowder (particle size 12nm) of the manganite La0.7Sr0.3MnO3 are investigated. It is shown that for temperatures below the Curie point the magnetization of the powder is of the ferromagnetic type with a relatively small value of the remanent magnetization. The minimum of the derivative of the spontaneous magnetization with respect to temperature lies 20K below the Curie temperature determined by extrapolation of the temperature dependence of the coercivity. These features of the magnetization are a consequence of a large variance of the anisotropy fields of the particles, the distribution function for which was determined from incremental hysteresis loops. It is also found that the Curie temperature of the powder has a strong variance, with an rms deviation of at least 20K. The mean value of the Curie temperature of the particles is 325K. The spontaneous magnetization of the powder particles does not have (even in the low-temperature region) a saturation region. This temperature dependence of the spontaneous magnetization influences the trend of the temperature dependence of the coercive field, leading to a deviation from the Néel–Brown law. It is also shown that for the given ensemble of particles the blocking temperature corresponds to the temperature of the maximum of the ratio of the magnetization measured after cooling in the zero-field regime to the spontaneous magnetization.
Theory of the absorption of a double ultrashort laser pulse by aspherical metallic particles of small size
Authors: Grigorchuk N. I. , Tomchuk P. M.
Published: July 2008

A theory is developed which permits calculation of the energy absorbed by aspherical particles of small size under irradiation by double ultrashort laser pulses of specified duration, in the excitation region of surface plasmons (Mie resonances). For particles of oblate or prolate spheroidal shape the dependence of the absorbed energy on the deviation of the particle shape from spherical, the pulse duration, the volume of the particle, and the polarization of the electric field of the laser beam relative to the axis of the revolution of the spheroid is determined. It is shown that, depending on the time delay between the two pulses, the energy absorbed by a particle can be greater or less than the total energy of absorption from two uncorrelated pulses.
Phosphorescence of vitreous 2-bromobenzophenone
Authors: Buravtseva L. M. , Pyshkin O. S. , Strzhemechny M. A. , Avdeenko A. A.
Published: July 2008

Spectroscopic studies of vitreous 2-bromobenzophenone have been carried out over the respective domain of its stability. Glassy 2-bromobenzophenone samples were obtained by abrupt cooling of the melt by cold helium vapor. Quantum yield measurements allowed us to establish that the upper boundary of stable glass is slightly above 100K, while at about 220K the glass melts. Phosphorescence measurements at 4.2K showed that even at this low temperature the emission contains a strong excimer component. The energy position and shape (two bands) of the excimer emission are close to those observed in the crystal of 2-bromobenzophenone at higher temperatures. Contrary to findings in the crystal, the monomeric emission of the glass contains only one C=O stretch series, every band of which is substantially broader than in the crystal. As the temperature is raised, the monomeric emission intensity falls, disappearing completely above 70K.
The effect of the noncentral impurity–matrix interaction upon the thermal expansion and polyamorphism of CO–C60 solid solutions at low temperatures
Authors: Dolbin A. V. , Esel’son V. B. , Gavrilko V. G. , Manzhelii V. G. , Vinnikov N. A. , Gadd G. E. , Moricca S. , Cassidy D. , Sundqvist B.
Published: July 2008

Orientational glasses with CO molecules occupying 26 and 90% of the octahedral interstitial sites in the C60 lattice have been investigated by the dilatometric method in a temperature interval of 2.5–22K. At temperatures of 4–6K the glasses undergo a first-order phase transition which is evident from the hysteresis of the thermal expansion and the maxima in the temperature dependences of the linear thermal expansion coefficients α(T) and the thermalization times τ1(T) of the samples. The effect of the noncentral CO–C60 interaction upon the thermal expansion and the phase transition in these glasses was clarified by comparing the behavior of the properties of the CO–C60 and N2–C60 solutions.
Excitonic absorption spectrum of Rb2ZnI4 thin films
Authors: Miloslavsky V. K. , Yunakova O. N. , Kovalenko E. N.
Published: July 2008

The absorption spectrum of Rb2ZnI4 thin films in the spectral region 3–6eV is investigated in the temperature range 90–290K. It is found that the compound is a direct-gap insulator and that the low-frequency excitations are localized in the ZnI42− structural layers of the crystal lattice and are of a quasi-two-dimensional character. For T<200K the temperature dependence of the spectral absorption and the half-widths of the long-wavelength exciton band exhibits thermal memory effects due to precursors of the low-temperature phases.
Photoluminescence of C60 single crystals intercalated with molecular hydrogen
Authors: Zinoviev P. V. , Zoryansky V. N. , Silaeva N. B.
Published: July 2008

The optical properties of C60 single crystals intercalated with molecular hydrogen are investigated in the temperature range 10–230K by means of photoluminescence studies. The intercalation was carried out at a temperature of 240°C and a pressure of 30atm for 200h. At 10K the emission spectrum of fullerite with an impurity of hydrogen molecules contains inhomogeneously broadened lines and is shifted to lower energies (it starts at 1.69eV). Analysis of the temperature studies of the photoluminescence spectra has for the first time revealed the temperature independence of the integrated emission intensity in the interval 10–150K. It is conjectured that the changes of the photoluminescence properties of fullerite are due to the strong influence of hydrogen impurity molecules on the formation of the orientational glass state.
Dynamical changes of hemoglobin and its surrounding water during thermal denaturation as studied by quasielastic neutron scattering and temperature modulated differential scanning calorimetry
Authors: Jansson H. , Swenson J.
Published: July 2008

We have investigated the dynamical behavior of both the protein hemoglobin and its surrounding water during the denaturation process using modulated temperature differential scanning calorimetry, quasielastic neutron scattering, and frequency dependent conductivity measurements. To distinguish between the scattering from the protein and its surrounding water, neutron scattering measurements were performed on both a fully hydrogenated sample as well as a sample where the water and the exchangeable hydrogen atoms on the protein surface were deuterated. The experimental data show that the unfolding and aggregation processes are substantially overlapping in temperature. The unfolding process occurs in the approximate temperature range of 315–345K, whereas the aggregation process starts around 330–335K and is completed at 360K. Furthermore, the results suggest that the secondary structure of the protein unfolds at about 325K, and that this leads to an increased number of water molecule hydrogen bonded to the protein. Thus, the unfolding of the secondary structure reduces the number of mobile (on the experimental time scale of about 50–100ps) water molecules. In contrast, the aggregation of protein molecules seems to have a minor effect on the dynamics of its surrounding water. In the case of the protein dynamics there are competing effects from unfolding and aggregation. The unfolding process increases the flexibility of the protein, whereas the initial aggregation reduces its dynamics. The conductivity seems to be negatively affected by both reduced water mobility and an aggregation of protein molecules.
Detecting anomalous phase synchronization from time series
Authors: Tokuda Isao T. , Kumar Dana Syamal , Kurths Jürgen
Published: July 2008

Modeling approaches are presented for detecting an anomalous route to phase synchronization from time series of two interacting nonlinear oscillators. The anomalous transition is characterized by an enlargement of the mean frequency difference between the oscillators with an initial increase in the coupling strength. Although such a structure is common in a large class of coupled nonisochronous oscillators, prediction of the anomalous transition is nontrivial for experimental systems, whose dynamical properties are unknown. Two approaches are examined; one is a phase equational modeling of coupled limit cycle oscillators and the other is a nonlinear predictive modeling of coupled chaotic oscillators. Application to prototypical models such as two interacting predator-prey systems in both limit cycle and chaotic regimes demonstrates the capability of detecting the anomalous structure from only a few sets of time series. Experimental data from two coupled Chua circuits shows its applicability to real experimental system.
The ground electronic state of KCs studied by Fourier transform spectroscopy
Authors: Ferber R. , Klincare I. , Nikolayeva O. , Tamanis M. , Knöckel H. , Tiemann E. , Pashov A.
Published: July 2008

We present here the first analysis of laser induced fluorescence (LIF) of the KCs molecule obtaining highly accurate data and perform a direct potential construction for the XΣ+1 ground state in a wide range of internuclear distances. KCs molecules were produced by heating a mixture of K and Cs metals in a heat pipe at a temperature of about 270°C. KCs fluorescence was induced by different laser sources: the 454.5, 457.9, 465.8, and 472.7nm lines of an Ar+ laser, a dye laser with Rhodamine 6G dye (excitation at around 16870cm−1), and 850 and 980nm diode lasers (11 500–11 900 and 10200–10450cm−1 tuning ranges, respectively). The LIF to the ground state was recorded by a Bruker IFS-125HR Fourier transform spectrometer with a spectral resolution of 0.03cm−1. Particularly, by applying the 850nm laser diode we were able to observe LIF progressions to very high vibrational levels of the ground state close to the dissociation limit. The present data field contains 7226 term values for the ground state XΣ+1 and covers a range from v″=0 to 97 with J″ varying from 12 to 209. More than 10 000 fluorescence lines were used to fit the ground state potential energy curve via the inverted perturbation approach procedure. The present empirical potential extends up to approximately 12.6Å and covers more than 99% of the potential well depth, it describes most of the spectral lines with an accuracy of about 0.003cm−1 and yields a dissociation energy of 4069.3±1.5cm−1 for the ground state XΣ+1. First observations of the triplet ground state aΣ+3 of KCs are presented, and preliminary values of few main molecular constants could be derived.
Edge state magnetism of single layer graphene nanostructures
Authors: Bhowmick Somnath , Shenoy Vijay B.
Published: July 2008

We study edge state magnetism in graphene nanostructures using a mean field theory of the Hubbard model. We investigate how the magnetism of the zigzag edges of graphene is affected by the presence of other types of terminating edges and defects. By a detailed study of both regular shapes, such as polygonal nanodots and nanoribbons, and irregular shapes, we conclude that the magnetism in zigzag edges is very robust. Our calculations show that the zigzag edges that are longer than three to four repeat units are always magnetic, irrespective of other edges, regular or irregular. We, therefore, clearly demonstrate that the edge irregularities and defects of the bounding edges of graphene nanostructures do not destroy the edge state magnetism.
Propagation of electron magnetohydrodynamic structures in a two-dimensional inhomogeneous plasma
Authors: Yadav Sharad Kumar , Das Amita , Kaw Predhiman
Published: July 2008

The fully three-dimensional governing equations in the electron magnetohydrodynamic (EMHD) regime for a plasma with inhomogeneous density are obtained. These equations in the two-dimensional limit can be cast in terms of the evolution of two coupled scalar fields. The nonlinear simulations for the two-dimensional case are carried out to understand the propagation of EMHD magnetic structures in the presence of inhomogeneity. A novel effect related to the trapping of dipolar magnetic structures in the high density plasma region in the EMHD regime is observed. The interpretation of this phenomena as well as its relevance to the problem of hot spot generation in the context of fast ignition is presented.
Chaotic dynamics on large networks
Authors: Sprott J. C.
Published: July 2008

Many systems in nature are governed by a large number of agents that interact nonlinearly through complex feedback loops. When the networks are sufficiently large and interconnected, they typically exhibit self-organization and chaos. This paper examines the prevalence and degree of chaos on large unweighted recurrent networks of ordinary differential equations with sigmoidal nonlinearities and unit coupling. The largest Lyapunov exponent is used as the signature and measure of the chaos, and the study includes the effects of damping, asymmetries in the distribution of coupling strengths, network symmetry, and sparseness of connections. Minimum conditions and optimal network architectures are determined for the existence of chaos. The results have implications for the design of social and other networks in the real world in which weak chaos is deemed desirable or as a way of understanding why certain networks might exist on “the edge of chaos.”
Ion acoustic vortices in quantum magnetoplasmas
Authors: Haque Q. , Saleem H.
Published: July 2008

A nonlinear equation for ion acoustic waves in dense quantum plasmas (which is analogous to the classical plasma case) has been obtained in a particular limit. Therefore it is proposed that electrostatic monopolar and dipolar vortices can appear in uniform dense quantum plasmas due to large amplitude acoustic fluctuations. It is noticed that the scale length of these structures will be very short. The main quantum effect appears through Fermi pressure.
Energetics and kinetics of the reaction of HOCO with hydrogen atoms
Authors: Yu Hua-Gen , Francisco Joseph S.
Published: July 2008

The potential energy surface for the reaction of HOCO radicals with hydrogen atoms has been explored using the CCSD(T)/aug-cc-pVQZ ab initio method. Results show that the reaction occurs via a formic acid (HOC(O)H) intermediate, and produces two types of products: H2O+CO and H2+CO2. Reaction enthalpies (0K) are obtained as −102.0kcal∕mol for the H2+CO2 products, and −92.7kcal∕mol for H2O+CO. Along the reaction pathways, there exists a nearly late transition state for each product channel. However, the transition states locate noticeably below the reactant asymptote. Direct ab initio dynamics calculations are also carried out for studying the kinetics of the H+HOCO reaction. At room temperature, the rate coefficient is predicted to be 1.07×10−10cm3molec−1s−1 with a negligible activation energy Ea=0.06kcal∕mol, and the branching ratios are estimated to be 0.87 for H2+CO2, and 0.13 for H2O+CO. In contrast, the product branching ratios have a strong T dependence. The branching ratio for H2O+CO could increase to 0.72 at T=1000K.
Silica-/titania-coated Y2O3:Tm3+, Yb3+ nanoparticles with improvement in upconversion luminescence induced by different thickness shells
Authors: Lü Qiang , Guo FengYun , Sun Liang , Li AiHua , Zhao LianCheng
Published: July 2008

In order to improve the upconversion (UC) luminescence of lanthanide-doped nanoparticles (NPs), different sized Y2O3:Tm3+, Yb3+ NPs were synthesized using the Pechini type sol-gel method, and their surfaces were coated with different thickness of SiO2 or TiO2 shells using the Stöber method. The results indicate that large-sized NPs have more intense UC luminescence intensities than small-sized NPs. The core-shell structures can enhance the UC luminescence intensities. Comparing with the UC luminescence intensity of noncoated NPs, the UC luminescence intensities of SiO2-coated NPs for the sintering time of 60 min and the coating time of 30, 60, 90, and 120 min are enhanced by 1.53, 1.54, 1.40, and 1.16 times, respectively. According to the relative variable ratios of the UC luminescence intensities, a competition process between two mechanisms was proposed to explain the effects of different thickness shells and different shell materials on the UC luminescence intensities. One mechanism is the role conversion of lanthanide ions on the NPs’ surfaces, which is from the “dormant” state to the “activated” state due to the complementary ligand fields from noncrystalline SiO2 shells. The other is the absorption effects of the shells on the incident pump light and the reabsorption effects of the shells on the UC luminescence. Therefore, it can be concluded that more intense UC luminescence can be achieved in doped core-shell NPs by selecting the appropriate shell materials and their thickness.
Forced synchronization of a self-sustained chaotic oscillator
Authors: González Salas J. S. , Campos Cantón E. , Ordaz Salazar F. C. , Campos Cantón I.
Published: July 2008

This work presents a forced synchronization phenomenon like the asymptotic correlated behavior between chaotic oscillators forced by an external signal. Different kinds of forced synchronization are presented and given a theoretical justification explaining why it is possible to find some of them. Numerical results are presented for different cases such as antisymmetric, lag, phase, and identical forced synchronization.
The discrete spectrum of the periodic Maxwell operator perturbed by a decreasing potential
Authors: Miao Dong
Published: July 2008

The propagation of electromagnetic waves in dielectric medium with decreasing perturbations (defects) is studied. We use the Maxwell operator M=∇×p(x)∇× and the perturbed operator Mλ=∇×(p(x)+λq(x))∇× to describe the “background” medium and perturbed medium, respectively, where λ>0 is the coupling constant. Under the assumption that M has a spectral gap G, we prove that a defect can create an eigenvalue of any given fixed value τ∊G for some λ>0, provided that the support of the defect is large enough. We also consider the asymptotic distribution of eigenvalues in the gap and bounds on the number of eigenvalue branches.
Laser pulse induced bumps in chalcogenide phase change films
Authors: Wei Jingsong , Jiao Xinbing , Gan Fuxin , Xiao Mufei
Published: July 2008

Formation of bumps in chalcogenide phase change thin films during the laser writing process is theoretically and experimentally investigated. The process involves basically fast heating and quenching stages. Circular bumps are formed after cooling, and the shape and size of the bumps depend on various parameters such as temperatures, laser power, beam size, laser pulse duration, etc. In extreme cases, holes are formed at the apex of the bumps. To understand the bumps and their formation is of great interest for data storage. In the present work, a theoretical model is established for the formation process, and the geometric characters of the formed bumps can be analytically and quantitatively evaluated from various parameters involved in the formation. Simulations based on the analytic solution are carried out taking Ag8In14Sb55Te23 as an example. The results are verified with experimental observations of the bumps.
Study of tungsten filament aging in hot-wire chemical vapor deposition with silacyclobutane as a source gas and the H2 etching effect
Authors: Tong Ling , Sveen Chris E. , Shi Yujun
Published: July 2008

The tungsten filament aging when using silacyclobutane (SCB) as a source gas in a hot-wire chemical vapor deposition reactor was systematically studied by the characterization of surface morphology using scanning electron microscopy and the chemical composition analysis of the filament surfaces using Auger electron spectroscopy. It is shown that filament aging involves the formation of silicides and under more severe conditions, a pure silicon deposit. At low pressures of SCB samples, e.g., 0.06 and 0.03Torr, only Si3W5 alloy was formed. Silicon-rich silicide, Si2W, was found when using a higher pressure of SCB at 0.12Torr. At the high SCB pressure of 0.12Torr and low temperatures, pure silicon was deposited on the W filament surface. It is also demonstrated that H2 can etch the aged filament at high temperatures above 1900°C. The etching products detected by the 10.5eV vacuum ultraviolet laser single photon ionization∕time-of-flight mass spectrometer include SiH4, SiCHx (x=2–5), and SiC2Hy (y=4–7).
Transient ordering in a quasi-two-dimensional liquid near freezing
Authors: Sheu Alice Shu-Yao , Rice Stuart
Published: July 2008

We report the results of a theoretical study of locally ordered fluctuations in a quasi-two-dimensional colloid fluid. The fluctuations in the equilibrium state are monitored by the aperture cross-correlation function of radiation scattered by the fluid, as calculated from molecular dynamics simulations of near hard spheres with diameter σ confined between smooth hard walls. These locally ordered fluctuations are transient; their decay can be monitored as a function of the time between the cross-correlated scattered radiation signals, but only the single-time cross-correlated signals are discussed in this paper. Systems with thicknesses less than two hard sphere diameters were studied. For wall separation H in the range 1σ⩽H⩽1.57σ, the liquid freezes into a single hexagonal layer and the locally ordered fluctuations only exhibit hexagonal symmetry that extends well into the liquid region. For H⩾1.57σ, hexagonal fluctuations persist in the dense liquid up to H=1.75σ, and fluctuations with square ordered symmetry, that of the solid to which the liquid freezes, only emerge at densities ∼2% below freezing. For H=1.8σ and 1.85σ, hexagonal ordered flucuations are no longer found, and the square ordered fluctuations dominate the dense liquid region as the system freezes into a two layer square solid. For H=1.9σ and 1.95σ, where the liquid freezes into a two layer hexagonal solid, both square and hexagonal ordered fluctuations are observed. At lower densities, the ordered fluctuations only exhibit square symmetry. Hexagonal ordered fluctuations appear at densities ∼7% below freezing and become more dominant as the density is increased, but the square ordered fluctuations persist until the system is converted into the solid.
Absolute level-resolved reactive and inelastic rate constants in Li+Li2∗
Authors: Coppage Steven , Matei Paula , Stewart Brian
Published: July 2008

We have used nuclear parity-changing collisions to obtain absolute level-to-level rate constants for reactive scattering in a triatomic system with identical nuclei. We have determined rate constants for the system L7i2∗(A 1Σu+)(vi=2,ji=19)+L7i→L7i+L7i2∗(A 1Σu+)(vf,jf), from laser-induced fluorescence spectra of lithium vapor in a heat pipe oven. Parity-preserving collisions yielded measurements of absolute rotationally and vibrationally inelastic rate constants as well. We compare the reactive rate constants with statistical prior distributions and the inelastic results with previously measured results on the Ne+L7i2∗ system.
Flexibility accompanies commitment of memory CD4 lymphocytes derived from IL-4 locus-activated precursors
Authors: Adeeku Eric , Gudapati Prathyusha , Mendez-Fernandez Yanice , Van Kaer Luc , Boothby Mark
Published: July 2008

Differentiation of T helper (Th) subset 2 effector lymphocytes is thought to foreclose on IFN-γ gene expression. Using an IL-4 locus modified to detect transcriptional induction of this effector cytokine gene in developing Th2 cells, we show here that these cells contributed effectively to a long-term memory population. A memory CD4 subset formed efficiently from an activated population after transcriptional induction of the IL-4 locus and differentiation into an IL-4-producing subset with Th2 characteristics. Memory lymphocytes derived from Th2 cells with IL-4 locus activation remained committed to transcriptional competence of Th2 cytokine genes when reactivated and cultured under strong Th1-polarizing conditions. This commitment to transcriptional competence at Th2 cytokine gene loci upon recall activation indicates that linear differentiation is a substantial component of type 2 memory. Strikingly, however, descendants of the Th2 population could turn on IFN-γ expression when reactivated after a quiescent period, revealing an unexpected flexibility allowing activation of the forbidden IFN-γ gene after reactivation and growth.
Mast cells inhibit intramacrophageFrancisella tularensisreplication via contact and secreted products including IL-4
Authors: Ketavarapu Jyothi M. , Rodriguez Annette R. , Yu Jieh-Juen , Cong Yu , Murthy Ashlesh K. , Forsthuber Thomas G. , Guentzel M. Neal , Klose Karl E. , Berton Michael T. , Arulanandam Bernard P.
Published: July 2008

Francisella tularensisis an intracellular, Gram-negative bacterium that is the causative agent of pulmonary tularemia. The pathogenesis and mechanisms related to innate resistance againstF. tularensisare not completely understood. Mast cells are strategically positioned within mucosal tissues, the major interface with the external environment, to initiate innate responses at the site of infection. Mast cell numbers in the cervical lymph nodes and the lungs progressively increased as early as 48 h after intranasalF. tularensislive vaccine strain (LVS) challenge. We established a primary bone marrow-derived mast cell–macrophage coculture system and found that mast cells significantly inhibitF. tularensisLVS uptake and growth within macrophages. Importantly, mice deficient in either mast cells or IL-4 receptor displayed greater susceptibility to the infection when compared with corresponding wild-type animals. Contact-dependent events and secreted products including IL-4 from mast cells, and IL-4 production from other cellular sources, appear to mediate the observed protective effects. These results demonstrate a previously unrecognized role for mast cells and IL-4 and provide a new dimension to our understanding of the innate immune mechanisms involved in controlling intramacrophageFrancisellareplication.
Egg size variation among tropical and temperate songbirds: An embryonic temperature hypothesis
Authors: Martin Thomas E.
Published: July 2008

Species with “slow” life history strategies (long life, low fecundity) are thought to produce high-quality offspring by investing in larger, but fewer, young. Larger eggs are indeed associated with fewer eggs across taxa and can yield higher-quality offspring. Tropical passerines appear to follow theory because they commonly exhibit slow life history strategies and produce larger, but fewer, eggs compared with northern species. Yet, I show here that relative egg mass (corrected for adult mass) varies extensively in the tropics and subtropics for the same clutch size, and this variation is unexplained. I propose a hypothesis to explain egg size variation both within the tropics and between latitudes: Relative egg mass increases in species with cooler egg temperatures and longer embryonic periods to offset associated increases in energetic requirements of embryos. Egg temperatures of birds are determined by parental incubation behavior and are often cooler among tropical passerines because of reduced parental attentiveness of eggs. Here, I show that cooler egg temperatures and longer embryonic periods explained the enigmatic variation in egg mass within and among regions, based on field studies in tropical Venezuela (36 species), subtropical Argentina (16 species), and north temperate Arizona (20 species). Alternative explanations are not supported. Thus, large egg sizes may reflect compensation for increased energetic requirements of cool egg temperatures and long embryonic periods that result from reduced parental attentiveness in tropical birds.
Role of hybrid tRNA-binding states in ribosomal translocation
Authors: Walker Sarah E. , Shoji Shinichiro , Pan Dongli , Cooperman Barry S. , Fredrick Kurt
Published: July 2008

During translation, tRNAs must move rapidly to their adjacent sites in the ribosome while maintaining precise pairing with mRNA. This movement (translocation) occurs in a stepwise manner with hybrid-state intermediates, but it is unclear how these hybrid states relate to kinetically defined events of translocation. Here we analyze mutations at position 2394 of 23S rRNA in a pre-steady-state kinetic analysis of translocation. These mutations target the 50S E site and are predicted to inhibit P/E state formation. Each mutation decreases growth rate, the maximal rate of translocation (
k
trans
), and the apparent affinity of EF-G for the pretranslocation complex (i.e., increases
K
1/2
). The magnitude of these defects follows the trend A > G > U. Because the C2394A mutation did not decrease the rate of single-turnover GTP hydrolysis, the >20-fold increase in
K
1/2
conferred by C2394A can be attributed to neither the initial binding of EF-G nor the subsequent GTP hydrolysis step. We propose that C2394A inhibits a later step, P/E state formation, to confer its effects on translocation. Replacement of the peptidyl group with an aminoacyl group, which is predicted to inhibit A/P state formation, decreases
k
trans
without increasing
K
1/2
. These data suggest that movements of tRNA into the P/E and A/P sites are separable events. This mutational study allows tRNA movements with respect to both subunits to be integrated into a kinetic model for translocation.
A sonic hedgehog signaling domain in the arterial adventitia supports resident Sca1
+
smooth muscle progenitor cells
Authors: Passman Jenna N. , Dong Xiu Rong , Wu San-Pin , Maguire Colin T. , Hogan Kelly A. , Bautch Victoria L. , Majesky Mark W.
Published: July 2008

We characterize a sonic hedgehog (Shh) signaling domain restricted to the adventitial layer of artery wall that supports resident Sca1-positive vascular progenitor cells (AdvSca1). Using patched-1 (

Ptc1
lacZ

) and patched-2 (

Ptc2
lacZ

) reporter mice, adventitial Shh signaling activity was first detected at embryonic day (E) 15.5, reached the highest levels between postnatal day 1 (P1) and P10, was diminished in adult vessels, and colocalized with a circumferential ring of Shh protein deposited between the media and adventitia. In
Shh
−/−
mice, AdvSca1 cells normally found at the aortic root were either absent or greatly diminished in number. Using a
Wnt1-cre
lineage marker that identifies cells of neural crest origin, we found that neither the adventitia nor AdvSca1 cells were labeled in arteries composed of neural crest-derived smooth muscle cells (SMCs). Although AdvSca1 cells do not express SMC marker proteins
in vivo
, they do express transcription factors thought to be required for SMC differentiation, including serum response factor (SRF) and myocardin family members, and readily differentiate to SMC-like cells
in vitro
. However, AdvSca1 cells also express potent repressors of SRF-dependent transcription, including Klf4, Msx1, and FoxO4, which may be critical for maintenance of the SMC progenitor phenotype of AdvSca1 cells
in vivo
. We conclude that a restricted domain of Shh signaling is localized to the arterial adventitia and may play important roles in maintenance of resident vascular SMC progenitor cells in the artery wall.
Critical regulation of TGFβ signaling by Hsp90
Authors: Wrighton Katharine H. , Lin Xia , Feng Xin-Hua
Published: July 2008

Transforming growth factor β (TGFβ) controls a diverse set of cellular processes by activating TGFβ type I (TβRI) and type II (TβRII) serine-threonine receptor kinases. Canonical TGFβ signaling is mediated by Smad2 and Smad3, which are phosphorylated in their SXS motif by activated TβRI. The 90-kDa heat-shock protein (Hsp90) is a molecular chaperone facilitating the folding and stabilization of many protein kinases and intracellular signaling molecules. Here, we present evidence identifying a critical role for Hsp90 in TGFβ signaling. Inhibition of Hsp90 function by using small-molecule inhibitors such as 17-allylamino-17-demethoxygeldanamycin (17AAG), and also at the genetic level, blocks TGFβ-induced signaling and transcriptional responses. Furthermore, we identify TβRI and TβRII as Hsp90-interacting proteins
in vitro
and
in vivo
and demonstrate that inhibition of Hsp90 function increases TβR ubiquitination and degradation dependent on the Smurf2 ubiquitin E3 ligase. Our data reveal an essential level of TGFβ signaling regulation mediated by Hsp90 by its ability to chaperone TβRs and also implicate the use of Hsp90 inhibitors in blocking undesired activation of TGFβ signaling in diseases.
Field evidence that ecosystem service projects support biodiversity and diversify options
Authors: Goldman Rebecca L. , Tallis Heather , Kareiva Peter , Daily Gretchen C.
Published: July 2008

Ecosystem service approaches to conservation are being championed as a new strategy for conservation, under the hypothesis that they will broaden and deepen support for biodiversity protection. Where traditional approaches focus on setting aside land by purchasing property rights, ecosystem service approaches aim to engage a much wider range of places, people, policies, and financial resources in conservation. This is particularly important given projected intensification of human impacts, with rapid growth in population size and individual aspirations. Here we use field research on 34 ecosystem service (ES) projects and 26 traditional biodiversity (BD) projects from the Western Hemisphere to test whether ecosystem service approaches show signs of realizing their putative potential. We find that the ES projects attract on average more than four times as much funding through greater corporate sponsorship and use of a wider variety of finance tools than BD projects. ES projects are also more likely to encompass working landscapes and the people in them. We also show that, despite previous concern, ES projects not only expand opportunities for conservation, but they are no less likely than BD projects to include or create protected areas. Moreover, they do not draw down limited financial resources for conservation but rather engage a more diverse set of funders. We also found, however, that monitoring of conservation outcomes in both cases is so infrequent that it is impossible to assess the effectiveness of either ES or BD approaches.
Structural basis of
Escherichia coli
single-stranded DNA-binding protein stimulation of exonuclease I
Authors: Lu Duo , Keck James L.
Published: July 2008

Bacterial single-stranded DNA (ssDNA)-binding proteins (SSBs) play essential protective roles in genome biology by shielding ssDNA from damage and preventing spurious DNA annealing. Far from being inert, ssDNA/SSB complexes are dynamic DNA processing centers where many different enzymes gain access to genomic substrates by exploiting direct interactions with SSB. In all cases examined to date, the C terminus of SSB (SSB-Ct) forms the docking site for heterologous proteins. We describe the 2.7-Å-resolution crystal structure of a complex formed between a peptide comprising the SSB-Ct element and exonuclease I (ExoI) from
Escherichia coli
. Two SSB-Ct peptides bind to adjacent sites on ExoI. Mutagenesis studies indicate that one of these sites is important for association with the SSB-Ct peptide in solution and for SSB stimulation of ExoI activity, whereas the second has no discernable function. These studies identify a correlation between the stability of the ExoI/SSB-Ct complex and SSB-stimulation of ExoI activity. Furthermore, mutations within SSB's C terminus produce variants that fail to stimulate ExoI activity, whereas the SSB-Ct peptide alone has no effect. Together, our findings indicate that SSB stimulates ExoI by recruiting the enzyme to its substrate and provide a structural paradigm for understanding SSB's organizational role in genome maintenance.
Coexpression of Argonaute-2 enhances RNA interference toward perfect match binding sites
Authors: Diederichs Sven , Jung Stephanie , Rothenberg S. Michael , Smolen Gromoslaw A. , Mlody Barbara G. , Haber Daniel A.
Published: July 2008

RNAi is widely applied to inhibit expression of specific genes, but it is limited by variable efficiency and specificity of empirically designed siRNA or shRNA constructs. This complicates studies targeting individual genes and significantly impairs large-scale screens using genome-wide knockdown libraries. Here, we show that ectopic expression of the RISC slicer Argonaute-2 (Ago2, eIF2C2) dramatically enhances RNAi specifically for mRNA targets with perfectly matched binding sites. This effect depends on its endonuclease activity and is uncoupled from its regulation of microRNA expression. To model the application of Ago2 coexpression with shRNA knockdown, we targeted the EGF receptor (EGFR) in lung cancer cells exhibiting oncogene addiction to EGFR. Whereas multiple empirically designed shRNA constructs exhibited highly divergent efficiencies in mediating EGFR knockdown and cell killing, coexpression of Ago2 resulted in uniform and highly specific target gene suppression and apoptosis in EGFR-dependent cells. Codelivery of Ago2 with shRNA constructs or siRNA duplexes thus provides a strategy to enhance the efficacy and the specificity of RNAi in experimental and potentially therapeutic settings.
Regulation of protein translation through mRNA structure influences MHC class I loading and T cell recognition
Authors: Tellam Judy , Smith Corey , Rist Michael , Webb Natasha , Cooper Leanne , Vuocolo Tony , Connolly Geoff , Tscharke David C. , Devoy Michael P. , Khanna Rajiv
Published: July 2008

Many viruses avoid immune surveillance during latent infection through reduction in the synthesis of virally encoded proteins. Although antigen presentation critically depends on the level of viral protein synthesis, the precise mechanism used to regulate the generation of antigenic peptide precursors remains elusive. Here, we demonstrate that a purine overloaded virally encoded mRNA lacking secondary structure significantly impacts the efficiency of protein translation and prevents endogenous antigen presentation. Reducing this purine bias through the generation of constructs expressing codon-modified sequences, while maintaining the encoded protein sequence, increased the stem–loop structure of the corresponding mRNA and dramatically enhanced self-synthesis of the viral protein. As a consequence, a higher number of HLA–peptide complexes were detected on the surface of cells expressing this viral protein. Furthermore, these cells were more efficiently recognized by virus-specific T cells compared with those expressing the same antigen expressed by a purine-biased mRNA. These findings delineate a mechanism by which viruses regulate self-synthesis of proteins and offer an effective strategy to evade CD8+T cell-mediated immune regulation.