bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of GPS zenith delay assimilation on convective‐scale prediction of Mediterranean heavy rainfall
Authors: Yan X. , Ducrocq V. , Poli P. , Hakam M. , Jaubert G. , Walpersdorf A.
Published: February 2009

The numerical weather prediction forecast skill of heavy precipitation events in the Mediterranean regions is currently limited, partly because of the paucity of water vapor observations assimilated today. An attempt to fill this observational gap is provided by Global Positioning System (GPS) ground station data over Europe that are now routinely processed into observations of Zenith Total Delay (ZTD), which is closely related to the tropospheric water vapor content. We evaluate here the impact of assimilating the GPS ZTD on the high‐resolution (2.4‐km) nonhydrostatic prediction of rainfall for the heavy precipitation event of 5–9 September 2005 over Southern France. First, we assimilate the GPS ZTD observations in the three‐dimensional variational (3DVAR) data assimilation system of the 9.5‐km horizontal resolution ALADIN/France hydrostatic model with parameterized convection. This one‐month‐long assimilation experiment includes the heavy rainfall period. Prior to the assimilation, a GPS ZTD observation preprocessing is carried out for quality control and bias correction. We find that the GPS ZTD observations impact mainly the representation of the humidity in the low to middle troposphere. We then conduct forecast trials with the Meso‐NH model, which explicitly resolves the deep convection, using the analyses of the 3DVAR ALADIN/France assimilation experiments as initial and boundary conditions. Our results indicate a benefit of GPS ZTD data assimilation for improving the Meso‐NH precipitation forecasts of the heavy rainfall event.
Hydrologic support of carbon dioxide flux revealed by whole‐lake carbon budgets
Authors: Stets Edward G. , Striegl Robert G. , Aiken George R. , Rosenberry Donald O. , Winter Thomas C.
Published: February 2009

Freshwater lakes are an important component of the global carbon cycle through both organic carbon (OC) sequestration and carbon dioxide (CO2) emission. Most lakes have a net annual loss of CO2 to the atmosphere and substantial current evidence suggests thatbiologic mineralization of allochthonous OC maintains this flux. Because net CO2 flux to the atmosphere implies net mineralization of OC within the lake ecosystem, it is also commonly assumed that net annual CO2 emission indicates negative net ecosystem production (NEP). We explored the relationship between atmospheric CO2 emission and NEP in two lakes known to have contrasting hydrologic characteristics and net CO2 emission. We calculated NEP for calendar year 2004 using whole‐lake OC and inorganic carbon (IC) budgets, NEPOC and NEPIC, respectively, and compared the resulting values to measured annual CO2 flux from the lakes. In both lakes, NEPOC and NEPIC were positive, indicating net autotrophy. Therefore CO2 emission from these lakes was apparently not supported by mineralization of allochthonous organic material. In both lakes, hydrologic CO2 inputs, as well as CO2 evolved from net calcite precipitation, could account for the net CO2 emission. NEP calculated from diel CO2 measurements was also affected by hydrologic inputs of CO2. These results indicate that CO2 emission and positive NEP may coincide in lakes, especially in carbonate terrain, and that all potential geologic, biogeochemical, and hydrologic sources of CO2 need to be accounted for when using CO2 concentrations to infer lake NEP.
Expression of the iron-regulatory protein haemojuvelin in retina and its regulation during cytomegalovirus infection
Authors: Gnana-Prakasam Jaya P. , Zhang Ming , Martin Pamela M. , Atherton Sally S. , Smith Sylvia B. , Ganapathy Vadivel
Published: February 2009

Haemochromatosis is a genetic disorder of iron overload resulting from loss-of-function mutations in genes coding for the iron-regulatory proteins HFE [HLA-like protein involved in iron (Fe) homoeostasis], transferrin receptor 2, ferroportin, hepcidin and HJV (haemojuvelin). Expression of the first four genes coding for these proteins in retina has been established. Here we report on the expression of HJV. Since infection of retina with CMV (cytomegalovirus) causes blindness, we also investigated the expression of HJV and other iron-regulatory proteins in retina during CMV infection. HJV (HJV gene) mRNA was expressed in RPE (retinal pigment epithelium)/eyecup and neural retina in mouse. In situ hybridization and immunohistochemistry confirmed the presence of HJV mRNA and protein in RPE, outer and inner nuclear layers, and ganglion cell layer. Immunocytochemistry with cell lines and primary cell cultures showed HJV expression in RPE and Müller cells. In RPE, the expression was restricted to apical membrane. Infection of primary cultures of mouse RPE with CMV increased HJV mRNA and protein levels. Under similar conditions, HFE (HFE gene) mRNA levels were not altered, but HFE protein was decreased. Hepcidin expression was, however, not altered. These findings were demonstrable in vivo with CMV-infected mouse retina. The CMV-induced up-regulation of HJV in RPE was independent of changes in HFE because the phenomenon was also seen in HFE-null RPE cells. CMV-infected primary RPE cells showed evidence of iron accumulation and oxidative stress, as indicated by increased levels of ferritin and hydroxynonenal. The observed changes in HJV expression and iron status during CMV infection in retina may have significance in the pathophysiology of CMV retinitis
Current-sweep-rate dependence of spin-torque driven dynamics in magnetic nanopillars
Authors: O’Gorman B. , Dietze S. , Tsoi M.
Published: February 2009

We report on the measurements of current-driven dynamics in magnetic nanopillars as a function of the current-sweep rate. These measurements were intended to verify the recently predicted thermal-activation nature of current-induced precessional states in spin-valve multilayers. For a fixed temperature and field (applied perpendicular to the layers), the critical current for dynamic excitations was found to increase logarithmically with the sweep rate as expected for a thermally activated process. However, we observed little if any dependence of this behavior on temperature. We discuss the implications of this in terms of a simple model of spin-torque driven magnetization dynamics.
Study of slider-defect interaction at ultralow flying height by dynamic flying height control
Authors: Tani H. , Kanda M. , Kubota M. , Tagawa N.
Published: February 2009

In this study, the interaction of the magnetic head slider and magnetic disk defects were studied as the function of the head flying height controlled by the dynamic flying height (DFH) control method. In the conventional glide test, the flying height is set as a function of the rotational velocity. However, in the glide test using the DFH control method, the flying height could be set as a function of DFH power on a constant rotational velocity. A magnetic disk with two types of defects—a crater and a 5nm bump—was prepared. The acoustic emission (AE) signal at the slider-defect contacts from the conventional glide test and the DFH glide test were then compared. The results of the experiment indicated that the DFH glide test could detect these defects at a few nanometers flying height, but the conventional glide test could not detect them. This was because the AE signal burst below a flying height of 3nm. The AE signal output of the DFH glide test was higher than that of the conventional glide test, and the AE signal of the defect contact increased at a greater rotational velocity. It was concluded that the DFH control glide testing was one of the most important techniques for the future high-density recording disks.
Control of the number of {110} grains and magnetic induction in inhibitor-free 3% Si–Fe strips
Authors: Kim S. B. , Soh J. Y. , Heo N. H.
Published: February 2009

After annealing with various heating rates, all the strips containing 58 ppm sulfur consisted of {110} grains, showing a magnetic induction over 1.95 T. Magnetic induction in the strips containing 11 ppm sulfur, on the contrary, varied from 1.98 to 1.48 T, depending on the additional amount of {100} and {111} grains. Direct isothermal annealing and a heating rate of 25 °C/h were advantageous for obtaining final {110} texture. These results are explained in terms of the segregation kinetics of sulfur affected by heating rate and the grain boundary pinning effect of the segregated sulfur.
First-order magnetic phase transition in FeRh–Pt thin films
Authors: Lu W. , Nam N. T. , Suzuki T.
Published: February 2009

The first-order antiferromagnetic/ferromagnetic phase transition in ordered FeRh100−XPtX (0≦X≦15) thin films grown onto MgO(100) substrate was investigated by temperature dependent magnetization measurements. It is shown that the phase transition temperature increases with increasing Pt content. The field dependence of transition temperature was also measured and a shift of −8 to −3.3 K/T is observed for FeRh100−XPtX thin films with increasing Pt contents. In addition, the entropy changes associated with the magnetic phase transition were studied, and it can be proposed that the change in electronic entropy associated with the magnetic moment of Rh atoms is the main mechanism for the first-order magnetic phase transition in ordered FeRh-based alloys.
Photoelectron imaging and theoretical investigation of bimetallic Bi1–2Ga–2− and Pb1–4− cluster anions
Authors: Sobhy M. A. , Reveles J. Ulises , Gupta Ujjwal , Khanna Shiv N. , Castleman A. W.
Published: February 2009

We present the results of photoelectron velocity-map imaging experiments for the photodetachment of small negatively charged BimGan (m=1–2, n=0–2), and Pbn (n=1–4) clusters at 527 nm. The photoelectron images reveal new features along with their angular distributions in the photoelectron spectra of these clusters. We report the vertical detachment energies of the observed multiple electronic bands and their respective anisotropy parameters for the BimGan and Pbn clusters derived from the photoelectron images. Experiments on the BiGan clusters reveal that the electron affinity increases with the number of Ga atoms from n=0 to 2. The BiGa2− cluster is found to be stable, both because of its even electron number and the high electron affinity of BiGa2. The measured photoelectron angular distributions of the BimGan and Pbn clusters are dependent on both the orbital symmetry and electron kinetic energies. Density-functional theory calculations employing the generalized gradient approximation for the exchange-correlation potential were performed on these clusters to determine their atomic and electronic structures. From the theoretical calculations, we find that the BiGa2−, Bi2Ga3− and Bi2Ga5− (anionic), and BiGa3, BiGa5, Bi2Ga4 and Bi2Ga6 (neutral) clusters are unusually stable. The stability of the anionic and neutral Bi2Gan clusters is attributed to an even-odd effect, with clusters having an even number of electrons presenting a larger gain in energy through the addition of a Ga atom to the preceding size compared to odd electron systems. The stability of the neutral BiGa3 cluster is rationalized as being similar to BiAl3, an all-metal aromatic cluster.
Layered discrete variable representations and their application within the multiconfigurational time-dependent Hartree approach
Authors: Manthe Uwe
Published: February 2009

The multiconfigurational time-dependent Hartree (MCTDH) approach facilitates multidimensional quantum dynamics calculations by employing a layered representation: in the upper layer of the representation the multidimensional wave function is expanded in a basis of time-dependent single-particle functions, in the lower layer then these single-particle functions are represented in a larger time-independent basis. This two layer approach can be generalized to a multilayer MCTDH representation to further increase the numerical efficiency. In recent work [U. Manthe, J. Chem. Phys. 128, 164116 (2008)], a quadrature scheme has been introduced which facilitates multilayer MCTDH calculations for Hamiltonians with general potential energy functions. Based on time-dependent discrete variable representation (DVR) grids corresponding to the single-particle function bases the scheme employs the correlation DVR (CDVR) approach. The present work shows that serious problems arise when this original multilayer CDVR approach is applied for accurate calculations of vibrational states. A solution to these problems is presented which uses a revised scheme to define the time-dependent DVR grids entering into the CDVR scheme. Applications studying the vibrational states of CH3 demonstrate that the resulting revised multilayer MCTDH/CDVR approach yields smoothly convergent and accurate results.
Initial rates of aggregation for dilute, granular flows of wet particles
Authors: Kantak A. A. , Hrenya C. M. , Davis R. H.
Published: February 2009

Molecular dynamics (MD) simulations are used to determine the agglomeration rates of wet grains (particles coated with a viscous, liquid layer) engaged in simple shear flow under dilute conditions. In this work, a closed-form model derived from the elastohydrodynamic theory describes the normal restitution coefficient for binary collisions. Unlike previous MD studies, the particle deformation is not assumed to depend on a particle “overlap” (penetration), but instead depends on the formal coupling of Hertzian deformation theory with lubrication theory. The initial rate of doublet formation is studied as a function of system properties and the energy input to the system. In addition to the system properties, the distribution of relative velocities in the system is found to be a key factor influencing the initial rates of clustering. A theory based on estimating the collision frequency and the critical velocity below which no rebound is observed—due to viscous dissipation—is found to provide a good approximation of the initial aggregation rate. The rate of aggregation is found to increase with increasing number of particles in the system, increasing solid fraction, decreasing overall Stokes number, and decreasing compliance parameter.
Understanding adsorption of hydrogen atoms on graphene
Authors: Casolo Simone , Løvvik Ole Martin , Martinazzo Rocco , Tantardini Gian Franco
Published: February 2009

Adsorption of hydrogen atoms on a single graphite sheet (graphene) has been investigated by first-principles electronic structure means, employing plane-wave based periodic density functional theory. A 5×5 surface unit cell has been adopted to study single and multiple adsorptions of H atoms. Binding and barrier energies for sequential sticking have been computed for a number of configurations involving adsorption on top of carbon atoms. We find that binding energies per atom range from ∼0.8 to ∼1.9 eV, with barriers to sticking in the range 0.0–0.15 eV. In addition, depending on the number and location of adsorbed hydrogen atoms, we find that magnetic structures may form in which spin density localizes on a 3×3R30° sublattice and that binding (barrier) energies for sequential adsorption increase (decrease) linearly with the site-integrated magnetization. These results can be rationalized with the help of the valence-bond resonance theory of planar π conjugated systems and suggest that preferential sticking due to barrierless adsorption is limited to formation of hydrogen pairs.
Influence of the power on the particles generated in a low pressure radio frequency nitrogen-rich methane discharge
Authors: Massereau-Guilbaud Véronique , Pereira Jérémy , Géraud-Grenier Isabelle , Plain André
Published: February 2009

Particles are generated in low pressure radio frequency (13.56 MHz) CH4/N2 discharges containing 90% of nitrogen. The influence of the radio frequency power supply on the particle presence within the plasma is studied. Particles are evidenced by laser light scattering. The particle formation leads to modifications in the discharge electrical parameters such as the dc self-bias voltage and the phase angle third harmonic. The plasma is analyzed by optical emission spectroscopy by following the temporal evolution of excited species such as CN, N2, N2+, Ar, and He. Finally, the particle morphology and size are analyzed by scanning electron microscopy. The correlation between these results allows a better understanding of the power influence on the particle growth within the plasma.
Vibron hopping and bond anharmonicity in hot dense hydrogen
Authors: Feldman J. L. , Johnson J. Karl , Hemley Russell J.
Published: February 2009

The Raman-active vibron of dense hydrogen has been shown to exhibit unexpected changes as a function of pressure and temperature to above 100GPa. To understand these results we have performed supercell-based calculations using Van Kranendonk theory taking into account the renormalization of the hopping parameter by the lattice vibrations. We find that the major temperature dependence at this level of theory comes from the differences in populations of rotational states. The theory provides a fair description of the experimental results up to 70GPa. We examine in detail a number of assumptions made in the application of the Van Kranendonk model to hydrogen as a function of pressure and temperature. We also present results of hybrid path integral molecular dynamics calculations in the fluid state at a low pressure (7GPa) near the melting temperature. An amorphous-solid model of the fluid predicts that the Raman vibron frequencies change little upon melting, in agreement with experiment. The Van Kranendonk theory with fixed rotational identities of the molecules tends to predict more peaks in the Raman spectrum than are observed experimentally.
Tuning the electronic properties of the golden buckyball by endohedral doping: M@Au16− (M=Ag,Zn,In)
Authors: Wang Lei-Ming , Pal Rhitankar , Huang Wei , Zeng Xiao Cheng , Wang Lai-Sheng
Published: February 2009

The golden Au16− cage is doped systematically with an external atom of different valence electrons: Ag, Zn, and In. The electronic and structural properties of the doped clusters, MAu16− (M=Ag,Zn,In), are investigated by photoelectron spectroscopy and theoretical calculations. It is observed that the characteristic spectral features of Au16−, reflecting its near tetrahedral (Td) symmetry, are retained in the photoelectron spectra of MAu16−, suggesting endohedral structures with little distortion from the parent Au16− cage for the doped clusters. Density functional calculations show that the endohedral structures of M@Au16− with Td symmetry are low-lying structures, which give simulated photoelectron spectra in good agreement with the experiment. It is found that the dopant atom does not significantly perturb the electronic and atomic structures of Au16−, but simply donate its valence electrons to the parent Au16− cage, resulting in a closed-shell 18-electron system for Ag@Au16−, a 19-electron system for Zn@Au16− with a large energy gap, and a 20-electron system for In@Au16−. The current work shows that the electronic properties of the golden buckyball can be systematically tuned through doping.
Electromechanical displacement of piezoelectric-electrostrictive monolithic bilayer composites
Authors: Ngernchuklin P. , Akdoğan E. K. , Safari A. , Jadidian B.
Published: February 2009

We examine the electromechanical displacement of piezoelectric-electrostrictive monolithic bilayer composites with various piezoelectric volume percentage obtained by cosintering piezoelectric 0.65Pb(Mg1/3Nb2/3)O3-0.35PbTiO3 and electrostrictive 0.9Pb(Mg1/3Nb2/.3)O3-0.1PbTiO3 under unipolar and bipolar electric field excitation up to 10 kV/cm experimentally. It is shown that the effective d33 of the composites is limited by the electrostrictive layer, which acts as a capacitor in series to the piezoelectric layer, causing incomplete poling. We show that by controlling the volume content of the piezoelectric layer and constraining it with an electrostrictor, substantial strain amplification (15 μm for bipolar excitation) can be achieved while inducing asymmetry to the displacement with respect to the polarity of the applied field, which we discuss in the context of symmetry superposition.
Magnetocaloric properties of Mn3Sn2 from heat capacity measurements
Authors: Recour Q. , Mazet T. , Malaman B.
Published: February 2009

The heat capacity of the Mn3Sn2 compound was measured between 2 and 300 K in magnetic fields up to 7 T. The isothermal magnetic entropy change (ΔSM) and the adiabatic temperature change (ΔTad) were calculated from these data. In agreement with previous magnetic measurements, three transitions are detected in the zero-field heat capacity versus temperature curve, two λ-like peaks close to TC1∼262 K and TC2∼227 K due to ferromagneticlike second-order transitions and a third anomaly at Tt∼197 K ascribed to the development of a weak antiferromagnetic interaction. The Debye temperature is estimated to be ∼303 K from the low-temperature data. The thermal dependences of ΔSM and ΔTad present a two-peak response with peak maxima near TC1 and TC2. For a field variation of 5 T, the values of ΔTad are found to be ∼2.1 and ∼1.6 K, respectively. The results are discussed and compared to previously published data concerning other magnetic refrigerants working near room temperature.
Multiple conduction paths in boron δ-doped diamond structures
Authors: Tumilty Niall , Welch Joseph , Ye Haitao , Balmer Richard S. , Wort Christopher , Lang Richard , Jackman Richard B.
Published: February 2009

Impedance spectroscopy has been used to investigate conductivity within boron-doped diamond in an intrinsic/delta-doped/intrinsic (i-δ-i) multilayer structure. For a 5 nm thick delta layer, three conduction pathways are observed, which can be assigned to transport within the delta layer and to two differing conduction paths in the i-layers adjoining the delta layer. For transport in the i-layers, thermal trapping/detrapping processes can be observed, and only at the highest temperature investigated (673 K) can transport due to a single conduction process be seen. Impedance spectroscopy is an ideal nondestructive tool for investigating the electrical characteristics of complex diamond structures.
Enhanced blue-violet emission by inverse energy transfer to the Ge-related oxygen deficiency centers via Er3+ ions in metal-oxide semiconductor structures
Authors: Kanjilal A. , Rebohle L. , Voelskow M. , Skorupa W. , Helm M.
Published: February 2009

It is generally believed that the 1.5 μm Er luminescence is enhanced by transferring energy from Si nanocrystals to the nearest Er3+ ions in Er-doped Si-rich SiO2 layers during optical pumping. Here, the influence of Ge nanocrystals instead of excess Si in the same environment is studied using electroluminescence technique on metal-oxide-semiconductor structures. An increase of the 400 nm electroluminescence intensity with a concomitant reduction of the Er-related emission is observed. This is explained in the light of an inverse energy transfer process from Er3+ to the Ge-related oxygen-deficiency centers.
Analytical modeling of electrical conduction through tunneling quasiresonant states in a one-atom metallic nanowire
Authors: Grado-Caffaro M. A. , Grado-Caffaro M.
Published: February 2009

An analytical study is carried out on a given one-atom metallic wire for describing quantitatively tunneling resonance relative to the atom-lead coupling and for determining the total density of quasiresonant conduction states and the current versus electrochemical potential. The sensitivity of the abovementioned density to the electrochemical potential is evaluated. The size of the coupling between the atom at the wire and the involved leads is discussed in relation to quantum transport at quasiresonance. In addition, the current intensity in the wire is expressed in terms of a commutative-semigroup structure.
Surface effect on the size- and orientation-dependent elastic properties of single-crystal ZnO nanostructures
Authors: Hu Jun , Pan B. C.
Published: February 2009

We studied the elastic properties of ZnO nanofilms (NFs) and nanowires (NWs) terminated by either (101¯0) or (112¯0) surfaces, based on the empirical Buckingham-type potential. It is found that the Young’s moduli of ZnO NFs increase as the thicknesses decrease and that of (101¯0)-surface terminated NFs are systematically larger than that of (112¯0)-surface terminated ones. In these NFs, the surface atomic layers of both types of NFs are stiffened significantly with respect to the bulk ZnO, and the (101¯0)-surface layer is much stiffer than the (112¯0)-surface layer. In contrast, all the interior atomic layers are only slightly stiffer than the bulk ZnO, and are independent on the orientations. The ZnO NWs show similar size- and orientation-dependent mechanical behaviors which also originate from the significant stiffening of the surface atomic layers. Through this study, we predict that the mechanical properties of ZnO nanostructures can be manipulated through controlling the size and orientations of these materials.
Microclimate determines community composition but not richness of epiphytic understory bryophytes of rainforest and cacao agroforests in Indonesia
Authors: Sporn S. Goda , Bos Merijn M. , Hoffstätter-Müncheberg Monika , Kessler Michael , Gradstein S. Robbert
Published: February 2009

Management intensification in cultivated, tropical forests drives changes in the microclimate that can threaten native forest flora and fauna. In this study, we use epiphytic bryophytes, known to be sensitive to microclimatic changes due to their lack of a protective cuticle and the exposed habitat, to investigate the predictive power of microclimate for changes in species richness and composition. Bryophytes were sampled from understory trees in natural forest and cacao (Theobroma cacao L.) trees in two types of cacao agroforests (natural shade trees and planted shade trees) in Central Sulawesi, Indonesia. The microclimate in the agroforests was characterised by low air humidity and high air temperature during the afternoon. Bryophyte species richness did not differ between habitat types but species composition changed markedly from the natural forest to the cacao agroforests. Although no correlation between species richness and microclimate values could be found, a series of matrix-based analyses revealed a significantly positive relationship between similarities in species composition and in maximum values for temperature and minimum values for humidity, which suggests that microclimatic changes are a good predictor for high turnover of bryophyte community composition from natural forests to cacao agroforests.
Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin
Authors: Tripathi Swarnendu , Portman John J.
Published: February 2009

We explore how inherent flexibility of a protein molecule influences the mechanism controlling allosteric transitions by using a variational model inspired from work in protein folding. The striking differences in the predicted transition mechanism for the opening of the two domains of calmodulin (CaM) emphasize that inherent flexibility is key to understanding the complex conformational changes that occur in proteins. In particular, the C-terminal domain of CaM (cCaM), which is inherently less flexible than its N-terminal domain (nCaM), reveals “cracking” or local partial unfolding during the open/closed transition. This result is in harmony with the picture that cracking relieves local stresses caused by conformational deformations of a sufficiently rigid protein. We also compare the conformational transition in a recently studied even–odd paired fragment of CaM. Our results rationalize the different relative binding affinities of the EF-hands in the engineered fragment compared with the intact odd–even paired EF-hands (nCaM and cCaM) in terms of changes in flexibility along the transition route. Aside from elucidating general theoretical ideas about the cracking mechanism, these studies also emphasize how the remarkable intrinsic plasticity of CaM underlies conformational dynamics essential for its diverse functions.
Wildfire responses to abrupt climate change in North America
Authors: Marlon J. R. , Bartlein P. J. , Walsh M. K. , Harrison S. P. , Brown K. J. , Edwards M. E. , Higuera P. E. , Power M. J. , Anderson R. S. , Briles C. , Brunelle A. , Carcaillet C. , Daniels M. , Hu F. S. , Lavoie M. , Long C. , Minckley T. , Richard P. J. H. , Scott A. C. , Shafer D. S. , Tinner W. , Umbanhowar C. E. , Whitlock C.
Published: February 2009

It is widely accepted, based on data from the last few decades and on model simulations, that anthropogenic climate change will cause increased fire activity. However, less attention has been paid to the relationship between abrupt climate changes and heightened fire activity in the paleorecord. We use 35 charcoal and pollen records to assess how fire regimes in North America changed during the last glacial–interglacial transition (15 to 10 ka), a time of large and rapid climate changes. We also test the hypothesis that a comet impact initiated continental-scale wildfires at 12.9 ka; the data do not support this idea, nor are continent-wide fires indicated at any time during deglaciation. There are, however, clear links between large climate changes and fire activity. Biomass burning gradually increased from the glacial period to the beginning of the Younger Dryas. Although there are changes in biomass burning during the Younger Dryas, there is no systematic trend. There is a further increase in biomass burning after the Younger Dryas. Intervals of rapid climate change at 13.9, 13.2, and 11.7 ka are marked by large increases in fire activity. The timing of changes in fire is not coincident with changes in human population density or the timing of the extinction of the megafauna. Although these factors could have contributed to fire-regime changes at individual sites or at specific times, the charcoal data indicate an important role for climate, and particularly rapid climate change, in determining broad-scale levels of fire activity.
Pituitary adenylyl cyclase-activating polypeptide is an intrinsic regulator of Treg abundance and protects against experimental autoimmune encephalomyelitis
Authors: Tan Yossan-Var , Abad Catalina , Lopez Robert , Dong Hongmei , Liu Shen , Lee Alice , Gomariz Rosa P. , Leceta Javier , Waschek James A.
Published: February 2009

Pituitary adenylyl cyclase-activating polypeptide (PACAP) is a widely expressed neuropeptide originally discovered in the hypothalamus. It closely resembles vasoactive intestinal peptide (VIP), a neuropeptide well known to inhibit macrophage activity, promote Th2-type responses, and enhance regulatory T cell (Treg) production. Recent studies have shown that administration of PACAP, like VIP, can attenuate dramatically the clinical and pathological features of murine models of autoimmune diseases such as experimental autoimmune encephalomyelitis (EAE) and collagen-induced arthritis. However, specific roles (if any) of endogenous VIP and PACAP in the protection against autoimmune diseases have not been explored. Here, we subjected PACAP-deficient mice to myelin oligodendrocyte glycoprotein (MOG35–55)-induced EAE. MOG immunization of PACAP-deficient mice triggered heightened clinical and pathological manifestations of EAE compared to wild-type mice. The increased sensitivity was accompanied by enhanced mRNA expression of proinflammatory cytokines (TNFα, IL-6, IFN-γ, IL-12p35, IL-23p19, and IL-17), chemokines (MCP-1/CCL2, MIP-1α/CCL3, and RANTES/CCL5), and chemotactic factor receptors (CCR1, CCR2, and CCR5), but downregulation of the anti-inflammatory cytokines (IL-4, IL-10, and TGF-β) in the spinal cord. Moreover, the abundance of CD4+CD25+FoxP3+Tregs in lymph nodes and levels of FoxP3 mRNA in the spinal cord were also diminished. The reduction in Tregs was associated with increased proliferation and decreased TGF-β secretion in lymph node cultures stimulated with MOG. These results demonstrate that endogenous PACAP provides protection in EAE and identify PACAP as an intrinsic regulator of Treg abundance after inflammation.
Following movement of the L1 stalk between three functional states in single ribosomes
Authors: Cornish Peter V. , Ermolenko Dmitri N. , Staple David W. , Hoang Lee , Hickerson Robyn P. , Noller Harry F. , Ha Taekjip
Published: February 2009

The L1 stalk is a mobile domain of the large ribosomal subunit E site that interacts with the elbow of deacylated tRNA during protein synthesis. Here, by using single-molecule FRET, we follow the real-time dynamics of the L1 stalk and observe its movement relative to the body of the large subunit between at least 3 distinct conformational states: open, half-closed, and fully closed. Pretranslocation ribosomes undergo spontaneous fluctuations between the open and fully closed states. In contrast, posttranslocation ribosomes containing peptidyl-tRNA and deacylated tRNA in the classical P/P and E/E states, respectively, are fixed in the half-closed conformation. In ribosomes with a vacant E site, the L1 stalk is observed either in the fully closed or fully open conformation. Several lines of evidence show that the L1 stalk can move independently of intersubunit rotation. Our findings support a model in which the mobility of the L1 stalk facilitates binding, movement, and release of deacylated tRNA by remodeling the structure of the 50S subunit E site between 3 distinct conformations, corresponding to the E/E vacant, P/E hybrid, and classical states.
Challenges of Implementing National Guidelines for the Control and Prevention of Methicillin-Resistant Staphylococcus aureus Colonization or Infection in Acute Care Hospitals in the Republic of Ireland
Authors: Fitzpatrick Fidelma , Roche Fiona , Cunney Robert , Humphreys Hilary ,   Strategy for the Control of Antimicrobial Resistance in Ireland Infection Control Subcommittee
Published: February 2009

Of the 49 acute care hospitals in Ireland that responded to the survey questionnaire drafted by the Infection Control Subcommittee of the Health Protection Surveillance Centre's Strategy for the Control of Antimicrobial Resistance in Ireland, 43 reported barriers to the full implementation of national guidelines for the control and prevention of methicillin-resistant Staphylococcus aureus infection; these barriers included poor infrastructure (42 hospitals), inadequate laboratory resources (40 hospitals), inadequate staffing (39 hospitals), and inadequate numbers of isolation rooms and beds (40 hospitals). Four of the hospitals did not have an educational program on hand hygiene, and only 17 had an antibiotic stewardship program.
Lightweight comparison of RNAs based on exact sequence–structure matches
Authors: Heyne Steffen , Will Sebastian , Beckstette Michael , Backofen Rolf
Published: February 2009

Motivation: Specific functions of ribonucleic acid (RNA) molecules are often associated with different motifs in the RNA structure. The key feature that forms such an RNA motif is the combination of sequence and structure properties. In this article, we introduce a new RNA sequence–structure comparison method which maintains exact matching substructures. Existing common substructures are treated as whole unit while variability is allowed between such structural motifs.

Based on a fast detectable set of overlapping and crossing substructure matches for two nested RNA secondary structures, our method ExpaRNA (exact pattern of alignment of RNA) computes the longest collinear sequence of substructures common to two RNAs in O(H·nm) time and O(nm) space, where H ≪ n·m for real RNA structures. Applied to different RNAs, our method correctly identifies sequence–structure similarities between two RNAs.

Results: We have compared ExpaRNA with two other alignment methods that work with given RNA structures, namely RNAforester and RNA_align. The results are in good agreement, but can be obtained in a fraction of running time, in particular for larger RNAs. We have also used ExpaRNA to speed up state-of-the-art Sankoff-style alignment tools like LocARNA, and observe a tradeoff between quality and speed. However, we get a speedup of 4.25 even in the highest quality setting, where the quality of the produced alignment is comparable to that of LocARNA alone.

Availability: The presented algorithm is implemented in the program ExpaRNA, which is available from our website (http://www.bioinf.uni-freiburg.de/Software).

Contact: {exparna@informatik.uni-freiburg.de,backofen@informatik.uni-freiburg.de}

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genetic network inference as a series of discrimination tasks
Authors: Kimura Shuhei , Nakayama Satoshi , Hatakeyama Mariko
Published: February 2009

Motivation: Genetic network inference methods based on sets of differential equations generally require a great deal of time, as the equations must be solved many times. To reduce the computational cost, researchers have proposed other methods for inferring genetic networks by solving sets of differential equations only a few times, or even without solving them at all. When we try to obtain reasonable network models using these methods, however, we must estimate the time derivatives of the gene expression levels with great precision. In this study, we propose a new method to overcome the drawbacks of inference methods based on sets of differential equations.

Results: Our method infers genetic networks by obtaining classifiers capable of predicting the signs of the derivatives of the gene expression levels. For this purpose, we defined a genetic network inference problem as a series of discrimination tasks, then solved the defined series of discrimination tasks with a linear programming machine. Our experimental results demonstrated that the proposed method is capable of correctly inferring genetic networks, and doing so more than 500 times faster than the other inference methods based on sets of differential equations. Next, we applied our method to actual expression data of the bacterial SOS DNA repair system. And finally, we demonstrated that our approach relates to the inference method based on the S-system model. Though our method provides no estimation of the kinetic parameters, it should be useful for researchers interested only in the network structure of a target system.

Contact:  kimura@ike.tottori-u.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Meta-analysis of age-related gene expression profiles identifies common signatures of aging
Authors: de Magalhães João Pedro , Curado João , Church George M.
Published: February 2009

Motivation: Numerous microarray studies of aging have been conducted, yet given the noisy nature of gene expression changes with age, elucidating the transcriptional features of aging and how these relate to physiological, biochemical and pathological changes remains a critical problem.

Results: We performed a meta-analysis of age-related gene expression profiles using 27 datasets from mice, rats and humans. Our results reveal several common signatures of aging, including 56 genes consistently overexpressed with age, the most significant of which was APOD, and 17 genes underexpressed with age. We characterized the biological processes associated with these signatures and found that age-related gene expression changes most notably involve an overexpression of inflammation and immune response genes and of genes associated with the lysosome. An underexpression of collagen genes and of genes associated with energy metabolism, particularly mitochondrial genes, as well as alterations in the expression of genes related to apoptosis, cell cycle and cellular senescence biomarkers, were also observed. By employing a new method that emphasizes sensitivity, our work further reveals previously unknown transcriptional changes with age in many genes, processes and functions. We suggest these molecular signatures reflect a combination of degenerative processes but also transcriptional responses to the process of aging. Overall, our results help to understand how transcriptional changes relate to the process of aging and could serve as targets for future studies.

Availability:  http://genomics.senescence.info/uarrays/signatures.html

Contact:  jp@senescence.info

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genetic Regulation of Meiotic Cross-Overs between Related Genomes inBrassica napusHaploids and Hybrids
Authors: Nicolas Stéphane D. , Leflon Martine , Monod Hervé , Eber Frédérique , Coriton Olivier , Huteau Virginie , Chèvre Anne-Marie , Jenczewski Eric
Published: February 2009

Although the genetic regulation of recombination in allopolyploid species plays a pivotal role in evolution and plant breeding, it has received little recent attention, except in wheat (Triticum aestivum). PrBn is the main locus that determines the number of nonhomologous associations during meiosis of microspore cultured Brassica napus haploids (AC; 19 chromosomes). In this study, we examined the role played by PrBn in recombination. We generated two haploid × euploid populations using two B. napus haploids with differing PrBn (and interacting genes) activity. We analyzed molecular marker transmission in these two populations to compare genetic changes, which have arisen during meiosis. We found that cross-over number in these two genotypes was significantly different but that cross-overs between nonhomologous chromosomes showed roughly the same distribution pattern. We then examined genetic recombination along a pair of A chromosomes during meiosis of B. rapa × B. napus AAC and AACC hybrids that were produced with the same two B. napus genotypes. We observed significant genotypic variation in cross-over rates between the two AAC hybrids but no difference between the two AACC hybrids. Overall, our results show that PrBn changes the rate of recombination between nonhomologous chromosomes during meiosis of B. napus haploids and also affects homologous recombination with an effect that depends on plant karyotype.
Curry spice allergy associated with pollen‐food allergy syndrome and latex fruit‐syndrome
Authors: YAGAMI Akiko , NAKAZAWA Yuri , SUZUKI Kayoko , MATSUNAGA Kayoko
Published: February 2009

We report a 22‐year‐old woman with urticaria, dyspnea and bronchial asthma‐like attacks after eating curried rice. We found the symptoms to be due to an immediate‐type allergy caused by spice antigens contained in curry spices by detailed questioning, skin test and measurement of specific immunoglobulin (Ig)E antibodies. This case was complicated with pollen‐food allergy syndrome (PFAS) from melon and latex allergy (LA) to natural rubber latex (NRL) antigen and she had also had atopic dermatitis, allergic rhinitis and pollinosis. Serum specific IgE antibodies to birch profilin (Bet v 2), latex profilin (Hev b 8), and timothy profilin (Phl p 12) were detected. She also showed positive reactions to several Apiaceae families, fruits and latex antigens in skin prick test. Based on these findings, we considered her symptoms to be involved with spice allergy, PFAS and latex‐fruit syndrome.
Lichen amyloidosis induced on the upper back by long‐term friction with a nylon towel
Authors: YOSHIDA Aki , TAKAHASHI Kazuhiro , TAGAMI Hachiro , AKASAKA Toshihide
Published: February 2009

Primary localized cutaneous amyloidosis can take several clinical forms. In Asia, macular amyloidosis caused by prolonged friction from a rough nylon towel or brush is common, and macular amyloidosis and lichen amyloidosis occasionally occur together, as so‐called biphasic amyloidosis. We report herein the case of an 83‐year‐old Japanese man with lichen amyloidosis caused by prolonged nylon towel friction. This patient presented with unique symmetrical papular lesions on the upper back and shoulders. Lesions comprised slightly shiny, brownish, fine uniform papules approximately 0.5 mm in diameter, showing a partially linear, annular or rippled arrangement. Although this case was caused by prolonged nylon towel friction, no coexisting macular lesions could be found. To the best of our knowledge, this represents the first case of lichen amyloidosis induced by nylon towel friction in the absence of the macular amyloidosis that is usually observed in such cases. We instructed the patient to stop the habit of nylon towel rubbing and prescribed a topical steroid ointment and cepharanthine. After 6 months of treatment, papular lesions became clearly flatter.
Allergic contact dermatitis from temporary henna tattoo
Authors: JOVANOVIC Dragan L. , SLAVKOVIC‐JOVANOVIC Maja R.
Published: February 2009

Temporary henna tattooing has been very popular during recent years. Henna (Lawsonia inermis) is a plant from the Lythraceae family. For henna tattooing, henna dye is used. It is a dark green powder, made from the leaves of the plant, used for hair dyeing and body tattooing. Very often, para‐phenylenediamine (PPD) is added to henna dye to make color blacker and to speed up dyeing. PPD may be a very potent contact sensitizer. We report a 9‐year‐old boy with allergic contact dermatitis due to temporary henna tattooing. Patch testing showed a positive reaction to PPD. After the treatment with topical corticosteroid and oral antihistamines, the lesion cleared with discrete residual hypopigmentation.
Comparison of the distribution patterns of BK polyomavirus lineages among China, Korea and Japan: Implications for human migrations in northeast Asia
Authors: Zhong Shan , Jeong Byung‐Hoon , Ikegaya Hiroshi , Kim Yong‐Sun , Xu Yawei , Zhu Mengyun , Chao Yuegen , Suzuki Makoto , Kitamura Tadaichi , Homma Yukio , Yogo Yoshiaki
Published: February 2009

BKV is widespread among humans, infecting children asymptomatically and then persisting in renal tissue. Based on the serological or phylogenetic method, BKV isolates worldwide are classified into four subtypes (I–IV), with subtypes I and IV further divided into several genetically‐distinct subgroups. Since, similarly to JCV, a close relationship exists between BKV lineages and human populations, BKV should be useful as a marker to trace human migrations. To elucidate ancient human migrations in northeast Asia, urine samples were collected from immunocompetent elderly patients in Shanghai, China; Anyang, South Korea; and various locations in Japan. Partial and complete BKV genomes from these samples were amplified and sequenced using PCR, and the determined sequences were classified into subtypes and subgroups by phylogenetic and SNP analyses. In addition, based on an SNP analysis, the major subtype I subgroup (I/c) was classified into two subdivisions, I/c/Ch and I/c/KJ. The distribution patterns of BKV subgroups and subdivisions among the three regions were compared. Some aspects of the subgroup and subdivision distribution were more similar between Korea and Japan, but others were more similar between China and Korea or between China and Japan. Based on these findings, we inferred various northeast Asian migrations. Most of the JCV‐based inferences of northeastern Asian migrations were consistent with those based on BKV, but the previously suggested migration route from the Asian continent to the Japanese archipelago seemed to need revision.