bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical variability of seawater in relation to particle concentration, composition, and size distribution in the nearshore marine environment at Imperial Beach, California
Authors: Woźniak Sławomir B. , Stramski Dariusz , Stramska Malgorzata , Reynolds Rick A. , Wright Vanessa M. , Miksic Ezra Y. , Cichocka Marta , Cieplak Agnieszka M.
Published: August 2010

We examined optical variability of seawater in relation to particle concentration, composition, and size distribution in the nearshore marine environment at Imperial Beach, California, over a period of 1.5 years. Measurements included the hyperspectral inherent optical properties (IOPs) of seawater (particulate beam attenuation, particulate and CDOM absorption coefficients within the spectral range 300–850 nm), particle size distribution (PSD) within the diameter range 2–60 μm, and the mass concentrations of suspended particulate matter (SPM), particulate organic carbon (POC), and chlorophyll a (Chl). The particulate assemblage spanned a wide range of concentrations and composition, from the dominance of mineral particles (POC/SPM < 0.06) with relatively steep PSDs to the high significance or dominance of organic particles (POC/SPM > 0.25) with considerably greater contribution of larger‐sized particles. Large variability in the particulate characteristics produced correspondingly large variability in the IOPs; up to 100‐fold variation in particulate absorption and scattering coefficients and several‐fold variation in the SPM‐specific and POC‐specific coefficients. Analysis of these data demonstrates that knowledge of general characteristics about the particulate composition and size distribution leads to improved interpretations of the observed optical variability. We illustrate a multistep empirical approach for estimating proxies of particle concentration (SPM and POC), composition (POC/SPM), and size distribution (median diameter) from the measured IOPs in a complex coastal environment. The initial step provides information about a proxy for particle composition; other particulate characteristics are subsequently derived from relationships specific to different categories of particulate composition.
An advection‐condensation model for subtropical water vapor isotopic ratios
Authors: Galewsky Joseph , Hurley John V.
Published: August 2010

The processes controlling the joint distribution of water vapor specific humidity (q) and isotopic ratios (δ) at the subtropical relative humidity (RH) minimum are investigated through the development of an advection‐condensation model that is applied to an idealized GCM and a GCM nudged by reanalysis data. The first‐order characteristics of the joint distribution of δ and q values from the subtropical RH minimum can be satisfactorily explained by the model. In an idealized GCM with physics that closely approximates the assumptions in the advection‐condensation model, the reconstructed δ and q distribution are quite close to that in the model. When compared to an isotopic simulation from a full‐physics GCM nudged by reanalysis data, the advection‐condensation model reproduces the first‐order aspects of the δ and q distribution but underestimates the variability. In both cases, the errors can potentially be attributed to insufficient variability in the representation of domains contributing water vapor to the subtropical RH minimum and, in the case of the isotopic reanalysis, to the omission of cloud microphysics. This study suggests that long‐term monitoring of water vapor isotopic ratios may provide a way to distinguish between different mechanisms for the projected moistening of the subtropics.
Estimating climatological planetary boundary layer heights from radiosonde observations: Comparison of methods and uncertainty analysis
Authors: Seidel Dian J. , Ao Chi O. , Li Kun
Published: August 2010

Planetary boundary layer (PBL) processes control energy, water, and pollutant exchanges between the surface and free atmosphere. However, there is no observation‐based global PBL climatology for evaluation of climate, weather, and air quality models or for characterizing PBL variability on large space and time scales. As groundwork for such a climatology, we compute PBL height by seven methods, using temperature, potential temperature, virtual potential temperature, relative humidity, specific humidity, and refractivity profiles from a 10 year, 505‐station radiosonde data set. Six methods are directly compared; they generally yield PBL height estimates that differ by several hundred meters. Relative humidity and potential temperature gradient methods consistently give higher PBL heights, whereas the parcel (or mixing height) method yields significantly lower heights that show larger and more consistent diurnal and seasonal variations (with lower nighttime and wintertime PBLs). Seasonal and diurnal patterns are sometimes associated with local climatological phenomena, such as nighttime radiation inversions, the trade inversion, and tropical convection and associated cloudiness. Surface‐based temperature inversions are a distinct type of PBL that is more common at night and in the morning than during midday and afternoon, in polar regions than in the tropics, and in winter than other seasons. PBL height estimates are sensitive to the vertical resolution of radiosonde data; standard sounding data yield higher PBL heights than high‐resolution data. Several sources of both parametric and structural uncertainty in climatological PBL height values are estimated statistically; each can introduce uncertainties of a few 100 m.
Changes in soil nitrogen storage andδ15N with woody plant encroachment in a subtropical savanna parkland landscape
Authors: Boutton T. W. , Liao J. D.
Published: August 2010

Subtropical woodlands dominated by N‐fixing tree legumes have largely replaced grasslands in the Rio Grande Plains, southwestern United States, during the past century. To evaluate the impact of this vegetation change on the N cycle, we measured the mass and isotopic composition (δ15N) of N in the soil system of remnant grasslands and woody plant stands ranging in age from 10 to 130 years. Nitrogen accumulated at linear rates following woody encroachment in the litter (0.10–0.14 g N m−2yr−1), roots (0.63–0.98 g N m−2yr−1), and soils (0.75–3.50 g N m−2yr−1), resulting in a 50%–150% increase in N storage in the soil system (0–30 cm) in woody stands older than 60 years. Simultaneous decreases in soilδ15N of up to 2‰ in the upper 30 cm of the profile are consistent with a scenario in which N inputs have exceeded losses following woody encroachment and suggest N accrual was derived from symbiotic N fixation by tree legumes and/or differential atmospheric N deposition to wooded areas. Vertical uplift and lateral transfer of N by the more deeply and intensively rooted woody plants may have contributed to N accumulation in wooded areas, but soilδ15N values are inconsistent with this explanation. N accumulation following woody encroachment may alter soil N availability, species interactions and successional dynamics, flux rates of key trace gases such as NOXand N2O and ecosystem C sequestration. Given the geographic dimensions of woody encroachment, these results may have implications for atmospheric composition and the climate system.
Is there regime behavior in monsoon convection in the late 20th century?
Authors: Turner A. G. , Hannachi A.
Published: August 2010

Mixture model techniques are applied to a daily index of monsoon convection from ERA‐40 reanalysis to show regime behavior. The result is the existence of two significant regimes showing preferred locations of convection within the Asia/Western‐North Pacific domain, with some resemblance to active‐break events over India. Simple trend analysis over 1958–2001 shows that the first regime has become less frequent while the second becomes much more dominant. Both undergo a change in structure contributing to the total OLR trend over the ERA‐40 period. Stratifying the data according to a large‐scale dynamical index of monsoon interannual variability, we show the regime occurrence to be strongly perturbed by the seasonal condition, in agreement with conceptual ideas. This technique could be used to further examine predictability issues relating the seasonal mean and intraseasonal monsoon variability or to explore changes in monsoon behavior in centennial‐scale model integrations.
CO oxidation on PdO surfaces
Authors: Hirvi Janne T. , Kinnunen Toni-Jani J. , Suvanto Mika , Pakkanen Tapani A. , Nørskov Jens K.
Published: August 2010

Density functional calculations were performed in order to investigate CO oxidation on two of the most stable bulk PdO surfaces. The most stable PdO(100) surface, with oxygen excess, is inert against CO adsorption, whereas strong adsorption on the stoichiometric PdO(101) surface leads to favorable oxidation via the Langmuir–Hinshelwood mechanism. The reaction with a surface oxygen atom has an activation energy of 0.66 eV, which is comparable to the lowest activation energies observed on metallic surfaces. However, the reaction rate may be limited by the coverage of molecular oxygen. Actually, the reaction with the site blocking molecular oxygen is slightly more favorable, enabling also possible formation of carbonate surface species at low temperatures. The extreme activity of strongly bonded surface oxygen atoms is more greatly emphasized on the PdO(100)–O surface. The direct reaction without adsorption, following the Eley–Rideal mechanism and taking advantage of the reaction tunnel provided by the adjacent palladium atom, has an activation energy of only 0.24 eV. The reaction mechanism and activation energy for the palladium activated CO oxidation on the most stable PdO(100)–O surface are in good agreement with experimental observations.
Enhancement of the hole injection into regioregular poly(3-hexylthiophene) by molecular doping
Authors: Zhang Yuan , Blom Paul W. M.
Published: August 2010

The hole injection in Schottky barriers formed between p-type doped regioregular poly(3-hexylthiophene-2,5-diyl) (rr-P3HT) and silver (Ag) is investigated. The rr-P3HT is controllably doped using the acceptor 2,3,5,6-Tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ). We demonstrate that only one order of magnitude increase in the background hole density p0, from 2×1016 to 2×1017 cm−3, enhances the hole injection with two orders of magnitude. The hole injection barrier is lowered by 0.5 eV and exhibits a linear dependence on p0, which can be explained by doping induced surface charges.
Photoionization of iodine atoms: Angular distributions and relative partial photoionization cross-sections in the energy region 11.0–23.0 eV
Authors: Eypper Marie , Innocenti Fabrizio , Morris Alan , Dyke John M. , Stranges Stefano , West John B. , King George C.
Published: August 2010

Relative partial photoionization cross-sections and angular distribution parameters, β, have been measured for the first, I+(P32)←I(P23/2), and fourth, I+(D12)←I(P23/2), (5p)−1 photoelectron (PE) bands of atomic iodine, by performing angle-resolved constant-ionic-state (CIS) measurements on these PE bands in the photon energy range 11.0–23.0 eV. Three Rydberg series, two ns and one nd series, which converge to the I+ P31 limit at 11.33 eV and four Rydberg series, two ns and two nd series, which converge to the I+ D12 limit at 12.15 eV were observed in the first PE band CIS spectra. The fourth band CIS spectrum showed structure in the 12.9–14.1eV photon energy range, which is also seen in the first band CIS spectra. This structure arises from excitation to ns and nd Rydberg states that are parts of series converging to the I+ S10 limit we reported on earlier, as well as 5s→5p excitations in the photon energy range 17.5–22.5 eV. These atomic iodine CIS spectra show reasonably good agreement with the equivalent spectra obtained for atomic bromine. The β-plots for the first PE band recorded up to the I+ P31 and I+ D12 limits only show resonances corresponding to some of the 5p→nd excitations observed in the first band CIS spectra scanned to the I+ D12 limit (12.15 eV). These plots are interpreted in terms of an angular momentum transfer model with the positive values of β obtained on resonances corresponding to parity allowed jt=1 and 3 channels and the off-resonance negative β values corresponding to parity unfavored channels, where jt is the quantum number for angular momentum transfer between the molecule, and the ion and photoelectron. The β-plots recorded for iodine are significantly different from those obtained for atomic bromine. Comparison of the experimental CIS spectra and β-plots with available theoretical results highlights the need for higher level calculations which include factors such as configuration interaction in the initial and final states, relativistic effects including spin-orbit interaction, and autoionization via resonant Rydberg states.
Molecular dynamics simulation of O2 sticking on Pt(111) using the ab initio based ReaxFF reactive force field
Authors: Valentini Paolo , Schwartzentruber Thomas E. , Cozmuta Ioana
Published: August 2010

The molecular dynamics technique with the ab initio based classical reactive force field ReaxFF is used to study the adsorption dynamics of O2 on Pt(111) for both normal and oblique impacts. Overall, good quantitative agreement with the experimental data is found at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF potential energy surface (PES) and the progressive suppression of a steering mechanism when increasing the translational kinetic energy (or the molecule’s rotational energy) because of steric hindrance. In the energy range between 0.1 and 0.4 eV, the sticking probability increases, similar to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3 due to an overall less attractive ReaxFF PES compared to experiments and density functional theory. For oblique impacts, the trapping probability is reduced by the nonzero parallel momentum because of the PES corrugation and does not scale with the total incident kinetic energy. Furthermore, our simulations predict quasispecular (slightly supraspecular) distributions of angles of reflection, in accordance with molecular beam experiments. Increasing the beam energy (between 1.2 and 1.7 eV) causes the angular distributions to broaden and to exhibit a tail toward the surface normal because molecules have enough momentum to get very near the surface and thus probe more corrugated repulsive regions of the PES.
On the magnetic field near the center of Helmholtz coils
Authors: Crosser M. S. , Scott Steven , Clark Adam , Wilt P. M.
Published: August 2010

We develop a series expansion for the calculation of the magnetic field near the center of Helmholtz coils and apply the result to a magnet of our design. Our analysis considers geometric details of the coils, the magnetic properties of the form and windings, conductor insulation effects, and several winding imperfections. We also consider the relaxation of coil symmetry which happens when the mean radius of each coil and the coil midplane separation distance are unequal. We compute the field uniformity near the coil’s center for three cases, including one where axial symmetry remains but geometric imperfections of the order of 10−3 of the coil “radius” exist.
Surface plasmon induced exciton redistribution in ZnCdO/ZnO coaxial multiquantum-well nanowires
Authors: Liu B. , Cheng C. W. , Chen R. , Ekahana S. A. , Yang W. F. , Wang S. J. , Sum T. C. , Shen Z. X. , Fan H. J. , Sun H. D.
Published: August 2010

The authors present the surface plasmon effects of Au nanoparticles on the photoluminescence properties of ZnCdO/ZnO coaxial multiquantum-well nanowires fabricated using chemical vapor deposition and pulse laser deposition methods. The spontaneous emission rate from ZnCdO quantum wells was increased by surface plasmon coupling by 1.29 times. The strong plasmon coupling between ZnO barriers and Au nanoparticles provides an extra fast decay channel for excitons generated in ZnO barrier layer and leads to exciton redistribution in ZnCdO/ZnO coaxial quantum wells, which promotes radiative recombination in ZnO barriers but reduces the number of excitons relaxing into the ZnCdO quantum wells.
Interface-controlled layer exchange in metal-induced crystallization of germanium thin films
Authors: Hu Shu , Marshall Ann F. , McIntyre Paul C.
Published: August 2010

Low-temperature synthesis of polycrystalline germanium (poly-Ge) thin films is of great interest in thin-film photovoltaic and electronics applications. We demonstrate metal (Al)-induced crystallization to form poly-Ge thin films on both glass and polymer substrates at temperatures as low as 200 °C. An interfacial diffusion control layer, intentionally interposed between the Al and the underlying amorphous Ge (a-Ge) layer, is found to achieve layer exchange while suppressing uncontrolled Ge crystallization within the bilayer samples. Germanium thin films with micron-size grains and (111)-preferred orientation are prepared by controlled Ge nucleation and Ge lateral overgrowth of Al during a-Ge crystallization.
A nanoscale Ti/GaAs metal-semiconductor hybrid sensor for room temperature light detection
Authors: Newaz A. K. M. , Chang W.-J. , Wallace K. D. , Edge L. C. , Wickline S. A. , Bashir R. , Gilbertson A. M. , Cohen L. F. , Solin S. A.
Published: August 2010

We report an individually addressable Ti/GaAs metal-semiconductor hybrid optical nanosensor with positive photoresistance and a sensitivity that increases as the device dimensions shrink. The underlying physics relates to the crossover from ballistic to diffusive transport of the photoinduced carriers and the geometric enhancement of the effect associated with a Schottky-barrier-coupled parallel metal shunt layer. For a 250 nm device under 633 nm illumination we observe a specific detectivity of D∗=5.06×1011 cm √Hz/W with a dynamic response of 40 dB.
The effect of secondary electrons on the separate control of ion energy and flux in dual-frequency capacitively coupled radio frequency discharges
Authors: Donkó Z. , Schulze J. , Hartmann P. , Korolov I. , Czarnetzki U. , Schüngel E.
Published: August 2010

Dual-frequency capacitive discharges are used to separately control the mean ion energy, ε¯ion, and flux, Γion, at the electrodes. We study the effect of secondary electrons on this separate control in argon discharges driven at 2+27 MHz at different pressures using Particle in Cell simulations. For secondary yield γ≈0, Γion decreases as a function of the low frequency voltage amplitude due to the frequency coupling, while it increases at high γ due to the effective multiplication of secondary electrons inside the sheaths. Therefore, separate control is strongly limited. ε¯ion increases with γ, which might allow an in situ determination of γ-coefficients.
Multiple localized states and magnetic orderings in partially open zigzag carbon nanotube superlattices: An ab initio study
Authors: Huang Bing , Li Zuanyi , Son Young-Woo , Kim Gunn , Duan Wenhui , Ihm Jisoon
Published: August 2010

Using ab initio calculations, we examine the electronic and magnetic properties of partially open (unzipped) zigzag carbon nanotube (CNT) superlattices. It is found that depending on their opening degree, these superlattices can exhibit multiple localized states around the Fermi energy. More importantly, some electronic states confined in some parts of the structure even have special magnetic orderings. We demonstrate that, as a proof of principle, some partially open zigzag CNT superlattices are by themselves giant (100%) magnetoresistive devices. Furthermore, the localized (and spin-polarized) states as well as the band gaps of the superlattices could be further modulated by external electric fields perpendicular to the tube axis. We believe that these results will open the way to the production of novel nanoscale electronic and spintronic devices.
White light emission from amorphous silicon oxycarbide (a-SiCxOy) thin films: Role of composition and postdeposition annealing
Authors: Gallis Spyros , Nikas Vasileios , Suhag Himani , Huang Mengbing , Kaloyeros Alain E.
Published: August 2010

The effects of carbon and postdeposition annealing on white luminescence are studied in amorphous silicon oxycarbide (a-SiCxOy) films grown by chemical vapor deposition. The films showed strong room-temperature luminescence in a broad spectral range from blue-violet to near infrared, depending on excitation energy. Photoluminescence (PL) intensity exhibited good correlation with SiOC bond concentration. At low C (<5%), matrix PL was completely quenched after annealing in O2 even at 500 °C. PL was unaffected by O2 annealing at higher C, and could be enhanced when excited by an ultraviolet laser. These findings are correlated to C- and Si-related O defect centers as luminescence sources in a-SiCxOy.
Nonlinear plasmonic directional couplers
Authors: Salgueiro José R. , Kivshar Yuri S.
Published: August 2010

A study on the nonlinear modes of plasmonic directional couplers created by two nonlinear dielectric slot waveguides with metallic claddings is presented. The calculated power diagram shows substantial differences from the case of nonlinear dielectric couplers. The power-dependent switching and the effect of losses on the coupler performance are studied using finite-difference time-domain numerical simulations.
Meir–Wingreen formula for heat transport in a spin-boson nanojunction model
Authors: Velizhanin Kirill A. , Thoss Michael , Wang Haobin
Published: August 2010

An analog of the Meir–Wingreen formula for the steady-state heat current through a model molecular junction is derived. The expression relates the heat current to correlation functions of operators acting only on the degrees of freedom of the molecular junction. As a result, the macroscopic heat reservoirs are not treated explicitly. This allows one to exploit methods based on a reduced description of the dynamics of a relatively small part of the overall system to evaluate the heat current through a molecular junction. The derived expression is applied to calculate the steady-state heat current in the weak coupling limit, where the Redfield theory is used to describe the reduced dynamics of the molecular junction. The results are compared with those of previously developed approximate and numerically exact methods.
Organic solar cells with remarkable enhanced efficiency by using a CuI buffer to control the molecular orientation and modify the anode
Authors: Cheng Chuan Hui , Wang Jin , Du Guo Tong , Shi Shao Hua , Du Zhi Jie , Fan Zhao Qi , Bian Ji Ming , Wang Min Shuai
Published: August 2010

CuI is used to control the molecular orientation of copper phthalocyanine (CuPc) and modify the anodes in organic solar cells based on CuPc/C60. By introducing a CuI buffer between indium tin oxide and CuPc, the power conversion efficiency is significantly enhanced by a factor of ∼70%. Because of the strong interactions between the CuI and CuPc, the stacking orientation of CuPc molecules is changed, resulting in a ∼65% increase in absorption coefficient, a larger carrier mobility and a smoother film surface. The anode work function is raised by the formation of a dipole layer.
The magnitude of diurnal variation in carbon isotopic composition of leaf dark respired CO2 correlates with the difference between δ13C of leaf and root material
Authors: Wegener Frederik , Beyschlag Wolfram , Werner Christiane
Published: August 2010

Spatial and temporal variations in δ13C of dark respired CO2 (δ13Cres) and total and water-soluble organic matter (WSOM) were analysed in four plant species. There was an increase in δ13Cres over the light period (measured 5 min after darkening) in leaves, whereas no distinct diurnal pattern was detected in roots. Furthermore, large differences in δ13Cres were found along the plant axis during day time. The amount of daily δ13Cres enrichment in leaves relative to the putative substrate (WSOM) varied largely between species (3.2–15.9‰), probably due to different carbon allocation strategies. Positional pyruvate labelling was used to detect whether variations in δ13Cres were related to changes in the relative activity of pyruvate dehydrogenase (PDH) and Krebs cycle (KC). The results indicate that one reason for the increase in δ13Cres in leaves during daylight is an increasing carbon flux through the PDH relative to the KC. Labelling experiments revealed no clear diurnal variations in PDH and KC activity in roots. Further, we found new evidence that the fractionation process that leads to the diurnal δ13C increase in leaf dark respiration is related to the well known 13C depletion of leaf material compared with heterotrophic tissues.
Operation and regulation of the lutein epoxide cycle in seedlings of Ocotea foetens
Authors: Esteban Raquel , Matsubara Shizue , Jiménez María Soledad , Morales Domingo , Brito Patricia , Lorenzo Roberto , Fernández-Marín Beatriz , Becerril José María , García-Plazaola José Ignacio
Published: August 2010

Two xanthophyll cycles are present in higher plants: the ubiquitous violaxanthin (V) cycle and the taxonomically restricted lutein epoxide (Lx) cycle. Conversions of V to zeaxanthin (Z) in the first and Lx to lutein (L) in the second happen in parallel under illumination. Unlike the V cycle, in which full epoxidation is completed overnight, in the Lx cycle, this reaction has been described as irreversible on a daily basis in most species (the ‘truncated’ Lx cycle). However, there are some species that display complete restoration of Lx overnight (‘true’ Lx cycle). So far, little is known about the physiological meaning of these two versions of the Lx cycle. Therefore, in the present work, the ‘true’ Lx cycle operation was studied in seedlings of Ocotea foetens (Aiton) Benth. under controlled and field conditions. Complete overnight recovery of the Lx pool in the presence of norfluorazon suggested that the inter-conversions between Lx and L represent a true cycle in this species. Furthermore, Lx responded dynamically to environmental conditions during long-term acclimation. Our data demonstrate the operation of a ‘true’ Lx cycle and, for the first time, its potential involvement in the regulation of non-photochemical quenching in situ. We propose dual regulation of Lx cycle in O. foetens, in which the extent of Lx restoration depends on the intensity and duration of illumination.
Respiration and temperature patterns in thermogenic flowers of Magnolia ovata under natural conditions in Brazil
Authors: Seymour Roger S. , Silberbauer-Gottsberger Ilse , Gottsberger Gerhard
Published: August 2010

The roles of floral thermogenesis in pollination biology include attraction and reward of insects. Magnolia ovata (A.St.-Hil.) Spreng. produces ~56 g, bisexual, protogynous and scented flowers. Two distinct episodes of thermogenesis occur during anthesis: one beginning at about sunset and lasting ~3 h in the female phase and another that occurs synchronously 24 h later and lasting 4 h in the male phase. Female stage flowers produce up to 0.36 W to reach 27.3°C, which is 3.9°C above ambient air. In the male stage, corresponding values are 0.79 W, 29.7°C and 5.4°C, respectively. Most heat is generated in the petals in both phases (74 and 65%). Maximum, mass-specific rate of respiration is 23 nmol s–1 g–1 in the petals and 100 nmol s–1 g–1 in the anthers. The flowers are apparently not thermoregulatory, because respiration rate decreases, rather than increases, with decreasing ambient temperature. Scarab beetles, Cyclocephala literata, enter the floral chamber created by the petals in the female phase, mate, consume floral parts (mainly petals) and then depart in the male phase. Temperatures maintained in the floral chamber are sufficient to provide beetles with significant energy savings during their activities in both phases. Thermogenesis is, therefore, consistent with volatilisation of floral fragrances and energy rewards to beetle visitors.
Evolution of growth-promoting plant hormones
Authors: Ross John J. , Reid James B.
Published: August 2010

The plant growth hormones auxin, gibberellins (GAs) and brassinosteroids (BRs) are major determinants of plant growth and development. Recently, key signalling components for these hormones have been identified in vascular plants and, at least for the GAs and BRs, biosynthetic pathways have been clarified. The genome sequencing of a range of species, including a few non-flowering plants, has allowed insight into the evolution of the hormone systems. It appears that the moss Physcomitrella patens can respond to auxin and contains key elements of the auxin signalling pathway, although there is some doubt as to whether it shows a fully developed rapid auxin response. On the other hand, P. patens does not show a GA response, even though it contains genes for components of GA signalling. The GA response system appears to be more advanced in the lycophyte Selaginella moellendorffii than in P. patens. Signalling systems for BRs probably arose after the evolutionary divergence of the mosses and vascular plants, although detailed information is limited. Certainly, the processes affected by the growth hormones (e.g. GAs) can differ in the different plant groups, and there is evidence that with the evolution of the angiosperms, the hormone systems have become more complex at the gene level. The intermediate nature of mosses in terms of overall hormone biology allows us to speculate about the possible relationship between the evolution of plant growth hormones and the evolution of terrestrial vascular plants in general.
Structure-based modeling of the functional HIV-1 intasome and its inhibition
Authors: Krishnan Lavanya , Li Xiang , Naraharisetty Hema L. , Hare Stephen , Cherepanov Peter , Engelman Alan
Published: August 2010

The intasome is the basic recombination unit of retroviral integration, comprising the integrase protein and the ends of the viral DNA made by reverse transcription. Clinical inhibitors preferentially target the DNA-bound form of integrase as compared with the free protein, highlighting the critical requirement for detailed understanding of HIV-1 intasome structure and function. Although previous biochemical studies identified integrase residues that contact the DNA, structural details of protein–protein and protein–DNA interactions within the functional intasome were lacking. The recent crystal structure of the prototype foamy virus (PFV) integrase–viral DNA complex revealed numerous details of this related integration machine. Structures of drug-bound PFV intasomes moreover elucidated the mechanism of inhibitor action. Herein we present a model for the HIV-1 intasome assembled using the PFV structure as template. Our results pinpoint previously identified protein–DNA contacts within the quaternary structure and reveal hitherto unknown roles for Arg20 and Lys266 in DNA binding and integrase function. Models for clinical inhibitors bound at the HIV-1 integrase active site were also constructed and compared with previous studies. Our findings highlight the structural basis for HIV-1 integration and define the mechanism of its inhibition, which should help in formulating new drugs to inhibit viruses resistant to first-in-class compounds.
Ezh2, the histone methyltransferase of PRC2, regulates the balance between self-renewal and differentiation in the cerebral cortex
Authors: Pereira João D. , Sansom Stephen N. , Smith James , Dobenecker Marc-Werner , Tarakhovsky Alexander , Livesey Frederick J.
Published: August 2010

Multipotent progenitor cells of the cerebral cortex balance self-renewal and differentiation to produce complex neural lineages in a fixed temporal order in a cell-autonomous manner. We studied the role of the polycomb epigenetic system, a chromatin-based repressive mechanism, in controlling cortical progenitor cell self-renewal and differentiation. We found that the histone methyltransferase of polycomb repressive complex 2 (PCR2), enhancer of Zeste homolog 2 (Ezh2), is essential for controlling the rate at which development progresses within cortical progenitor cell lineages. Loss of function of Ezh2 removes the repressive mark of trimethylated histone H3 at lysine 27 (H3K27me3) in cortical progenitor cells and also prevents its establishment in postmitotic neurons. Removal of this repressive chromatin modification results in marked up-regulation in gene expression, the consequence of which is a shift in the balance between self-renewal and differentiation toward differentiation, both directly to neurons and indirectly via basal progenitor cell genesis. Although the temporal order of neurogenesis and gliogenesis are broadly conserved under these conditions, the timing of neurogenesis, the relative numbers of different cell types, and the switch to gliogenesis are all altered, narrowing the neurogenic period for progenitor cells and reducing their neuronal output. As a consequence, the timing of cortical development is altered significantly after loss of PRC2 function.
Extracellular DNA traps promote thrombosis
Authors: Fuchs Tobias A. , Brill Alexander , Duerschmied Daniel , Schatzberg Daphne , Monestier Marc , Myers Daniel D. , Wrobleski Shirley K. , Wakefield Thomas W. , Hartwig John H. , Wagner Denisa D.
Published: August 2010

Neutrophil extracellular traps (NETs) are part of the innate immune response to infections. NETs are a meshwork of DNA fibers comprising histones and antimicrobial proteins. Microbes are immobilized in NETs and encounter a locally high and lethal concentration of effector proteins. Recent studies show that NETs are formed inside the vasculature in infections and noninfectious diseases. Here we report that NETs provide a heretofore unrecognized scaffold and stimulus for thrombus formation. NETs perfused with blood caused platelet adhesion, activation, and aggregation. DNase or the anticoagulant heparin dismantled the NET scaffold and prevented thrombus formation. Stimulation of platelets with purified histones was sufficient for aggregation. NETs recruited red blood cells, promoted fibrin deposition, and induced a red thrombus, such as that found in veins. Markers of extracellular DNA traps were detected in a thrombus and plasma of baboons subjected to deep vein thrombosis, an example of inflammation-enhanced thrombosis. Our observations indicate that NETs are a previously unrecognized link between inflammation and thrombosis and may further explain the epidemiological association of infection with thrombosis.
A Trojan horse mechanism of bacterial pathogenesis against nematodes
Authors: Niu Qiuhong , Huang Xiaowei , Zhang Lin , Xu Jianping , Yang Dongmei , Wei Kangbi , Niu Xuemei , An Zhiqiang , Bennett Joan Wennstrom , Zou Chenggang , Yang Jinkui , Zhang Ke-Qin
Published: August 2010

Understanding the mechanisms of host–pathogen interaction can provide crucial information for successfully manipulating their relationships. Because of its genetic background and practical advantages over vertebrate model systems, the nematode
Caenorhabditis elegans
model has become an attractive host for studying microbial pathogenesis. Here we report a “Trojan horse” mechanism of bacterial pathogenesis against nematodes. We show that the bacterium
Bacillus nematocida
B16 lures nematodes by emitting potent volatile organic compounds that are much more attractive to worms than those from ordinary dietary bacteria. Seventeen
B. nematocida
-attractant volatile organic compounds are identified, and seven are individually confirmed to lure nematodes. Once the bacteria enter the intestine of nematodes, they secrete two proteases with broad substrate ranges but preferentially target essential intestinal proteins, leading to nematode death. This Trojan horse pattern of bacterium–nematode interaction enriches our understanding of microbial pathogenesis.
Metallic ferromagnetism in the Kondo lattice
Authors: Yamamoto Seiji J. , Si Qimiao
Published: August 2010

Metallic magnetism is both ancient and modern, occurring in such familiar settings as the lodestone in compass needles and the hard drive in computers. Surprisingly, a rigorous theoretical basis for metallic ferromagnetism is still largely missing. The Stoner approach perturbatively treats Coulomb interactions when the latter need to be large, whereas the Nagaoka approach incorporates thermodynamically negligible holes into a half-filled band. Here, we show that the ferromagnetic order of the Kondo lattice is amenable to an asymptotically exact analysis over a range of interaction parameters. In this ferromagnetic phase, the conduction electrons and local moments are strongly coupled but the Fermi surface does not enclose the latter (i.e., it is “small”). Moreover, non-Fermi-liquid behavior appears over a range of frequencies and temperatures. Our results provide the basis to understand some long-standing puzzles in the ferromagnetic heavy fermion metals, and raise the prospect for a new class of ferromagnetic quantum phase transitions.
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription
Authors: Huang Xuhui , Wang Dong , Weiss Dahlia R. , Bushnell David A. , Kornberg Roger D. , Levitt Michael
Published: August 2010

A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis of RNA polymerase II (pol II) transcription elongation. Recently resolved X-ray structures showed that the trigger loop forms direct interactions with the β-phosphate and base of the matched nucleotide triphosphate (NTP) through residues His1085 and Leu1081, respectively. In order to understand the role of these two critical residues in stabilizing active site conformation in the dynamic complex, we performed all-atom molecular dynamics simulations of the wild-type pol II elongation complex and its mutants in explicit solvent. In the wild-type complex, we found that the trigger loop is stabilized in the “closed” conformation, and His1085 forms a stable interaction with the NTP. Simulations of point mutations of His1085 are shown to affect this interaction; simulations of alternative protonation states, which are inaccessible through experiment, indicate that only the protonated form is able to stabilize the His1085-NTP interaction. Another trigger loop residue, Leu1081, stabilizes the incoming nucleotide position through interaction with the nucleotide base. Our simulations of this Leu mutant suggest a three-component mechanism for correctly positioning the incoming NTP in which (
i
) hydrophobic contact through Leu1081, (
ii
) base stacking, and (
iii
) base pairing work together to minimize the motion of the incoming NTP base. These results complement experimental observations and provide insight into the role of the trigger loop on transcription fidelity.
Natural killer cells in NOD.NK1.1 mice acquire cytolytic function during viral infection and provide protection against cytomegalovirus
Authors: Orr Mark T. , Beilke Joshua N. , Proekt Irina , Lanier Lewis L.
Published: August 2010

Resting natural killer (NK) cells in nonobese diabetic (NOD) mice have impaired immune functions compared with NK cells from other mouse strains. Here we investigated how NOD NK cells respond after mouse cytomegalovirus (MCMV) infection, using NOD mice congenic for the protective NK gene complex from C57BL/6 mice. Compared with C57BL/6 mice congenic for theH2gene complex from NOD mice (B6.g7), NOD.NK1.1 mice fail to control early infection with MCMV. After MCMV infection, however, NOD.NK1.1 NK cells demonstrate increased cytolytic function, associated with higher expression of granzyme B, and undergo robust expansion. One week after infection, NOD.NK1.1 NK cells control MCMV replication as effectively as B6.g7 NK cells, even in the absence of T cells and B cells. Thus, the impaired cytotoxic function of NK cells in NOD mice is alleviated by viral infection, which enables NOD NK cells to efficiently control MCMV infection.
Competition dynamics of second-language listening
Authors: Broersma Mirjam , Cutler Anne
Published: August 2010

Spoken-word recognition in a nonnative language is particularly difficult where it depends on discrimination between confusable phonemes. Four experiments here examine whether this difficulty is in part due to phantom competition from “near-words” in speech. Dutch listeners confuse English /æ/ and /ε/, which could lead to the sequence daf being interpreted as deaf, or lemp being interpreted as lamp. In auditory lexical decision, Dutch listeners indeed accepted such near-words as real English words more often than English listeners did. In cross-modal priming, near-words extracted from word or phrase contexts ( daf from DAFfodil, lemp from eviL EMPire) induced activation of corresponding real words ( deaf; lamp) for Dutch, but again not for English, listeners. Finally, by the end of untruncated carrier words containing embedded words or near-words ( definite; daffodil) no activation of the real embedded forms ( deaf in definite) remained for English or Dutch listeners, but activation of embedded near-words ( deaf in daffodil) did still remain, for Dutch listeners only. Misinterpretation of the initial vowel here favoured the phantom competitor and disfavoured the carrier (lexically represented as containing a different vowel). Thus, near-words compete for recognition and continue competing for longer than actually embedded words; nonnative listening indeed involves phantom competition.
Phonological Facilitation from Pictures in a Word Association Task: Evidence for Routine Cascaded Processing in Spoken Word Production
Authors: Humphreys Karin R. , Boyd Candice H. , Watter Scott
Published: August 2010

While most authors now agree that the language production system is in principle cascaded, the strength with which cascaded lemma-to-phoneme activation typically occurs is debated. Picture naming has been shown to be facilitated by phonologically related distractor pictures, but no such facilitation from pictures has been shown for word reading. Picture–picture paradigms have recently been suggested to represent an attentionally facilitated and unusually strong case of cascaded phonological facilitation, not typical of a more general weakly cascaded production system. We used a novel procedure based on picture–word interference paradigms, where participants made speeded verbal free association responses to presented words, with irrelevant picture distractors that were phonologically related to their predicted high-associate responses. Phonological facilitation effects from related picture names were observed on free associate verbal production latencies. These findings represent a far more general demonstration of routine cascaded language production and suggest that the strength and extent of cascaded activation is more substantial than that suggested by traditional picture–word paradigms.
DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas
Authors: Lai Anne Y. , Fatemi Mehrnaz , Dhasarathy Archana , Malone Christine , Sobol Steve E. , Geigerman Cissy , Jaye David L. , Mav Deepak , Shah Ruchir , Li Leping , Wade Paul A.
Published: August 2010

Aberrant DNA methylation commonly occurs in cancer cells where it has been implicated in the epigenetic silencing of tumor suppressor genes. Additional roles for DNA methylation, such as transcriptional activation, have been predicted but have yet to be clearly demonstrated. The BCL6 oncogene is implicated in the pathogenesis of germinal center–derived B cell lymphomas. We demonstrate that the intragenic CpG islands within the first intron of the human BCL6 locus were hypermethylated in lymphoma cells that expressed high amounts of BCL6 messenger RNA (mRNA). Inhibition of DNA methyltransferases decreased BCL6 mRNA abundance, suggesting a role for these methylated CpGs in positively regulating BCL6 transcription. The enhancer-blocking transcription factor CTCF bound to this intronic region in a methylation-sensitive manner. Depletion of CTCF by short hairpin RNA in neoplastic plasma cells that do not express BCL6 resulted in up-regulation of BCL6 transcription. These data indicate that BCL6 expression is maintained during lymphomagenesis in part through DNA methylation that prevents CTCF-mediated silencing.
Annotare—a tool for annotating high-throughput biomedical investigations and resulting data
Authors: Shankar Ravi , Parkinson Helen , Burdett Tony , Hastings Emma , Liu Junmin , Miller Michael , Srinivasa Rashmi , White Joseph , Brazma Alvis , Sherlock Gavin , Stoeckert Christian J. , Ball Catherine A.
Published: August 2010

Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis.

Availability and Implementation: Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows.

Contact:  rshankar@stanford.edu
4. Contributions to the Osteology of Birds.—Part IX. Tyranni; Hirundines; Muscicapæ, Lanii, and Gymno‐rhines
Authors: Pycraft W. P.
Published: August 2010

Summary.

I have ventured, on the evidence chiefly of osteological and inyological characters, to associate many Families which have hitherto been separated, often widely. Furthermore I have endeavoured, in the course of this summary, to show that the ranks of these Families must be enlarged to receive forms which till now have been regarded a9 having no ailhities therewith.

It will be remarked that I have included in this paper the Families Phytotomidæ, Pittidæ, arid Tyrannidæ. This I have done because there seems good reason to regard these three nearly related Families as close allies of the Diacroniyodean Passeres.
The Skull of the False Killer Dolphin, Pseudorca crassidens (Owen)
Authors: Cowley Lionel F.
Published: August 2010

The skull of the False Killer Dolphin, Pseudorca crassidens, has been described and points of difference with allied forms mentioned. Measurements of the fœtal and adult skull have been compared and it has been shown that increase in size is accompanied by a change in form; and that in its anteroposterior dimension the cranial region of the skull grows at a slower rate than does the facial portion.
Some Structural Variations in the Second Upper Premolar of the Lesser One‐horned Rhinoceros (Rhinoceros sondaicus).
Authors: POCOCK R. I.
Published: August 2010

Two main conclusions may be deduced from the foregoing description:—(1) In Rh. sondaicus pm2 of the permanent dentition, when unworn, may differ from pm3 and pm4, as well as from the molars, in having the ectoloph and protoloph superficially separated and the anterior fossa opening in front between them. This at all events is the case in two youngish skulls, one without locality, the other from Lower Tenasserim. These may be set aside for the time being, pending the examination of additional skulls, if any, to prove that the newly erupted pm2 is always so constructed.

(2) In two fully adult, if not oldish, skulls from the Sanderbans, with pm2 considerably worn, the condition above described persists, whereas in several skulls from the Sunda Islands, younger than the last, or about the same age, with pm2 less or about equally worn, the ectoloph and protoloph are connected by a vertical crest which completely closes the anterior fossa in front. I provisionally attach racial significance to this difference and restore the name inermis for the now extinct Rhinoceros of the Sanderbans, restricting sondaicus in a racial sense to the form from the Sunda Islands.