bluuebunny/crossref_metadata_2025 huggingface dataset:
The relationship between microstructure and dislocation density distribution in multicrystalline silicon
Authors: Würzner Sindy , Helbig René , Funke Claudia , Möller Hans Joachim
Published: October 2010

The investigation of the grain structure is important to understand the origin of dislocations during crystal growth of multicrystalline silicon. This paper studies the dislocation density distribution for different grain orientations that occur during crystal growth. Single grains are analyzed in detail, including their microstructure. The grain orientations are determined by means of the electron backscatter diffraction technique. The obtained information reveals grain orientations, which allow a higher number of active slip planes during crystal growth process. The number of active slip planes during solidification seems to influence the dislocation density in the final crystal.
Dynamics of coupled oscillators with convex interaction potential
Authors: Qin Wen-Xin , Xu Chun-Lan
Published: October 2010

In this paper we study via the monotonicity approach the dynamical behavior of a class of coupled oscillators with periodic on-site potential and convex interaction potential. It is shown that under periodic or Neumann boundary conditions the Poincaré map admits an invariant curve, on which the Poincaré map is actually an orientation preserving circle homeomorphism. Some consequences are then obtained, including a Massera type theorem and the existence of running periodic solutions. For the Dirichlet boundary conditions, each solution is asymptotic to a periodic solution if it is not periodic.
Doppler coherence imaging and tomography of flows in tokamak plasmas (invited)
Authors: Howard J. , Diallo A. , Creese M. , Blackwell B. D. , Allen S. L. , Ellis R. M. , Porter G. D. , Meyer W. , Fenstermacher M. E. , Brooks N. H. , Van Zeeland M. E. , Boivin R. L.
Published: October 2010

This article describes the results of spatial heterodyne Doppler “coherence imaging” of carbon ion flows in the divertor region of the DIII-D tokamak. Spatially encoded interferometric projections of doubly ionized carbon emission at 465 nm have been demodulated and tomographically inverted to obtain the spatial distribution of the carbon ion parallel flow and emissivity. The operating principles of the new instruments are described, and the link between measured properties and line integrals of the flow field are established. An iterative simultaneous arithmetic reconstruction procedure is applied to invert the interferometric phase shift projections, and the reconstructed parallel flow field amplitudes are found to be in reasonable agreement with UEDGE modeling.
A novel method for digital ultrasonic time-of-flight measurement
Authors: Wang X. F. , Tang Z. A.
Published: October 2010

Most ultrasonic ranging measurements are based on the determination of the ultrasonic time-of-flight (TOF). This paper develops a novel method for the TOF measurement which combines both the improved self-interference driving technique and the optional optimization signal processing algorithms. By stimulating the transmitter with the amplitude modulation and the phase modulation envelope square waveforms (APESWs), the proposed system can effectively reduce the errors caused by inertia delay and amplitude attenuation. In addition, based on different signal-to-noise ratio test conditions, the resultant received zero-crossing samples, which are deteriorated by noise, can be precisely inspected and calculated with two optimized algorithms named zero-crossing tracking (ZCT) and time-shifted superposition (TSS) method. The architecture of the designed system is divided into two parts. The novel APESW driving module, the received envelope zero-crossings phase detection module, and the ZCT method processing module are designed in a complex programable logic device. The TSS signal processing module and the optimization algorithm discrimination program module are integrated in a digital signal processor. The TOF measurements calibrated in ultrasonic ranging experiments indicate that the relative errors of the method are limited in ±0.8%. Therefore, a feasible method is provided with the advantages of high noise immunity, accuracy, low cost, and ease of implementation.
A topology preserving method for generating equilibrated polymer melts in computer simulations
Authors: Subramanian Gopinath
Published: October 2010

A new method for generating equilibrated configurations of polymer melts is presented. In this method, the molecular weight of an equilibrated melt of polymers is successively doubled by affinely scaling the simulation box and adding beads along the contour of the chains. At each stage of molecular weight doubling, compressive deformations are produced on all length scales, while the random walk nature of the polymers is preserved, thereby requiring relaxation times significantly smaller than the reptation time to fully equilibrate the melt. This method preserves the topological state of individual polymers in the melt and its effectiveness is demonstrated for linear polymers with molecular weight N up to 1024, and cyclic polymers with N up to 8192. For the range of N studied, the method requires simulation time that scales as N2 and is thought to be applicable to a variety of polymer architectures.
Identification of metastable states in peptide’s dynamics
Authors: Ruzhytska Svitlana , Jacobi Martin Nilsson , Jensen Christian H. , Nerukh Dmitry
Published: October 2010

A recently developed spectral method for identifying metastable states in Markov chains is used to analyze the conformational dynamics of a four-residue peptide valine-proline-alanine-leucine. We compare our results to empirically defined conformational states and show that the found metastable states correctly reproduce the conformational dynamics of the system.
A model proton-transfer system in the condensed phase: NH4+OOH−, a crystal with short intermolecular H-bonds
Authors: Churakov Andrei V. , Prikhodchenko Petr V. , Lev Ovadia , Medvedev Alexander G. , Tripol’skaya Tatiana A. , Vener Mikhail V.
Published: October 2010

The crystal structure of NH4+OOH− is determined from single-crystal x-ray data obtained at 150 K. The crystal belongs to the space group P21/c and has four molecules in a unit cell. The structure consists of discrete NH4+ and OOH− ions. The OOH− ions are linked by short hydrogen bonds (2.533 Å) to form parallel infinite chains. The ammonium ions form links between these chains (the N⋯O distances vary from 2.714 to 2.855 Å) giving a three-dimensional network. The harmonic IR spectrum and H-bond energies are computed at the Perdew–Burke–Ernzerhof (PBE)/6-31G∗∗ level with periodic boundary conditions. A detailed analysis of the shared (bridging) protons' dynamics is obtained from the CPMD simulations at different temperatures. PBE functional with plane-wave basis set (110 Ry) is used. At 10 K the shared proton sits near the oxygen atom, only a few proton jumps along the chain are detected at 70 K while at 270 K numerous proton jumps exist in the trajectory. The local-minimum structure of the space group Cc is localized. It appears as a result of proton transfer along a chain. This process is endothermic (∼2 kJ/mol) and is described as P21/c↔2Cc. The computed IR spectrum at 10 K is close to the harmonic one, the numerous bands appear at 70 K while at 270 K it shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm−1. The advantages of the NH4+OOH− crystal as a promising model for the experimental and DFT based molecular dynamics simulation studies of proton transfer along the chain are discussed.
New printed circuit boards magnetic coils in the vacuum vessel of J-TEXT tokamak for position measurement
Authors: Qiu S. S. , Zhuang G. , Zhang M. , Xia D. H. , Rao B. , Zhang X. Q. , Pan Y. , Gentle K.
Published: October 2010

Four sets of magnetic diagnostic coils, which are printed on machinable ceramic printed circuit boards (PCB), are designed, fabricated, installed, and tested in the Joint Texas Experimental Tokamak (J-TEXT) vacuum vessel for detecting the plasma radial and vertical displacements relative to the geometric center of the vacuum vessel in Ohmic discharges. Each coordinate is determined by a pair of variable cross-section Rogowski and saddle coils, which measure the tangential and normal magnetic fields (relative to the coil surface). These coils are suitable for mass production and offer advantages in vacuum compatibility and temperature tolerance that are important for J-TEXT. Position measurements using PCB coils are compared with those from soft x-ray image system and match the position well.
Ab initioinvestigation of benzene clusters: Molecular tailoring approach
Authors: Mahadevi A. Subha , Rahalkar Anuja P. , Gadre Shridhar R. , Sastry G. Narahari
Published: October 2010

An exhaustive study on the clusters of benzene (Bz)n, n=2–8, at MP2/6-31++G∗∗ level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (∼0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n−1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.
Multidimensional partial differential equation systems: Nonlocal symmetries, nonlocal conservation laws, exact solutions
Authors: Cheviakov Alexei F. , Bluman George W.
Published: October 2010

For systems of partial differential equations (PDEs) with n≥3 independent variables, construction of nonlocally related PDE systems is substantially more complicated than is the situation for PDE systems with two independent variables. In particular, in the multidimensional situation, nonlocally related PDE systems can arise as nonlocally related subsystems as well as potential systems that follow from divergence-type or lower-degree conservation laws. The theory and a systematic procedure for the construction of such nonlocally related PDE systems is presented in Part I [A. F. Cheviakov and G. W. Bluman, J. Math. Phys. 51, 103521 (2010)]. This paper provides many new examples of applications of nonlocally related systems in three and more dimensions, including new nonlocal symmetries, new nonlocal conservation laws, and exact solutions for various nonlinear PDE systems of physical interest.
Stochastic hybrid modeling of intracellular calcium dynamics
Authors: Choi TaiJung , Maurya Mano Ram , Tartakovsky Daniel M. , Subramaniam Shankar
Published: October 2010

Deterministic models of biochemical processes at the subcellular level might become inadequate when a cascade of chemical reactions is induced by a few molecules. Inherent randomness of such phenomena calls for the use of stochastic simulations. However, being computationally intensive, such simulations become infeasible for large and complex reaction networks. To improve their computational efficiency in handling these networks, we present a hybrid approach, in which slow reactions and fluxes are handled through exact stochastic simulation and their fast counterparts are treated partially deterministically through chemical Langevin equation. The classification of reactions as fast or slow is accompanied by the assumption that in the time-scale of fast reactions, slow reactions do not occur and hence do not affect the probability of the state. Our new approach also handles reactions with complex rate expressions such as Michaelis–Menten kinetics. Fluxes which cannot be modeled explicitly through reactions, such as flux of Ca2+ from endoplasmic reticulum to the cytosol through inositol 1,4,5-trisphosphate receptor channels, are handled deterministically. The proposed hybrid algorithm is used to model the regulation of the dynamics of cytosolic calcium ions in mouse macrophage RAW 264.7 cells. At relatively large number of molecules, the response characteristics obtained with the stochastic and deterministic simulations coincide, which validates our approach in the limit of large numbers. At low doses, the response characteristics of some key chemical species, such as levels of cytosolic calcium, predicted with stochastic simulations, differ quantitatively from their deterministic counterparts. These observations are ubiquitous throughout dose response, sensitivity, and gene-knockdown response analyses. While the relative differences between the peak-heights of the cytosolic [Ca2+] time-courses obtained from stochastic (mean of 16 realizations) and deterministic simulations are merely 1%–4% for most perturbations, it is specially sensitive to levels of Gβγ (relative difference as large as 90% at very low Gβγ).
Ab initio characterization of the Mg–HF van der Waals complex
Authors: Koput Jacek , Makarewicz Jan
Published: October 2010

The equilibrium structure and the three-dimensional potential energy surface of the Mg–HF van der Waals complex in its ground electronic state have been determined from accurate ab initio calculations using the coupled-cluster method, CCSD(T), in conjunction with the basis sets of triple- through quintuple-zeta quality. The core-electron correlation, high-order valence-electron correlation, and scalar relativistic effects were investigated. The Mg–HF complex was confirmed to be linear at equilibrium, with a vibrationless dissociation energy (into Mg and HF) De of 280 cm−1. The vibration-rotation energy levels of two isotopologues, M24g–HF and M24g–DF, were predicted using the variational method. The predicted spectroscopic constants can be useful in a further analysis of high-resolution vibration-rotation spectra of the Mg–HF complex.
The isotropic-nematic interface of colloidal goethite in an external magnetic field
Authors: van den Pol E. , Lupascu A. , Davidson P. , Vroege G. J.
Published: October 2010

Polarization microscopy was used to study the behavior around the isotropic-nematic interface of colloidal goethite dispersions in a magnetic field. It has been found before that the nematic phase is favored in an external field. In the case of goethite this was also observed; nematic droplets formed inside the isotropic phase and coalesced with the nematic phase. However, the behavior was found to be much richer because of the particle rotation around a certain critical field strength. The simultaneous occurrence of (parallel)nematic-(perpendicular)nematic phase separation under the influence of a magnetic field also plays a role here.
A digital method for separation and reconstruction of pile-up events in germanium detectors
Authors: Nakhostin M. , Podolyak Zs. , Regan P. H. , Walker P. M.
Published: October 2010

The problem of pulse pile-up is very often encountered in precise measurements of γ-rays using germanium detectors. The standard method of treating the pile-up events is to identify and reject them using an appropriate electronic system. Digital acquisition techniques now allow the recording of waveforms of pile-up events that can be analyzed and the contributing single pulses recovered, rather than simply tolerating the losses associated with pile-up. In this paper, a method for the off-line digital processing of pile-up events from germanium detectors is demonstrated. The method is based on an appropriate fitting of the detector signals, shaped with a suitable digital pulse shaper. It is shown that the method is able to recover the pile-up events with good accuracy even when the constituent signals are in close proximity. The method is very useful for γ-ray spectroscopy in nuclear physics experiments, where the low intensity signals can be lost due to the pile-up in a high-rate environment.
The temperature dependence of magnetic properties for cobalt ferrite nanoparticles by the hydrothermal method
Authors: Zhang Yue , Liu Yong , Fei Chunlong , Yang Zhi , Lu Zhihong , Xiong Rui , Yin Di , Shi Jing
Published: October 2010

Cobalt ferrite nanoparticles were synthesized via the hydrothermal route with the addition of trisodium citrate dihydrate (Na3CA⋅2H2O). The characterizations including x-ray diffraction (XRD) and transmission electron microscope showed that the products of this hydrothermal reaction are composed of cobalt ferrite nanocrystallite and a small amount of FeOOH, and the average crystallite size of the nanoparticles is 7.6±0.3 nm by XRD. The magnetic measurements revealed the temperature-dependent magnetic properties: The superparamagnetism occurs above 380 K due to the overcoming of energy barrier for the flip of spins, which arises from the magnetocrystalline anisotropy energy and the interparticle interactions due to the aggregation of the nanoparticles; a frozen spin-glasslike state was observed below 20 K, which is accompanied with the decrease in coercivity and high-field paramagnetic susceptibility, as well as the enhancement of saturated magnetization and the effective magnetic anisotropy constant.
Use of the Far Infrared Tangential Interferometer/Polarimeter diagnostic for the study of rf driven plasma waves on NSTX
Authors: Kim J. , Lee K. C. , Kaita R. , Phillips C. K. , Domier C. W. , Valeo E. , Luhmann N. C. , Bonoli P. T. , Park H.
Published: October 2010

A rf detection system for waves in the 30 MHz range has been constructed for the Far Infrared Tangential Interferometer/Polarimeter on National Spherical Torus Experiment (NSTX). It is aimed at monitoring high frequency density fluctuations driven by 30 MHz high harmonic fast wave fields. The levels of density fluctuations at various radial chords and antenna phase angles can be estimated using the electric field calculated by TORIC code and linearized continuity equation for the electron density. In this paper, the experimental arrangement for the detection of rf signal and preliminary results of simulation will be discussed.
Relaxation of a semiflexible grafted polymer
Authors: Nam Gimoon , Johner Albert , Lee Nam-Kyung
Published: October 2010

The relaxation of single grafted semiflexible chains freely rotating around the grafting point is investigated by means of two dimensional computer simulations and scaling arguments. Both free chains and chains surrounded by topological obstacles are considered. We compute the autocorrelation of the end-to-end vector for the whole chain and for terminal sections of various lengths. Our results are relevant for the relaxation of star polymers with stiff arms or branched semiflexible polymers moving in an array of obstacles.
Micromagnetic study of fieldlike spin torque effect on the magnetization switching in tunnel junctions with perpendicular anisotropy
Authors: Zhang Zongzhi , Qiu Yongcheng , Jin Q. Y. , Liu Yaowen
Published: October 2010

Micromagnetic simulation is employed to study the effect of fieldlike spin torque in a perpendicularly magnetized tunnel junction. We find that the effect of fieldlike spin torque strongly depends on the current direction, showing the torque significantly reduces the switching time for the electrons flowing from free layer to pinned layer while has less effect for the opposite current. This asymmetric behavior is consistent with the theoretical prediction on the bias dependence of the fieldlike spin torque. The observed absence of preswitching and postswitching oscillations can be attributed to the opposite precession phase of local magnetic moments within the free layer.
Hydrogen-related n-type conductivity in hydrothermally grown epitaxial ZnO films
Authors: Zhang Y. B. , Goh G. K. L. , Ooi K. F. , Tripathy S.
Published: October 2010

Epitaxial ZnO films were grown on single crystal spinel substrates at 90 °C in water. Hall measurements showed that the n-type carrier concentration and conductivity of the ZnO films decreased as postgrowth annealing temperature increases or pH of the growth solution decreases. At the same time, x-ray photoelectron spectroscopy, room temperature and low-temperature photoluminescence, and secondary ion mass spectroscopy observations revealed that H incorporation was enhanced at a higher pH value but reduced with increasing annealing temperature. All these observations show that the unintentionally-incorporated hydrogen in solution grown ZnO acts as a shallow donor and enhances the n-type carrier density.
ITER-relevant calibration technique for soft x-ray spectrometer
Authors: Rzadkiewicz J. , Książek I. , Zastrow K-D. , Coffey I. H. , Jakubowska K. , Lawson K. D. ,   JET EFDA Contributors
Published: October 2010

The ITER-oriented JET research program brings new requirements for the low-Z impurity monitoring, in particular for the Be—the future main wall component of JET and ITER. Monitoring based on Bragg spectroscopy requires an absolute sensitivity calibration, which is challenging for large tokamaks. This paper describes both “component-by-component” and “continua” calibration methods used for the Be IV channel (75.9 Å) of the Bragg rotor spectrometer deployed on JET. The calibration techniques presented here rely on multiorder reflectivity calculations and measurements of continuum radiation emitted from helium plasmas. These offer excellent conditions for the absolute photon flux calibration due to their low level of impurities. It was found that the component-by-component method gives results that are four times higher than those obtained by means of the continua method. A better understanding of this discrepancy requires further investigations.
Lateral spatial switching of excitons using vertical electric fields in semiconductor quantum rings
Authors: McDonald P. G. , Shumway J. , Galbraith I.
Published: October 2010

We study the response of exciton complexes in semiconductor quantum rings to vertical electric fields, using path integral quantum Monte Carlo simulations. The interaction of a vertical applied field and the piezoelectric fields of the ring with correlated excitonic complexes switches excitons between two different lateral locations within the ring. This control should be observable through polarizability and dipole measurements, and, for biexcitons, an energy shift beyond the normal Stark shift.
Electronic structure of cleaved InAsP/InP(001) quantum dots measured by scanning tunneling spectroscopy
Authors: Fain B. , Girard J. C. , Elvira D. , David C. , Beaudoin G. , Beveratos A. , Robert-Philip I. , Sagnes I. , Wang Z. Z.
Published: October 2010

We investigate the structural and electronic properties of cleaved InAsP quantum dots grown by metal organic chemical vapor deposition on a (001) InP substrate by means of cross-sectional scanning tunneling microscopy and spectroscopy. We performed spatially and energetically resolved differential conductance measurements on several dots and thus mapped their electronic wave functions. Five distinct quantum dot energy levels are identified, all of them strongly confined inside the quantum dot. We further discuss the structural characteristics inferred from topographical images in the specific case of parallelogram-based InAsP/InP(001) quantum dots as a mean of investigating the size of a buried quantum dot.
Isotope effects in liquid water by infrared spectroscopy. IV. No free OH groups in liquid water
Authors: Max Jean-Joseph , Chapados Camille
Published: October 2010

The presence of free OH (OH not H-bonded) in bulk water is a key element for the determination of its molecular structure. The OH covalent bond infrared (IR) absorption is highly sensitive to the molecular environment. For this reason, IR spectroscopy is used for the determination of free OH. A workable definition of this is obtained with methanol (MeOH) in hexane where minute quantities of free OH are present. These absorb at 3654 cm−1 (a 27 cm−1 redshift from the gas position) with a full width at half height of 35 cm−1. The IR spectrum of water between room temperature and 95 °C does not display such a band near 3650 cm−1. This indicates that we do not see, in the IR spectra, the “free” OH group. From this we conclude that it is not present in liquid water at least down to the 1000 ppm level which is the limit of detectivity of our spectrometer. Other spectroscopic considerations of methanol and water in acetonitrile solutions indicate that weak H-bonds are also not present in liquid water.
Correlation between second-order optical response and structure in thermally poled sodium niobium-germanate glass
Authors: Guimbretière G. , Dussauze M. , Rodriguez V. , Kamitsos E. I.
Published: October 2010

We have carried out Raman and second harmonic generation (SHG) measurements to probe thermal poling-induced phenomena in glass 20Na2O-80[0.35Nb2O5-0.65GeO2]. A SHG response of 0.6 pm/V was measured after poling in a ∼3 μm thick layer under the anode and found to deviate from the widely used electric field-induced SHG model. This effect was associated with complex structural rearrangements in the subanode layer involving destruction of nonbridging oxygen atoms, formation of molecular oxygen, and enhancement of cross-linking in the glass network.
Hypersonic rugate filters based on porous silicon
Authors: Thomas L. , Aliev G. N. , Snow P. A.
Published: October 2010

Periodic solid state structures exhibit transmission stopbands for waves of certain frequencies. We demonstrate porous silicon based rugate filters with 40 dB rejection first-order stopbands for longitudinal acoustic waves at hypersonic frequencies and the predicted suppression of higher order bands.
Evolving science of marine reserves: New developments and emerging research frontiers
Authors: Gaines Steven D. , Lester Sarah E. , Grorud-Colvert Kirsten , Costello Christopher , Pollnac Richard
Published: October 2010

The field of marine reserve science has matured greatly over the last decade, moving beyond studies of single reserves and beyond perspectives from single disciplines. This Special Feature exemplifies recent advances in marine reserve research, showing insights gained from synthetic studies of reserve networks, long-term changes within reserves, integration of social and ecological science research, and balance between reserve design for conservation as well as fishery and other commercial objectives. This rich body of research helps to inform conservation planning for marine ecosystems but also poses new challenges for further study, including how to best design integrated fisheries management and conservation systems, how to effectively evaluate the performance of entire reserve networks, and how to examine the complex coupling between ecological and socioeconomic responses to reserve networks.
Evolutionary history of partible paternity in lowland South America
Authors: Walker Robert S. , Flinn Mark V. , Hill Kim R.
Published: October 2010

Partible paternity, the conception belief that more than one man can contribute to the formation of a fetus, is common in lowland South America and characterized by nonexclusive mating relationships and various institutionalized forms of recognition and investment by multiple cofathers. Previous work has emphasized the fitness benefits for women where partible paternity beliefs facilitate paternal investment from multiple men and may reduce the risk of infanticide. In this comparative study of 128 lowland South American societies, the prevalence of partible paternity beliefs may be as much as two times as common as biologically correct beliefs in singular paternity. Partible paternity beliefs are nearly ubiquitous in four large language families—Carib, Pano, Tupi, and Macro-Je. Phylogenetic reconstruction suggests that partible paternity evolved deep in Amazonian prehistory at the root of a tentative Je-Carib-Tupi clade. Partible paternity often occurs with uxorilocal postmarital residence (males transfer), although there are exceptions. Partible paternity may have benefits for both sexes, especially in societies where essentially all offspring are said to have multiple fathers. Despite a decrease in paternity certainty, at least some men probably benefit (or mitigate costs) by increasing their number of extramarital partners, using sexual access to their wives to formalize male alliances, and/or sharing paternity with close kin.
Driving forces of global wildfires over the past millennium and the forthcoming century
Authors: Pechony O. , Shindell D. T.
Published: October 2010

Recent bursts in the incidence of large wildfires worldwide have raised concerns about the influence climate change and humans might have on future fire activity. Comparatively little is known, however, about the relative importance of these factors in shaping global fire history. Here we use fire and climate modeling, combined with land cover and population estimates, to gain a better understanding of the forces driving global fire trends. Our model successfully reproduces global fire activity record over the last millennium and reveals distinct regimes in global fire behavior. We find that during the preindustrial period, the global fire regime was strongly driven by precipitation (rather than temperature), shifting to an anthropogenic-driven regime with the Industrial Revolution. Our future projections indicate an impending shift to a temperature-driven global fire regime in the 21st century, creating an unprecedentedly fire-prone environment. These results suggest a possibility that in the future climate will play a considerably stronger role in driving global fire trends, outweighing direct human influence on fire (both ignition and suppression), a reversal from the situation during the last two centuries.
Neuropeptide S facilitates cue-induced relapse to cocaine seeking through activation of the hypothalamic hypocretin system
Authors: Kallupi Marsida , Cannella Nazzareno , Economidou Daina , Ubaldi Massimo , Ruggeri Barbara , Weiss Friedbert , Massi Maurizio , Marugan Juan , Heilig Markus , Bonnavion Patricia , de Lecea Luis , Ciccocioppo Roberto
Published: October 2010

Drug addiction is a chronic relapsing disorder characterized by compulsive drug seeking and use. Environmental conditioning factors are among the major determinants of relapse in abstinent cocaine users. Here we describe a role of the neuropeptide S (NPS) system in regulating relapse. In rats with a history of cocaine self-administration, presentation of stimuli predictive of drug availability reinstates drug seeking, triggering relapse. Intracerebroventricular (ICV) injection of NPS increased conditioned reinstatement of cocaine seeking, whereas peripheral administration of the NPS receptor antagonist SHA 68 reduced it. Manipulation of the NPS receptor system did not modify cocaine self-administration. We also found that ICV NPS administration activates c-Fos expression in hypocretin-1/orexin-A (Hcrt-1/Ox-A) immunoreactive neurons in the lateral hypothalamus (LH) and in the perifornical area (PeF). Of note, intra-LH and intra-PeF administration of NPS increased conditioned reinstatement of cocaine responding, an effect that was selectively blocked with the Hcrt-1/Ox-A receptor selective antagonist SB334867. Finally, results showed that intra-LH injection of the NPS antagonist [D-Cys(tBu) (5)]NPS blocked cue-induced cocaine seeking, indicating a role for this system in the pathophysiology of drug relapse.
αβγ-Synuclein triple knockout mice reveal age-dependent neuronal dysfunction
Authors: Greten-Harrison Becket , Polydoro Manuela , Morimoto-Tomita Megumi , Diao Ling , Williams Andrew M. , Nie Esther H. , Makani Sachin , Tian Ning , Castillo Pablo E. , Buchman Vladimir L. , Chandra Sreeganga S.
Published: October 2010

Synucleins are a vertebrate-specific family of abundant neuronal proteins. They comprise three closely related members, α-, β-, and γ-synuclein. α-Synuclein has been the focus of intense attention since mutations in it were identified as a cause for familial Parkinson's disease. Despite their disease relevance, the normal physiological function of synucleins has remained elusive. To address this, we generated and characterized αβγ-synuclein knockout mice, which lack all members of this protein family. Deletion of synucleins causes alterations in synaptic structure and transmission, age-dependent neuronal dysfunction, as well as diminished survival. Abrogation of synuclein expression decreased excitatory synapse size by ∼30% both in vivo and in vitro, revealing that synucleins are important determinants of presynaptic terminal size. Young synuclein null mice show improved basic transmission, whereas older mice show a pronounced decrement. The late onset phenotypes in synuclein null mice were not due to a loss of synapses or neurons but rather reflect specific changes in synaptic protein composition and axonal structure. Our results demonstrate that synucleins contribute importantly to the long-term operation of the nervous system and that alterations in their physiological function could contribute to the development of Parkinson's disease.
Importance of representing optical depth variability for estimates of global line-shaped contrail radiative forcing
Authors: Kärcher Bernd , Burkhardt Ulrike , Ponater Michael , Frömming Christine
Published: October 2010

Estimates of the global radiative forcing by line-shaped contrails differ mainly due to the large uncertainty in contrail optical depth. Most contrails are optically thin so that their radiative forcing is roughly proportional to their optical depth and increases with contrail coverage. In recent assessments, the best estimate of mean contrail radiative forcing was significantly reduced, because global climate model simulations pointed at lower optical depth values than earlier studies. We revise these estimates by comparing the probability distribution of contrail optical depth diagnosed with a climate model with the distribution derived from a microphysical, cloud-scale model constrained by satellite observations over the United States. By assuming that the optical depth distribution from the cloud model is more realistic than that from the climate model, and by taking the difference between the observed and simulated optical depth over the United States as globally representative, we quantify uncertainties in the climate model’s diagnostic contrail parameterization. Revising the climate model results accordingly increases the global mean radiative forcing estimate for line-shaped contrails by a factor of 3.3, from 3.5 mW/m
2
to 11.6 mW/m
2
for the year 1992. Furthermore, the satellite observations and the cloud model point at higher global mean optical depth of detectable contrails than often assumed in radiative transfer (off-line) studies. Therefore, we correct estimates of contrail radiative forcing from off-line studies as well. We suggest that the global net radiative forcing of line-shaped persistent contrails is in the range 8–20 mW/m
2
for the air traffic in the year 2000.
CO
2
enhancement of forest productivity constrained by limited nitrogen availability
Authors: Norby Richard J. , Warren Jeffrey M. , Iversen Colleen M. , Medlyn Belinda E. , McMurtrie Ross E.
Published: October 2010

Stimulation of terrestrial plant production by rising CO
2
concentration is projected to reduce the airborne fraction of anthropogenic CO
2
emissions. Coupled climate–carbon cycle models are sensitive to this negative feedback on atmospheric CO
2
, but model projections are uncertain because of the expectation that feedbacks through the nitrogen (N) cycle will reduce this so-called CO
2
fertilization effect. We assessed whether N limitation caused a reduced stimulation of net primary productivity (NPP) by elevated atmospheric CO
2
concentration over 11 y in a free-air CO
2
enrichment (FACE) experiment in a deciduous
Liquidambar styraciflua
(sweetgum) forest stand in Tennessee. During the first 6 y of the experiment, NPP was significantly enhanced in forest plots exposed to 550 ppm CO
2
compared with NPP in plots in current ambient CO
2
, and this was a consistent and sustained response. However, the enhancement of NPP under elevated CO
2
declined from 24% in 2001–2003 to 9% in 2008. Global analyses that assume a sustained CO
2
fertilization effect are no longer supported by this FACE experiment. N budget analysis supports the premise that N availability was limiting to tree growth and declining over time —an expected consequence of stand development, which was exacerbated by elevated CO
2
. Leaf- and stand-level observations provide mechanistic evidence that declining N availability constrained the tree response to elevated CO
2
; these observations are consistent with stand-level model projections. This FACE experiment provides strong rationale and process understanding for incorporating N limitation and N feedback effects in ecosystem and global models used in climate change assessments.
Ecological contingency in the effects of climatic warming on forest herb communities
Authors: Harrison Susan , Damschen Ellen I. , Grace James B.
Published: October 2010

Downscaling from the predictions of general climate models is critical to current strategies for mitigating species loss caused by climate change. A key impediment to this downscaling is that we lack a fully developed understanding of how variation in physical, biological, or land-use characteristics mediates the effects of climate change on ecological communities within regions. We analyzed change in understory herb communities over a 60-y period (1949/1951–2007/2009) in a complex montane landscape (the Siskiyou Mountains, Oregon) where mean temperatures have increased 2 °C since 1948, similar to projections for other terrestrial communities. Our 185 sites included primary and secondary-growth lower montane forests (500–1.200 m above sea level) and primary upper montane to subalpine forests (1,500–2,100 m above sea level). In lower montane forests, regardless of land-use history, we found multiple herb-community changes consistent with an effectively drier climate, including lower mean specific leaf area, lower relative cover by species of northern biogeographic affinity, and greater compositional resemblance to communities in southerly topographic positions. At higher elevations we found qualitatively different and more modest changes, including increases in herbs of northern biogeographic affinity and in forest canopy cover. Our results provide community-level validation of predicted nonlinearities in climate change effects.
Biogeographic and evolutionary implications of a diverse paleobiota in amber from the early Eocene of India
Authors: Rust Jes , Singh Hukam , Rana Rajendra S. , McCann Tom , Singh Lacham , Anderson Ken , Sarkar Nivedita , Nascimbene Paul C. , Stebner Frauke , Thomas Jennifer C. , Solórzano Kraemer Monica , Williams Christopher J. , Engel Michael S. , Sahni Ashok , Grimaldi David
Published: October 2010

For nearly 100 million years, the India subcontinent drifted from Gondwana until its collision with Asia some 50 Ma, during which time the landmass presumably evolved a highly endemic biota. Recent excavations of rich outcrops of 50–52-million-year-old amber with diverse inclusions from the Cambay Shale of Gujarat, western India address this issue. Cambay amber occurs in lignitic and muddy sediments concentrated by near-shore chenier systems; its chemistry and the anatomy of associated fossil wood indicates a definitive source of Dipterocarpaceae. The amber is very partially polymerized and readily dissolves in organic solvents, thus allowing extraction of whole insects whose cuticle retains microscopic fidelity. Fourteen orders and more than 55 families and 100 species of arthropod inclusions have been discovered thus far, which have affinities to taxa from the Eocene of northern Europe, to the Recent of Australasia, and the Miocene to Recent of tropical America. Thus, India just prior to or immediately following contact shows little biological insularity. A significant diversity of eusocial insects are fossilized, including corbiculate bees, rhinotermitid termites, and modern subfamilies of ants (Formicidae), groups that apparently radiated during the contemporaneous Early Eocene Climatic Optimum or just prior to it during the Paleocene-Eocene Thermal Maximum. Cambay amber preserves a uniquely diverse and early biota of a modern-type of broad-leaf tropical forest, revealing 50 Ma of stasis and change in biological communities of the dipterocarp primary forests that dominate southeastern Asia today.
Giant virus with a remarkable complement of genes infects marine zooplankton
Authors: Fischer Matthias G. , Allen Michael J. , Wilson William H. , Suttle Curtis A.
Published: October 2010

As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a critical link in aquatic foodwebs. Here, we show that a major marine microflagellate grazer is infected by a giant virus,
Cafeteria roenbergensis
virus (CroV), which has the largest genome of any described marine virus (≈730 kb of double-stranded DNA). The central 618-kb coding part of this AT-rich genome contains 544 predicted protein-coding genes; putative early and late promoter motifs have been detected and assigned to 191 and 72 of them, respectively, and at least 274 genes were expressed during infection. The diverse coding potential of CroV includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22 tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2γ, and an Elp3-like histone acetyltransferase are usually not found in viruses. We also discovered a 38-kb genomic region of putative bacterial origin, which encodes several predicted carbohydrate metabolizing enzymes, including an entire pathway for the biosynthesis of 3-deoxy-
d
-
manno
-octulosonate, a key component of the outer membrane in Gram-negative bacteria. Phylogenetic analysis indicates that CroV is a nucleocytoplasmic large DNA virus, with
Acanthamoeba polyphaga
mimivirus as its closest relative, although less than one-third of the genes of CroV have homologs in Mimivirus. CroV is a highly complex marine virus and the only virus studied in genetic detail that infects one of the major groups of predators in the oceans.
Nanoparticles activate the NLR pyrin domain containing 3 (Nlrp3) inflammasome and cause pulmonary inflammation through release of IL-1α and IL-1β
Authors: Yazdi Amir S. , Guarda Greta , Riteau Nicolas , Drexler Stefan K. , Tardivel Aubry , Couillin Isabelle , Tschopp Jürg
Published: October 2010

Nanoparticles are increasingly used in various fields, including biomedicine and electronics. One application utilizes the opacifying effect of nano-TiO
2
, which is frequently used as pigment in cosmetics. Although TiO
2
is believed to be biologically inert, an emerging literature reports increased incidence of respiratory diseases in people exposed to TiO
2
. Here, we show that nano-TiO
2
and nano-SiO
2
, but not nano-ZnO, activate the NLR pyrin domain containing 3 (Nlrp3) inflammasome, leading to IL-1β release and in addition, induce the regulated release of IL-1α. Unlike other particulate Nlrp3 agonists, nano-TiO
2
–dependent-Nlrp3 activity does not require cytoskeleton-dependent phagocytosis and induces IL-1α/β secretion in nonphagocytic keratinocytes. Inhalation of nano-TiO
2
provokes lung inflammation which is strongly suppressed in IL-1R– and IL-1α–deficient mice. Thus, the inflammation caused by nano-TiO
2
in vivo is largely caused by the biological effect of IL-1α. The current use of nano-TiO
2
may present a health hazard due to its capacity to induce IL-1R signaling, a situation reminiscent of inflammation provoked by asbestos exposure.
Boundary crossing in epithelial wound healing
Authors: Fong Eileen , Tzlil Shelly , Tirrell David A.
Published: October 2010

The processes of wound healing and collective cell migration have been studied for decades. Intensive research has been devoted to understanding the mechanisms involved in wound healing, but the role of cell-substrate interactions is still not thoroughly understood. Here we probe the role of cell-substrate interactions by examining in vitro the healing of monolayers of human corneal epithelial (HCE) cells cultured on artificial extracellular matrix (aECM) proteins. We find that the rate of wound healing is dependent on the concentration of fibronectin-derived (RGD) cell-adhesion ligands in the aECM substrate. The wound closure rate varies nearly sixfold on the substrates examined, despite the fact that the rates of migration and proliferation of individual cells show little sensitivity to the RGD concentration (which varies 40-fold). To explain this apparent contradiction, we study collective migration by means of a dynamic Monte Carlo simulation. The cells in the simulation spread, retract, and proliferate with probabilities obtained from a simple phenomenological model. The results indicate that the overall wound closure rate is determined primarily by the rate at which cells cross the boundary between the aECM protein and the matrix deposited under the cell sheet.
Xenopus furry
contributes to release of microRNA gene silencing
Authors: Goto Toshiyasu , Fukui Akimasa , Shibuya Hiroshi , Keller Ray , Asashima Makoto
Published: October 2010

A transcriptional corepressor,
Xenopus furry
(
Xfurry
)
,
is expressed in the chordamesodermal region and induces secondary dorsal axes when overexpressed on the ventral side of the embryo. The N-terminal furry domain functions as a repressor, and the C-terminal leucine zipper (LZ) motifs /coiled-coil structure, found only in vertebrate homologs, contributes to the nuclear localization. The
engrailed repressor
(
enR
)
+LZ
repressor construct, which has properties similar to
Xfurry
, induced several chordamesodermal genes. In contrast, an antisense morpholino oligonucleotide,
Xfurry
-MO, and the activating construct,
herpes simplex virus protein
(
VP16
)
+LZ,
had effects opposite those of
Xfurry
overexpression. Because blocking protein synthesis with cycloheximide superinduced several
Xfurry
transcriptional targets, and because expression of
enR+LZ
induced such genes under cycloheximide treatment, we analyzed the role of an
Xfurry
transcriptional target, microRNA
miR-15
. Cycloheximide reduced the expression of
primary miR-15
(
pri-miR-15
), whereas
miR-15
reduced the expression of genes superinduced by cycloheximide treatment. These results show that
Xfurry
regulates chordamesodermal genes by contributing to repression of pretranscriptional gene silencing by
miR-15
.