bluuebunny/crossref_metadata_2025 huggingface dataset:
A nested grid model of the Oregon Coastal Transition Zone: Simulations and comparisons with observations during the 2001 upwelling season
Authors: Springer S. R. , Samelson R. M. , Allen J. S. , Egbert G. D. , Kurapov A. L. , Miller R. N. , Kindle J. C.
Published: February 2009

The Oregon Coastal Transition Zone (OCTZ) extends several hundred kilometers offshore where shelf flows interact with the northern California Current. A primitive‐equation numerical ocean model is used to study the upwelling circulation in this region from 1 May to 1 November 2001. This OCTZ model obtains initial and boundary conditions from a larger‐scale model of the California Current System and forcing from a regional atmospheric model product. The model results are compared with extensive in situ and remotely sensed data, and the model is found to provide a realistic representation of flows both over the shelf and in the broader OCTZ. Simulation of coastal sea level and shelf currents over the complex topography of the central Oregon coast is improved quantitatively relative to previous regional models. A particularly significant qualitative improvement is realistic representation of coastal jet separation and eddy formation offshore of Cape Blanco. Three‐dimensional Lagrangian analysis of water parcel displacement shows that the surface waters inshore of the separated jet are upwelled from near the bottom along the shelf as far north as 45.5°N. A large eddy, which incorporates some of this upwelled water and carries it farther westward, forms offshore in the late summer. Ensemble simulations show a distinction between the strongly deterministic response to wind forcing over the shelf and the more unstable, less predictable jet separation and offshore eddy formation processes in the region near Cape Blanco.
Formation mechanisms of latitudinal CO2 gradients in the upper troposphere over the subtropics and tropics
Authors: Miyazaki Kazuyuki , Machida Toshinobu , Patra Prabir K. , Iwasaki Toshiki , Sawa Yousuke , Matsueda Hidekazu , Nakazawa Takakiyo
Published: February 2009

Aircraft observations and numerical simulations using an atmospheric transport model exhibit large latitudinal gradients in the carbon dioxide (CO2) mixing ratio around the subtropics and equator throughout the troposphere. The formation mechanisms of the latitudinal CO2 gradients are investigated at aircraft flight altitudes (350–260 hPa) by considering the influences of atmospheric transport and carbon fluxes at the earth's surface. A meridional transport analysis demonstrates how various transport processes create the latitudinal CO2 gradients in the upper troposphere. The analysis result shows that around the northern subtropics, the suppression of meridional mixing sharpens the CO2 gradient during boreal winter and spring. In other words, extratropical cyclonic activity effectively flattens the mixing ratio along isentropic surfaces at midlatitudes and induces gradients around the subtropics. The southern subtropical CO2 gradient is also induced by the subtropical mixing barrier and convergence of the cross‐equatorial eddy flux. Different from the subtropical gradients, a CO2 gradient in the tropical upper troposphere is not created by the suppression of meridional transport but is created by the uplifting of low‐level air during boreal winter and spring. The latitudinal CO2 gradient in the tropical upper troposphere decreases due to interhemispheric transport. The seasonal migration of the mean Hadley circulation yields efficient interhemispheric transport and reduces the tropical CO2 gradient.
Links between iron supply, marine productivity, sea surface temperature, and CO2 over the last 1.1 Ma
Authors: Martínez‐Garcia Alfredo , Rosell‐Melé Antoni , Geibert Walter , Gersonde Rainer , Masqué Pere , Gaspari Vania , Barbante Carlo
Published: February 2009

Paleoclimatic reconstructions have provided a unique data set to test the sensitivity of climate system to changes in atmospheric CO2 concentrations. However, the mechanisms behind glacial/interglacial (G/IG) variations in atmospheric CO2 concentrations observed in the Antarctic ice cores are still not fully understood. Here we present a new multiproxy data set of sea surface temperatures (SST), dust and iron supply, and marine export productivity, from the marine sediment core PS2489‐2/ODP Site 1090 located in the subantarctic Atlantic, that allow us to evaluate various hypotheses on the role of the Southern Ocean (SO) in modulating atmospheric CO2 concentrations back to 1.1 Ma. We show that Antarctic atmospheric temperatures are closely linked to changes in SO surface temperatures over the last 800 ka and use this to synchronize the timescales of our marine and the European Project for Ice Coring in Antarctica (EPICA) Dome C (EDC) records. The close correlation observed between iron inputs and marine export production over the entire interval implies that the process of iron fertilization of marine biota has been a recurrent process operating in the subantarctic region over the G/IG cycles of the last 1.1 Ma. However, our data suggest that marine productivity can only explain a fraction of atmospheric CO2 changes (up to around 40–50 ppmv), occurring at glacial maxima in each glacial stage. In this sense, the good correlation of our SST record to the EDC temperature reconstruction suggests that the initial glacial CO2 decrease, as well as the change in the amplitude of the CO2 cycles observed around 400 ka, was most likely driven by physical processes, possibly related to changes in Antarctic sea ice extent, surface water stratification, and westerly winds position.
Extending the timescale for using beryllium 7 measurements to document soil redistribution by erosion
Authors: Walling D. E. , Schuller P. , Zhang Y. , Iroumé A.
Published: February 2009

The need for spatially distributed information on soil mobilization, transfer, and deposition within the landscape by erosion has focused attention on the potential for using fallout radionuclides (i.e., 137Cs, excess 210Pb, and 7Be) to document soil redistribution rates. Whereas 137Cs and excess 210Pb are used to estimate medium‐ and longer‐term erosion rates (i.e., approximately 45 years and 100 years, respectively), 7Be, by virtue of its short half‐life (53 days), provides potential for estimating short‐term soil redistribution on bare soils. However, the approach commonly used with this radionuclide means that it can only be applied to individual events or short periods of heavy rain. In addition, it is also frequently difficult to ensure that the requirement for spatially uniform 7Be inventories across the study area immediately prior to the study period is met. If the existing approach is applied to longer periods with several rainfall events (e.g., several weeks or more) soil redistribution is likely to be substantially underestimated. These problems limit the potential for using the 7Be approach, particularly in investigations where there is a need to assemble representative information on soil redistribution occurring during the entire wet season. This paper reports the development of a new or refined model for converting radionuclide measurements to estimates of soil redistribution (conversion model) for use with 7Be measurements, which permits much longer periods to be studied. This refined model aims to retain much of the simplicity of the existing approach, but takes account of the temporal distribution of both 7Be fallout and erosion during the study period and of the evolution of the 7Be depth distribution during this period. The approach was successfully tested using 7Be measurements from a study of short‐term soil redistribution undertaken within an area of recently harvested forest located near Valdivia in Southern Chile. The study period extended over about 3 months and included the main part of the winter wet season of 2006. The estimates of soil redistribution obtained using the new conversion model were consistent with those obtained from erosion pins deployed within the same study area and were two to three times greater than those obtained using the approach and conversion model employed in existing studies.
Sensitivity and resolution of tomographic pumping tests in an alluvial aquifer
Authors: Bohling Geoffrey C.
Published: February 2009

Various investigators have proposed hydraulic tomography, the simultaneous analysis of responses to multiple well tests, as a means to obtain a high‐resolution characterization of aquifer flow properties. This study assesses the information content of drawdown records from a set of tomographic pumping tests in an alluvial aquifer, comparing the parameter sensitivity and resolution associated with transient and steady‐shape formulations of the objective function for the parameter estimation problem. The steady‐shape approach takes advantage of the rapid establishment of constant gradients within the region surrounding a pumping well, comparing observed drawdown differences within this region with drawdown differences predicted by a steady state model. Both the transient and steady‐shape approaches resolve K variations only within a limited distance of the pumping intervals and observation points. Relative to the transient approach, the steady‐shape approach reduces the influence of poorly resolved property variations, including K variations outside the region of investigation and storage coefficient variations throughout the model domain.
The NS3 protein of rice hoja blanca virus complements the RNAi suppressor function of HIV‐1 Tat
Authors: Schnettler Esther , de Vries Walter , Hemmes Hans , Haasnoot Joost , Kormelink Richard , Goldbach Rob , Berkhout Ben
Published: February 2009

The question of whether RNA interference (RNAi) acts as an antiviral mechanism in mammalian cells remains controversial. The antiviral interferon (IFN) response cannot easily be distinguished from a possible antiviral RNAi pathway owing to the involvement of double‐stranded RNA (dsRNA) as a common inducer molecule. The non‐structural protein 3 (NS3) protein of rice hoja blanca virus (RHBV) is an RNA silencing suppressor (RSS) that exclusively binds to small dsRNA molecules. Here, we show that this plant viral RSS lacks IFN antagonistic activity, yet it is able to substitute the RSS function of the Tat protein of human immunodeficiency virus type 1. An NS3 mutant that is deficient in RNA binding and its associated RSS activity is inactive in this complementation assay. This cross‐kingdom suppression of RNAi in mammalian cells by a plant viral RSS indicates the significance of the antiviral RNAi response in mammalian cells and the usefulness of well‐defined RSS proteins.
Preparation of Nd–Fe–B nanoparticles by surfactant-assisted ball milling technique
Authors: Yue M. , Wang Y. P. , Poudyal N. , Rong C. B. , Liu J. P.
Published: February 2009

Nd–Fe–B nanoparticles have been obtained by using surfactant-assisted ball milling and subsequent size-selection technique. Structural analyses show that nanoparticles with two particle sizes around 10 and 100nm were obtained. The partially amorphous Nd–Fe–B nanoparticles give their room-temperature coercivities around 0.1 and 1.5kOe for the small and large nanoparticles, respectively. As the temperature decreases to 200K, the coercive force of the large nanoparticles increases by 50% due to the enhancement of the magnetocrystalline anisotropy of the Nd2Fe14B phase in the particles.
Magnetic properties of epitaxially grown Fe3Si/Ge(111) layers with atomically flat heterointerfaces
Authors: Ando Y. , Hamaya K. , Kasahara K. , Ueda K. , Nozaki Y. , Sadoh T. , Maeda Y. , Matsuyama K. , Miyao M.
Published: February 2009

We study magnetic properties of epitaxial Fe3Si layers grown on Ge(111) with atomically flat interfaces. An unexpected uniaxial magnetic anisotropy is observed in the film plane for all as-grown samples, and the direction of the uniaxial easy axis is different for each of these samples. By postgrowth annealing, surprisingly, the random orientation of the uniaxial easy axis is aligned to a direction along about [01¯1], together with a reduction in the saturation magnetization. We discuss a possible mechanism of the variation in the magnetic properties after the annealing.
Pressure and magnetic field effects in heavy-fermion UCu3.5Al1.5
Authors: Nasreen F. , Kothapalli K. , Nakotte H. , Alsmadi A. M. , Zapf V. , Fabris F. , Lacerda A. , Kamarad J.
Published: February 2009

UCu 3.5 Al 1.5 is a heavy-fermion compound, which crystallizes in the hexagonal CaCu5 structure, and it was reported to exhibit non-Fermi-liquid scaling at low temperatures. We report on the measurements of the electrical resistivity and magnetoresistance as a function of temperature (2–150 K), pressure (0–10 kbar), and applied magnetic field (0–18 T). The results provide evidence that, for UCu3.5Al1.5, application of pressure and/or magnetic field tends to suppress non-Fermi-liquid scaling and a tendency toward long-range magnetic correlations is observed for temperatures below 20 K, although there is no clear evidence of long-range order in the available pressure and field range.
Movable algebraic singularities of second-order ordinary differential equations
Authors: Filipuk G. , Halburd R. G.
Published: February 2009

Any nonlinear equation of the form y″=∑n=0Nan(z)yn has a solution with leading behavior proportional to (z−z0)−2/(N−1) about a point z0, where the coefficients an are analytic at z0 and aN(z0)≠0. Equations are considered for which each possible leading term of this form extends to a Laurent series solution in fractional powers of z−z0. For these equations we show that the only movable singularities that can be reached by analytic continuation along finite-length curves are of the algebraic type just described. This generalizes results of Shimomura [“On second order nonlinear differential equations with the quasi-Painlevé property II,” RIMS Kokyuroku 1424, 177 (2005)]. The possibility that these algebraic singularities could accumulate along infinitely long paths ending at a finite point is considered. Smith [“On the singularities in the complex plane of the solutions of y″+y′f(y)+g(y)=P(x),” Proc. Lond. Math. Soc. 3, 498 (1953)] showed that such singularities do occur in solutions of a simple equation outside this class.
Evaluating nucleation rates in direct simulations
Authors: Chkonia Guram , Wölk Judith , Strey Reinhard , Wedekind Jan , Reguera David
Published: February 2009

We compare different methods for obtaining nucleation rates from molecular dynamics simulations of nucleation, using the condensation of Lennard-Jones argon as an example. All methods yield the same nucleation rate at the conditions where they can be applied correctly, with discrepancies smaller than a factor of 2. We critically examine the different approaches and highlight their respective strengths and possible limitations.
Calculations of trapping and desorption in heavy atom collisions with surfaces
Authors: Fan Guoqing , Manson J. R.
Published: February 2009

Calculations are carried out for the scattering of heavy rare gas atoms with surfaces using a recently developed classical theory that can track particles trapped in the physisorption potential well and follow them until ultimate desorption. Comparisons are made with recent experimental data for xenon scattering from molten gallium and indium, systems for which the rare gas is heavier than the surface atoms. The good agreement with the data obtained for both time-of-flight energy-resolved spectra and for total scattered angular distributions yields an estimate of the physisorption well depths for the two systems.
Experimental verification of rank 1 chaos in switch-controlled Chua circuit
Authors: Oksasoglu Ali , Ozoguz Serdar , Demirkol Ahmet S. , Akgul Tayfun , Wang Qiudong
Published: February 2009

In this paper, we provide the first experimental proof for the existence of rank 1 chaos in the switch-controlled Chua circuit by following a step-by-step procedure given by the theory of rank 1 maps. At the center of this procedure is a periodically kicked limit cycle obtained from the unforced system. Then, this limit cycle is subjected to periodic kicks by adding externally controlled switches to the original circuit. Both the smooth nonlinearity and the piecewise linear cases are considered in this experimental investigation. Experimental results are found to be in concordance with the conclusions of the theory.
Crystallization and dynamical arrest of attractive hard spheres
Authors: Babu Sujin , Gimel Jean-Christophe , Nicolai Taco
Published: February 2009

Crystallization of hard spheres interacting with a square well potential was investigated by numerical simulations using so-called Brownian cluster dynamics. The phase diagram was determined over a broad range of volume fractions. The crystallization rate was studied as a function of the interaction strength expressed in terms of the second virial coefficient. For volume fractions below about 0.3 the rate was found to increase abruptly with increasing attraction at the binodal of the metastable liquid-liquid phase separation. The rate increased until a maximum was reached after which it decreased with a power law dependence on the second virial coefficient. Above a critical percolation concentration, a transient system spanning network of connected particles was formed. Crystals were formed initially as part of the network, but eventually crystallization led to the breakup of the network. The lifetime of the transient gels increased very rapidly over a small range of interaction energies. Weak attraction destabilized the so-called repulsive crystals formed in pure hard sphere systems and shifted the coexistence line to higher volume fractions. Stronger attraction led to the formation of a denser, so-called attractive, crystalline phase. Nucleation of attractive crystals in the repulsive crystalline phase was observed close to the transition.
Structural, dielectric, and insulating properties of barium strontium titanate thin films grown on various oriented LaAlO3 substrates
Authors: Chen Hongwei , Yang Chuanren , Wang Bo , Ji Hong , Zhang Jihua
Published: February 2009

( Ba 0.6 Sr 0.4 ) TiO 3 (BST) thin films were deposited on (100) and (110) oriented LaAlO3 (LAO) single-crystal substrates by radio-frequency magnetron sputtering system, respectively. X-ray diffraction θ-2θ and Φ-scans results showed that the BST thin films grown on LaAlO3 (100) displayed (h00) preferred orientation, while the films grown on LaAlO3 (110) indicated (110) preferred orientation. Atomic force microscope revealed that BST films grown on LAO (110) had smoother surface and smaller grain size than that BST films grown on LAO (100). Compared with BST films grown on LAO (100), the BST films grown on LAO (110) had higher tunability and better figure of merit. Additionally, the current-voltage (I-V) measurement indicated that the leakage current density of BST films grown on LAO (110) was obviously reduced compared to that of BST films grown on LAO (100).
Colossal dielectric behavior of semiconducting Sr2TiMnO6 ceramics
Authors: Meher K. R. S. Preethi , Varma K. B. R.
Published: February 2009

Manganitelike double perovskite Sr2TiMnO6 (STMO) ceramics fabricated from the powders synthesized via the solid-state reaction route, exhibited dielectric constants as high as ∼105 in the low frequency range (100 Hz–10 kHz) at room temperature. The Maxwell–Wagner type of relaxation mechanism was found to be more appropriate to rationalize such high dielectric constant values akin to that observed in materials such as KxTiyNi(1−x−y)O and CaCu3Ti4O12. The dielectric measurements carried out on the samples with different thicknesses and electrode materials reflected the influence of extrinsic effects. The impedance studies (100 Hz–10 MHz) in the 180–300 K temperature range revealed the presence of two dielectric relaxations corresponding to the grain boundary and the electrode. The dielectric response of the grain boundary was found to be weakly dependent on the dc bias field (up to 11 V/cm). However, owing to the electrode polarization, the applied ac/dc field had significant effect on the low frequency dielectric response. At low temperatures (100–180 K), the dc conductivity of STMO followed a variable range hopping behavior. Above 180 K, it followed the Arrhenius behavior because of the thermally activated conduction process. The bulk conductivity relaxation owing to the localized hopping of charge carriers obeyed the typical universal dielectric response.
Electronic structure and carrier dynamics in InAs/InP double-cap quantum dots
Authors: Miska P. , Even J. , Marie X. , Dehaese O.
Published: February 2009

The carrier dynamics in InAs double-cap quantum dots (DC-QDs) grown on InP(113)B are investigated. The shape of these QDs can be controlled during the growth, yielding an emission wavelength of the system of about 1.55 μm at room temperature. The DC-QD dynamics is studied by time-resolved photoluminescence experiments at low temperature for various excitation densities. A simplified dynamic model is developed, yielding results consistent with experimental data. This analysis yields the determination of the Auger coefficients and the intradot relaxation time in this system.
Electroluminescence from TiO2/p+-Si heterostructure
Authors: Zhang Yuanyuan , Ma Xiangyang , Chen Peiliang , Li Dongsheng , Yang Deren
Published: February 2009

Titanium films sputtered on heavily boron-doped (p+) silicon substrates were thermally oxidized to form electroluminescent TiO2/p+-Si heterostructures. The electroluminescence (EL) features a broad spectrum covering red, green, and blue regions. We believe that in TiO2 recombinations between electrons at oxygen-vacancy-related energy levels and holes in the valence band result in the EL. Furthermore, the EL mechanism has been explained in terms of the energy band diagram of the TiO2/p+-Si heterostructure, which possesses an intermediate ultrathin SiOx layer revealed by high resolution transmission microscopy.
Application of triangular atomic force microscopy cantilevers to friction measurement with the improved parallel scan method
Authors: Wang Yu-Liang , Zhao Xue-Zeng
Published: February 2009

The atomic force microscopy (AFM) can provide tribological information in micro/nanoscale. However, the general measurement techniques require rigorous value of stiffness and relationship between AFM cantilever deformation and corresponding photodetector response. In this study, triangular AFM cantilevers with different dimensions are applied to quantitatively measure the coefficient of friction with the improved parallel scan method [Y. L. Wang, X. Z. Zhao, and F. Q. Zhou, Rev. Sci. Instrum. 78, 036107 (2007)]. An analytical model is first presented with the plan-view geometrical dimensions of cantilevers. Finite element analysis (FEA) models are set up to validate the analytical model. The results show good agreement between analytical calculation and FEA simulation. More importantly, the coefficient of friction obtained with different cantilevers on silicon surface shows a good consistency. At last, the factors which may affect measurement are discussed. The advantage of the model presented here is that the general uncertainties of thickness and Young’s modulus are not necessary to be known for the friction force calibration in AFM application.
Correlation between average melting temperature and glass transition temperature in metallic glasses
Authors: Lu Zhibin , Li Jiangong
Published: February 2009

The correlation between average melting temperature (⟨Tm⟩) and glass transition temperature (Tg) in metallic glasses (MGs) is analyzed. A linear relationship, Tg=0.385⟨Tm⟩, is observed. This correlation agrees with Egami’s suggestion [Rep. Prog. Phys. 47, 1601 (1984)]. The prediction of Tg from ⟨Tm⟩ through the relationship Tg=0.385⟨Tm⟩ has been tested using experimental data obtained on a large number of MGs. This relationship can be used to predict and design MGs with a desired Tg.
Energy level alignment at a charge generation interface between 4,4′-bis(N-phenyl-1-naphthylamino)biphenyl and 1,4,5,8,9,11-hexaazatriphenylene-hexacarbonitrile
Authors: Kim Yong-Ki , Won Kim Jeong , Park Yongsup
Published: February 2009

We have determined the electronic energy level alignment at the interface between 4,4′-bis(N-phenyl-1-naphthylamino)biphenyl (NPB) and 1,4,5,8,9,11-hexaazatriphenylene-hexacarbonitrile (HAT-CN) using ultraviolet photoelectron spectroscopy. The highest occupied molecular orbital (HOMO) of 20 nm thick HAT-CN film was located at 3.8 eV below the Fermi level. Thus the lowest unoccupied molecular orbital (LUMO) is very close to the Fermi level. The HOMO position of NPB was only about 0.3 eV below Fermi level at NPB/HAT-CN interface. This enables an easy excitation of electrons from the NPB HOMO to the HAT-CN LUMO, creating electron-hole pairs across this organic-organic interface.
Intercoupling of free-space radiation to s-polarized confined modes via nanocavities
Authors: Nikitin A. Yu. , García-Vidal F. J. , Martín-Moreno L.
Published: February 2009

The interaction of the s-polarized waveguide mode in the dielectric layer placed on a metal film with one-dimensional indentations in the metal is studied. The efficiency of the coupling to the out-of-plane radiation is considered. It is shown that varying the parameters of the cavities, the periodical array of resonant indentations can almost totally reflect back the incident waveguide mode or, on the contrary, efficiently transform it into a narrow-directional outgoing beam. An efficient waveguide mode launcher is examined on the basis of the results for Bragg mirror. The differences and similarities between scattering of surface plasmon polaritons and waveguide modes are discussed.
Floral structure and development in the dioecious Australian endemic Lomandra longifolia (Lomandraceae)
Authors: Ahmad Nabil M. , Martin Peter M. , Vella John M.
Published: February 2009

The micromorphology and histology of the development of male and female flowers of the dioecious Australian endemic species Lomandra longifolia Labill. was studied by means of scanning electron microscopy and light microscopy of entire and sectioned material. Although mature flowers are functionally unisexual, in the early stages of development pistillate and staminate flowers are identical and apparently bisexual. In a sequential fashion, six perianth parts are initiated within two alternating whorls, the sepals first and the petals second; six stamens are initiated in two alternating whorls of three stamens each, the first opposite the sepals and the second opposite the petals; and last, a central gynoecium is initiated. Following initiation, the two flower types diverge developmentally when the stamens become bilobed. In male flowers, cytological analysis of the slowly growing abortive pistil shows that megasporogenesis does not occur. Pistil abortion happens before meiosis whereas the stamens continue to develop until maturity and dehiscence. In female flowers, stamen arrest occurs before the onset of meiosis in microspore mother cells, after which the pistil continues its development through megasporogenesis and megagametogenesis. In all, 14 stages of floral development of both male and female flowers have been designated. Stages 1–6 of the two flower types were common to both sexes.
Impacts of experimental warming and fire on phenology of subalpine open-heath species
Authors: Jarrad Frith C. , Wahren Carl-Henrik , Williams Richard J. , Burgman Mark A.
Published: February 2009

The present study examined experimentally the phenological responses of a range of plant species to rises in temperature. We used the climate-change field protocol of the International Tundra Experiment (ITEX), which measures plant responses to warming of 1 to 2°C inside small open-topped chambers. The field study was established on the Bogong High Plains, Australia, in subalpine open heathlands; the most common treeless plant community on the Bogong High Plains. The study included areas burnt by fire in 2003, and therefore considers the interactive effects of warming and fire, which have rarely been studied in high mountain environments. From November 2003 to March 2006, various phenological phases were monitored inside and outside chambers during the snow-free periods. Warming resulted in earlier occurrence of key phenological events in 7 of the 14 species studied. Burning altered phenology in 9 of 10 species studied, with both earlier and later phenological changes depending on the species. There were no common phenological responses to warming or burning among species of the same family, growth form or flowering type (i.e. early or late-flowering species), when all phenological events were examined. The proportion of plants that formed flower buds was influenced by fire in half of the species studied. The findings support previous findings of ITEX and other warming experiments; that is, species respond individualistically to experimental warming. The inter-year variation in phenological response, the idiosyncratic nature of the responses to experimental warming among species, and an inherent resilience to fire, may result in community resilience to short-term climate change. In the first 3 years of experimental warming, phenological responses do not appear to be driving community-level change. Our findings emphasise the value of examining multiple species in climate-change studies.
The use of pre-dawn leaf water potential and MODIS LAI to explore seasonal trends in the phenology of Australian and southern African woodlands and savannas
Authors: Palmer Anthony R. , Fuentes Sigfredo , Taylor Daniel , Macinnis-Ng Cate , Zeppel Melanie , Yunusa Isa , February Edmund , Eamus Derek
Published: February 2009

Trends in global soil moisture are needed to inform models of soil–plant–atmosphere interactions. Predawn leaf water potential (Ψpd), a surrogate for soil moisture and an index of plant water stress, has been routinely collected in Australian forests, woodlands and savannas, but the associated leaf area index (LAI) has seldom been available to enable the preparation of a Ψpd on LAI relationship. Following an analysis of Ψpd and MODIS LAI data from Australian forests, woodlands and savannas, we identified patterns in Ψpd which provide an understanding of the role of soil-moisture status in controlling LAI. In the savanna of northern Australia, the MODIS LAI product had a basal value of 0.96 during the dry season as compared with a mean value of 2.5 for the wet season. The dry season value is equivalent to the LAI of the tree component and corresponds with ground-truthed LAI. Ψpd is lowest (more negative) during the height of the dry season (late October) at −2.5 MPa, and highest (−0.1 MPa) during the wet season (early March). We present two models which predict Ψpd from the MODIS LAI product. These may be useful surrogates for studying trends in soil moisture in highly seasonal climates and may contribute to climate change research.
Climate change and other factors influencing the decline of the Tasmanian cider gum (Eucalyptus gunnii)
Authors: Calder J. A. , Kirkpatrick J. B.
Published: February 2009

Global climatic change has been strongly implicated in the decline of many species. However, other processes can contribute towards the extinction risk of these species. Could management of these processes arrest or slow climatically related decline? We test the relationship between climate change, and other potential threatening factors, and the decline of Eucalyptus gunnii, a tree endemic to the subalpine regions of Tasmania, Australia. Through observing the spatial patterns of both climatic change and dieback, we found there was a stronger pattern of increasing droughts in the eastern part of the species range, the region which also displayed the worst dieback. A time series of aerial photographs revealed that the most severe drought periods in the last several decades have coincided with the most rapid tree decline. However, the sites that suffered the worst dieback were also more heavily used for stock grazing, a factor which had a stronger spatial relationship with tree decline than climate. Other factors were also implicated in the decline, including possum browsing. The good health of some populations in the most climatically stressed areas suggests that the amelioration of non-climatic stresses could be effective in maintaining the health of the surviving populations.
Ring Contractions of 3-Azido-4H-quinolizin-4-ones and 3-Azido-4H-azino[1,2 - x]pyrimidin-4-ones: a Novel Approach to 3-Aminoindolizines and their Aza Analogues
Authors: Rečnik Simon , Meden Anton , Stanovnik Branko , Svete Jurij
Published: February 2009

Thermal transformations of 3-azido-4H-quinolizin-4-ones 4a,b and 3-azido-4H-azino[1,2–x]pyrimidin-4-ones 4c,d, available from the corresponding heteroarylamines 2a–d, were studied. The reaction products were mostly dependent on the solvent. Thus, heating of 3-azido-1-cyano-4H-quinolizin-4-one (4a) in toluene afforded 2-(pyridin-2-yl)fumaronitrile 5a, whereas 3-amino-1-cyano-4H-quinolizin-4-one (8) was obtained on treatment of 4a in a mixture of toluene and trifluoroacetic anhydride. However, heating of 4a in acetic anhydride and in acetic acid resulted in a ring contraction to produce 3-(diacetylamino)indolizine-1-carbonitrile 6a and 3-(acetylamino)indolizine-1-carbonitrile 7a, respectively. Similarly, ring contractions took place on heating ethyl 3-azido-4-oxo-4H-quinolizin-1-carboxylate 4b and 3-azido-4H-azino[1,2–x]pyrimidin-4-ones 4c,d in acetic anhydride or acetic acid to produce the N-acetylated 3-aminoindolizine derivatives 6b, 7b and 3-aminoimidazo[1,2–x]azine derivatives 6c,d in 30–89% yields. The structures of compounds 5–8 were determined by NMR spectroscopy and X-ray diffraction.
Convenient and Efficient Synthesis of Thiol Esters using Zinc Oxide as a Heterogeneous and Eco-Friendly Catalyst
Authors: Bandgar Babasaheb Pandurang , More Parmeshwar Eknath , Kamble Vinod Tribhuvannathji , Sawant Sanjay Suresh
Published: February 2009

A catalytic method was developed to synthesize thiol esters from the reaction of acyl chlorides and thiols using zinc oxide as a catalyst under solvent-free conditions at room temperature. Mild reaction conditions, short reaction time, excellent yields of products and recyclability of the catalyst are noteworthy features of this methodology.
Surface-Enhanced Raman Scattering Spectroscopy of Resveratrol
Authors: Vongsvivut Jitraporn , Robertson Evan G. , McNaughton Don
Published: February 2009

We report here, for the first time, the surface-enhanced Raman scattering (SERS) spectra of resveratrol using KNO3-aggregated citrate-reduced silver (Ag) colloids. The technique provided a substantial spectral enhancement and therefore good quality spectra of resveratrol at parts per million (ppm) concentrations. The detection limit was found to be <1 μM, equivalent to <0.2 ppm. The SERS profile additionally closely resembled its normal solid-state Raman spectrum with some changes in relative intensity. These intensity changes, together with a precise band assignment aided by density functional theory calculations at the B3LYP/6–31G(d) level, allowed the determination of the structural orientation of the adsorbed resveratrol on the surface of the metal nanoparticles. In particular, the SERS spectra obtained at different resveratrol concentrations exhibited concentration-dependent features, suggesting an influence of surface coverage on the orientation of the adsorbed molecules. At a high concentration, an adoption of close-to-upright orientation of resveratrol adsorbed on the metal surface through the p-OH phenyl ring is favoured. The binding structure is, however, altered at lower surface coverage when the concentration decreases to a tilted orientation with the trans-olefin C=C bond aligning closer to parallel to the surface of the Ag nanoparticles.
Synthesis and Preliminary Pharmacological Evaluation of 4′-Arylalkyl Analogues of Clozapine. IV. The Effects of Aromaticity and Isosteric Replacement
Authors: Capuano Ben , Crosby Ian T. , Lloyd Edward J. , Podloucka Anna , Taylor David A.
Published: February 2009

We report the synthesis and preliminary pharmacological activity of a new series of tricyclic analogues of clozapine as potential antipsychotic agents for the treatment of schizophrenia. These compounds were designed based on a revised structural model, and investigate the length and nature of a designated linker (alkyl and alkyloxy) and the nature of the introduced aryl group (aromatic and heteroaromatic). The chemistry and structural characterization of this series of 4′-arylalkyl(oxy) analogues of clozapine are described. Preliminary results on the pharmacological effects of the selected linkers and introduced aryl groups on affinity for dopamine D4 and serotonin 5-HT2A receptors are discussed. Psychosis-related animal behavioural data for promising compounds identified from the receptor binding screen are also presented.
Non-Selective Stereoablation for the Synthesis of Enantioenriched Compounds
Authors: Ahamed Muneer
Published: February 2009

Muneer Ahamed is a Ph.D. candidate under the supervision of Dr Matthew H. Todd at the University of Sydney. His research is focussed on asymmetric catalysis.
Electrochemical Detection of Short DNA Sequences Related to the Escherichia coli Pathogen Using a Zirconia-Modified Screen-Printed DNA Biosensor
Authors: Zuo Shao-Hua , Zhang Ling-Fan , Zhao Yan-Hui , Yuan Hui-Hui , Lan Min-Bo , Lawrance Geoffrey A. , Wei Gang
Published: February 2009

A simple, disposable and inexpensive electrochemical DNA biosensor based on a zirconia (ZrO2) modified thin film screen-printed electrode (ZrO2/SPE) has been developed. Short DNA sequences (21 monomer units) from the Escherichia coli pathogen, modified with a phosphate group at the 5′ end, were attached to the surface of the electrode through the affinity of the phosphate group for zirconia, to produce an effective DNA probe (ssDNA/ZrO2/SPE). DNA immobilization and hybridization were characterized using differential pulse voltammetry by employing methylene blue as redox indicator. Target sequences hybridized with the probe resulted in a decrease of the reduction peak current of methylene blue intercalated into the probe. The response of a non-complementary sequence and a single base pair mismatch sequence were both clearly distinguished from that of a complementary sequence. The developed biosensor had a high selectivity and sensitivity towards hybridization detection (10–10 M complementary DNA detectable). Making use of screen-printed technology, the fabrication of the biosensors exhibited satisfactory reproducibility, investigated by cyclic voltammetry and differential pulse voltammetry. The relative standard deviation was found to be <3.0% for six bare SPEs and six ssDNA-modified SPEs (ssDNA/ZrO2/SPE) from a batch.
Fitzroy River Basin, Queensland, Australia. IV. Identification of flood sediment sources in the Fitzroy River
Authors: Douglas G. B. , Ford P. W. , Palmer M. R. , Noble R. M. , Packett R. J. , Krull E. S.
Published: February 2009

Environmental context. During flood events, the Fitzroy River is a major contributor to the loads of suspended sediment and nutrients to the southern Great Barrier Reef. The present geochemical and modelling study provides for the first time a quantitative estimate of the temporal variation in sediment sources over an entire flood hydrograph. Basaltic soils are substantially enriched in this flood event relative to their catchment abundance.
Abstract. Suspended sediment collected over a complete flood hydrograph in the Fitzroy River provided an insight into the origin and transport of sediment in this system. Strong temporal trends are evident in the proportions of catchment soil types estimated using a Bayesian mixing model in the fine (<10 μm) fraction of the suspended sediment. These temporal trends were also manifested in changes in mineralogy, major and trace element and Nd–Sr and C–N isotope geochemistry. Tertiary Basaltic soils were the most abundant catchment soil type transported in the flood event studied here, constituting 39% of the <10-μm sediment fraction, but varied between an estimated 20 and 50% of the suspended solids over the course of the flood event. The techniques used here allow quantification and comparison between flow and suspended sediment sources and are widely applicable to other river systems.
FLUXY: a simple code for computing steady-state metal fluxes at consuming (bio)interfaces, in natural waters
Authors: Zhang Zeshi , Buffle Jacques , Startchev Konstantin , Alemani Davide
Published: February 2009

Environmental context. Until now there was no user-friendly code for metal flux computations in natural mixtures of aquatic complexants, which are however essential for prediction of metal bioavailability. The present paper describes the capabilities and limitations of one of the only two such codes presently available, called FLUXY. The results of FLUXY are compared with those of another code, and it is shown that it enables quick computation and is applicable to natural ligands under many environmental conditions.
Abstract. The computation of metal fluxes at consuming interfaces like microorganisms or bioanalogical sensors is of great importance in ecotoxicology. The present paper describes the application of a simple code, FLUXY, for the computation of steady-state metal fluxes in the presence of a very large number of complexes, with broadly varying values of equilibrium constants, rate constants and diffusion coefficients. This code includes two major limiting assumptions, namely, (i) the existence of excess of ligand (L) compared with metal (M), and (ii) the fact that in a series of successive MLn complexes, the reaction is the rate-limiting step in flux computation. The domains of rate constants for which these assumptions are valid are tested systematically, and the corresponding errors are evaluated by comparison with the exact results given by another code: MHEDYN. FLUXY is then applied and compared with MHEDYN for case studies typical of aquatic systems, namely (i) a culture medium containing simple ligands; (ii) solutions of fulvic compounds including a broad distribution of complex stability and rate constants; and (iii) suspensions of aggregates with a broad size distribution. It is shown that FLUXY gives good results for cases (i) and (iii). Application to case (ii) (fulvic compounds) is also feasible under conditions that are clearly described. Altogether, FLUXY and MHEDYN are complementary. In particular, FLUXY only computes steady-state fluxes and requires the fulfilment of a few conditions, but when these are met, computations require much less computer time than MHEDYN.
Systematics of the Australo-Papuan tree frogs known as Litoria bicolor (Anura:Hylidae) in the Papuan region
Authors: Menzies J. I. , Richards S. J. , Tyler M. J.
Published: February 2009

We examined differences in morphology and advertisement calls of a large sample of frogs from the Australo-Papuan Region that resemble Litoria bicolor, and compared them with examples of that species from Australia. Consistent differences in body size, body proportions, and advertisement call structure among populations demonstrate that at least seven distinct species occur in the Australo-Papuan region, and that only the population represented by the holotype from the Northern Territory of Australia is Litoria bicolor s.s. Herein we describe four new species from the Papuan Region and comment on the origin and evolution of the Papuan members of the Litoria bicolor complex in the region.
Cyclin A–Cdk1 regulates the origin firing program in mammalian cells
Authors: Katsuno Yuko , Suzuki Ayumi , Sugimura Kazuto , Okumura Katsuzumi , Zineldeen Doaa H. , Shimada Midori , Niida Hiroyuki , Mizuno Takeshi , Hanaoka Fumio , Nakanishi Makoto
Published: February 2009

Somatic mammalian cells possess well-established S-phase programs with specific regions of the genome replicated at precise times. The ATR–Chk1 pathway plays a central role in these programs, but the mechanism for how Chk1 regulates origin firing remains unknown. We demonstrate here the essential role of cyclin A2–Cdk1 in the regulation of late origin firing. Activity of cyclin A2–Cdk1 was hardly detected at the onset of S phase, but it was obvious at middle to late S phase under unperturbed condition. Chk1 depletion resulted in increased expression of Cdc25A, subsequent hyperactivation of cyclin A2–Cdk1, and abnormal replication at early S phase. Hence, the ectopic expression of cyclin A2–Cdk1AF (constitutively active mutant) fusion constructs resulted in abnormal origin firing, causing the premature appearance of DNA replication at late origins at early S phase. Intriguingly, inactivation of Cdk1 in temperature-sensitive Cdk1 mutant cell lines (FT210) resulted in a prolonged S phase and inefficient activation of late origin firing even at late S phase. Our results thus suggest that cyclin A2–Cdk1 is a key regulator of S-phase programs.
Simulation of large-scale rule-based models
Authors: Colvin Joshua , Monine Michael I. , Faeder James R. , Hlavacek William S. , Von Hoff Daniel D. , Posner Richard G.
Published: February 2009

Motivation: Interactions of molecules, such as signaling proteins, with multiple binding sites and/or multiple sites of post-translational covalent modification can be modeled using reaction rules. Rules comprehensively, but implicitly, define the individual chemical species and reactions that molecular interactions can potentially generate. Although rules can be automatically processed to define a biochemical reaction network, the network implied by a set of rules is often too large to generate completely or to simulate using conventional procedures. To address this problem, we present DYNSTOC, a general-purpose tool for simulating rule-based models.

Results: DYNSTOC implements a null-event algorithm for simulating chemical reactions in a homogenous reaction compartment. The simulation method does not require that a reaction network be specified explicitly in advance, but rather takes advantage of the availability of the reaction rules in a rule-based specification of a network to determine if a randomly selected set of molecular components participates in a reaction during a time step. DYNSTOC reads reaction rules written in the BioNetGen language which is useful for modeling protein–protein interactions involved in signal transduction. The method of DYNSTOC is closely related to that of StochSim. DYNSTOC differs from StochSim by allowing for model specification in terms of BNGL, which extends the range of protein complexes that can be considered in a model. DYNSTOC enables the simulation of rule-based models that cannot be simulated by conventional methods. We demonstrate the ability of DYNSTOC to simulate models accounting for multisite phosphorylation and multivalent binding processes that are characterized by large numbers of reactions.

Availability: DYNSTOC is free for non-commercial use. The C source code, supporting documentation and example input files are available at http://public.tgen.org/dynstoc/.

Contact:  dynstoc@tgen.org

Supplementary information:  Supplementary data are available at Bioinformatics online.