bluuebunny/crossref_metadata_2025 huggingface dataset:
Bulk magnetic domain structures visualized by neutron dark-field imaging
Authors: Grünzweig C. , David C. , Bunk O. , Dierolf M. , Frei G. , Kühne G. , Schäfer R. , Pofahl S. , Rønnow H. M. R. , Pfeiffer F.
Published: September 2008

We report on how a neutron grating interferometer can yield projection images of the internal domain structure in bulk ferromagnetic samples. The image contrast relies on the ultrasmall angle scattering of unpolarized neutrons at domain wall structures in the specimen. The results show the basic domains of (110)-oriented sheets in an FeSi test sample. The obtained domain structures could be correlated with surface sensitive magneto-optical Kerr effect micrographs.
Coulomb scattering in high-κ gate stack silicon-on-insulator metal-oxide-semiconductor field effect transistors
Authors: Jiménez-Molinos F. , Gámiz F. , Donetti L.
Published: September 2008

A new model for calculating Coulomb perturbation potentials in bidimensional semiconductor structures is proposed. The main advantage of this model is that it can be applied for an arbitrary number of layers with different permittivities. As an example of how it could be used, we studied the influence on Coulomb scattering of high-κ materials used as gate insulators in silicon-on-insulator structures. This study was carried out with insulators of different physical and effective oxide thicknesses. The results show that when a silicon dioxide is replaced by a high-κ dielectric with the same thickness, Coulomb scattering is reduced. However, the strength of this beneficial effect might be diminished in actual devices for two reasons. The first is that an interfacial layer of silicon dioxide is usually placed between the silicon slab and the high-κ dielectric, lessening its influence. Second, a gate high-κ dielectric is normally wider than its silicon dioxide counterpart. As a consequence, the metal or polysilicon gate is further from the silicon channel, and its beneficial screening effect on the perturbation charges is then reduced. Both these effects on Coulomb scattering were examined in this study.
On Painlevé VI transcendents related to the Dirac operator on the hyperbolic disk
Authors: Lisovyy O.
Published: September 2008

Dirac Hamiltonian on the Poincaré disk in the presence of an Aharonov–Bohm flux and a uniform magnetic field admits a one-parameter family of self-adjoint extensions. We determine the spectrum and calculate the resolvent for each element of this family. Explicit expressions for Green’s functions are then used to find Fredholm determinant representations for the tau function of the Dirac operator with two branch points on the Poincaré disk. Isomonodromic deformation theory for the Dirac equation relates this tau function to a one-parameter class of solutions of the Painlevé VI equation with γ=0. We analyze long-distance behavior of the tau function, as well as the asymptotics of the corresponding Painlevé VI transcendents as s→1. Considering the limit of flat space, we also obtain a class of solutions of the Painlevé V equation with β=0.
Lamellar-in-lamellar structure of binary linear multiblock copolymers
Authors: Klymko T. , Subbotin A. , ten Brinke G.
Published: September 2008

A theoretical description of the lamellar-in-lamellar self-assembly of binary A-b-(B-b-A)m-b-B-b-A multiblock copolymers in the strong segregation limit is presented. The essential difference between this binary multiblock system and the previously considered C-b-(B-b-A)m-b-B-b-C ternary multiblock copolymer system is discussed. Considering the situation with long end blocks, the free energy of the lamellar-in-lamellar self-assembled state is analyzed as a function of the number k of “thin” internal lamellar domains for different numbers m of repeating (B-b-A) units and different values of the Flory–Huggins χAB interaction parameter. The theoretical predictions are in excellent agreement with the available experimental data.
Transverse susceptibility study of the effect of varying dipolar interactions on anisotropy peaks in a three-dimensional assembly of soft ferrite nanoparticles
Authors: Poddar Pankaj , Morales Marienette B. , Frey Natalie A. , Morrison Shannon A. , Carpenter Everett E. , Srikanth Hariharan
Published: September 2008

Collective magnetization dynamics in nanoparticle assemblies is of current interest as it forms the basis of high density storage media. It is important to understand how interparticle interactions in a three-dimensional (3D) arrangement of superparamagnetic nanoparticles would affect the overall effective magnetic anisotropy of the system. We have studied the influence of varying strengths of dipolar interaction on the static and dynamic magnetic properties of surfactant-coated monodispersed manganese zinc ferrite nanoparticles using reversible transverse susceptibility. We track the evolution of the anisotropy peaks with varying magnetic field, temperature, and interaction strength. The blocking temperature shows an increase from 28 to 32 K and the coercive field (at 10 K) shows an increase from 144 to 192 Oe as the system changes from the case of weakly interacting to strongly interacting 3D assembly of the particles.
First order simultaneous optimization of molecular geometry and electronic wave function
Authors: Moss Christopher L. , Li Xiaosong
Published: September 2008

We present a very efficient simultaneous optimization method for both molecular geometry and electronic wave function. We introduce a simultaneous least squares scheme to minimize errors in a full local quadratic space of both geometric and wave function vectors. Several self-consistent-field iterations are taken until a uniform search direction is achieved in every geometry optimization step. Not only does this new simultaneous optimization method significantly reduce the number of self-consistent-field iterations to reach convergence, it is able to overcome shallow potential wells to find a better stationary point. This new method exhibits up to ∼60% savings in computational cost compared to conventional geometry optimization methods.
Monte Carlo simulation study of scanning electron microscopy images of rough surfaces
Authors: Li Y. G. , Mao S. F. , Li H. M. , Xiao S. M. , Ding Z. J.
Published: September 2008

In this paper, we have developed a Monte Carlo (MC) simulation method for calculation of scanning electron microscopy (SEM) images of rough surfaces. The roughness structure is constructed in a finite element triangulated mesh by using a Gaussian function to describe the distribution of amplitude of the random rough peaks. Further spatial subdividing can accelerate the calculation and improves MC simulation efficiency. The MC model is based on the using of the Mott cross section for description of the electron elastic scattering and the using of the full Penn algorithm in a dielectric functional approach to the electron inelastic scattering. This simulation relates directly a defined rough surface structure modeling described by exact values of roughness parameters to the contrast observed in a SEM image, enabling the investigation of the influence of line edge roughness to the critical dimension (CD) metrology of a metal-oxide-semiconductor device by SEM. Example calculation of line images with sidewall roughness demonstrates that the present MC simulation method is useful for CD metrology of nanostructures by CD-SEM and, especially, for the linewidth measurement in the integrated circuit industry.
Morphology and electrical conduction of Si:P δ-doped layers on vicinal Si(001)
Authors: Reusch T. C. G. , Goh K. E. J. , Pok W. , Lo W.-C. N. , McKibbin S. R. , Simmons M. Y.
Published: September 2008

We present a combined scanning tunneling microscopy (STM) and low-temperature magnetotransport study of Si:P δ-doped layers on vicinal Si(001) substrates. The substrates were misoriented 4° toward [110] resulting in a high step density on the starting growth surface. Atomically resolved STM was used to study all stages of the fabrication. We find only a weak influence of the high step density and discuss the implications for the fabrication δ-doped layers and planar nanoscale Si:P devices by scanning tunneling lithography.
Photoluminescence from ZnO nanoparticles in vapor phase
Authors: Mohanta Antaryami , Singh V. , Thareja R. K.
Published: September 2008

Photoluminescence (PL) is observed from ZnO nanoclusters formed in ZnO plasma due to cooling of plasma species by passing a collimated beam of fourth harmonic (266 nm) of Nd:YAG (yttrium aluminum garnet) laser through ZnO plasma formed by third harmonic (355 nm) of Nd:YAG laser. A shift of 42 meV in peak position of PL profile of ZnO clusters from that observed in bulk ZnO is seen, which shows the effect of quantum confinement. The behaviors of PL profiles are studied at varying ablating intensities with fixed probe intensity. A superlinear increase in PL peak intensity with narrowing of emission linewidth above a particular ablating intensity is observed. The defect related emission band, usually occurring due to oxygen vacancy, is not observed from the ZnO clusters formed due to cooling of laser induced ZnO plasma. The observed redshift of PL peak positions with increasing ablating intensities could be due to temperature-induced band gap shrinkage arising due to enhancement of electron temperature.
Monte Carlo modeling of geminate recombination in polymer-polymer photovoltaic devices
Authors: Groves C. , Marsh R. A. , Greenham N. C.
Published: September 2008

A Monte Carlo model is used to examine geminate pair dissociation in polymer-polymer photovoltaic devices. It is found that increasing one or both carrier mobilities aids geminate separation yield ηGS particularly at low fields. This, in turn, leads to improved maximum power output from polymer-polymer blend photovoltaics, even when carrier mobilities are unbalanced by a factor of 10. The dynamic behaviors of geminate charges that eventually separate and recombine are examined for the first time. It is shown that geminate pairs in a bilayer become effectively free when separated by ∼4nm, which is far smaller than the thermal capture radius of 16nm here. This may lead one to expect that ηGS would not be limited by the separation allowed by the morphology once the domain size has increased above 4nm. In fact it is found that ηGS in a blend improves continuously as the average domain size increases from 4to16nm. We show that although a small degree of separation may be available in a blend, the limited number of possible routes to further separation makes charge pairs in blends more susceptible to recombination than charge pairs in a bilayer.
Modulational instability of electromagnetic electron-cyclotron wave packets in the magnetosphere with non-Maxwellian electron distribution
Authors: Abbasi H. , Hakimi Pajouh H.
Published: September 2008

The satellite observations of the magnetosphere in the low-frequency ion dynamics revealed several facts: (1) localized structures for electric field signal parallel to the magnetic field; (2) anisotropy for the electron velocity distribution such that T⊥⪡T∥; and (3) non-Maxwellian distribution function for the electrons. Based on these evidences, a nonlinear model is presented to develop the electromagnetic electron-cyclotron (EMEC) theory to the non-Maxwellian plasmas. Then, the modulational instability analysis of EMEC waves is investigated.
Spectroscopic evidence of extended states in the quantized Hall phase of weakly coupled GaAs/AlGaAs multilayers
Authors: Pusep Yu. A. , Guimarães F. E. G. , Arakaki A. H. , de Souza C. A.
Published: September 2008

The influence of interlayer coupling on the formation of the quantized Hall phase at the filling factor ν=2 was studied in multilayer GaAs/AlGaAs heterostructures. The disorder broadened Gaussian photoluminescence line due to localized electrons was found in the quantized Hall phase of the isolated multi-quantum-well structure. On the other hand, the quantized Hall phase of weakly coupled multilayers emitted an unexpected asymmetrical line similar to that observed in metallic electron systems. We demonstrated that the observed asymmetry is caused by the partial population of extended electron states formed in the insulating quantized Hall phase due to spin-assisted interlayer percolation. A sharp decrease in the single-particle scattering time associated with these extended states was observed for the filling factor ν=2.
Writing ferroelectric domain bits on the PbZr0.48Ti0.52O3 thin film
Authors: Son J. Y. , Park C. S. , Kim S.-K. , Shin Y.-H.
Published: September 2008

PbZr 0.48 Ti 0.52 O 3 thin films were fabricated on (111) Pt/TiO2/SiO2/Si substrate by eclipse pulsed laser deposition with the very low deposition rate of 0.02 Å/pulse. High crystalline PbZr0.48Ti0.52O3 thin films showed a good ferroelectric property with the high remanent polarization of 48 μC/cm2 as well as an enhanced fatigue behavior. The small roughness of PZT thin films makes a negligible influence on electron force microscope images, which gave the enhanced resolution for the observation of a minimum ferroelectric bit size. We demonstrated the minimum ferroelectric bits below 9 nm, which were clearly observed.
Interfacial and electrical properties of SrBi2Ta2O9/ZrO2/Si heterostructures for ferroelectric memory devices
Authors: Roy A. , Dhar A. , Ray S. K.
Published: September 2008

We have investigated the interfacial and frequency dependent electrical properties of metal-ferroelectric-insulator-semiconductor capacitors with SrBi2Ta2O9 (SBT) ferroelectric films grown on ZrO2 buffer layer coated Si. Heterostructure SBT and ZrO2 thin films were deposited using rf magnetron sputtering. Interfacial and surface roughness parameters of heterostructures were extracted from the simulation of specular x-ray reflectivity data. The structure exhibited clockwise capacitance-voltage hysteresis with a maximum memory window of 2.0 V at a bias voltage of ±7 V. Frequency dependent (5 kHz–1 MHz) measurements at room temperature indicated that the clockwise hysteresis originates from the ferroelectric domain reversal. A minimum leakage current density of 4×10−8 A/cm2 of fabricated capacitors at an applied voltage of ±5 V revealed that the ZrO2 buffer layer prevents the interfacial diffusion between SBT thin film and the substrate, resulting in an improvement of interface quality. The charge retention time of the ferroelectric capacitor was studied as a function of buffer layer thickness.
Formation of linear carbon chains during the initial stage of nanostructured carbon film growth
Authors: Ma Tian-Bao , Hu Yuan-Zhong , Wang Hui
Published: September 2008

The initial stage of nanostructured carbon film growth is investigated by molecular dynamics simulations. The carbon film exhibits amorphous structures with linear chains and cyclic rings on the surface at low incident energies. The structural transformations from linear chains to cyclic rings and to atom networks are observed during the growth process, which is explained in terms of system stability. The atomic adsorption behavior is analyzed through the calculation of the surface potential field. The formation of linear chain structure is due to the predominance of inhomogeneous adsorption of incident atoms on the surface and preferential growth at the tip of the chain. The formation of nanostructures on the surface is argued to be the initial nucleation process of amorphous carbon films.
Motor entropy in response to task demands and environmental information
Authors: Hong S. Lee , Newell Karl M.
Published: September 2008

This experiment tested the hypothesis that human motor adaptation can be represented as the conservation of entropy across the task, organism, and environment. Healthy young individuals generated a submaximal isometric force with the index finger of their dominant hand. Subjects performed this task under different task demands (error tolerance) and environmental information (feedback frequency) conditions. In order to extend previous findings, we employ the use of approximate entropy (ApEn) to capture the temporal aspects of the variability in the isometric force and to create links to other studies of time-series in human behavior. We showed that ApEn of the force time-series, made conditional upon satisfying the task demands, decreased as the task demands were increased and the environmental information reduced. There was a compensatory interaction between task and environment on the force dynamics that could be represented by a quadratic surface, capturing 92% of the total variance. Our results show that when faced with a reduced likelihood of achieving the task goal (increased task entropy) and an environment that provides little information (increased environmental entropy), the subjects employed similar force production strategies over time, resulting in a more regular pattern.
Optimization of the output and efficiency of a high power cascaded arc hydrogen plasma source
Authors: Vijvers W. A. J. , van Gils C. A. J. , Goedheer W. J. , van der Meiden H. J. , Schram D. C. , Veremiyenko V. P. , Westerhout J. , Lopes Cardozo N. J. , van Rooij G. J.
Published: September 2008

The operation of a cascaded arc hydrogen plasma source was experimentally investigated to provide an empirical basis for the scaling of this source to higher plasma fluxes and efficiencies. The flux and efficiency were determined as a function of the input power, discharge channel diameter, and hydrogen gas flow rate. Measurements of the pressure in the arc channel show that the flow is well described by Poiseuille flow and that the effective heavy particle temperature is approximately 0.8eV. Interpretation of the measured I-V data in terms of a one-parameter model shows that the plasma production is proportional to the input power, to the square root of the hydrogen flow rate, and is independent of the channel diameter. The observed scaling shows that the dominant power loss mechanism inside the arc channel is one that scales with the effective volume of the plasma in the discharge channel. Measurements on the plasma output with Thomson scattering confirm the linear dependence of the plasma production on the input power. Extrapolation of these results shows that (without a magnetic field) an improvement in the plasma production by a factor of 10 over where it was in van Rooij et al. [Appl. Phys. Lett. 90, 121501 (2007)] should be possible.
Testing asymmetry in plasma-ball growth seeded by a nanoscale absorbing defect embedded in a SiO2 thin-film matrix subjected to UV pulsed-laser radiation
Authors: Papernov S. , Schmid A. W.
Published: September 2008

Previous studies of ultraviolet, nanosecond-pulsed-laser damage in thin films revealed nanoscale absorbing defects as a major source of damage initiation. It was also demonstrated that damage (crater formation) is facilitated by plasma-ball formation around absorbing defects. In this work an attempt is made to verify the symmetry of the plasma ball by irradiating SiO2 thin film with embedded gold nanoparticles from the side of either the air/film or substrate/film interfaces. Crater-formation thresholds derived in each case support preferential plasma-ball growth in the direction of the laser-beam source. The strong impact of internal E-field distribution is identified.
Nonlinear dynamics of rotating drift-tearing modes in tokamak plasmas
Authors: Nishimura S. , Benkadda S. , Yagi M. , Itoh S.-I. , Itoh K.
Published: September 2008

The rotation frequency of the drift-tearing mode is investigated with numerical simulations of reduced two-fluid equations. An extended analytical formula of the rotation frequency of the drift-tearing mode is derived, and is used to analyze numerical results. It is found that the rotation frequency depends strongly on the poloidal zonal flow generated by the drift-tearing mode. The dependence of the rotation frequency on transport coefficients is examined in the nonlinear saturation phase. It is found that ion viscosity μ and parallel resistivity η∥ play important roles by controlling the self-generated zonal flow through the change of the balance between the Reynolds stress and the Maxwell stress. The dependence of the rotation frequency on the magnetic Prandtl number μ∕η∥ shows a monotonic increase.
Characterization and investigation of the anomalous behavior of the immersed-Bz diode during operation at 4 to 5 MV
Authors: Rovang D. C. , Bruner N. , Johnston M. D. , Madrid E. A. , Maenchen J. E. , Oliver B. V. , Portillo S. , Welch D. R.
Published: September 2008

The immersed-Bz diode is being developed as a high-brightness, flash x-ray radiography source at Sandia National Laboratories. This diode is a foil-less electron-beam diode with a long, thin, needlelike cathode which is inserted into the bore of a solenoid. The solenoidal magnetic field guides the electron beam emitted from the cathode to the anode while maintaining a small beam radius. The electron beam strikes a thin, high-atomic-number anode and produces forward-directed bremsstrahlung. In addition, electron beam heating of the anode produces surface plasmas allowing ion emission. Two different operating regimes for this diode have been identified: A nominal operating regime where the total diode current is characterized as classically bipolar with stable impedance [see D. C. Rovang et al., Phys. Plasmas 14, 113107 (2007)] and an anomalous operating regime characterized by a rapid impedance collapse where the total diode current greatly exceeds the bipolar limit. The operating regimes are approximately separated by cathode diameters greater than 3mm for the nominal regime and less than 3mm for the anomalous impedance collapse regime. Results from a comprehensive series of experiments conducted at 4–5MV characterizing the transition from this nominal operating regime to the anomalous operating regime as the cathode diameter is reduced are presented. Results from experiments investigating the effects of anode-cathode gap, anode material, and cryogenic modification of the anode surface are also presented. Although these investigations were unsuccessful in completely mitigating the anomalous behavior, insight gained from these experiments has elucidated several key physics issues that are discussed.
Nature of quasi-LO phonon in ZnO
Authors: Tay Y. Y. , Tan T. T. , Liang M. H. , Boey F. , Li S.
Published: September 2008

The quasi-LO phonon mode is related to the specific defects that strongly affect the photonic properties of materials such as zinc oxide (ZnO). The line shapes of the quasi-LO phonon of ZnO annealed in different environments have been investigated. The experimental results show that this mode has the greatest Raman shift to lower wavenumber for the ZnO annealed in ambient atmosphere, suggesting that it has the largest concentration of defects that may be related to its green emission.
Continuous terahertz-wave generation using a monolithically integrated horn antenna
Authors: Peytavit E. , Beck A. , Akalin T. , Lampin J-F. , Hindle F. , Yang C. , Mouret G.
Published: September 2008

A transverse electromagnetic horn antenna is monolithically integrated with a standard ultrafast interdigitated electrode photodetector on low-temperature-grown GaAs. Continuous-wave terahertz radiation is generated at frequencies up to 2 THz with a maximum power of approximately 1 μW at 780 GHz. Experimental variations in the terahertz power as function of the frequency are explained by means of electromagnetic simulations of the antenna and the photomixer vicinity.
Nanoelectromechanical switch with low voltage drive
Authors: Jang J. E. , Cha S. N. , Choi Y. , Butler T. P. , Kang D. J. , Hasko D. G. , Jung J. E. , Jin Y. W. , Kim J. M. , Amaratunga G. A. J.
Published: September 2008

The triode structure vertical carbon nanotube based nanoelectromechanical switch shows excellent low voltage drive (∼4.5 V), owing to its vertical gate and the narrow gap between structural elements. The insulator deposition and the selective etching process steps simplify fabrication through self-alignment. The thickness of the insulator determines the width of the gap and the etching process, used to produce the vertical gate, removes the need for a complicated lithography step. The low drive voltage increases device stability and reliability and allows the device to be deployed in a wide range of applications.
Measurement of electron density by Stark broadening in an ablative pulsed plasma thruster
Authors: Liu Feng , Nie Zongfu , Xu Xu , Zhou Qianhong , Li Linsen , Liang Rongqing
Published: September 2008

Electron density was measured by Stark broadening in an ablative pulsed plasma thruster. The asymmetrical deconvolution is used to obtain Stark broadening. The result shows that the electron density in the discharge channel is 2.534×1022 m−3 when the discharge energy is 5 J and the measured electron temperature is 18 000 K, and it is in excellent agreement with other experimental and theoretical data. The electron density in the discharge channel increases very minimally with increasing discharge energy.
Characterization of n-n Ge/SiC heterojunction diodes
Authors: Gammon P. M. , Pérez-Tomás A. , Jennings M. R. , Roberts G. J. , Davis M. C. , Shah V. A. , Burrows S. E. , Wilson N. R. , Covington J. A. , Mawby P. A.
Published: September 2008

In this paper we investigate the physical and electrical properties of germanium deposited on 4H silicon carbide substrates by molecular beam epitaxy. Layers of highly doped and intrinsic germanium were deposited at 300 and 500 °C and compared. Current-voltage measurements reveal low turn-on voltages. The intrinsic samples display ideality factors of 1.1 and a reverse leakage current of 9×10−9 A/cm2, suggesting a high quality electrical interface. X-ray diffraction analysis reveals the polycrystalline nature of the high-temperature depositions, whereas the low-temperature depositions are amorphous. Atomic force microscopy shows that the low-temperature layers have a rms roughness of 3 nm.
A microfluidic platform for studying the effects of small temperature gradients in an incubator environment
Authors: Das Sarit K. , Chung Seok , Zervantonakis Ioannis , Atnafu Joseph , Kamm Roger D.
Published: September 2008

Studies on the effects of variations in temperature and mild temperature gradients on cells, gels, and scaffolds are important from the viewpoint of biological function. Small differences in temperature are known to elicit significant variations in cell behavior and individual protein reactivity. For the study of thermal effects and gradients in vitro, it is important to develop microfluidic platforms which are capable of controlling temperature gradients in an environment which mimics the range of physiological conditions. In the present paper, such a microfluidic thermal gradient system (μTGS) system is proposed which can create and maintain a thermal gradient throughout a cell-seeded gel matrix using the hot and cold water supply integrated in the system in the form of a countercurrent heat exchanger. It is found that a uniform temperature gradient can be created and maintained in the device even inside a high temperature and high humidity environment of an incubator. With the help of a hot and cold circuit controlled from outside the incubator the temperature gradient can be regulated. A numerical simulation of the device demonstrates the thermal feature of the chip. Cell viability and activity under a thermal gradient are examined by placing human breast cancer cells in the device.
Variability of optimum sowing time for wheat yield in Western Australia
Authors: Sharma D. L. , D'Antuono M. F. , Anderson W. K. , Shackley B. J. , Zaicou-Kunesch C. M. , Amjad M.
Published: September 2008

Sowing wheat (Triticum aestivum L.) at the right time is one of the most important means of maximising grain yield in dryland agriculture. Objectives of this study were to understand the variation in estimates of optimum sowing time as influenced by cultivar and environmental characteristics, and to assess the relative importance of location, season, sowing time, and cultivar factors in maximising grain yield in Western Australia. Twenty-seven cultivar × time of sowing experiments were conducted over three seasons (2003–05) at a range of locations (annual rainfall 300–450 mm, lat. 28–35°S).
There were four types of cultivar × sowing time responses, namely, quadratic, linear declining, flat, and linear increasing, associated with opening rains before mid-May, opening rains after mid-May, low-yielding sites, and good spring rains, respectively. Regression-tree analysis revealed that differences among cultivars in Tmax (sowing time when maximum grain yield was achieved) were much less in the eastern sites (mostly drier seasons). A biplot differentiated cultivars for Tmax across the range of environments used, while the subset regression analysis specifically indicated an association of average temperature and growing-season rainfall with variation for Tmax of individual cultivars.
The yield penalty for sowing before the optimum time in quadratic-type responses was clearly greater for shorter season cultivars but no clear relationship was apparent between maturity class of cultivars and the penalty for late sowing, possibly due to differential plasticity of cultivars for grain weight under harsh finishing conditions. The duration of the optimum sowing window at a given location was inversely proportional to the yield potential, implying that it is critical to sow at or close to the optimum time when the yield potential is high, most common when the season breaks early. Yield component analysis showed that the relative change in grain yield over sowing dates was significantly correlated with relative changes in grain numbers/m2 in the late May sowings but other yield components were also important in the early May experiments. Sowing time accounted for 10% of grain yield variation compared with cultivar (1%), while the rest was due to uncontrollable factors of location and season.
Relationships between carbon isotope discrimination and leaf morphophysiological traits in spring-planted spring wheat under drought and salinity stress in Northern China
Authors: Zhu Lin , Liang Zong Suo , Xu Xing , Li Shu Hua , Jing Ji Hai , Monneveux P.
Published: September 2008

The relationships between carbon isotope discrimination (Δ) and some morphophysiological traits such as specific leaf dry weight (SLDW), gas exchange parameters, and relative water content (RWC) were studied in a collection of 20 bread wheat cultivars (landraces, released cultivars and advanced lines) in three locations of the Ningxia region (North-East China), i.e. Yinchuan (limited irrigation conditions), Huinong (limited irrigation conditions + salinity) and Guyuan (rain-fed conditions). Relationships between Δ, grain yield (GY), and harvest index (HI) and above-ground biomass (AGB) were also analysed. Differences in the measured traits between different locations were highly related to the variation in water availability. Positive correlations were noted between Δ and HI and grain yield. Flag leaf Δ was positively correlated with RWC at anthesis, and negatively associated with SLDW at grain filling. Significant and negative correlations between Δ and dry matter weight per plant at anthesis and biomass at maturity were noted. Leaf temperature (LT) was found to be negatively correlated with Δ and gs. The findings suggest that Δ may be a useful indicator reflecting wheat yield, harvest index, and water status under irrigation and rain-fed conditions in the Ningxia region.
Allelic variation for the high- and low-molecular-weight glutenin subunits in wild diploid wheat (Triticum urartu) and its comparison with durum wheats
Authors: Caballero L. , Martín M. A. , Alvarez J. B.
Published: September 2008

Triticum urartu is a wild diploid wheat identified as donor of the A genome in polyploid wheats. This species could be used as a genetic resource for wheat quality breeding. The HMWGs and B-LMWGs of this species were analysed by SDS-PAGE in 169 accessions from Armenia, Iran, Iraq, Lebanon, the former Soviet Union, and Turkey. Seventeen alleles for the Glu-Au1 locus and 24 for the Glu-Au3 locus were found. The allelic variation was asymmetrically distributed, Turkey being the country where the largest number of alleles was found. Genetic diversity was high, although a great part of this diversity is at risk of erosion given that the distribution of the combinations among the evaluated accessions was not random. Consequently, the loss of these accessions could mean the disappearance of the allelic variants. The alleles found for both loci were different from those detected in cultivated wheats. These results provided new basic knowledge regarding the genetic variability of the seed storage proteins synthesised by the Au genome, as well as their potential to create novel germplasm for quality breeding in wheat programs.
Variation in fatty acid composition among genetically homogeneous seeds of canola (Brassica napus), and implications for genotypic selection based on single seeds
Authors: Aslam M. N. , Kailis S. , Nelson M. N. , Bayliss K. L. , Cowling W. A.
Published: September 2008

Selection of canola (Brassica napus L.) for fatty acid (FA) composition is often based on single seeds or small seed lots, but information is lacking on variation among repeated samples. Variation in FA composition was measured among repeated samples of B. napus seeds by gas chromatography on oil extracted by cold solvents, from a selfed doubled-haploid line (Monty-028DH), and an open-pollinated B. napus cv. Surpass 501TT. The variation in FA composition among repeated samples of 1, 3, 5, and 10 whole seeds was compared with the equivalent weight of ground seeds or Soxhlet-extracted oil. The standard deviation of oleic acid for whole seeds of Monty-028DH decreased from 2.12% (single-seed samples) to 0.12% (groups of 10 seeds), but was constant across an equivalent range in weight of ground seed (0.15%) and in volume of Soxhlet-extracted oil (0.05%). A single-seed sample is not sufficient to separate two B. napus genotypes differing in mean oleic acid content of 60% and 70% at the 95% confidence interval, based on the sampling variance measured in these experiments. Similar trends were found for all the major FAs in both varieties.
Orchestration of transpiration, growth and carbohydrate dynamics in rice during a dry-down cycle
Authors: Luquet D. , Clément-Vidal A. , Fabre D. , This D. , Sonderegger N. , Dingkuhn M.
Published: September 2008

The regulation of carbohydrate metabolism and source–sink relationships among organs play a key role in plant adaptation to drought. This study aimed at characterising the dynamics of transpiration, development, growth and carbon metabolism, as well as the expression of invertase genes, in response to drought during a dry-down cycle. Three 1-month experiments were conducted in controlled environment using the rice genotype IR64 (Oryza sativa L., indica). Plant leaf relative transpiration and expansion rates decreased linearly when fraction of transpirable soil water (FTSW) dropped below 0.66 and 0.58, respectively. Hexose and starch concentration responses to FTSW in a given organ were generally linear and opposite: in source leaves, hexose concentration increased and starch decreased, and vice versa in sink leaves and roots. Sucrose remained constant in source leaves and increased slightly in sink leaves. Starch reserves built up during stress in sink organs were rapidly mobilised upon rewatering, indicating its involvement in a mechanism to ensure recovery. Expression of cell-wall and vacuolar invertase genes under stress increased in sink leaves, interpreted as a mechanism to maintain sink activity (cell wall) and osmotic adjustment (vacuolar). It is concluded that carbohydrate metabolism in sink organs under drought is highly regulated, and important for stress adaptation.
Enhanced sensitivity of Arabidopsis anthocyanin mutants to photooxidation: a study with fluorescence imaging
Authors: Shao Ling , Shu Zhan , Peng Chang-Lian , Lin Zhi-Fang , Yang Cheng-Wei , Gu Qun
Published: September 2008

Chlorophyll fluorescence imaging and antioxidative capability in detached leaves of the wild-type Arabidopsis thaliana ecotype Landsberg erecta (Ler) and in three mutants deficient in anthocyanin biosynthesis (tt3, tt4 and tt3tt4) were investigated under photooxidation stress induced by methyl viologen (5 μm) in the light. In comparison with the wild-type (WT) plant, photooxidation resulted in significant decreases in the contents of total phenolics and flavonoid, total antioxidative capability and chlorophyll fluorescence parameters (Fv/Fm, qP, ΦPSII, NPQ and ETR) as determined by chlorophyll fluorescence imaging, and in an increase in cell-membrane leakiness in the three anthocyanin mutants. The sequence of sensitivity to photooxidation in the leaves of the four phenotypes were tt3tt4 (deficient in both chalcone synthase locus (CHS) and dihydroflavonol 4-reductase locus (DFR)) > tt4 (deficient in CHS) > tt3 (deficient in DFR) > WT. The results demonstrate that anthocyanins might, along with other antioxidants, protect the photosynthetic apparatus against photooxidative damage. An interesting phenomenon was observed over the 270 min of the photooxidative treatment, that is, fluorescence imaging revealed that qP, ΦPSII and ETR appeared in three phases (fall → partial recovery → rapid fall). This was considered to be a modulation of reversible deactivation in PSII to cope with the moderate oxidative stress in the first two stages of short-term treatment (<150 min), followed finally by damage to PSII under severe oxidative stress with prolonged treatment.
HilD-mediated transcriptional cross-talk between SPI-1 and SPI-2
Authors: Bustamante Víctor H. , Martínez Luary C. , Santana Francisco J. , Knodler Leigh A. , Steele-Mortimer Olivia , Puente José L.
Published: September 2008

The acquisition of new genetic traits by horizontal gene transfer and their incorporation into preexisting regulatory networks have been essential events in the evolution of bacterial pathogens. An example of successful assimilation of virulence traits is
Salmonella enterica
, which acquired, at distinct evolutionary times,
Salmonella
pathogenicity island 1 (SPI-1), required for efficient invasion of the intestinal epithelium and intestinal disease, and SPI-2, essential for
Salmonella
replication and survival within macrophages and the progression of a systemic infection. A positive regulatory cascade mainly composed of HilD, HilA, and InvF, encoded in SPI-1, controls the expression of SPI-1 genes, whereas the two-component regulatory system SsrA/B, encoded in SPI-2, controls expression of SPI-2 genes. In this study, we report a previously undescribed transcriptional cross-talk between SPI-1 and SPI-2, where the SPI-1–encoded regulator HilD is essential for the activation of both the SPI-1 and SPI-2 regulons but at different times during the stationary phase of growth in Luria-Bertani medium. Our data indicate that HilD counteracts the H-NS–mediated repression exerted on the OmpR-dependent activation of the
ssrAB
operon by specifically interacting with its regulatory region. In contrast, HilD is not required for SPI-2 regulon expression under the
in vitro
growth conditions that are thought to resemble the intracellular environment. Our results suggest that two independent SPI-2 activation pathways evolved to take advantage of the SPI-2–encoded information at different niches and, in consequence, in response to different growth conditions.
The human ERG1 channel polymorphism, K897T, creates a phosphorylation site that inhibits channel activity
Authors: Gentile Saverio , Martin Negin , Scappini Erica , Williams Jason , Erxleben Christian , Armstrong David L.
Published: September 2008

Single-nucleotide polymorphisms (SNPs) in the human ether-a-go-go-related gene 1, hERG1, are associated with cardiac arrhythmias. The Kv11.1 channels encoded by hERG1 are also essential for rhythmic excitability of the pituitary, where they are regulated by thyroid hormone through a signal transduction cascade involving the phosphatidylinositol 3-kinase (PI3K) and the Ser/Thr-directed protein phosphatase, PP5. Here, we show that the hERG1 polymorphism at codon 897, which is read as a Thr instead of a Lys, creates a phosphorylation site for the Akt protein kinase on the Kv11.1 channel protein. Consequently, hormonal signaling through the PI3K signaling cascade, which normally stimulates K897 channels through PP5-mediated dephosphorylation, inhibits T897 channels through Akt-mediated phosphorylation. Thus, hormonal regulation of Kv11.1 in humans with the T897 polymorphism is predicted to prolong the QT interval of cardiac myocytes. A systematic bioinformatics search for SNPs in human ion channel genes identified 15 additional candidates for such “phosphorylopathies,” which are predicted to create or destroy putative phosphorylation sites. Changes in protein phosphorylation might represent a general mechanism for the interaction of genetic variation and environment on human health.
Dominance and the evolutionary accumulation of
cis
- and
trans
-effects on gene expression
Authors: Lemos Bernardo , Araripe Luciana O. , Fontanillas Pierre , Hartl Daniel L.
Published: September 2008

Gene expression levels appear to be under pervasive stabilizing selection. Yet the genetic architecture underlying abundant gene expression diversity within and between populations remains elusive. Here, we investigated the role of dominance in the segregation of
cis
- and
trans
-regulation within and between populations. We used chromosome substitution lines of
Drosophila melanogaster
to show that (
i
) >70% of the genes that are differentially expressed between two homozygous lines are masked in the heterozygous, suggesting that one of the substituted chromosomes contains a recessive allele; (
ii
) such large masking is already obtained with heterozygous chromosomes originating from the same population, with the time of divergence between chromosomes in heterozygous lines making only a small but significant contribution to the masking of variation observed in homozygous lines; (
iii
) variation in gene expression due to
trans
-regulation is biased toward greater deviations from additivity because of recessive and dominant alleles, whereas variation due to
cis
-regulation shows higher additivity; and (
iv
) genetic divergence between second chromosomes is associated with increased
cis
-regulation, whereas the level of
trans
-regulation shows little increase over the time scale studied. Our results indicate that
cis
-acting alleles may be preferentially fixed by positive natural selection because of their higher additivity, and that the disruption of gene expression by recessive variation with pervasive
trans
-effects may be important for understanding gene expression variation within populations. We suggest that widespread regulatory effects of recessive low-frequency homozygous variation may provide a general mechanism mediating disease phenotypes and the genetic load of natural populations.
Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen
Histoplasma capsulatum
Authors: Webster Rachael Hanby , Sil Anita
Published: September 2008

The human fungal pathogen
Histoplasma capsulatum
grows in a sporulating filamentous form in the soil and, after inhalation of infectious spores, converts to a pathogenic yeast form inside host macrophages in response to temperature. Here we report the identification of two genes (
RYP2
and
RYP3
)
r
equired for
y
east-
p
hase growth. Ryp2 and Ryp3 are homologous to each other and to the Velvet A family of regulatory proteins in
Aspergillus
species and other filamentous fungi. Wild-type
H. capsulatum
grows as filaments at room temperature and as yeast cells at 37°C, but
ryp2
and
ryp3
mutants constitutively grow as filaments independent of temperature.
RYP2
and
RYP3
transcripts accumulate to higher levels at 37°C than at room temperature. This differential expression is similar to the previously identified
RYP1
transcript, which encodes a transcriptional regulator required for the yeast-phase expression program. Ryp1 associates with the upstream region of
RYP2
, and each of the three
RYP
genes is required for the differential expression of the others at 37°C. In addition to responding to the elevated temperature of the mammalian host,
RYP2
and
RYP3
are essential for viable spore production and regulation of sporulation at room temperature. This regulatory function is strikingly similar to the role of the
Aspergillus
Velvet A protein family in spore development in response to light, with the notable distinction that the
H. capsulatum
circuit responds to temperature.
Prevolutionary dynamics and the origin of evolution
Authors: Nowak Martin A. , Ohtsuki Hisashi
Published: September 2008

Life is that which replicates and evolves. The origin of life is also the origin of evolution. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here, we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. Therefore, any theory for the origin of life must address the emergence of such a system. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication: Polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. Yet, there is competition between life and prelife. There is a phase transition: If the effective replication rate exceeds a critical value, then life outcompetes prelife. Replication is not a prerequisite for selection, but instead, there can be selection for replication. Mutation leads to an error threshold between life and prelife.
Hydrophobic surfaces for enhanced differentiation of embryonic stem cell-derived embryoid bodies
Authors: Valamehr Bahram , Jonas Steven J. , Polleux Julien , Qiao Rong , Guo Shuling , Gschweng Eric H. , Stiles Bangyan , Kam Korey , Luo Tzy-Jiun M. , Witte Owen N. , Liu Xin , Dunn Bruce , Wu Hong
Published: September 2008

With their unique ability to differentiate into all cell types, embryonic stem (ES) cells hold great therapeutic promise. To improve the efficiency of embryoid body (EB)-mediated ES cell differentiation, we studied murine EBs on the basis of their size and found that EBs with an intermediate size (diameter 100–300 μm) are the most proliferative, hold the greatest differentiation potential, and have the lowest rate of cell death. In an attempt to promote the formation of this subpopulation, we surveyed several biocompatible substrates with different surface chemical parameters and identified a strong correlation between hydrophobicity and EB development. Using self-assembled monolayers of various lengths of alkanethiolates on gold substrates, we directly tested this correlation and found that surfaces that exhibit increasing hydrophobicity enrich for the intermediate-size EBs. When this approach was applied to the human ES cell system, similar phenomena were observed. Our data demonstrate that hydrophobic surfaces serve as a platform to deliver uniform EB populations and may significantly improve the efficiency of ES cell differentiation.