bluuebunny/crossref_metadata_2025 huggingface dataset:
Asymmetric flank uplift of the Yinchuan graben, north central China: Implications for lateral variation of crustal rheology from the Alashan to the Ordos
Authors: He Jiankun , Li Yanxing , Teng Chunkai
Published: November 2005

The Yinchuan graben in north central China is an intense active zone that is bordered by the Alashan to the west and the Ordos to the east. Analysis of high‐resolution digital topography shows that the present elevation on two shoulders of the graben exists drastic contrast (∼1.5–2 km). We use two‐dimensional finite element modeling to investigate the mechanical relation between crustal rheology and flank uplift of this graben. Models are simplified as an elastoplastic upper crust and a viscoelastic lower crust. Two antithetic faults on the graben's margins are simulated as Coulomb‐type frictional zones. Rheological tests show that the asymmetric flank uplift of the graben can be reconciled with lateral variations of crustal rheology; With the lower‐crust viscosity of the Ordos being ∼1–2 orders greater than that of the Alashan, we predict that even with the same effective friction of the two antithetic faults (0.1), the flank uplift will localize mainly on the west shoulder, consistent with present topographic contrast. This means that the crustal strength of the Alashan is weak relative to the Ordos, resulting in the active deformation and the seismicity being occurred heavily within the Alashan.
Material contrast does not predict earthquake rupture propagation direction
Authors: Harris Ruth A. , Day Steven M.
Published: November 2005

Earthquakes often occur on faults that juxtapose different rocks. The result is rupture behavior that differs from that of an earthquake occurring on a fault in a homogeneous material. Previous 2D numerical simulations have studied simple cases of earthquake rupture propagation where there is a material contrast across a fault and have come to two different conclusions: 1) earthquake rupture propagation direction can be predicted from the material contrast, and 2) earthquake rupture propagation direction cannot be predicted from the material contrast. In this paper we provide observational evidence from 70 years of earthquakes at Parkfield, CA, and new 3D numerical simulations. Both the observations and the numerical simulations demonstrate that earthquake rupture propagation direction is unlikely to be predictable on the basis of a material contrast.
The wrinkle‐like slip pulse is not important in earthquake dynamics
Authors: Andrews D. J. , Harris Ruth A.
Published: November 2005

A particular solution for slip on an interface between different elastic materials, the wrinkle‐like slip pulse, propagates in only one direction with reduced normal compressive stress. More general solutions, and natural earthquakes, need not share those properties. In a 3D dynamic model with a drop in friction and heterogeneous initial stress, the wrinkle‐like slip pulse is only a small part of the solution. Rupture propagation is determined primarily by the potential stress drop, not by the wrinkle‐like slip pulse. A 2D calculation with much finer resolution shows that energy loss to friction might not be significantly reduced in the wrinkle‐like slip pulse.
Simulation study of penetration electric field effects on the low‐ to mid‐latitude ionosphere
Authors: Huba J. D. , Joyce G. , Sazykin S. , Wolf R. , Spiro R.
Published: November 2005

The first self‐consistent study of the impact of storm‐time penetration electric fields on the low‐ to mid‐latitude ionosphere is presented. The inner magnetosphere is described by the Rice Convection Model (RCM) and the ionosphere is described by the Naval Research Laboratory (NRL) code SAMI3. The codes are coupled electrodynamically through the electrostatic potential equation, and the storm is modeled via changes in the polar cap potential. Neutral wind driven electric fields are estimated from the Fejer/Scherliess quiet time model. It is found that temporal changes in the polar cap potential produce electric fields that modify the F region equatorial E × B drift velocities: the velocities increase in the daytime and decrease in the nighttime by up to a factor of two. This causes the total electron content (TEC) in the daytime, mid‐latitude ionosphere to increase by up to 35%. In addition, the ‘fountain effect’ is enhanced in the post‐sunset period.
Late crustal growth on Mars: Evidence from lithospheric extension
Authors: Grott M.
Published: November 2005

We apply the pure shear model of lithospheric extension to rifting on Mars and investigate the range of initial ambient conditions that allow for narrow rifting. The results are applied to the Coracis Fossae, constraining the crustal thickness at the time the rift formed. We thus find that the crustal thickness at 3.5–3.9 Gyr is unlikely to have exceeded ∼50 km. This is significantly lower than the estimates for the present day crustal thickness in that region (∼70 km) and interpreted as an indication for continued crustal production at that time.
ICESat's new perspective on ice shelf rifts: The vertical dimension
Authors: Fricker H. A. , Bassis J. N. , Minster B. , MacAyeal D. R.
Published: November 2005

The small footprint (∼70 m) and ∼172 m along‐track spacing of the Geoscience Laser Altimeter System (GLAS) on the Ice, Cloud and land Elevation Satellite (ICESat) provides unprecedented horizontal resolution for a satellite altimeter. This enables ICESat to map many previously unresolved features on ice shelves, such as crevasses, rifts, grounding zones and ice fronts. We present examples of ICESat‐derived elevation data showing topography over rifts on the Amery and Ross ice shelves, widths of rifts and as estimates of the thickness of mélange (a collection of ice and snow trapped inside the rifts). We show that mélange thickness remains constant over the ICESat data period and tends to be thicker in older rifts. We validate the ICESat‐derived mélange depth estimate with an in situ measurement on the Ross Ice Shelf.
Single‐particle characterization of four aerosol samples collected in ChunCheon, Korea, during Asian dust storm events in 2002
Authors: Hwang HeeJin , Ro Chul‐Un
Published: November 2005

A single‐particle analytical technique, named low‐Z particle electron probe X‐ray microanalysis (low‐Z particle EPMA), employing an ultrathin window X‐ray detector and enabling the quantitative determination of even low‐Z elements such as C, N, and O, was applied to characterize “Asian dust” samples, collected in ChunCheon, Korea, during four Asian dust storm events on 21 March, 9 April, 17 April, and 11 November in 2002. In this study, it is demonstrated that single‐particle analysis using the low‐Z particle EPMA provides detailed information on various types of chemical species in the samples. The most abundantly encountered particles, both in coarse and fine fractions, are soil‐derived particles such as aluminosilicates and silicon dioxide, except for the sample collected on 11 November 2002, where reacted CaCO3 particles are the most abundantly encountered. All four samples are found to have experienced chemical modifications during long‐range transport because the samples contain a significant number of particles composed of chemical species, such as nitrate and sulfate, which resulted from atmospheric reactions of CaCO3 and sea‐salt particles. This finding implies that CaCO3 and sea‐salt particles reacted with sulfur and nitrogen oxide species during long‐range transport. The sample collected on 11 November 2002 experienced the most extensive chemical modification during its transport. For this sample, the overall relative abundances of reacted CaCO3 and reacted sea‐salt particles are 29.9% and 23.2%, respectively. In addition to the observation of the reacted CaCO3 and sea‐salt particles, reacted K‐containing particles are also encountered in this sample. In this work, it is observed that chemical modification of sea‐salt particles was more extensive than that of CaCO3 particles. By considering the relative abundances of nitrate‐ and sulfate‐containing particles, nitrate formation from CaCO3 and sea‐salt particles in the air is found to be more favorable than sulfate formation.
Experimental and modeling approach to the study of the critical slope for the initiation of rill flow erosion
Authors: Shao Xuejun , Wang Hong , Hu Huiwu
Published: November 2005

Critical conditions for rill erosion are determined through laboratory experiments and one‐dimensional numerical simulations. Relationships between rill flow characteristics and slope angle θ or plot size are studied both experimentally and numerically for realistic rainfall intensities. The experimental results show that maximum rill flow velocities occur within a specific range of slope angles, θ = 30°–40°, which is independent of plot size and degree of overland flow concentration. For a given plot size and rainfall intensity the threshold slope angle for rill erosion depends on a number of factors, including soil erodibility, the degree of overland flow concentration, and the effect of gravity on soil erosion. The effect of plot size on the stable rill width generated by rill erosion is also discussed along with its implications for soil loss predictions.
On the long‐term behavior of meandering rivers
Authors: Camporeale C. , Perona P. , Porporato A. , Ridolfi L.
Published: November 2005

In spite of notable advances in the description of river morphodynamics, the long‐term dynamics of meandering rivers is still an open question, in particular, regarding the existence of a possible statistical steady state and its scaling properties induced by the competing action of cutoffs and reach elongation. By means of extensive numerical simulations, using three fluid dynamic models of different complexity and analysis of real data from the Amazon, North America, and Russia, we show that the reach cutoffs, besides providing stability and self‐confinement to the meander belt, also act as a dynamical filter on several hydrodynamic mechanisms, selecting only those that really dominate the long‐term dynamics. The results show that the long‐term equilibrium conditions are essentially governed by only one spatial scale (proportional to the ratio of the river depth and the friction coefficient) and one temporal scale (proportional to the square of the spatial scale divided by the river width, the mean longitudinal velocity, and the erodibility coefficient) that contain the most important fluid dynamic quantities. The ensuing statistical long‐term behavior of meandering rivers proves to be universal and largely unaffected by the details of the fluid dynamic processes that govern the short‐term river behavior.
N
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K
near-edge x-ray-absorption fine structures of acetonitrile in gas phase
Authors: Carniato Stéphane , Taïeb Richard , Kukk Edwin , Luo Yi , Brena Barbara
Published: November 2005

The dynamic processes of N(1s) core-hole excitation in gas-phase CH3CN molecule have been studied at both Hartree-Fock and hybrid density-functional theory levels. The vibrational structure is analyzed for fully optimized core-excited states. Frank-Condon factors are obtained using the linear coupling model for various potential surfaces. It is found that the vibrational profile of the N-K absorption can be largely described by a summation of two vibrational progressions: a structure-rich profile of ν(CN) stretching mode and a large envelope of congestioned vibrational levels related to the strong (–C–CN) terminal bending bond. Excellent agreement between theoretical and experimental spectra is obtained.
Ultrasoft spin-dependent pseudopotentials
Authors: Cocula Vincent , Pickard Chris J. , Carter Emily A.
Published: November 2005

The use of the spin-dependent pseudopotentials has been shown to markedly enhance the transferability of the commonly used spin-neutral pseudopotential method for the study of the structural and magnetic properties of transition-metal-containing materials. Unfortunately, because the method was based on the rather expensive norm-conserving pseudopotential formalism, the method was limited to the study of fairly small systems. Here we present an extension of the spin-dependent pseudopotential method for the far more computationally advantageous ultrasoft formalism and show that it is very easy to add such a feature to any preexisting computer code. We benchmark our new method by comparing to previously published results and then apply it to the study of several relevant test cases: bulk Ni, Fe, and Co, as well as a Pd atomic wire.
Low-temperature phonon transport in 3D point-contacts (Review)
Authors: Feher A. , Mamaluĭ A. A. , Dul’fan A. Ya. , Syrkin E. S. , Shkorbatov A. G.
Published: November 2005

This review is devoted to describing nonequilibrium carrier systems and relaxational and kinetic phenomena in three-dimensional point-contacts. Attention is focused on describing a phonon system which becomes substantially modified under conditions of ballistic transport. In such systems the energy fluxes are limited by the presence of weakly coupled layers of impurity atoms, planar defects, or microscopic-size contacts. The small size of point-contacts, ranging from several to 1000 nm, makes it possible to investigate low-temperature heat and charge transfer on scales less than the characteristic inelastic scattering lengths. A mechanism of phonon transport in the presence of an interface is analyzed, and various models of a planar defect are examined. The special features of interfacial phonon transport, where the transport coefficients are determined not by scattering processes in the volume of a bulk crystal but rather by the properties of the intercrystalline boundary, are studied. The quantum phonon thermal conductivity of point-contacts is studied in detail.
Crystallization thermometer for ultralow temperatures with a cooled FET oscillator
Authors: Maĭdanov V. A. , Mil’chenko M. I. , Mikhin N. P. , Neoneta A. S. , Polev A. V. , Repin V. N. , Rubets S. P. , Rybalko A. S. , Semenov S. F. , Syrnikov E. V. , Shilin V. A. , Vekhov E. O.
Published: November 2005

The existing methods of measuring pressure in a crystallization thermometer used for measuring ultralow temperatures are analyzed. It is shown that a method based on measuring the resonance frequency of a resonance circuit, which includes a capacitive pressure gauge, can be used to increase measurement sensitivity and accuracy. A low-temperature FET oscillator is described. This oscillator makes it possible to increase the sensitivity and accuracy of temperature measurements in the range 0.9 mK–1 K by more than an order of magnitude.
An anomalous x-ray diffraction study of the hydration structures of Cs+ and I− in concentrated solutions
Authors: Ramos S. , Neilson G. W. , Barnes A. C. , Buchanan P.
Published: November 2005

Anomalous x-ray diffraction experiments were carried out on concentrated aqueous solutions of sodium iodide (6molal) and cesium iodide (3molal). Data were gathered at two energies below the absorption edges of the Cs+ and I− ions in order to avoid contributions from fluorescence. The statistics and quality of the raw data were improved by the use of a focusing analyzer crystal. Differences were taken between the data sets and used to calculate the hydration structures of Cs+ and I−. The structures found are more complex than anticipated for such large ions with relatively low charge densities and show evidence of ion-pair formation in both solutions. A two-Gaussian fit to the Cs+ data gives information about the Cs+–O and Cs+–I− correlations. The central position of the Gaussian representing the Cs+–O was fixed at 3.00Å, that is, the maximum of this contribution. The other parameters were allowed to vary freely, giving a Cs+–I− distance of 3.84±0.05Å and coordination numbers of 7.9 and 2.7, respectively, for the Cs+–O and Cs+–I− correlations. The results on the structure of I− in the 6molal NaI aqueous solution were also fitted to a model based on Gaussians; this gives correlations for I−–O and I−–Na+ at 3.17±0.06 and 3.76±0.06Å with respective coordination numbers of 8.8 and 1.6. The structure of I− in the 3molal CsI solution shows overlapping contributions due to I−–H, I−–O, and I−–Cs+. The best Gaussian fit gives two peaks centered at 3.00±0.08 and 3.82±0.04Å and shows that the latter two correlations are unresolved. The hydration structures are compared with those of other alkali and halide ions. The results are also found to be in good agreement with those obtained from standard x-ray diffraction and computer simulation.
Rotational effects in the band oscillator strengths and predissociation linewidths for the lowest Πu1–XΣg+1 transitions of N2
Authors: Haverd V. E. , Lewis B. R. , Gibson S. T. , Stark G.
Published: November 2005

A coupled-channel Schrödinger equation (CSE) model of N2 photodissociation, which includes the effects of all interactions between the b, c, and oΠu1 and the C and C′Πu3 states, is employed to study the effects of rotation on the lowest-υΠu1–XΣg+1(υ,0) band oscillator strengths and Πu1 predissociation linewidths. Significant rotational dependences are found which are in excellent agreement with recent experimental results, where comparisons are possible. New extreme-ultraviolet (EUV) photoabsorption spectra of the key bΠu1←XΣg+1(3,0) transition of N2 are also presented and analyzed, revealing a b(υ=3) predissociation linewidth peaking near J=11. This behavior can be reproduced only if the triplet structure of the C state is included explicitly in the CSE-model calculations, with a spin-orbit constant A≈15cm−1 for the diffuse C(υ=9) level which accidentally predissociates b(υ=3). The complex rotational behavior of the b–X(3,0) and other bands may be an important component in the modeling of EUV transmission through nitrogen-rich planetary atmospheres.
Tunneling-assisted Poole-Frenkel conduction mechanism in HfO2 thin films
Authors: Jeong Doo Seok , Hwang Cheol Seong
Published: November 2005

Tunneling-assisted Poole-Frenkel (TAPF) mechanism, which represents electron tunneling from a metal electrode to traps in a nearby insulator layer followed by detrapping of the electrons from the traps by virtue of a lowered potential well due to an applied electric field, is suggested in this study to precisely describe the electrical conduction behavior of a Pt∕HfO2∕Si capacitor. The current density versus the applied electric-field curves of the TAPF conduction show a similar electric-field dependency to that of the Poole-Frenkel (PF) conduction. However, unlike the PF mechanism, the activation energy of the leakage current density corresponds to the value of the Schottky barrier height (SBH) of a metal/insulator junction minus a lowered potential-well height by the applied electric field in the TAPF mechanism. In addition, the SBH of the Pt∕HfO2 junction is calculated considering a high space-charge density (>∼1018cm−3) in the HfO2 layer. The measured activation energy for the electrical conduction from an atomic-layer-deposited HfO2 film is compared to the value that is expected from this model.
Correlation between structural quality and magnetic properties of IrMn-based multilayers
Authors: Malinowski G. , Hehn M. , Robert S. , Lenoble O. , Schuhl A.
Published: November 2005

Structural and magnetic characterizations have been performed on exchange-biased multilayers, namely, Ta∕X∕IrMn∕Y∕Ta where X and Y are Py and/or Co. In agreement with earlier calculations, magnetic hysteresis loops reveal a clear correlation between the structural quality of the IrMn layer and the variation of the surface exchange energy constant versus its thickness. Moreover, we observe a direct link between the exchange bias variation with temperature and the magnetic disorder.
Tailoring the surface topography and wetting properties of oxygen-plasma treated polydimethylsiloxane
Authors: Tserepi Angeliki , Gogolides Evangelos , Tsougeni Katerina , Constantoudis Vassilios , Valamontes Evangelos S.
Published: November 2005

In this work, we address the issue of controlled modification of the surface topography of polydimethylsiloxane (PDMS) when subjected to oxygen-based plasma treatments, and we investigate the resulting enhanced surface area as a means of controlling the surface wetting properties. We fabricate wavy structures of controllable nanoscale amplitude and periodicity in the range 50–300nm, spontaneously formed on PDMS surfaces, by means of appropriate plasma processing conditions and radiation pretreatment. Such structures are desirable for applications in sensor microdevices, the development of biocompatible materials, and micro- and nanosystems in general. Ordered structures fabricated on polydimethylsiloxane of relatively high amplitude and small periodicity are chosen as appropriate surfaces for the enhancement of the surface wetting properties, which can be tuned from highly hydrophilic to hydrophobic when combined with a hydrophobic coating applied on the rich surface nanotexture. This fact underlines the potential application of the proposed technique in the field of microfluidics, where polydimethylsiloxane is gaining popularity as structural material for microfluidic devices.
Angular-dependent polarization-based plasmon light scattering for bioaffinity sensing
Authors: Aslan Kadir , Lakowicz Joseph R. , Geddes Chris D.
Published: November 2005

We describe an approach to affinity biosensing based on the depolarization of plasmon scatter of biotinylated-bovine serum albumin coated 20nm gold colloids crosslinked by streptavidin. Our model system employs nanoparticles which initially scatter incident light with P≈1, in a Rayleigh-like manner. However, upon aggregation, the nanoparticles show a decreased polarization and an increased forward scatter, consistent with both plasmon near-field coupling and Mie like scatter, enabling large changes in polarization detectable at angles approaching 180°.
Spatially selective and reversible doping control in cuprate films
Authors: Oh Seongshik , Bonetti Joseph A. , Inderhees Kevin , Van Harlingen D. J. , Eckstein J. N.
Published: November 2005

We describe a reversible, spatially controlled doping method for cuprate films. The technique has been used to create superconductor-antiferromagnetic insulator-superconductor (S-AFI-S) junctions and optimally doped superconductor-underdoped superconductor-optimally doped superconductor cuprate structures. We demonstrate how the S-AFI-S structure can be employed to reliably measure the transport properties of the antiferromagnetic insulator region at cryogenic temperatures using the superconductors as seamless electrical leads. We also discuss applied and fundamental issues which may be addressed with the structures created with this doping method. Although it is implemented on a cuprate film (YBa2Cu3O7−δ) in this work, the method can also be applied to any mixed-valence transition metal oxide whose physical properties are determined by oxygen content.
Top-down structure and device fabrication using in situ nanomachining
Authors: Li Xiaodong , Wang Xinnan , Xiong Qihua , Eklund Peter C.
Published: November 2005

We demonstrate the potential of an alternative tool for the fabrication of nanoscale structures and devices. A nanoindenter integrated with an atomic force microscope is shown to be a powerful machine tool for cutting precise length nanowires or nanobelts and for manipulating the shortened wires. We also demonstrate its utility in cutting grooves and fabricating dents (or periodic arrays of dents) in ZnS nanobelts. This approach permits the direct mechanical machining of nanodevices that are supported on a substrate without the inherent complications of e beam or photolithography.
Hafnium-doped tantalum oxide high-k dielectrics with sub-2 nm equivalent oxide thickness
Authors: Lu Jiang , Kuo Yue
Published: November 2005

Hafnium-doped tantalum oxide high dielectric constant films, i.e., with an equivalent oxide thickness as low as 1.3 nm, have been prepared and studied. The doped film has a bulk layer dielectric constant greater than 28 and an interface layer (formed with silicon substrate) dielectric constant greater than 8. The doping process changed the bulk and the interface layer structures as well as energy band gaps. The postdeposition annealing atmosphere showed major impacts on material and electrical properties. The new high-k material is a viable gate dielectric film for future metal-oxide-semiconductor transistors.
Photocurrent-modulated optical nuclear polarization in bulk GaAs
Authors: Paravastu Anant K. , Coles Patrick J. , Reimer Jeffrey A. , Ladd Thaddeus D. , Maxwell Robert S.
Published: November 2005

Application of a dc electric field to bulk, semi-insulating, GaAs during laser irradiation was observed to significantly affect optically pumped nuclear spin polarizations. Changes to nuclear polarizations correlated with nonlinear photoconductivity, and both depended significantly on excitation photon energy. Many aspects of the data could be explained by electric field-dependent population transfer between trapped and delocalized electronic spin reservoirs. These results indicate that semi-insulating GaAs could be a platform for localized optical and electric field control of nuclear spin polarization.
Location control of giant silicon grains using organic lenses
Authors: Oh Jae Hwan , Kim Eun Hyun , Kim Sang Kyu , Cheon Jun Hyuk , Son Yong Duck , Jang Jin
Published: November 2005

We studied the location control of a giant grain of polycrystalline silicon produced by Ni-mediated crystallization of amorphous silicon (a-Si) using a cap layer. An organic lens made of acryl was used for the focusing of light for the seed formation and subsequent crystallization. A single grain 62μm in diameter was made using an 80-μm-square SiNx cap layer on the a-Si. The position of a thin-film transistor (TFT) on a grain can be controlled, so that a single grain TFT can be fabricated at a predetermined position without use of the laser annealing technique.
Oxyfluoride glass for high-energy laser windows: Thermal lensing issue
Authors: Klein Claude A.
Published: November 2005

Recently, a glass composition identified as oxyfluoride glass (OFG™) has stimulated great expectations in terms of creating “athermal” high-energy laser (HEL) windows. A proper evalution of the two thermal lensing coefficients, however, indicates that (a) the intrinsic stress birefringence cannot be ignored (χ−=−2.88×10−7K−1), and (b) the evaluation of χ+(χ+=5.87×10−7K−1) must include the stress-optic contribution. Strehl-ratio calculations demonstrate that, in the absence of stress-driven failure modes, HEL windows made of OFG outperform fused-silica windows but may not match the capability of windows made of fusion-cast CaF2.
Breakdown kinetics of Pr2O3 films by conductive-atomic force microscopy
Authors: Fiorenza Patrick , Lo Nigro Raffaella , Raineri Vito , Lombardo Salvatore , Toro Roberta G. , Malandrino Graziella , Fragalà Ignazio L.
Published: November 2005

The dielectric breakdown (BD) kinetics of praseodymium thin films has been determined by comparison between current-voltage measurements on large-area (up to 78.54μm2) metal-oxide-semiconductor structures and conductive-atomic force microscopy (C-AFM). C-AFM clearly images the weak BD single spots under constant voltage stresses. The stress time on the single C-AFM tip dot was varied from 2.5×10−3 to 8×10−2s. The density of BD spots, upon increasing the stress time, exhibits an exponential trend. The Weibull slope and the characteristic time of the dielectric BD have been determined by direct measurements at nanometer scale.
All-optical control of the resonant-photon tunneling effect observed in GaAs∕AlGaAs multilayered structures containing quantum dots
Authors: Yamamoto Naokatsu , Akahane Kouichi , Gozu Shin-Ichirou , Ohtani Naoki
Published: November 2005

We observed the resonant-photon tunneling (RPT) effect at the 1.5μm optical communications waveband in a GaAs∕AlGaAs multilayered structure containing InGaSb quantum dots (QDs) as an active medium by a silicon prism total-reflection measurement. A sharp reflectance dip due to the RPT effect was clearly observed at a resonant-incidence angle in the total reflection region. The resonant-incidence angle clearly shifted when control light was irradiated onto the QD active layer. We demonstrated that the reflectance around the resonant-incidence angle can be controlled all-optically using the control light irradiation. These results clearly indicate the possibility of creating RPT devices for all-optical signal processing in the optical communication wavebands.
Phenological variation among Israeli populations of Cicer judaicum Boiss.
Authors: Ben-David Roi , Abbo Shahal
Published: November 2005

To obtain knowledge about the phenological adaptation of wild Cicer, we studied Israeli populations of Cicer judaicum and quantified the flowering time and morphological vernalisation response. Vernalisation treatment led to a similar advance in flowering time in Israeli C. judaicum and in Turkish C. reticulatum. The two wild taxa, however, showed differential response in main shoot development following the vernalisation treatment. Between- and within-population variance components of the measured traits were estimated. Phenological variation between populations exceeded the variation between accessions within populations. We suggest that increasing the number of sampling sites at the expense of more intensive collection within sites is likely to optimise collection strategy for this species.
Differential effects of soil water deficit on the basic plant functions and their significance to analyse crop responses to water deficit in indeterminate plants
Authors: Wery Jacques
Published: November 2005

On the basis of a large set of experiments conducted on legumes, cotton, and vineyards, we propose a framework to analyse the functioning of an indeterminate crop in response to soil water deficit. Indicators of basic plant functions (e.g. leaf carbon exchange rate as an indicator of production of assimilates) have been correlated with soil water status in the root zone (quantified with the fraction of transpirable soil water, FTSW), across a range of soil water deficit. Leaf area development was the most sensitive process to soil water deficits, with branching being more sensitive than leaf emission and growth on the main stem. Net carbon exchange rate and the various steps of reproductive development were less sensitive to drought, thereby explaining why grain/fruit yield can be increased by a moderate drought in indeterminate plants. Other traits of plant adaptation to drought at the crop level, such as reduction of flowering duration and increase of harvest index (in case of early drought), can be explained by the observed differential effects of soil dehydration on the various plant functions. These results have been used to develop regulated deficit irrigation strategies using tensiometers and tools for in-field diagnosis, especially for seed production and grape production.
Developmental sequences for simulating crop phenology for water-limiting conditions
Authors: McMaster Gregory S. , Wilhelm W. W. , Frank A. B.
Published: November 2005

The timing, duration, and pace of developmental events, or phenology, are among the many responses of plants to limited soil water. Understanding and predicting plant responses to availability of soil water are important in improving the efficacy of management practices. However, the first steps towards gaining this understanding, summarising the complete developmental sequence of the shoot apex and correlating the timing of these events, have rarely been reported. Also, the effect of water-limiting conditions on crop phenology and shoot apex development is variable. The objective of this paper is to present the developmental sequence of the wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and corn (Zea mays L.) shoot apices and correlate events in these sequences with growth stages for both well-watered and water-limiting conditions. We note that phenological responses to water availability occur at 3 different scales: among crops, among cultivars of a crop, and among growth stages within a cultivar or crop. Clearly, genotype × environment interaction affects the accuracy of predicting phenology. However, the fact that plants develop in an orderly, predictable pattern allows a general foundation for synthesising the complete sequence of developmental events of the shoot apex and correlate these with growth stages when water is not limiting. These patterns and relationships are the foundation to build upon in quantifying our understanding of crop phenology under water-limiting environments.
Drought resistance, water-use efficiency, and yield potential—are they compatible, dissonant, or mutually exclusive?
Authors: Blum A.
Published: November 2005

This presentation is a concept review paper dealing with a central dilemma in understanding, designing, and acting upon crop plant improvement programs for drought conditions. The association among yield potential (YP), drought resistance (DR), and water-use efficiency (WUE) is often misunderstood, which in turn can lead to conceptual oversight and wrong decisions in implementing breeding programs for drought-prone environments. Although high YP is the target of most crop breeding programs, it might not be compatible with superior DR. On the other hand, high YP can contribute to yield in moderate stress environments. Plant production in water-limited environments is very often affected by constitutive plant traits that allow maintenance of a high plant water status (dehydration avoidance). Osmotic adjustment (OA) is a major cellular stress adaptive response in certain crop plants that enhances dehydration avoidance and supports yield under stress. Despite past voiced speculations, there is no proof that OA entails a cost in terms of reduced YP. WUE for yield is often equated in a simplistic manner with DR. The large accumulation of knowledge on crop WUE as derived from research on carbon isotope discrimination allows some conclusions on the relations between WUE on the one hand, and DR and YP on the other, to be made. Briefly, apparent genotypic variations in WUE are normally expressed mainly due to variations in water use (WU; the denominator). Reduced WU, which is reflected in higher WUE, is generally achieved by plant traits and environmental responses that reduce YP. Improved WUE on the basis of reduced WU is expressed in improved yield under water-limited conditions only when there is need to balance crop water use against a limited and known soil moisture reserve. However, under most dryland situations where crops depend on unpredictable seasonal rainfall, the maximisation of soil moisture use is a crucial component of drought resistance (avoidance), which is generally expressed in lower WUE. It is concluded that the effect of a single ‘drought adaptive’ gene on crop performance in water-limited environments can be assessed only when the whole system is considered in terms of YP, DR, and WUE.
Monitoring standing dead wood for carbon accounting in tropical savanna
Authors: Fensham R. J.
Published: November 2005

Changes in the biomass of dead wood can be substantial in tropical woodland and should be included in complete carbon budgets. A recent estimate of biomass changes from long-term, permanent monitoring sites within the eucalypt woodlands of Queensland suggests that carbon accumulated in dead standing wood is similar to the amount of carbon accumulated within live woody biomass. However, this assessment did not include trees that were dead at the commencement of monitoring but have since been burnt or fallen over. Original data are presented from a permanent monitoring site, suggesting that on average 27% of dead standing biomass is consumed per low-intensity fire. The consumption of standing dead wood by fire, together with likely ‘fall-down rates’, could offset a substantial proportion of recently estimated dead standing wood carbon sink. The potential for using existing allometric equations to ascribe biomass to the components of dead standing wood (trunks, branches, bark) on permanent monitoring plots is reviewed. Some valid generalisations can be recognised but a lack of standardisation in allometric studies presents problems. It is suggested that data from survey, monitoring and experiments could drive worthwhile models of dead standing wood biomass. This pool will probably vary substantially through time and space, depending on climatic conditions, fire and termite activity.
The utility of the eddy covariance techniques as a tool in carbon accounting: tropical savanna as a case study
Authors: Hutley Lindsay B. , Leuning Ray , Beringer Jason , Cleugh Helen A.
Published: November 2005

Global concern over rising atmospheric CO2 concentrations has led to a proliferation of studies of carbon cycling in terrestrial ecosystems. Associated with this has been widespread adoption of the eddy covariance method to provide direct estimates of mass and energy exchange between vegetation surfaces and the atmosphere. With the eddy covariance method, fast-response instruments (10–20Hz) are typically mounted above plant canopies and the fluxes are calculated by correlating turbulent fluctuations in vertical velocity with fluctuations in various scalars such as CO2, water vapour and temperature. These techniques allow the direct and non-destructive measurement of the net exchange of CO2 owing to uptake via photosynthesis and loss owing to respiration, evapotranspiration and sensible heat. Eddy covariance measurements have a high temporal resolution, with fluxes typically calculated at 30-min intervals and can provide daily, monthly or annual estimates of carbon uptake or loss from ecosystems. Such measurements provide a bridge between ‘bottom-up’ (e.g. leaf, soil and whole plant measures of carbon fluxes) and ‘top-down’ approaches (e.g. satellite remote sensing, air sampling networks, inverse numerical methods) to understanding carbon cycling. Eddy covariance data also provide key measurements to calibrate and validate canopy- and regional-scale carbon balance models. Limitations of the method include high establishment costs, site requirements of flat and relatively uniform vegetation and problems estimating fluxes accurately at low wind speeds. Advantages include spatial averaging over 10–100ha and near-continuous measurements. The utility of the method is illustrated in current flux studies at ideal sites in northern Australia. Flux measurements spanning 3years have been made at a mesic savanna site (Howard Springs, Northern Territory) and semi-arid savanna (Virginia Park, northern Queensland). Patterns of CO2 and water vapour exchange at diurnal, seasonal and annual scales are detailed. Carbon dynamics at these sites are significantly different and reflect differences in climate and land management (impacts of frequent fire and grazing). Such studies illustrate the utility of the eddy covariance method and its potential to provide accurate data for carbon accounting purposes. If full carbon accounting is implemented, for ideal sites, the eddy covariance method provides annual estimates of carbon sink strength accurate to within 10%. The impact of land-use change on carbon sink strength could be monitored on a long-term basis and provide a valuable validation tool if carbon trading schemes were implemented.
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
Authors: Foat Barrett C. , Houshmandi S. Sean , Olivas Wendy M. , Bussemaker Harmen J.
Published: November 2005

The steady-state abundance of an mRNA is determined by the balance between transcription and decay. Although regulation of transcription has been well studied both experimentally and computationally, regulation of transcript stability has received little attention. We developed an algorithm, MatrixREDUCE, that discovers the position-specific affinity matrices for unknown RNA-binding factors and infers their condition-specific activities, using only genomic sequence data and steady-state mRNA expression data as input. We identified and computationally characterized the binding sites for six mRNA stability regulators inSaccharomyces cerevisiae, which include two members of the Pumilio-homology domain (Puf) family of RNA-binding proteins, Puf3p and Puf4p. We provide computational and experimental evidence that regulation of mRNA stability by these factors is modulated in response to a variety of environmental stimuli.
Allergen-induced peribronchial fibrosis and mucus production mediated by IκB kinase β-dependent genes in airway epithelium
Authors: Broide David H. , Lawrence Toby , Doherty Taylor , Cho Jae Youn , Miller Marina , McElwain Kirsti , McElwain Shauna , Karin Michael
Published: November 2005

In response to inflammation or injury, airway epithelial cells express inducible genes that may contribute to allergen-induced airway remodeling. To determine the contribution of epithelial cell NF-κB activation to the remodeling response, we generatedCC10-Cretg/IkkβΔ/Δmice in which NF-κB signaling through IκB kinase β (IKKβ) is selectively ablated in the airway epithelium by conditional Cre-recombinase expression from the Clara cell (CC10) promoter. Repetitive ovalbumin challenge of mice deficient in airway epithelial IKKβ prevented nuclear translocation of the RelA NF-κB subunit only in airway epithelial cells, resulting in significantly lower peribronchial fibrosis inCC10-Cretg/IkkβΔ/Δmice compared with littermate controls as assessed by peribronchial trichrome staining and total lung collagen content. Levels of airway mucus, airway eosinophils, and peribronchial CD4+cells in ovalbumin-challenged mice were also reduced significantly upon airway epithelialIkkβ ablation. The diminished inflammatory response was associated with reduced expression of NF-κB-regulated chemokines, including eotaxin-1 and thymus- and activation-regulated chemokine, which attract eosinophils and Th2 cells, respectively, into the airway. The number of peribronchial cells expressing TGF-β1, as well as TGF-β1 amounts in bronchoalveolar lavage, were also significantly reduced in mice deficient in airway epithelium IKKβ. Overall, these studies show an important role for NF-κB regulated genes in airway epithelium in allergen-induced airway remodeling, including peribronchial fibrosis and mucus production.
Paircoil2: improved prediction of coiled coils from sequence
Authors: McDonnell A. V. , Jiang T. , Keating A. E. , Berger B.
Published: November 2005

Summary: We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled–coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure.

Availability: Paircoil2 is freely available as a web application and for download at

Contact:  keating@mit.edu; bab@mit.edu

Supplementary information: Available at Bioinformatics online and at the Paircoil website.
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
Authors: Beerli Peter
Published: November 2005

Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic parameters, such as population sizes and migration rates, using coalescence theory. Both inference methods use the same Markov chain Monte Carlo algorithm and differ from each other in only two aspects: parameter proposal distribution and maximization of the likelihood function. Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance.

Motivation: The Markov chain Monte Carlo-based ML framework can fail on sparse data and can deliver non-conservative support intervals. A Bayesian framework with appropriate prior distribution is able to remedy some of these problems.

Results: The program MIGRATE was extended to allow not only for ML(-) maximum likelihood estimation of population genetics parameters but also for using a Bayesian framework. Comparisons between the Bayesian approach and the ML approach are facilitated because both modes estimate the same parameters under the same population model and assumptions.

Availability: The program is available from

Contact:  beerli@csit.fsu.edu
SimShift: Identifying structural similarities from NMR chemical shifts
Authors: Ginzinger Simon W. , Fischer Johannes
Published: November 2005

Motivation: An important quantity that arises in NMR spectroscopy experiments is the chemical shift. The interpretation of these data is mostly done by human experts; to our knowledge there are no algorithms that predict protein structure from chemical shift sequences alone. One approach to facilitate this process could be to compare two such sequences, where the structure of one protein has already been resolved. Our claim is that similarity of chemical shifts thereby found implies structural similarity of the respective proteins.

Results: We present an algorithm to identify structural similarities of proteins by aligning their associated chemical shift sequences. To evaluate the correctness of our predictions, we propose a benchmark set of protein pairs that have high structural similarity, but low sequence similarity (because with high sequence similarity the structural similarities could easily be detected by a sequence alignment algorithm). We compare our results with those of HHsearch and SSEA and show that our method outperforms both in >50% of all cases.

Contact:  Simon.Ginzinger@bio.ifi.lmu.de
Application of compression-based distance measures to protein sequence classification: a methodological study
Authors: Kocsor András , Kertész-Farkas Attila , Kaján László , Pongor Sándor
Published: November 2005

Motivation: Distance measures built on the notion of text compression have been used for the comparison and classification of entire genomes and mitochondrial genomes. The present study was undertaken in order to explore their utility in the classification of protein sequences.

Results: We constructed compression-based distance measures (CBMs) using the Lempel-Zlv and the PPMZ compression algorithms and compared their performance with that of the Smith–Waterman algorithm and BLAST, using nearest neighbour or support vector machine classification schemes. The datasets included a subset of the SCOP protein structure database to test distant protein similarities, a 3-phosphoglycerate-kinase sequences selected from archaean, bacterial and eukaryotic species as well as low and high-complexity sequence segments of the human proteome, CBMs values show a dependence on the length and the complexity of the sequences compared. In classification tasks CBMs performed especially well on distantly related proteins where the performance of a combined measure, constructed from a CBM and a BLAST score, approached or even slightly exceeded that of the Smith–Waterman algorithm and two hidden Markov model-based algorithms.

Contact:  kocsor@inf.u-szeged.hu

Supplementary information: