bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical study of the adsorption of H on Sin clusters, (n=3–10)
Authors: Tiznado William , Oña Ofelia B. , Bazterra Víctor E. , Caputo María C. , Facelli Julio C. , Ferraro Marta B. , Fuentealba Patricio
Published: November 2005

A recently proposed local Fukui function is used to predict the binding site of atomic hydrogen on silicon clusters. To validate the predictions, an extensive search for the more stable SinH (n=3–10) clusters has been done using a modified genetic algorithm. In all cases, the isomer predicted by the Fukui function is found by the search, but it is not always the most stable one. It is discussed that in the cases where the geometrical structure of the bare silicon cluster suffers a considerable change due to the addition of one hydrogen atom, the situation is more complicated and the relaxation effects should be considered.
Integral equation theory of randomly coupled multiblock copolymer melts: Effect of block size on the phase behavior
Authors: Sung Bong June , Yethiraj Arun
Published: November 2005

The phase behavior of randomly coupled multiblock copolymer melts is studied using the polymer reference interaction site model integral equation theory. The molecules are modeled as flexible chains with random sequences of two types of blocks, each of which consists of the same number (R) of monomer beads. In the random copolymer (R=1) limit the theory predicts macrophase separation as the temperature is decreased for all values of the monomer correlation length λ. For R>2, however, the theory predicts a microphase separation for values of λ less than some critical value which increases as the block size increases.
Oscillator strength and linewidth measurements of dipole-allowed transitions in N214 between 93.5 and 99.5nm
Authors: Stark G. , Huber K. P. , Yoshino K. , Smith Peter L. , Ito K.
Published: November 2005

Line oscillator strengths in 16 electric dipole-allowed bands of N214 in the 93.5–99.5nm(106950−100500cm−1) region have been measured at an instrumental resolution of 6.5×10−4nm(0.7cm−1). The transitions terminate on vibrational levels of the 3pσΣu+1, 3pπΠu1, and 3sσΠu1 Rydberg states and of the b′Σu+1 and bΠu1 valence states. The J dependences of band f values derived from the experimental line f values are reported as polynomials in J′(J′+1) and are extrapolated to J′=0 in order to facilitate comparisons with results of coupled-Schrödinger-equation calculations that do not take into account rotational interactions. Most bands in this study reveal a marked J dependence of the f values and/or display anomalous P-, Q- and R-branch intensity patterns. These patterns should help inform future spectroscopic models that incorporate rotational effects, and these are critical for the construction of realistic atmospheric radiative transfer models. Linewidth measurements are reported for four bands. Information provided by the J dependences of the experimental linewidths should be of use in the development of a more complete understanding of the predissociation mechanisms in N2.
Solidification and epitaxial regrowth in surface nanostructuring with laser-assisted scanning tunneling microscope
Authors: Wang Xinwei , Lu Yongfeng
Published: November 2005

In this work, parallel molecular-dynamics simulation is conducted to study the long-time (up to 2ns) behavior of argon crystal in surface nanostructuring with a laser-assisted scanning tunneling microscope. A large system consisting of more than 1×108at. is explored. The study is focused on the solidification procedure after laser irradiation, which is driven by heat conduction in the material. Epitaxial regrowth is observed in the solidification. Atomic dislocation due to thermal strain-induced structural damages is observed as well in epitaxial regrowth. During solidification, the liquid is featured with decaying normal compressive stresses and negligible shear stresses. Two functions are designed to capture the structure and distinguish the solid and liquid regions. These functions work well in terms of reflecting the crystallinity of the material and identifying the atomic dislocations. The study of the movement of the solid-liquid interface reveals an accelerating moving speed in the order of 3–5m∕s. The spatial distribution of the moving speed at the solid-liquid interface indicates a nonuniform epitaxial regrowth in space. The bottom of the liquid solidifies slower than that at the edge.
Ferroelectric properties of epitaxial BaTiO3 thin films and heterostructures on different substrates
Authors: Trithaveesak O. , Schubert J. , Buchal Ch.
Published: November 2005

Ferroelectric thin films of BaTiO3 and BaTiO3∕SrRuO3 epitaxial heterostructures on different single-crystalline substrates were fabricated by pulsed laser deposition. The BaTiO3 films of 100–400nm thickness show high structural perfection and c-axis-oriented growth. For the electrical characterization of the BaTiO3 in a thin-film capacitor structure, Pt top electrodes were deposited by e-beam evaporation. The results are compared to the current experimental and theoretical models. Special consideration is given to the model of charge injection from the electrodes.
Tuning magnetic hysteresis of electrodeposited Fe3O4
Authors: Chatman Shawn , Noel Adam J. G. , Poduska Kristin M.
Published: November 2005

We demonstrate that changes in electrolyte composition and applied potential during aqueous electrodeposition can be used to tune the magnetic hysteresis response of thin-film Fe3O4 (magnetite) on polycrystalline metal substrates. X-ray diffraction data confirmed that magnetite formation in electrolytes containing KCH3COO (0.04–2.0M) and Fe(SO4)2(NH4)2 (0.01M) required temperatures between 60 and 85°C, and deposition potentials between −0.300 and −0.575V or galvanostatic current densities between 50 and 88μA∕cm2. Scanning electron microscopy studies show that magnetite crystallites tend to adopt different habits depending on the electrolyte composition. Room-temperature magnetic hysteresis responses (squareness and coercivity) are dependent upon the crystal habit of deposits, implying that the electrolyte’s acetate concentration influences the magnetic domain structure of the resulting magnetite deposits. Magnetite crystallites grown from electrolytes with low acetate concentrations showed pseudo-single-domain magnetic response, while magnetite grown from acetate-enriched electrolytes showed multidomain magnetic response.
Diamond synthesis under atmospheric pressure from ethanol-water solution using hot-filament chemical vapor deposition method assisted by electrospray
Authors: Matsushima Yuta , Naganuma Miya , Yamazaki Tsutomu , Maeda Kazuyuki , Suzuki Takeyuki
Published: November 2005

The effect of water on diamond synthesis was investigated in the hot-filament chemical vapor deposition process under atmospheric pressure. We adopted an ethanol-water-hydrogen system; an ethanol-water mixture was supplied by an electrospraying technique. With increasing the water content, the morphology of deposited diamond varied from mirror-ball-like to small-crystalline particles. Dense diamond films with distinct facets were obtained at 5.58mol% ethanol with 1.39mol% water and 5.27mol% ethanol with 2.26mol% water. In Raman spectroscopy, the full width at half maximum (FWHM) of the diamond peak at 1333cm−1 decreased with the water content and a broad peak of nondiamond carbon around 1550cm−1 was markedly reduced. The FWHM also decreased by lowering the ethanol concentration in an ethanol-hydrogen system. Only the ethanol-water-hydrogen system yielded the high-quality diamond with a relatively high deposition rate. The major roles of water were cleaning the filament and removing nondiamond carbon in the deposit with the water-gas reaction, H2O+C→H2+CO.
Evidence of material mixing during local anodic oxidation nanolithography
Authors: Mori G. , Lazzarino M. , Ercolani D. , Biasiol G. , Sorba L. , Heun S. , Locatelli A.
Published: November 2005

We investigate the chemical properties of nanostructures fabricated by local anodic oxidation (LAO) on epitaxial GaAs∕AlAs∕GaAs layers. We find evidence for the presence of Al compounds located in the topmost surface layers of the LAO structures. Our results cannot be explained within the framework of the commonly accepted mechanism that describes the growth of the LAO oxides in terms of diffusion of oxygen-rich ions through the growing oxide. A more general mechanism that explains our experimental findings is proposed.
Surface instability of a bilayer elastic film due to surface van der Waals forces
Authors: Yoon J. , Ru C. Q. , Mioduchowski A.
Published: November 2005

The paper studies surface instability of a bilayer elastic film interacting with another flat rigid body through surface van der Waals forces under plane-strain conditions. The analysis is based on an approximate model which reduces the two-dimensional plane-strain problem of the bilayer elastic film to a one-dimensional problem on its surface. The critical value of the interaction coefficient for surface instability and the associated instability mode can be determined easily by identifying the minimum of the interaction coefficient as a function of the wavelength of the instability mode. Among others, the present analysis shows that a stiff bottom layer of a bilayer film can be approximately treated as a rigid substrate only when the surface compliance ratio of the top layer to the bottom layer exceeds a certain critical value. In contrast to a common assumption that nonequal Poisson ratios of the two layers have a minor effect, it is found that different Poisson ratio combinations could have a significant effect on the surface instability of a bilayer elastic film even when the thickness ratio and modulus ratio keep unchanged. In particular, the present study confirms that, unlike a single-layer elastic film which has only one instability mode, a bilayer elastic film can have two distinct surface instability modes when the top layer is more compliant and much thinner than the bottom layer.
Spin transfer switching and spin polarization in magnetic tunnel junctions with MgO and AlOx barriers
Authors: Diao Zhitao , Apalkov Dmytro , Pakala Mahendra , Ding Yunfei , Panchula Alex , Huai Yiming
Published: November 2005

We present spin transfer switching results for MgO based magnetic tunneling junctions (MTJs) with large tunneling magnetoresistance (TMR) ratio of up to 150% and low intrinsic switching current density of 2–3×106A∕cm2. The switching data are compared to those obtained on similar MTJ nanostructures with AlOx barrier. It is observed that the switching current density for MgO based MTJs is 3 to 4 times smaller than that for AlOx based MTJs, and that can be attributed to higher tunneling spin polarization (TSP) in MgO based MTJs. In addition, we report a qualitative study of TSP for a set of samples, ranging from 0.22 for AlOx to 0.46 for MgO based MTJs, and that shows the TSP (at finite bias) responsible for the current-driven magnetization switching is suppressed as compared to zero-bias tunneling spin polarization determined from TMR.
Index and gain dynamics of optically pumped GaInNAs vertical-cavity semiconductor optical amplifiers
Authors: Laurand Nicolas , Calvez Stephane , Dawson Martin D. , Kelly Anthony E.
Published: November 2005

To study the dynamic effects in GaInNAs vertical-cavity semiconductor amplifiers (VCSOAs), we carried out a pump-probe experiment on an optically biased VCSOA, first at antiresonance and then in gain. At antiresonance, the highest absorption region of the amplifier, the carrier-population-depletion-induced shift in the wavelength of the absorption was measured as a function of pump-probe delay. The corresponding index recovery time was measured to be τ∼50ps±5ps. In the amplification regime, we observed that the carrier depletion induced by the pump pulse decreased the available gain. The recovery time for the device gain in dB under these conditions was measured at τ∼55±15ps. These results indicate that GaInNAs VCSOAs can process data at 10Gbits∕s with no patterning effect.
Mechanism of electrical polarization of silica glass
Authors: Doremus Robert H.
Published: November 2005

When an electrical potential is applied to silica glass at 250 °C, there is a residual electrical field after the applied potential is removed. The profile of this field with distance is modeled as resulting from interdiffusion of sodium and hydronium ions; the shapes of the measured and calculated profiles of electrical field agree reasonably well, showing that this model describes the mechanism of poling the glass.
Thermal stability of ion-implanted ZnO
Authors: Coleman V. A. , Tan H. H. , Jagadish C. , Kucheyev S. O. , Zou J.
Published: November 2005

Zinc oxide single crystals implanted at room temperature with high-dose (1.4×1017cm−2) 300 keV As+ ions are annealed at 1000–1200 °C. Damage recovery is studied by a combination of Rutherford backscattering/channeling spectrometry (RBS/C), cross-sectional transmission electron microscopy (XTEM), and atomic force microscopy. Results show that such a thermal treatment leads to the decomposition and evaporation of the heavily damaged layer instead of apparent defect recovery and recrystallization that could be inferred from RBS/C and XTEM data alone. This study shows that heavily damaged ZnO has relatively poor thermal stability compared to as-grown ZnO which is a significant result and has implications for understanding results on thermal annealing of ion-implanted ZnO.
Short-channel polymer field-effect-transistor fabrication using spin-coating-induced edge template and ink-jet printing
Authors: P. Li S. , Chu D. P. , Newsome C. J. , Russell D. M. , Kugler T. , Ishida M. , Shimoda T.
Published: November 2005

A method to fabricate polymer field-effect transistors with submicron channel lengths is described. A thin polymer film is spin coated on a prepatterned resist with a low resolution to create a thickness contrast in the overcoated polymer layer. After plasma and solvent etching, a submicron-sized line structure, which templates the contour of the prepattern, is obtained. A further lift-off process is applied to define source-drain electrodes of transistors. With a combination of ink-jet printing, transistors with channel length down to 400 nm have been fabricated by this method. We show that drive current density increases as expected, while the on/off current ratio 106 is achieved.
GaAs-based room-temperature continuous-wave 1.59μm GaInNAsSb single-quantum-well laser diode grown by molecular-beam epitaxy
Authors: Niu Z. C. , Zhang S. Y. , Ni H. Q. , Wu D. H. , Zhao H. , Peng H. L. , Xu Y. Q. , Li S. Y. , He Z. H. , Ren Z. W. , Han Q. , Yang X. H. , Du Y. , Wu R. H.
Published: November 2005

Starting from the growth of high-quality 1.3μmGaInNAs∕GaAs quantum well (QW), the QW emission wavelength has been extended up to 1.55μm by a combination of lowering growth rate, using GaNAs barriers and incorporating some amount of Sb. The photoluminescence properties of 1.5μm range GaInNAsSb∕GaNAs QWs are quite comparable to the 1.3μm QWs, revealing positive effect of Sb on improving the optical quality of the QWs. A 1.59μm lasing of a GaInNAsSb∕GaNAs single-QW laser diode is obtained under continuous current injection at room temperature. The threshold current density is 2.6kA∕cm2 with as-cleaved facet mirrors.
Experimental determination of electron and hole sublevels in modulation-doped InAs∕GaAs quantum dots
Authors: Jang Y. D. , Yim J. S. , Lee D. , Kim Gil-Ho , Liang C.-T. , Farrer I. , Ritchie D. A.
Published: November 2005

Electron and hole sublevels in quantum dots (QDs) are experimentally determined using the excitation-power dependence of photoluminescence spectrum for a modulation-doped QD structure. The sublevel spacing between n=1 and n=2 electron states can be obtained from the photoluminescence (PL) spectrum under very low excitation and the spacing between n=1 and n=2 hole states can be obtained by comparing the PL spectrum under high excitation with the one under low excitation. The proposed method should give useful information in the design of QD devices, as well as for the verification of theoretical calculations of QD energy levels.
Current crowding in graded contact layers of intracavity-contacted oxide-confined vertical-cavity surface-emitting lasers
Authors: Lysak V. V. , Chang K. S. , Lee Y. T.
Published: November 2005

In this work we present the simulation of the intracavity-contacted oxide-confined vertical-cavity surface-emitting lasers including the thermal effects. We analyze the thermal, electrical, and optical properties of such devices with the different thicknesses of graded layers between the contact and oxide confined layers. Results of simulations for the devices with graded layer thickness of 40–60 Å show a reduced current crowding effect.
A review of drought adaptation in crop plants: changes in vegetative and reproductive physiology induced by ABA-based chemical signals
Authors: Liu Fulai , Jensen Christian R. , Andersen Mathias N.
Published: November 2005

This review discusses the role of abscisic acid (ABA)-based drought stress chemical signalling in regulating crop vegetative and reproductive development and its contributions to crop drought adaptation. Increased concentrations of ABA in the root induced by soil drying may maintain root growth and increase root hydraulic conductivity; both lead to an increase in water uptake and thereby postpone the development of water deficit in the shoot. Root ABA is also transported in the xylem to the shoot and is perceived at the acting sites, where it causes stomatal closure and reduced leaf expansion, thereby preventing dehydration of leaf tissues and enhancing the chance for survival under prolonged drought. ABA-based chemical signalling can be amplified by several factors, particularly increased pH in the xylem/apoplast, which retains anionic ABA. Such an increase in xylem pH detected in field-grown maize might have been brought about by reduced nitrate uptake by plants during soil drying. In contrast, xylem sap alkalinisation was not found in soybeans, which depend on fixing nitrogen through their association with Rhizobium japonicum. Evidence has also shown that the xylem-borne ABA can be transported to plant reproductive structures and influence their development, presumably by regulating gene expression that controls cell division and carbohydrate metabolic enzyme activity under drought conditions. The possible involvement of ABA in the up- and down-regulation of acid invertase in crop source (adult leaves) v. sink (young ovaries) organs indicates a crucial role of the hormone in balancing source and sink relationship in plants according to the availability of water in the soil. A novel irrigation technique named partial root-zone drying (PRD), has been developed to allow exploitation of ABA-based drought stress signalling to improve water-use efficiency (WUE) based on its roles in regulating stomatal aperture and leaf expansion. However, little is known about how crop reproductive development is regulated when irrigated under PRD. We suggest that more attention should be paid to the latter aspect as it directly relates to crop yield and quality.
Physiology of abscisic acid (ABA) in roots under stress—a review of the relationship between root ABA and radial water and ABA flows
Authors: Hartung Wolfram , Schraut Daniela , Jiang Fan
Published: November 2005

Abscisic acid (ABA), the universal plant stress hormone, is accumulated in roots subjected to a range of external stresses, including drought, salinity, and nutrient deficiencies. This accumulation is regulated by ABA-metabolism (biosynthesis and degradation), -recirculation, and -exudation. Stress ABA serves as a long-distance signal regulating the water relations of shoots (stomata, meristems) and roots (hydraulic conductivity, root development, desiccation tolerance). Endogenous ABA, radial water flows (JV), and radial ABA flows (JABA) are closely coupled. Here we described the relations between these processes that are crucial factors for the role of ABA as a stress hormone and a long-distance stress signal. Crop varieties with high ABA concentrations exhibit an intensified long distance ABA signalling that reduces water consumption and, in the case of grapevine, improves the quality of the berries.
Root penetration ability of wheat through thin wax-layers under drought and well-watered conditions
Authors: Acuña T. L. Botwright , Wade L. J.
Published: November 2005

Sand over clay duplex soils and those compacted by heavy farm machinery restrict water infiltration and root growth because roots cannot penetrate hard soil. Under drought, restriction of roots to soil above the hard layer results in the early onset of plant water-deficit, unless roots can penetrate the hard layer to reach soil water and nutrients at depth. There is little to no information on the ability of roots of bread wheat (Triticum aestivum L.) to penetrate hardpans. Here we report on 3 experiments undertaken in a controlled environment in pots that validate and explore the use of thin Paraffin wax–Vaseline (WV) layers of different strengths to simulate a hardpan under contrasting water regimes. Seeds produced an average of 5 seminal roots, which all penetrated the low-impedance wax-layer (0.03WV), in such a way that seminal root dry matter (DM) was evenly distributed throughout the soil profile. The number and depth of penetrating seminal root axes declined as wax-layer strength increased, and a significant proportion of total length and DM of main seminal root axes was instead restricted to the 0–0.12-m soil layer above the wax layer. No roots penetrated the 0.60WV, which was equivalent to ~1.50 MPa penetrometer resistance. The distribution of seminal roots was less affected by water regime than nodal roots, which were severely reduced in number when drought was imposed at 14 days after sowing (DAS), compared with well-watered conditions. Growth of the seminal roots into soil beneath the wax-layer determined the pattern of stomatal conductance and volumetric soil water content (Jv) over the period of drought stress, as few nodal roots reached and penetrated the wax layer. Stomatal conductance declined suddenly at 19 days after the last irrigation, and partially recovered as water extraction increased in the 0.40–0.60-m soil depth. Reasons for this are discussed. The wax-layer technique requires validation for wheat in the field, but the technique offers promise for screening breeding lines for the ability to penetrate a hardpan.
Policy issues impacting on crop production in water-limiting environments
Authors: Radcliffe John C
Published: November 2005

Policy issues have impacted on cropping since the earliest days of European colonial settlement. Following emigration to Australia, secure land titles were required, with the Torrens title system being progressively introduced from 1858. This provided the basis for landholders to be able to borrow to develop land. Closer settlement policies were adopted, underpinned by the development of transport infrastructure. The demand for education resulted in Agricultural Colleges in the colonies from the 1880s, with Departments of Agriculture soon afterwards. Federation of the colonies into the Commonwealth of Australia and the creation of the states resulted in a separation of powers, with the Commonwealth assuming responsibility for external powers including overseas marketing, import quarantine, health and quality standards of exports and credit and financial powers. Natural resource management matters and education were among those remaining with the states. Regular intergovernmental meetings were held to discuss research from 1927 and a broader range of agricultural issues from 1935. The Great Depression in the 1930s, poor commodity prices and serious land degradation led to government support for debt reconstruction and the introduction of soil conservation services. Realising the need for innovation to successfully compete on world markets, farmers, led by cereal growers, petitioned for the establishment of statutory research programs with joint grower/government funding from the 1950s. These have been remarkably successful, with the uptake of new technologies contributing to an average multifactor productivity growth of Australian grain farms by 3.3% per year between 1977–78 and 2001–02.
With community and policy recognition of the need to conserve natural resources, the Commonwealth Government is playing an increasing role in this area. Farmers are required to meet standards for the use of agricultural chemicals and for occupational safety, welfare and environmental protection. The states have taken a conservative stand against the growing of genetically modified food crops in the name of protecting overseas markets. New water management regimes are coming into place with the separation of water titles from land. Market-based instruments are being introduced to encourage more sustainable production systems and saleable ecosystem services. Research and innovation along with complementary policy initiatives will continue to underpin farmers’ adaptive management skills to ensure dryland crop producers have sustainable production systems while remaining competitive in world markets.
Optimal sowing time and seeding rate for winter-sown, rain-fed chickpea in a cool, semi-arid Mediterranean area
Authors: Yau Sui-Kwong
Published: November 2005

Chickpea (Cicer arietinum) is one of the 3 most important legume crops in West Asia and North Africa. Winter sowing of chickpea has been advocated recently in the region, but detailed research on date and rate of sowing has not been conducted. The objectives of this study were to find the optimal sowing month and to test the hypothesis that a lower than normal seeding rate is needed for winter-sown chickpea. Two series of field experiments were conducted under rain-fed conditions at the Agricultural Research and Educational Center in the Bekaa Valley of Lebanon. In the sowing-date experiment, which was conducted over 3 years, seed was sown in November, December or January and February. The seeding-rate by sowing-date experiment, which was conducted over 2 years, consisted of 3 seeding rates: 25, 40 and 55 seeds/m2, and 2 sowing dates: one each in November and March. Sowing in December or January gave similar seed yield as November sowing, and both gave higher yield than sowing in February. Sowing in December or January should be preferable than sowing in November because it is expected to give adequate time for weed control and less chance of ascochyta blight infestation. Seeding rates had no significant effects on yield, and seeding-rate by sowing-date interaction was non-significant, indicating that there is no yield advantage of a reduced seeding rate with winter sowing. However, sowing at 25 seeds/m2 yielded bigger seeds, which usually fetch higher prices. In conclusion, chickpea farmers in the semi-arid areas of the high-elevation Bekaa Valley of Lebanon or in other areas with similar environments should shift their sowing date from early spring to December or January and sow at a lower (25 seeds/m2) than normal seeding rate.
Productivity, sustainability, and rainfall-use efficiency in Australian rainfed Mediterranean agricultural systems
Authors: Turner Neil C. , Asseng Senthold
Published: November 2005

Mediterranean environments are characterised by hot, dry summers and cool, wet winters. The native vegetation in Mediterranean-climatic regions is predominantly perennial shrubs and trees intermixed with annual forbs. In south-western Australia, the spread of agriculture has seen the well adapted perennial vegetation replaced by rainfed annual crops and pastures. This has increased waterlogging and secondary salinity, thereby causing loss of productivity in ~10% of the cleared land area. To reduce deep drainage and make the agricultural systems environmentally sustainable requires the re-introduction of perennial vegetation in the form of belts of trees or shrubs, and phase-farming systems with perennials such as lucerne replacing annual pastures between the cropping years. To be economically viable, agricultural productivity needs to increase by at least 3% per annum. Yields of dryland wheat, the predominant crop in the Mediterranean agricultural regions of Australia, have increased at ~1%/year for the century preceding the 1980s and since then by nearly 4%/year. Increases have arisen from both genotypic and agronomic improvements. Genotypic increases have arisen from selection for earliness, early vigour, deep roots, osmotic adjustment, increased transpiration efficiency, improved disease resistance, and an improved harvest index from high ear weight (grain number) at flowering and high assimilate storage and remobilisation. Agronomic increases have arisen from early sowing that has been enabled by minimum tillage, increased fertiliser use, especially nitrogen, weed control, and rotations to improve weed control, minimise disease risk, and increase nitrogen availability. Evidence is presented suggesting that the rapid increase in yield of wheat in the last two decades has likely arisen from the rapid adoption of new technologies. For productivity to be maintained in the face of the increasing requirement to be environmentally sustainable will be a challenge and will require better integration of breeding and agronomy.
The improvement of crop yield in marginal environments using 'on-farm' seed priming: nodulation, nitrogen fixation and disease resisitance
Authors: Harris D. , Breese W. A. , Rao J. V. D. K. Kumar
Published: November 2005

On-farm seed priming with water is a low-cost, low-risk technology that is easily adopted by resource-poor farmers. It increases the yield of tropical and subtropical annual crops in marginal areas by a combination of better crop establishment and improved individual plant performance. The effects of seed priming, i.e. soaking seeds overnight in water before sowing, on plant growth and development are consequences of faster germination, emergence, and more vigorous early growth. Results from in-vitro, on-station and on-farm experiments are discussed.
Recent work has tested opportunities for resource-poor farmers to use seed priming as a vehicle for applying biofertilisers (Rhizobia). Preliminary results from field experiments suggest that these interventions are very effective over and above the already demonstrated benefits of priming with water alone. In a pot experiment using chickpea, combining a Rhizobium inoculation with seed priming significantly increased nodulation but had little effect on yield. Nevertheless, the results confirmed that Rhizobium inoculation is compatible with on-farm seed priming.
Observations in the field have shown that some primed crops show enhanced resistance to disease, either as a consequence of increased vigour, altered phenology, or due to some more fundamental mechanism associated with exposure of seeds to anaerobic conditions during priming. Priming seeds of a highly susceptible cultivar of pearl millet in water for 8 h before sowing significantly reduced the incidence of downy mildew in artificially infected seedlings from 80% to less than 60%.
Lupin: the largest grain legume crop in Western Australia, its adaptation and improvement through plant breeding
Authors: French Robert J. , Buirchell Bevan J.
Published: November 2005

Between 500 000 and 1 000 000 tonnes of narrow-leafed lupins (Lupinus angustifolius L.) are produced in Western Australia each year. It has become the predominant grain legume in Western Australian agriculture because it is peculiarly well adapted to acid sandy soils and the Mediterranean climate of south-western Australia. It has a deep root system and root growth is not reduced in mildly acid soils, which allows it to fully exploit the water and nutrients in the deep acid sandplain soils that cover much of the agricultural areas of Western Australia. It copes with seasonal drought through drought escape and dehydration postponement. Drought escape is lupin’s main adaptation to drought, and has been strengthened by plant breeders over the past 40 years by removal of the vernalisation requirement for flowering, and further selection for earlier flowering and maturity. Lupin postpones dehydration by several mechanisms. Its deep root system allows it to draw on water from deep in the soil profile. Lupin stomata close to reduce crop water demand at a higher leaf water potential than wheat, but photosynthetic rates are higher when well watered. It has been proposed that stomata close in response to roots sensing receding soil moisture, possibly at a critical water potential at the root surface. This is an adaptation to sandy soils, which hold a greater proportion of their water at high matric potentials than loamy or clayey soils, since the crop needs to moderate its water use while there is still sufficient soil water left to complete its life cycle. Lupin has limited capacity for osmotic adjustment, and does not tolerate dehydration as well as other crops such as wheat or chickpea. Plant breeding has increased the yield potential of lupin in the main lupin growing areas of Western Australia by 2–3 fold since the first adapted cultivar was released in 1967. This has been due largely to selecting earlier flowering and maturing cultivars, but also to improved pod set and retention, resistance to Phomopsis leptostromiformis (Kühn) Bubák, and more rapid seed filling. We propose a model for reproductive development in lupin where vegetative growth is terminated in response to receding soil moisture and followed by a period in which all assimilate is devoted to seed filling. This should allow lupin to adjust its developmental pattern in response to seasonal conditions to something like the optimum that mathematical optimal control theory would choose for that season. This is the type of pattern that has evolved in lupin, and the task of future plant breeders will be to fine-tune it to better suit the environment in the lupin growing areas of Western Australia.
Adaptation of olive (Olea europaea L.) to water-limited environments
Authors: Connor David J.
Published: November 2005

Olive has been widely grown around the Mediterranean Basin for around 5000 years, where productivity and survival of this long-lived evergreen tree in environments of low and variable rainfall depend on physiological characteristics but also on management. The tree exercises effective control of water loss by transpiration and can also withstand intense internal water deficit that in turn increases extraction of water from soil. Critical aspects of management that maintain, albeit limited, transpiration and metabolic activity during hot dry summer months, are directed at both crop and understorey. Strategic decisions are selection of cultivar, tree density, and canopy size, together with surface management as tilled soil or as cover crop of selected species. Tactical adjustments are seen in extra pruning of olives and timing of tillage, or of grazing, mowing, or herbicides to restrict growth and water use of the understorey, especially following dry winters and during dry summers. Survival of olive orchards in low-rainfall climates requires that canopies intercept a small proportion of incident radiation, depending upon rainfall amount, distribution, and soil water storage capacity. Crop water balance models can assist in defining optimum canopy size for productivity and survival. New olive production in the Mediterranean and now extending widely in the ‘New World’, including in Australia, deviates widely from traditional practice. Orchards are planted at higher density, are generally irrigated, and trees are formed to suit mechanical pruning and harvesting. The environmental adaptation and understanding of water relations of olive in traditional systems are of limited applicability to these new production systems. Rather, there are now new emphases on nutrition, irrigation, canopy management, assimilate relationships, and fruiting performance to add to the existing questions of the suitability of cultivars to new environments in terms of productivity and oil quality.
Conservation analysis of large biochemical networks
Authors: Vallabhajosyula Ravishankar Rao , Chickarmane Vijay , Sauro Herbert M.
Published: November 2005

Motivation: Large biochemical networks pose a unique challenge from the point of view of evaluating conservation laws. The computational problem in most cases exceeds the capability of available software tools, often resulting in inaccurate computation of the number and form of conserved cycles. Such errors have profound effects on subsequent calculations, particularly in the evaluation of the Jacobian which is a critical quantity in many other calculations. The goal of this paper is to outline a new algorithm that is computationally efficient and robust at extracting the correct conservation laws for very large biochemical networks.

Results: We show that our algorithm can perform the conservation analysis of large biochemical networks, and can evaluate the correct conserved cycles when compared with other similar software tools. Biochemical simulators such as Jarnac and COPASI are successful at extracting only a subset of the conservation laws that our algorithm can. This is illustrated with examples for some large networks which show the advantages of our method.

Availability: The software is available as part of the latest release of Systems Biology Workbench (SBW version 2.5.0) and can be downloaded from . The software is licensed under the BSD open source license and is freely available at sourceforge.

Contact:  rrao@kgi.edu
Application of latent semantic analysis to protein remote homology detection
Authors: Dong Qi-wen , Wang Xiao-long , Lin Lei
Published: November 2005

Motivation: Remote homology detection between protein sequences is a central problem in computational biology. The discriminative method such as the support vector machine (SVM) is one of the most effective methods. Many of the SVM-based methods focus on finding useful representations of protein sequence, using either explicit feature vector representations or kernel functions. Such representations may suffer from the peaking phenomenon in many machine-learning methods because the features are usually very large and noise data may be introduced. Based on these observations, this research focuses on feature extraction and efficient representation of protein vectors for SVM protein classification.

Results: In this study, a latent semantic analysis (LSA) model, which is an efficient feature extraction technique from natural language processing, has been introduced in protein remote homology detection. Several basic building blocks of protein sequences have been investigated as the ‘words’ of ‘protein sequence language’, including N-grams, patterns and motifs. Each protein sequence is taken as a ‘document’ that is composed of bags-of-word. The word-document matrix is constructed first. The LSA is performed on the matrix to produce the latent semantic representation vectors of protein sequences, leading to noise-removal and smart description of protein sequences. The latent semantic representation vectors are then evaluated by SVM. The method is tested on the SCOP 1.53 database. The results show that the LSA model significantly improves the performance of remote homology detection in comparison with the basic formalisms. Furthermore, the performance of this method is comparable with that of the complex kernel methods such as SVM-LA and better than that of other sequence-based methods such as PSI-BLAST and SVM-pairwise.

Availability: The source codes are freely available at or upon request from the authors.

Contact:  qwdong@insun.hit.edu.cn
Identification of plant microRNA homologs
Authors: Dezulian Tobias , Remmert Michael , Palatnik Javier F. , Weigel Detlef , Huson Daniel H.
Published: November 2005

Summary: MicroRNAs (miRNAs) are a recently discovered class of non-coding RNAs that regulate gene and protein expression in plants and animals. MiRNAs have so far been identified mostly by specific cloning of small RNA molecules, complemented by computational methods. We present a computational identification approach that is able to identify candidate miRNA homologs in any set of sequences, given a query miRNA. The approach is based on a sequence similarity search step followed by a set of structural filters.

Availability: microHARVESTER is offered as a web-service and additionally as source code upon request at

Contact:  dezulian@informatik.uni-tuebingen.de
Elastic Properties of the Ascending Aorta and Left Ventricular Function in Patients with Hypothyroidism
Authors: Özhan Hakan , Yazici Mehmet , Albayrak Sinan , Erbilen Enver , Bulur Serkan , Akdemir Ramazan , Uyan Cihangir
Published: November 2005

Background: We sought to clarify the possible role of elastic properties of the ascending aorta in the development of cardiac disease associated with hypothyroidism (HT). Methods: A total of 37 patients with HT (age: 39.3 ± 8.9 years) and 29 control subjects were studied. Ascending Aortic (Ao) diameter, Ao elastic indexes, strain (AoST), distensibility (AoD), stiffness index (AoSI), and pressure strain modulus were calculated from the echocardiographically derived Ao diameters. Myocardial performance index (MPI), E/A ratio, isovolumetric relaxation time (IVRT), deceleration time (DT) were measured by Doppler echocardiography to assess diastolic LV function. Patients were treated with levothyroxine and followed‐up for 6 months. Thyroid function tests and echocardiographic measurements were repeated at the end of the study. Results: AoD (cm2 dyn−1 10−3) and AoST (%) were significantly lower (3.8 vs. 6.1; P < 0.001, 7.4 vs. 12.6, P < 0.001; respectively), whereas AoSI was higher in HT patients (6.2 vs. 3.3; P < 0.001). After treatment, AoD and AoST were increased (5.7; P < 0.001 and 11.8; P < 0.001; respectively), whereas AoSI was decreased significantly (3.7; P < 0.001). Also, early/late mitral peak velocity ratio (Emax/Amax) was significantly lower in HT patients (1.19 vs 1.34; P < 0.01), whereas MPI was higher (0.52 vs. 0.42; P < 0.001). MPI showed a strong correlation with aortic root indexes [AoST (r =−0.61/P < 0.001); AoD, (r =−0.57/P < 0.002); AoSI, (r = 0.53/P < 0.005)] in the HT group. After 6 months of therapy, MPI significantly decreased P < 0.001) and E/A ratios were normalized (P < 0.001). Conclusions: Ao root functions have an important role on diastolic LV function. Levothyroxine replacement therapy can reverse all of these adverse effects of HT.
Induced inaccessibility and accessibility in the oat powdery mildew system: insights gained from use of metabolic inhibitors and silicon nutrition
Authors: PRATS ELENA , CARVER TIMOTHY L. W. , LYNGKJÆR MICHAEL F. , ROBERTS PETE C. , ZEYEN RICHARD J.
Published: November 2005

Fungal‐induced inaccessibility in oat to Blumeria graminis requires active cell processes. These are reiterative de novo cell processes involved in inherent penetration resistance. Therefore, induced inaccessibility may well involve cellular memory of the initial attack. Phenylpropanoid biosynthesis inhibitors (AOPP and OH‐PAS) and phosphate scavengers (DDG and d‐mannose) strongly suppressed induced inaccessibility, but silicon nutrition had no effect. Induced accessibility was modulated by the presence of fungal haustoria inside cells. Haustoria actively suppress or reprogram infected plant cells toward a constant state of penetration susceptibility. Neither inhibitor treatments nor silicon nutrition affected fungal‐induced accessibility.
National audit of continence care for older people: results of a pilot study*
Authors: Wagg Adrian , Mian Sarah , Lowe Derek , Potter Jonathan , Michael Pearson MD FRCP
Published: November 2005

Introduction and aim  Bladder and bowel problems are common in the elderly and are associated with a considerable morbidity and impact on quality of life. Inequalities in service provision and access to services have been recognized but there has been no systematic approach to measuring the quality of continence care for older people. This study aimed to develop quality standards, to assess the reliability and utility of the resulting audit package and to report on the standards of care provided in primary care, secondary care and care home setting.

Method  Fifteen sites in secondary care, primary care and in long‐term care settings were randomly selected to pilot the audit package. Data collectors completed audit questionnaires relating to the structure [organization] of care, the outcomes of care, and the process of care for 20 subjects with urinary incontinence and 10 subjects with faecal or double incontinence.  

Results  The audit tool was reliable (median kappa score of 0.7). Access to integrated continence services, as defined by Good Practice in Continence Services was inadequate. Eighty‐five per cent of hospitals had no written policy for continence care. There were deficiencies in obtaining information, in carrying out basic and specialist examinations and investigations and in determining the cause of incontinence. There was a high prevalence of catheter use in secondary care settings.

Conclusion  The pilot has indicated significant inadequacies in continence care and demonstrates that in many sites the National Service Framework milestone for integrated continence services has not been met. A national audit of continence care is required to determine the extent of inadequate continence care.
Measuring the perceived impact of facilitation on implementing recommendations from external assessment: lessons from the Dutch visitatie programme for medical specialists
Authors: Lombarts M. J. M. H. (Kiki) , Klazinga N. S. (Niek) , Redekop K (Ken)
Published: November 2005

Objective  To evaluate the impact of facilitation by management consultants on implementing recommendations from external quality assessment (visitatie).

Design  Data collection through a postal survey amongst 205 medical specialists, representing 50 hospital‐based specialist groups in  the  Netherlands. 

Setting  Under the auspices of the specialty societies of surgeons, paediatricians and gynaecologists, 25 groups were offered ∼20 h of management consulting to support the implementation of recommendations for quality improvement and were compared to 25 specialist groups not receiving the support.

Intervention  The Quality Consultation (QC) took a site‐specific multifaceted implementation approach.

Main measures  Self‐reported degree of implementation of recommendations, specialists’ judgement of implementation result and process; experienced obstructing factors in implementing recommendations.

Results  The response rate was 54% (n = 110). The supported specialist groups were more successful in partially or fully implementing the recommendations from external peer assessment: 66.1% vs. 53.8%. The implementation result and process were also rated significantly higher for the supported groups. The supported groups reported significantly less (P < 0.005) obstructing factors; in particular for the barriers ‘expectation of implementation advantages’, ‘acceptance of the recommendations’ and ‘assessed self‐efficacy’. The experienced obstructing factors are strongly related with the degree of implementation (spearman rho 0.57–32.5%).

Conclusions  This study suggests QC is a powerful implementation strategy. It also shows the limitations of merely quantitatively analysing multifaceted strategies: it does not offer any insight into the ‘black box’ of the QC. It is recommended that these limitations are met by also exploring multifaceted strategies qualitatively.