bluuebunny/crossref_metadata_2025 huggingface dataset:
Determining the equation of state of amorphous solids at high pressure using optical microscopy
Authors: Amin Samrat A. , Rissi Erin N. , McKiernan Keri , Yarger Jeffery L.
Published: March 2012

A method to determine the volumetric equation of state of amorphous solids using optical microscopy in a diamond anvil cell is described. The method relies on two- dimensional image acquisition and analysis to quantify changes in the projected image area with compression. The area analysis methods prove to be robust against improper focusing and lighting conditions while providing the accuracy necessary to deduce small area changes, which correspond to small volume changes in an isotropic material. The image capture, area analysis method is used to determine the compression of cubic crystals, yielding results in good agreement with diffraction and volumetric measurements. As a proof of concept, the equation of state of amorphous red phosphorus is measured up to 12 GPa under hydrostatic conditions where the quantified volume change between the red and black phases is approximately ΔV/V0 ≈ 0.05 after a reduction of volume nearing 35% at 8 GPa. A large hysteresis is present during decompression and eventually results in a 15% permanent densification relative to the starting volume, which is attributed to a pressure induced crystallization from red to black phosphorus. The robustness of the technique is also demonstrated by measuring the equation of state of GeSe2 glasses for semi transparent samples and As2O3 in which gold coating is used as a contrasting aid.
Hyperpolarizability of two electron atoms under spherically confined Debye plasma
Authors: Sen Subhrangsu , Mandal Puspajit , Mukherjee Prasanta Kumar
Published: March 2012

Pilot calculations on the hyperpolarizability of He, the first neutral member of the two electron sequence, have been performed under spherical confinement with a view to analyse the effect of pressure on such non linear optical properties. Detailed investigations have also been performed for the first time on the hyperpolarizability due to the effect of screened Coulomb potential obtained from a surrounding Debye plasma environment. Variation perturbation theory within coupled Hartree-Fock scheme has been adopted to estimate the non linear optical properties under such external confinement. For a given plasma coupling strength, the hyperpolarizability value is found to reduce systematically with decrease of radius of confinement, while the same is found to increase continuously with increasing plasma coupling strength determined by gradual enhancement of the screening parameter for a given radius of confinement. Under strong confinement the hyperpolarizability value is found to be negative. The estimated free atom hyperpolarizability is consistent with the existing coupled Hartree-Fock result.
Multiferroic properties in orthorhombic perovskite manganites: Monte Carlo simulation
Authors: Qin M. H. , Tao Y. M. , Dong S. , Zeng M. , Wu S. J. , Zhao H. B. , Gao X. S. , Liu J.-M.
Published: March 2012

In this work, a random field method (based on Mochizuki-Furukawa model) is used to study the effect of the R-site ionic disorder and inhomogeneity on the multiferroic behavior in orthorhombic manganites. It is shown that both the R-site ionic disorder and inhomogeneity can drive the reorientation of the plane in which cycloidal spin order takes place and actually lead to the flop of the spins from the ab-plane to the bc-plane. The simulated results can be understood as the consequence of the competition between exchange interactions and spin-orbit coupling.
A study for the static properties of symmetric linear multiblock copolymers under poor solvent conditions
Authors: Theodorakis Panagiotis E. , Fytas Nikolaos G.
Published: March 2012

We use a standard bead-spring model and molecular dynamics simulations to study the static properties of symmetric linear multiblock copolymer chains and their blocks under poor solvent conditions in a dilute solution from the regime close to theta conditions, where the chains adopt a coil-like formation, to the poorer solvent regime where the chains collapse obtaining a globular formation and phase separation between the blocks occurs. We choose interaction parameters as is done for a standard model, i.e., the Lennard-Jones fluid and we consider symmetric chains, i.e., the multiblock copolymer consists of an even number n of alternating chemically different A and B blocks of the same length NA = NB = N. We show how usual static properties of the individual blocks and the whole multiblock chain can reflect the phase behavior of such macromolecules. Also, how parameters, such as the number of blocks n can affect properties of the individual blocks, when chains are in a poor solvent for a certain range of n. A detailed discussion of the static properties of these symmetric multiblock copolymers is also given. Our results in combination with recent simulation results on the behavior of multiblock copolymer chains provide a complete picture for the behavior of these macromolecules under poor solvent conditions, at least for this most symmetrical case. Due to the standard choice of our parameters, our system can be used as a benchmark for related models, which aim at capturing the basic aspects of the behavior of various biological systems.
Surface thermocouples for measurement of pulsed heat flux in the divertor of the Alcator C-Mod tokamak
Authors: Brunner D. , LaBombard B.
Published: March 2012

A novel set of thermocouple sensors has been developed to measure heat fluxes arriving at divertor surfaces in the Alcator C-Mod tokamak, a magnetic confinement fusion experiment. These sensors operate in direct contact with the divertor plasma, which deposits heat fluxes in excess of ∼10 MW/m2 over an ∼1 s pulse. Thermoelectric EMF signals are produced across a non-standard bimetallic junction: a 50 μm thick 74% tungsten-26% rhenium ribbon embedded in a 6.35 mm diameter molybdenum cylinder. The unique coaxial geometry of the sensor combined with its single-point electrical ground contact minimizes interference from the plasma/magnetic environment. Incident heat fluxes are inferred from surface temperature evolution via a 1D thermal heat transport model. For an incident heat flux of 10 MW/m2, surface temperatures rise ∼1000 °C/s, corresponding to a heat flux flowing along the local magnetic field of ∼200 MW/m2. Separate calorimeter sensors are used to independently confirm the derived heat fluxes by comparing total energies deposited during a plasma pulse. Langmuir probes in close proximity to the surface thermocouples are used to test plasma-sheath heat transmission theory and to identify potential sources of discrepancies among physical models.
Elimination of spurious solutions from k·p theory with Fourier transform technique and Burt-Foreman operator ordering
Authors: Zhao Qiuji , Mei Ting , Zhang Dao Hua
Published: March 2012

To eliminate spurious solutions in the multiple-band k·p theory, we developed the Fourier transform-based k·p approach through combining the Fourier transform technique with Burt-Foreman operator ordering. The performance is perfect for the six-band k·p calculation, and the spurious solutions in the conduction band met in the eight-band calculation can also be easily screened away in the inborn cut-off step in FTM, i.e., choosing a proper order of Fourier truncation. Truncating high-order terms of Fourier coefficients of the envelope function prevents the occurrence of a wild-spreading spectrum of the Fourier expansion coefficients, which can be taken as the signature of spurious solutions.
Infrared spectroscopy and modeling of co-crystalline CO2·C2H2 aerosol particles. I. The formation and decomposition of co-crystalline CO2·C2H2 aerosol particles
Authors: Preston Thomas C. , Wang Chia C. , Signorell Ruth
Published: March 2012

Aerosol particles composed of co-crystalline CO2·C2H2 were generated in a bath gas cooling cell at cryogenic temperatures and investigated with infrared spectroscopy between 600 and 4000 cm−1. Similar to results obtained for thin films of the co-crystal [T. E. Gough and T. E. Rowat, J. Chem. Phys. 109, 6809 (1998)], this phase was found to be metastable and decomposed into pure CO2 and pure C2H2. These decomposed aerosols were characterized through (i) a comparison to experimentally prepared aerosols of mixed CO2 and C2H2 of known architectures and (ii) the modeling of infrared spectra. A likely architecture after decomposition are C2H2-CO2 core-shell particles with a disk-like shape. The co-crystalline CO2·C2H2 aerosols prior to decomposition are modeled and analyzed in detail in the subsequent paper (Part II).
Magneto-Rayleigh-Taylor experiments on a MegaAmpere linear transformer driver
Authors: Zier J. C. , Gilgenbach R. M. , Chalenski D. A. , Lau Y. Y. , French D. M. , Gomez M. R. , Patel S. G. , Rittersdorf I. M. , Steiner A. M. , Weis M. , Zhang P. , Mazarakis M. , Cuneo M. E. , Lopez M.
Published: March 2012

Experiments have been performed on a nominal 100 ns rise time, MegaAmpere (MA)-class linear transformer driver to explore the magneto-Rayleigh-Taylor (MRT) instability in planar geometry. Plasma loads consisted of ablated 400 nm-thick, 1 cm-wide aluminum foils located between two parallel-plate return-current electrodes. Plasma acceleration was adjusted by offsetting the position of the foil (cathode) between the anode plates. Diagnostics included double-pulse, sub-ns laser shadowgraphy, and machine current B-dot loops. Experimental growth rates for MRT on both sides of the ablated aluminum plasma slab were comparable for centered-foils. The MRT growth rate was fastest (98 ns e-folding time) for the foil-offset case where there was a larger magnetic field to accelerate the plasma. Other cases showed slower growth rates with e-folding times of about ∼106 ns. An interpretation of the experimental data in terms of an analytic MRT model is attempted.
Nonplanar dust-ion acoustic Gardner solitons in a dusty plasma with q-nonextensive electron velocity distribution
Authors: Kumar Ghosh Deb , Chatterjee Prasanta , Narayan Ghosh Uday
Published: March 2012

The basic features of planar and nonplanar time-dependent dust-ion acoustic Gardner solitary waves have been studied in an unmagnetized dusty plasma system consisting of positively and negatively charged dust, Boltzmann distributed ions and nonextensive q-distributed electrons. The modified Gardner equation is derived by employing the reductive perturbation technique, which is beyond the Korteweg-de Vries (KdV) limit (corresponding to the vanishing of nonlinear coefficient of the KdV equation). It has been observed that the nonextensive q-distribution of electrons has a significant effect on the MG equation and also plays an important role beyond the KdV limit.
Dispersion and damping of potential surface waves in a degenerate plasma
Authors: Tyshetskiy Yu. , Williamson D. J. , Kompaneets R. , Vladimirov S. V.
Published: March 2012

Potential (electrostatic) surface waves (SWs) in a semi-bounded plasma with degenerate electrons are studied using the quasi-classical mean-field kinetic model. The SW spectrum and the collisionless damping rate are obtained numerically for a wide range of wavelengths. In the limit of long wavelengths, the SW frequency ω approaches the cold-plasma limit ω=ωp/2 with ωp being the plasma frequency, while at short wavelengths, the SW spectrum asymptotically approaches the spectrum of zero-sound mode propagating along the boundary. It is shown that the surface waves in this system remain weakly damped at all wavelengths (in contrast to strongly damped surface waves in Maxwellian electron plasmas), and the damping rate nonmonotonically depends on the wavelength, with the maximum (yet small) damping occurring for surface waves with wavelength of ≈5πλF, where λF is the Thomas-Fermi length. The applicability of the used approximations and of the obtained results is discussed in detail.
Study of high frequency parallel propagating modes in a weakly magnetized relativistic degenerate electron plasma
Authors: Abbas Gohar , Bashir M. F. , Ali Muddasir , Murtaza G.
Published: March 2012

Using the Vlasov-Maxwell’s model, the generalized dispersion relations for parallel propagating electromagnetic modes (R- and L-waves) and electrostatic mode (Langmuir wave) for weakly magnetized relativistic degenerate plasma are derived. The propagation characteristics of these modes are analyzed both analytically and graphically in order to highlight the relativistic and the ambient magnetic field effects in different degenerate plasma environments. Furthermore, the analytical expressions of these modes are extracted for the limiting cases, i.e., non-relativistic (pF/moc≪1) and ultra-relativistic (pF/moc≫1). It is noted that the relativistic effects shift the cut-off point towards the lower value of frequency and resultantly broaden the propagation domain. Moreover, the cut-off point of R-wave/L-wave move towards the higher/lower frequency as the strength of ambient magnetic field is increased. The shifting of frequency due to the ambient magnetic field becomes more prominent in the non-relativistic regime than in the highly relativistic one because the relativistic effect suppresses the contribution of the ambient magnetic field.
Magnetized electronegative plasma presheath-sheath containing two positive ion species
Authors: Aslaninejad Morteza , Yasserian Kiomars
Published: March 2012

The structure of the presheath-sheath for a magnetized electronegative discharge in the presence of two species of positive ions is investigated. In the absence of collision, for different magnetic field strength, the densities of the charges and the profiles of the positive ions velocities and electric potentials are obtained. It is shown that a slightly magnetized uniform structure discharge converts to a stratified multiple layer oscillatory structure for an intermediate magnetic field. But, in contrast to a single positive ion species up to high values of magnetic field, oscillatory behavior continues to exist. We also observe oscillations in the profile of electron densities which are hidden in the single positive ion species case. A competition between the two positive ions species exists which depends on their different masses. The density profiles of the species follow each other along the sheath and the heavier component always occupies higher density values. The influence of the elastic collisions between positive ions and neutrals on the structure of a magnetized electronegative discharge is also investigated. Finally, the positive ion flux at the plasma-sheath edge for each species is obtained as a function of magnetic field strength, for different values of the collision frequency.
Vesicle tumbling inhibited by inertia
Authors: Laadhari Aymen , Saramito Pierre , Misbah Chaouqi
Published: March 2012

Vesicles under flow constitute a model system for the study of red blood cells (RBCs) dynamics and blood rheology. In the blood circulatory system the Reynolds number (at the scale of the RBC) is not always small enough for the Stokes limit to be valid. We develop a numerical method in two dimensions based on the level set approach and solve the fluid/membrane coupling by using an adaptive finite element technique. We find that a Reynolds number of order one can destroy completely the vesicle tumbling motion obtained in the Stokes regime. We analyze in details this phenomenon and discuss some of the far reaching consequences. We suggest experimental tests on vesicles.
Rotational excitation of H2O by para-H2 from an adiabatically reduced dimensional potential
Authors: Scribano Yohann , Faure Alexandre , Lauvergnat David
Published: March 2012

Cross sections and rate coefficients for low lying rotational transitions in H2O colliding with para-hydrogen pH2 are computed using an adiabatic approximation which reduces the dimensional dynamics from a 5D to a 3D problem. Calculations have been performed at the close-coupling level using the recent potential of Valiron et al. [J. Chem. Phys. 129, 134306 (2008)10.1063/1.2988314]. A good agreement is found between the reduced adiabatic calculations and the 5D exact calculations, with an impressive time saving and memory gain. This adiabatic reduction of dimensionality seems very promising for scattering studies involving the excitation of a heavy target molecule by a light molecular projectile.
Structure and magnetic properties of Y1−xLuxFeO3 (0 ≤ x ≤ 1) ceramics
Authors: Yuan Xue-ping , Tang Yan-kun , Sun Yue , Xu Ming-xiang
Published: March 2012

Polycrystalline Lu-doped YFeO3 samples with perovskite structure were synthesized by solid-state reaction. Powder X-ray diffraction, scanning electron microscopy, and energy dispersive X-ray analysis manifest the high quality of the samples. Room temperature 57Fe Mössbauer spectra indicate that only the Fe3+ exists in the samples, which excludes the formation of multiple valence of Fe. The large effective magnetic moments of Fe3+ obtained from the temperature dependence of magnetization data can be explained in terms of the formation of ferromagnetic clusters. Field-dependent magnetization reveals that all the samples show weak ferromagnetic property due to the small canting of the Fe3+ moments. The field-induced spin-reorientation was detected on YFeO3 and was gradually suppressed by Lu3+ doping. Polarization hysteresis loops of Y1−xLuxFeO3 (0 ≤ x ≤ 1) were observed at room temperature. Our results suggest that the multiferroic properties may exist in the Y1−xLuxFeO3 (0 ≤ x ≤ 1) ceramics.
Parabolic temperature profile and second-order temperature jump of a slightly rarefied gas in an unsteady two-surface problem
Authors: Takata Shigeru , Aoki Kazuo , Hattori Masanari , Hadjiconstantinou Nicolas G.
Published: March 2012

The behavior of a slightly rarefied monatomic gas between two parallel plates whose temperature grows slowly and linearly in time is investigated on the basis of the kinetic theory of gases. This problem is shown to be equivalent to a boundary-value problem of the steady linearized Boltzmann equation describing a rarefied gas subject to constant volumetric heating. The latter has been recently studied by Radtke, Hadjiconstantinou, Takata, and Aoki (RHTA) as a means of extracting the second-order temperature jump coefficient. This correspondence between the two problems gives a natural interpretation to the volumetric heating source and explains why the second-order temperature jump observed by RHTA is not covered by the general theory of slip flow for steady problems. A systematic asymptotic analysis of the time-dependent problem for small Knudsen numbers is carried out and the complete fluid-dynamic description, as well as the related half-space problems that determine the structure of the Knudsen layer and the coefficients of temperature jump, are obtained. Finally, a numerical solution is presented for both the Bhatnagar-Gross-Krook model and hard-sphere molecules. The jump coefficient is also calculated by the use of a symmetry relation; excellent agreement is found with the result of the numerical computation. The asymptotic solution and associated second-order jump coefficient obtained in the present paper agree well with the results by RHTA that are obtained by a low variance stochastic method.
Improved AC conductance and Gray-Brown methods to characterize fast and slow traps in Ge metal–oxide–semiconductor capacitors
Authors: Sun Xiao , Merckling Clement , Brammertz Guy , Lin Dennis , Dekoster Johan , Cui Sharon , Ma T. P.
Published: March 2012

We use an improved AC conductance method and a modified Gray-Brown method to study fast interface traps and slow border traps in Ge-based MOS capacitors. The combined methods provide the corrected Fermi energy level (E) versus gate voltage (Vg) relationship, even in samples with high densities of traps that cause significant C-V distortion, the energy distribution of interface traps, their capture cross sections (σ), as well as slow border traps. A wide range of σ’s in p-type Ge is found, indicating that there is more than one type of interface trap near the Ge valence band edge. In contrast, a constant σ near the Ge conduction band edge is observed in n-type Ge. XPS results indicate that Ge suboxides near the interface are accountable for the detected slow border traps.
Contacting nanowires and nanotubes with atomic precision for electronic transport
Authors: Qin Shengyong , Hellstrom Sondra , Bao Zhenan , Boyanov Boyan , Li An-Ping
Published: March 2012

Making contacts to nanostructures with atomic precision is an important process in the bottom-up fabrication and characterization of electronic nanodevices. Existing contacting techniques use top-down lithography and chemical etching, but lack atomic precision and introduce the possibility of contamination. Here, we report that a field-induced emission process can be used to make local contacts onto individual nanowires and nanotubes with atomic spatial precision. The gold nano-islands are deposited onto nanostructures precisely by using a scanning tunneling microscope tip, which provides a clean and controllable method to ensure both electrically conductive and mechanically reliable contacts. To demonstrate the wide applicability of the technique, nano-contacts are fabricated on silicide atomic wires, carbon nanotubes, and copper nanowires. The electrical transport measurements are performed in situ by utilizing the nanocontacts to bridge the nanostructures to the transport probes.
Control of coherent acoustic phonon generation with external bias in InGaN/GaN multiple quantum wells
Authors: Kim C. S. , Kim J. H. , Jeong H. , Jho Y. D. , Kwon H. K. , Lee H. S. , Park J. S. , Song K. , Kim S. H. , Kim Y. J. , Lee D. , Yee K. J.
Published: March 2012

Control of acoustic phonon generation with external bias is demonstrated for an InGaN light-emitting diode by performing femtosecond pump–probe measurements. The evolution of both the carrier dynamics and the acoustic phonon strength with an external bias reveals that the acoustic wave is generated during the carrier sweeping process of the depletion field, where electric field screening accompanies stress of the lattice for a piezoelectric material.
Frequency-doubled photons can measure current density
Authors: Blau Steven K.
Published: March 2012

The possibility, anticipated theoretically 16 years ago, could be applied as a semiconductor diagnostic.
Criegee chemistry is captured
Authors: Miller Johanna L.
Published: March 2012

An elusive but atmospherically important molecule yields to kinetic measurement for the first time.
A blind quantum computer makes its laboratory debut
Authors: Miller Johanna L.
Published: March 2012

Quantum computing promises great efficiency advantages over classical computing. Quantum communication promises tamper-proof security. Combine them, and you get blind quantum computing.
Predicting and managing extreme weather events
Authors: Lubchenco Jane , Karl Thomas R.
Published: March 2012

Earth’s climate is warming, and destructive weather is growing more prevalent. Coping with the changes will require collaborative science, forward-thinking policy, and an informed public.
Water in Earth’s mantle
Authors: Hirschmann Marc , Kohlstedt David
Published: March 2012

In the form of ionic impurities in rocks and minerals, water lubricates tectonic plates, influences rock viscosities and melting processes, and slows down seismic waves.
Finding genes for economically important traits: Brahman cattle puberty
Authors: Fortes M. R. S. , Lehnert S. A. , Bolormaa S. , Reich C. , Fordyce G. , Corbet N. J. , Whan V. , Hawken R. J. , Reverter A.
Published: March 2012

Age at puberty is an important component of reproductive performance in beef cattle production systems. Brahman cattle are typically late-pubertal relative to Bos taurus cattle and so it is of economic relevance to select for early age at puberty. To assist selection and elucidate the genes underlying puberty, we performed a genome-wide association study (GWAS) using the BovineSNP50 chip (~54 000 polymorphisms) in Brahman bulls (n = 1105) and heifers (n = 843) and where the heifers were previously analysed in a different study. In a new attempt to generate unbiased estimates of single-nucleotide polymorphism (SNP) effects and proportion of variance explained by each SNP, the available data were halved on the basis of year and month of birth into a calibration and validation set. The traits that defined age at puberty were, in heifers, the age at which the first corpus luteum was detected (AGECL, h2 = 0.56 ± 0.11) and in bulls, the age at a scrotal circumference of 26 cm (AGE26, h2 = 0.78 ± 0.10). At puberty, heifers were on average older (751 ± 142 days) than bulls (555 ± 101 days), but AGECL and AGE26 were genetically correlated (r = 0.20 ± 0.10). There were 134 SNPs associated with AGECL and 146 SNPs associated with AGE26 (P < 0.0001). From these SNPs, 32 (~22%) were associated (P < 0.0001) with both traits. These top 32 SNPs were all located on Chromosome BTA 14, between 21.95 Mb and 28.4 Mb. These results suggest that the genes located in that region of BTA 14 play a role in pubertal development in Brahman cattle. There are many annotated genes underlying this region of BTA 14 and these are the subject of current research. Further, we identified a region on Chromosome X where markers were associated (P < 1.00E–8) with AGE26, but not with AGECL. Information about specific genes and markers add value to our understanding of puberty and potentially contribute to genomic selection. Therefore, identifying these genes contributing to genetic variation in AGECL and AGE26 can assist with the selection for early onset of puberty.
A review of how dairy farmers can use and profit from genomic technologies
Authors: Pryce Jennie , Hayes Ben
Published: March 2012

New genomic technologies can help farmers to (1) achieve higher annual rates of genetic gain through using genomically tested bulls in their herds, (2) select for ‘difficult’ to measure traits, such as feed conversion efficiency, methane emissions and energy balance, (3) select the best heifers to become herd replacements, (4) sell pedigree heifers at a premium, (5) use mating plans to optimise rates of genetic gain while controlling inbreeding, (6) achieve certainty in parentage of individual cows and (7) avoid genetic defects that could arise from mating cows to bulls that are known carriers of genetic diseases that are the result of a single lethal mutation. The first use does not require genotyping females and could approximately double the net income per cow that arises due to genetic improvement, mainly through a reduction in generation interval. On the basis of current rates of genetic gain, the net profit from using genotyped bulls could be worth AU$20/cow per year and is permanent and cumulative. One of the most powerful uses of genomic selection is to select for economically important, yet difficult- or expensive-to-measure traits, such as residual feed intake or energy balance. Provided the accuracy of genomic breeding values is high enough (i.e. correlation between the true and estimated breeding values), these traits lend themselves well to genomic selection. For selecting replacement heifers, if genotyping costs are AU$50/cow, the net profit of genotyping 40 heifers to select the top 20 as replacements (per 100 cows) would be worth approximately AU$41 per cow. However, using parent average estimated breeding-value information is free and can already be used to select replacement heifers. So, genotyping costs would need to be very low to be more profitable than selecting on parent average estimated breeding value. However, extra value from genotyping can also be captured by using other strategies. For example, mating plans that use genomic relationships rather than pedigree relationships to capture inbreeding are superior in terms of reducing progeny inbreeding at a desired level of genetic gain, although pedigree does an adequate job. So, again, the benefits of genotyping are small (<AU$10). Ascertainment of pedigree is an additional use of genotyping and is potentially worth ~AU$30 per cow. Avoidance of genetic diseases and selling of pedigree heifers have a value that should be estimated case-by-case. Because genotyping costs continue to fall, it may become increasingly popular to capture the extra value from genotyping females.
Effect of replacing barley with corn or sorghum grain on rumen fermentation characteristics and performance of Iranian Baluchi lamb fed high concentrate rations
Authors: Yahaghi M. , Liang J. B. , Balcells J. , Valizadeh R. , Alimon A. R. , Ho Y. W.
Published: March 2012

The present study, conducted in Iran, was aimed to evaluate the effects of partial substitution of barley with corn or sorghum (slowly fermenting grains) on in situ dry matter (DM) and starch degradability and in vivo digestion characteristics and performance in finishing Iranian Baluchi lambs. In the first experiment, samples of ground barley (B), corn (C), sorghum (S) and their combinations [%: 70 barley : 30 corn (LC), 70 barley : 30 sorghum (LS), 30 barley : 70 corn (HC) and 30 barley : 70 sorghum (HS)] were incubated in nylon bags in rumen of three fistulated Holstein steers. Effective degradability (ED) for DM and starch were different (P < 0.05) among treatments. In both cases, ED was higher (P < 0.05) for B than that for C, S, HC and HS. Results of the present study confirmed previous reports that ruminal degradability of barley is higher than that of corn and sorghum, and further suggested that there may be benefits in replacing barley with ~70% of corn or sorghum. In Experiment 2, 30 Iranian Baluchi male lambs weaned at 65 days of age (BW 32 ± 2.3 kg) were divided into five equal weight groups (6 animals per group) in a complete randomised design. Lambs received a mixed diet in the form of total mixed rations (TMR), consisting of 32.5% alfalfa hay [89% DM, 43% natural detergent fibre (NDF) and 16% crude protein (CP) in diet DM basis] and 67.5% of the respective concentrates. The five iso-caloric (10.73 MJ ME/kg) and iso-nitrogenous (14% CP/kg DM) concentrates with different sources of starch used in the study were (1) barley, as the control cereal source for starch, and in the other treatments barley substituted with (2) 30% corn (LC), (3) 30% sorghum (LS), (4) 70% corn (HC) and (5) 70% sorghum (HS). Lambs in HC and HS diets recorded increases of 20 and 50 g/day in average daily gain, respectively, compared with lambs in B. Substitution of B with 70% C and S significantly (P < 0.01) improved ruminal pH and, presumably, resulted in higher starch outflow for post-ruminal digestion, as reflected by a higher blood glucose concentration, particularly for lambs in the HS diet. Results of the present study reaffirmed the advantages of feeding a mixture of grains with differing fermentation rates and, as previously reported, also suggested that the inclusion rate of slowly degradable grains should be ~70% so as to enhance animal performance.
Incidence of subclinical toxicity in goats and dairy cows consuming leucaena (Leucaena leucocephala) in Thailand
Authors: Phaikaew C. , Suksaran W. , Ted-arsen J. , Nakamanee G. , Saichuer A. , Seejundee S. , Kotprom N. , Shelton H. M.
Published: March 2012

A survey of the leucaena toxicity status in four major goat-producing provinces of Thailand where leucaena is fed as the principal dietary component was conducted. Three adjacent dairy farms in one province where leucaena silage was being fed were also sampled. Urine samples were collected from 63 animals on six goat farms and from 32 cows on three dairy farms. Samples were acidified, cleaned and analysed by high performance liquid chromatography for 3,4-DHP and 2,3-DHP concentrations, using a modified procedure developed at the University of Queensland. Total DHP concentrations varied from 375 to 3357 μg/mL on goat farms, and from 142 to 182 μg/mL on dairy farms. These concentrations are indicative of subclinical toxicity that might cause reduced feed intake and productivity. The impact of high DHP on productivity needs to be further studied because leucaena is a readily available source of high-protein forage for ruminant industries in Thailand.
Grapevine varieties exhibiting differences in stomatal response to water deficit
Authors: Costa Joaquim M. , Ortuño Maria F. , Lopes Carlos M. , Chaves Maria M.
Published: March 2012

Knowledge on variety traits and physiological responses to stress is still scarce in Vitis vinifera L., limiting the optimisation of irrigation and breeding for high water use efficiency. We have characterised five grapevine varieties using thermal imaging, leaf gas exchange, leaf morphology and carbon isotope composition. Plants of the varieties Aragonez, Trincadeira, Cabernet Sauvignon, Syrah and Touriga Nacional were grown in field conditions. Two experiments were performed. In Experiment I (2006), vines of Aragonez and Trincadeira were either well irrigated (WI, 80% ETc), non-irrigated but rain fed (NI) or subjected to regulated deficit irrigation (RDI, 40% ETc) and studied along the summer season. In Experiment II (2006 and 2007), vines of the five varieties were subjected to RDI (30–40% ETc) and studied at veraison. In Experiment I, leaf temperature (Tleaf) correlated negatively with stomatal conductance (gs) and leaf water potential (Ψpd). The inverse relationship between gs and Tleaf was highly significant in the afternoon. In Experiment II, the different genotypes showed different Tleaf for similar Ψpd. Stomatal density did not correlate with gs suggesting that varieties have different stomatal control. Our results show that combined measurements of canopy temperature and Ψpd can aid in better understanding of stomatal regulation in different grapevine varieties. Such variation in stomatal regulation should be taken into account in determining irrigation strategies.
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily
Authors: Lukk Tiit , Sakai Ayano , Kalyanaraman Chakrapani , Brown Shoshana D. , Imker Heidi J. , Song Ling , Fedorov Alexander A. , Fedorov Elena V. , Toro Rafael , Hillerich Brandan , Seidel Ronald , Patskovsky Yury , Vetting Matthew W. , Nair Satish K. , Babbitt Patricia C. , Almo Steven C. , Gerlt John A. , Jacobson Matthew P.
Published: March 2012

The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in
Eschericiha coli
and
Bacillus subtilis
, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (
i
) a new group of presumed Ala-Glu epimerases; (
ii
) several enzymes with specificity for hydrophobic dipeptides, including one from
Cytophaga hutchinsonii
that epimerizes D-Ala-D-Ala; and (
iii
) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion.
Isotope composition and volume of Earth’s early oceans
Authors: Pope Emily C. , Bird Dennis K. , Rosing Minik T.
Published: March 2012

Oxygen and hydrogen isotope compositions of Earth’s seawater are controlled by volatile fluxes among mantle, lithospheric (oceanic and continental crust), and atmospheric reservoirs. Throughout geologic time the oxygen mass budget was likely conserved within these Earth system reservoirs, but hydrogen’s was not, as it can escape to space. Isotopic properties of serpentine from the approximately 3.8 Ga Isua Supracrustal Belt in West Greenland are used to characterize hydrogen and oxygen isotope compositions of ancient seawater. Archaean oceans were depleted in deuterium [expressed as
δ
D relative to Vienna standard mean ocean water (VSMOW)] by at most 25 ± 5‰, but oxygen isotope ratios were comparable to modern oceans. Mass balance of the global hydrogen budget constrains the contribution of continental growth and planetary hydrogen loss to the secular evolution of hydrogen isotope ratios in Earth’s oceans. Our calculations predict that the oceans of early Earth were up to 26% more voluminous, and atmospheric CH
4
and CO
2
concentrations determined from limits on hydrogen escape to space are consistent with clement conditions on Archaean Earth.
Chemokine receptor CXCR3 agonist prevents human T-cell migration in a humanized model of arthritic inflammation
Authors: O'Boyle Graeme , Fox Christopher R. J. , Walden Hannah R. , Willet Joseph D. P. , Mavin Emily R. , Hine Dominic W. , Palmer Jeremy M. , Barker Catriona E. , Lamb Christopher A. , Ali Simi , Kirby John A.
Published: March 2012

The recruitment of T lymphocytes during diseases such as rheumatoid arthritis is regulated by stimulation of the chemokine receptors expressed by these cells. This study was designed to assess the potential of a CXCR3-specific small-molecule agonist to inhibit the migration of activated human T cells toward multiple chemokines. Further experiments defined the molecular mechanism for this anti-inflammatory activity. Analysis in vitro demonstrated agonist induced internalization of both CXCR3 and other chemokine receptors coexpressed by CXCR3
+
T cells. Unlike chemokine receptor-specific antagonists, the CXCR3 agonist inhibited migration of activated T cells toward the chemokine mixture in synovial fluid from patients with active rheumatoid arthritis. A humanized mouse air-pouch model showed that intravenous treatment with the CXCR3 agonist prevented inflammatory migration of activated human T cells toward this synovial fluid. A potential mechanism for this action was defined by demonstration that the CXCR3 agonist induces receptor cross-phosphorylation within CXCR3-CCR5 heterodimers on the surface of activated T cells. This study shows that generalized chemokine receptor desensitization can be induced by specific stimulation of a single chemokine receptor on the surface of activated human T cells. A humanized mouse model was used to demonstrate that this receptor desensitization inhibits the inflammatory response that is normally produced by the chemokines present in synovial fluid from patients with active rheumatoid arthritis.
On a fundamental structure of gene networks in living cells
Authors: Kravchenko-Balasha Nataly , Levitzki Alexander , Goldstein Andrew , Rotter Varda , Gross A. , Remacle F. , Levine R. D.
Published: March 2012

Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like transcripts vary greatly, even among tumors of the same type from different individuals. Two distinguishable classes could be identified within the hardware-like component: those transcripts that are highly expressed and stable and an adaptable subset with lower expression that respond to external stimuli. Importantly, we demonstrate that this structure is conserved across organisms. Deletions of transcripts from the highly stable core are predicted to result in cell mortality. The approach provides a conceptual thermodynamic-like framework for the analysis of gene-expression levels and networks and their variations in diseased cells.
Fish Species of Greatest Conservation Need in Wadeable Iowa Streams: Current Status and Effectiveness of Aquatic Gap Program Distribution Models
Authors: Sindt Anthony R. , Pierce Clay L. , Quist Michael C.
Published: March 2012

Effective conservation of fish species of greatest conservation need (SGCN) requires an understanding of species–habitat relationships and distributional trends. Thus, modeling the distribution of fish species across large spatial scales may be a valuable tool for conservation planning. Our goals were to evaluate the status of 10 fish SGCN in wadeable Iowa streams and to test the effectiveness of Iowa Aquatic Gap Analysis Project (IAGAP) species distribution models. We sampled fish assemblages from 86 wadeable stream segments in the Mississippi River drainage of Iowa during 2009 and 2010 to provide contemporary, independent fish species presence–absence data. The frequencies of occurrence in stream segments where species were historically documented varied from 0.0% for redfin shiner Lythrurus umbratilis to 100.0% for American brook lamprey Lampetra appendix, with a mean of 53.0%, suggesting that the status of Iowa fish SGCN is highly variable. Cohen's kappa values and other model performance measures were calculated by comparing field-collected presence–absence data with IAGAP model–predicted presences and absences for 12 fish SGCN. Kappa values varied from 0.00 to 0.50, with a mean of 0.15. The models only predicted the occurrences of banded darter Etheostoma zonale, southern redbelly dace Phoxinus erythrogaster, and longnose dace Rhinichthys cataractae more accurately than would be expected by chance. Overall, the accuracy of the twelve models was low, with a mean correct classification rate of 58.3%. Poor model performance probably reflects the difficulties associated with modeling the distribution of rare species and the inability of the large-scale habitat variables used in IAGAP models to explain the variation in fish species occurrences. Our results highlight the importance of quantifying the confidence in species distribution model predictions with an independent data set and the need for long-term monitoring to better understand the distributional trends and habitat associations of fish SGCN.

Received April 16, 2011; accepted November 19, 2011
Highly ordered nanoscale surface ripples produced by ion bombardment of binary compounds
Authors: Motta Francis C , Shipman Patrick D , Bradley R Mark
Published: March 2012

Nanoscale surface ripples generated by oblique-incidence ion bombardment of a solid are generally full of defects, and this has prevented the widespread adoption of ion bombardment as a nanofabrication tool. We advance a theory that predicts that remarkably defect-free ripples can be produced by ion bombardment of a binary material if the ion species, energy and angle of incidence are appropriately chosen. This high degree of order results from the coupling between the surface height and composition, and cannot be achieved by bombarding an elemental material.
Pump–probe photothermal spectroscopy using quantum cascade lasers
Authors: Farahi R H , Passian A , Tetard L , Thundat T
Published: March 2012

Obtaining compositional information for objects from a distance remains a major challenge in chemical and biological sensing. Capitalizing on mid-infrared (IR) excitation of molecules by using quantum cascade lasers (QCLs) and invoking a pump–probe technique, we present a variation of the photothermal process that can provide spectral fingerprints of substances from a variable standoff distance. We have evaluated the modal variations of the QCL beam that must be taken into account when applying QCLs for photothermal measurements. The results compare well with spectra obtained from conventional IR spectroscopy. Guided by the results, the potential of the measurements to be extended such that each point within a target region may be spectrally interrogated to form a hyperspectral image is discussed.
Nanoscale stoichiometric modifications and surface charge patterning of La1.975Sr0.025CuO4+δ crystals with a biased atomic force microscope tip
Authors: Strojnik M , Strle J , Jenko M , Mihailovic D
Published: March 2012

The application of a positive or negative local bias to the surface of La1.975Sr0.025CuO4+δ (LSCO) crystal by a conducting atomic force microscope tip results in accumulation of a (positive or negative, respectively) metastable charge on the surface. The surface charge initially shows diffusive dynamics with a timescale of hours, but thereafter it is shown to be stable for months. The charged regions are found by Auger electron spectroscopy to have a different stoichiometry from the surrounding material. Apart from fundamental implications for the heterostructure device construction, such surface charge manipulation could lead to AFM nanopatterning of superconducting nanoscale devices and applications in memories.
Intersection multiplicity on blow-ups
Authors: Dutta S.
Published: March 2012

A conjecture on vanishing and non-negativity of intersection multiplicity on the blow-up of a regular local ring at its closed point has been proposed. Proofs of vanishing, several special cases of non-negativity and a sufficient condition for non-negativity of this conjecture are described. The topic on intersection multiplicity on vector bundles is also addressed.
1-(2-Hydroxyethyl)pyrrole-2,5-dione
Authors: Tan Xue-Jie , Du Ting-Wen , Xing Dian-Xiang , Liu Yun
Published: March 2012

The asymmetric unit of the title compound, C6H7NO3, contains two molecules (AandB) related by a non-crystallographic twofold pseudo-axis. The molecules are joined in the (AABB)nmanner by O—H...O hydrogen bonds between their hydroxy groups, thus formingC(2) chains along thea-axis direction. Neighboring molecules of the same kind (AandA, orBandB) are related by inversion centers, so that all hydroxy H atoms are disordered other two sets of sites with half occupancies (superimposed O—H...O and O...H—O fragments). The molecules are further linked by C—H...O interactions, which can be considered to be weak hydrogen bonds.
(Carbonato-κ2O,O′)bis(5,5′-dimethyl-2,2′-bipyridyl-κ2N,N′)cobalt(III) bromide trihydrate
Authors: Arun Kumar Kannan , Meera Parthsarathi , Amutha Selvi Madhavan , Dayalan Arunachalam
Published: March 2012

In the title complex, [Co(CO3)(C12H12N2)2]Br·3H2O, the CoIIIcation has a distorted octahedral coordination environment. It is chelated by four N atoms of two different 5,5′-dimethyl-2,2′-bipyridyl (dmbpy) ligands in axial and equatorial positions, and by two O atoms of a carbonate anion completing the equatorial positions. Although the water molecules are disordered and their H atoms were not located, there are typical O...O distances between 2.8 and 3.0 Å, indicating O—H...O hydrogen bonding. The crystal packing is consolidated by C—H...O and C—H...Br hydrogen bonds, as well as π–π stacking interactions between adjacent pyridine rings of the dmbpy ligands, with centroid–centroid distances of 3.694 (3) and 3.7053 (3) Å.
2-[2-(3-Chlorophenyl)-2-oxoethyl]-4-hydroxy-3-(3-methoxybenzoyl)-2H-1λ6,2-benzothiazine-1,1-dione
Authors: Siddiqui Hamid Latif , Ahmad Matloob , Gul Salman , Siddiqui Waseeq Ahmad , Parvez Masood
Published: March 2012

In the title molecule, C24H18ClNO6S, the heterocyclic thiazine ring adopts a half chair conformation with the S and N atoms displaced by 0.318 (3) and 0.387 (3) Å, respectively, on the opposite sides from the mean plane formed by the remaining ring atoms. The benzene rings of the benzothiazin unit and methoxybenzoyl group are more or less coplanar, the dihedral angle between the mean planes of these rings being 12.37 (10)° while the chlorophenyl ring is inclined at 81.87 (4) and 73.30 (5)°, respectively, to these rings. The molecular structure is consolidated by intramolecular O—H...O and C—H...N interactions and the crystal packing is stabilized by weak intermolecular C—H...O hydrogen bonds.