bluuebunny/crossref_metadata_2025 huggingface dataset:
Upper critical field and vortex phase diagram of polycrystalline δ-Mo1-xZrxN thin films by sol-gel
Authors: Hui Zhenzhen , Tang Xianwu , Wei Renhuai , Lei Hechang , Gao Guanyin , Hu Ling , Yang Jie , Yang Zhaorong , Song Wenhai , Zhu Xuebin , Sun Yuping
Published: February 2014

Upper critical field of polycrystalline δ-Mo1-xZrxN (0 ≤ x ≤ 0.3) thin films by sol-gel was investigated. It showed that the upper critical field was continuously improved with Zr doping content, and the improvement of ∼10 T in upper critical field was mainly attributed to the combined effects of obvious enhancements in normal-state resistivity with slight changes in Tc, obvious decrease in crystallite/grain size and enhanced microstrains. Flux jump was observed in low-level doped thin films due to enhanced critical current density by Zr doping. Finally, the vortex phase diagram of δ-Mo0.95Zr0.05N thin films was presented, which will provide guidance for investigation about the vortex mechanisms of δ-Mo1-xZrxN thin films.
Simple analytical model for fiber tensile failure due to droplet impact
Authors: Lopatnikov Sergey L. , Gillespie John W.
Published: February 2014

We present a simple model of the mechanics of the transverse impact of a water droplet of finite size on a free-standing fiber. There are two major differences between the transversal impact of a liquid droplet and the impact of a solid projectile. The first difference is that the segment of the fiber interacting with the droplet is not required to move with the speed of the droplet as in the case of an impact of a solid projectile. The second difference is related to the duration of interaction between the fiber and impactor. In the case of a solid projectile, interaction is complete when either the fiber fails or the projectile is defeated. However, failure in the case of the impact of a droplet is governed particularly by the time of interaction with the liquid droplet, which is governed by the flow around the accelerating fiber that may lead to fiber failure. The analytical model assumes a droplet diameter much larger than the diameter of the fiber and predicts the transverse forces acting on the fiber at the impact site, transversal wave propagation, and associated tensile stress in the fiber. The model identifies droplet size/velocity combinations that cause tensile failure of fibers with prescribed mechanical properties.
Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO2–H2O systems
Authors: Liu Ping , Zhao Jing , Liu Jinxiang , Zhang Meng , Bu Yuxiang
Published: February 2014

In view of the important implications of excess electrons (EEs) interacting with CO2–H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2–H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π* orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2− oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n]− systems. Interestingly, hydration occurs not only on the O atoms of the core CO2− through formation of O⋯H–O H–bond(s), but also on the C atom, through formation of a C⋯H–O H–bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H–O H–bonds, and vice versa. The number of water molecules associated with the CO2− anion in the first hydration shell is about 4∼7. No dimer-core (C2O4−) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2–H2O media.
Correlation functions for the fractional generalized Langevin equation in the presence of internal and external noise
Authors: Sandev Trifce , Metzler Ralf , Tomovski Živorad
Published: February 2014

We study generalized fractional Langevin equations in the presence of a harmonic potential. General expressions for the mean velocity and particle displacement, the mean squared displacement, position and velocity correlation functions, as well as normalized displacement correlation function are derived. We report exact results for the cases of internal and external friction, that is, when the driving noise is either internal and thus the fluctuation-dissipation relation is fulfilled or when the noise is external. The asymptotic behavior of the generalized stochastic oscillator is investigated, and the case of high viscous damping (overdamped limit) is considered. Additional behaviors of the normalized displacement correlation functions different from those for the regular damped harmonic oscillator are observed. In addition, the cases of a constant external force and the force free case are obtained. The validity of the generalized Einstein relation for this process is discussed. The considered fractional generalized Langevin equation may be used to model anomalous diffusive processes including single file-type diffusion.
Influence of gap spacing on the characteristics of Trichel pulse generated in point-to-plane discharge gaps
Authors: Li Zhen , Zhang Bo , He Jinliang , Xu Yongsheng
Published: February 2014

In this paper, the specific characteristics of the Trichel pulse generated in wide point-to-plane discharge gaps are investigated and compared with those of the currents generated in narrow gaps. A set of empirical formulas are derived to describe the specific characteristics. The influence of the gap spacing both on the current characteristics and on the coefficients of the formulas is studied. Based on the experiment results, an improvement is made to the space charge calculation method proposed by Lama and Gallo [J. Appl. Phys. 45, 103–113 (1974)] and the calculation results are compared to the ones obtained with Lama and Gallo's original method. With the influence of the space charge considered, the modified method obtains more accurate results of the space charge accumulating in the gap and gives a more precise description of the motion of the space charge in the gap. Based on the calculation results, the influence of the space charge on the distribution of the electric field is examined and the influence of the gap spacing on the current characteristics is also studied.
Formation of toroidal bubbles from acoustic droplet vaporization
Authors: Li David S. , Kripfgans Oliver D. , Fabiilli Mario L. , Brian Fowlkes J. , Bull Joseph L.
Published: February 2014

Acoustic droplet vaporization (ADV) is the selective vaporization of liquid microdroplets using ultrasound to produce stable gas bubbles. ADV is the primary mechanism in an ultrasound based cancer therapy, called gas embolotherapy, where the resulting bubbles are used to create localized occlusions leading to tumor necrosis. In this investigation, early time scale events including phase change are directly visualized using ultra-high speed imaging. Modulating elevated acoustic pressure or pulse length resulted in toroidal bubbles. For sufficiently short pulses (4 cycles at 7.5 MHz), toroidal bubble formation could be avoided, regardless of acoustic pressures tested.
Optically erasable samarium-doped fluorophosphate glasses for high-dose measurements in microbeam radiation therapy
Authors: Morrell B. , Okada G. , Vahedi S. , Koughia C. , Edgar A. , Varoy C. , Belev G. , Wysokinski T. , Chapman D. , Sammynaiken R. , Kasap S. O.
Published: February 2014

Previous work has demonstrated that fluorophosphate (FP) glasses doped with trivalent samarium (Sm3+) can be used as a dosimetric detector in microbeam radiation therapy (MRT) to measure high radiation doses and large dose variations with a resolution in the micrometer range. The present work addresses the use of intense optical radiation at 405 nm to erase the recorded dose information in Sm3+-doped FP glass plates and examines the underlying physics. We have evaluated both the conversion and optical erasure of Sm3+-doped FP glasses using synchrotron-generated high-dose x-rays at the Canadian Light Source. The Sm-ion valency conversion is accompanied by the appearance of x-ray induced optical absorbance due to the trapping of holes and electrons into phosphorus-oxygen hole (POHC) and electron (POEC) capture centers. Nearly complete Sm2+ to Sm3+ reconversion (erasure) may be achieved by intense optical illumination. Combined analysis of absorbance and electron spin resonance measurements indicates that the optical illumination causes partial disappearance of the POHC and the appearance of new POEC. The suggested model for the observed phenomena is based on the release of electrons during the Sm2+ to Sm3+ reconversion process, the capture of these electrons by POHC (and hence their disappearance), or by PO groups, with the appearance of new and/or additional POEC. Optical erasure may be used as a practical means to erase the recorded data and permits the reuse of these Sm-doped FP glasses in monitoring dose in MRT.
Numerical investigation on the partial return to isotropy of freely decaying homogeneous axisymmetric turbulence
Authors: Mons V. , Meldi M. , Sagaut P.
Published: February 2014

The return to isotropy of freely decaying homogeneous axisymmetric turbulence is numerically studied using the Eddy-Damped Quasi-Normal Markovian closure. The model, whose classical formulation has been extended to moderately anisotropic flows by Cambon, Jeandel, and Mathieu [“Spectral modelling of homogeneous non-isotropic turbulence,” J. Fluid Mech. 104, 247–262 (1981)], allows for an accurate description of the turbulence decay for very long times. More specifically, the observed results encompass both the high and low Reynolds number asymptotic regimes. Such an analysis escapes both wind tunnel experiments and direct numerical simulations possibilities at the present time. Anisotropy generation mechanisms considered in the present paper do not affect the nature of nonlinear interactions and the related energy cascade mechanisms. Their influence on the decay regime is quantified by the investigation of the features of the initial three dimensional kinetic energy spectrum. The initial anisotropy level is always chosen in agreement with experimental grid turbulence observations. The present results show that the relaxation towards an isotropic state is observed in the inertial range of the energy spectrum E(k, t) during the initial high Reynolds regime, while the large scales conserve the imposed anisotropy level if the permanence of large eddies hypothesis is verified. A direct consequence is that the ratio between axial and transverse kinetic energies γ increases when the low Reynolds asymptotic regime is reached. Saturation effects, i.e., effects related to the boundedness of the physical domain under consideration, are also investigated. Isotropic saturation (same cut off scale in every direction) leads to the relaxation towards a fully isotropic state in all cases, whereas anisotropic saturation (unbounded domain in the axial direction) leads to an amplification of the initial anisotropy.
The role of density discontinuity in the inviscid instability of two-phase parallel flows
Authors: Behzad M. , Ashgriz N.
Published: February 2014

We re-examine the inviscid instability of two-phase parallel flows with piecewise linear velocity profiles. Although such configuration has been theoretically investigated, we employ the concept of waves resonance to physically interpret the instability mechanism as well as the essential role of density discontinuity in the flow. Upon performing linear stability analysis, we demonstrate the existence of neutrally stable “density” and “density-vorticity” waves which are emerged due to the density jump in the flow, in addition to the well-known vorticity waves. Such waves are capable of resonating with each other to form unstable modes in the flow. Although unstable modes in this study are classified as the “shear instability” type, we demonstrate that they are not necessarily of the Rayleigh type. The results also show that the density can have both stabilizing and destabilizing effects on the flow stability. We verify that the difference in the resonating pair of neutral waves leads to such distinct behavior of the density variation.
A simple grand canonical approach to compute the vapor pressure of bulk and finite size systems
Authors: Factorovich Matías H. , Molinero Valeria , Scherlis Damián A.
Published: February 2014

In this article we introduce a simple grand canonical screening (GCS) approach to accurately compute vapor pressures from molecular dynamics or Monte Carlo simulations. This procedure entails a screening of chemical potentials using a conventional grand canonical scheme, and therefore it is straightforward to implement for any kind of interface. The scheme is validated against data obtained from Gibbs ensemble simulations for water and argon. Then, it is applied to obtain the vapor pressure of the coarse-grained mW water model, and it is shown that the computed value is in excellent accord with the one formally deduced using statistical thermodynamics arguments. Finally, this methodology is used to calculate the vapor pressure of a water nanodroplet of 94 molecules. Interestingly, the result is in perfect agreement with the one predicted by the Kelvin equation for a homogeneous droplet of that size.
A perspective on optical developments in microfluidic platforms for Caenorhabditis elegans research
Authors: Aubry Guillaume , Lu Hang
Published: February 2014

Microfluidics offers unique ways of handling and manipulating microorganisms, which has particularly benefited Caenorhabditis elegans research. Optics plays a major role in these microfluidic platforms, not only as a read-out for the biological systems of interest but also as a vehicle for applying perturbations to biological systems. Here, we describe different areas of research in C. elegans developmental biology and behavior neuroscience enabled by microfluidics combined with the optical components. In particular, we highlight the diversity of optical tools and methods in use and the strategies implemented in microfluidics to make the devices compatible with optical techniques. We also offer some thoughts on future challenges in adapting advancements in optics to microfluidic platforms.
Translation and integration of numerical atomic orbitals in linear molecules
Authors: Heinäsmäki Sami
Published: February 2014

We present algorithms for translation and integration of atomic orbitals for LCAO calculations in linear molecules. The method applies to arbitrary radial functions given on a numerical mesh. The algorithms are based on pseudospectral differentiation matrices in two dimensions and the corresponding two-dimensional Gaussian quadratures. As a result, multicenter overlap and Coulomb integrals can be evaluated effectively.
Triple band polarization-independent ultra-thin metamaterial absorber using electric field-driven LC resonator
Authors: Bhattacharyya Somak , Vaibhav Srivastava Kumar
Published: February 2014

In this paper, a triple band polarization-independent metamaterial absorber using electric field-driven LC resonators is proposed over wide angle of incidence. The unit cell is designed by parametric optimization in such a way that triple band absorption occurs in C-band. The proposed structure exhibits triple band absorption property for any angle of polarization under normal incidence. It also shows high absorption for wide angle of incidence upto 60° for both TE and TM polarizations. The proposed structure is also fabricated and experimental results provide good agreement with the simulated responses. The constitutive electromagnetic parameters viz. effective permittivity and effective permeability are extracted from the simulated response, which support the absorption phenomena at all these three frequencies. The reflection from the structure is numerically computed and verified with simulated response, and it shows good agreement between them.
Non-radiative relaxation and rectification behavior of metal/semiconductor tetrapod heterostructures
Authors: Kanta Haldar Krishna , Kundu Simanta , Patra Amitava
Published: February 2014

The metal-semiconductor hetero-structures have recently emerged as functional materials for their potential applications in the areas of photonic, optoelectronic, and other fields. Here, we discuss the structural characterization of Au/CdSe tetrapod hetero-structures by using high-resolution transmission electron microscope, high angle annular dark field-scanning transmission electron microscopic, and X-ray diffraction. The blue shifting of the plasmonic band and red shifting of the excitonic band suggest a strong surface plasmon-exciton interaction between Au and CdSe in Au/CdSe tetrapod heterostructure. A significant photoluminescence quenching (83.4%) of CdSe nanorod (NR) is observed in the presence of Au nanoparticle in Au/CdSe tetrapod heterostructure. The radiative and nonradiative decay rates of CdSe nanorods are found to be modified in Au/CdSe tetrapod structures and the nonradiative rate changes from 1.91 × 107 s−1 to 9.33 × 109 s−1 for CdSe NR to Au/CdSe tetrapod structure, respectively. Current-voltage characteristics of Au/CdSe heterostructure exhibit the rectification property with a threshold voltage of about 0.85 V and the rectifying ratio is 140 which can open up avenues for developing challenging devices.
Controllable perpendicular hysteresis steps in highly perpendicular magnetic anisotropic CoPt/AlN layered structures
Authors: Yu Youxing , Shi Ji , Nakamura Yoshio
Published: February 2014

Magnetic properties of Sub/AlN (20 nm)/[CoPt (2 nm)/AlN (2 nm)](y-1)/CoPt (2 nm)/AlN (x)/CoPt (4 nm) layered structures (x is the thickness of AlN interlayer between the CoPt top layer (TL) and the base multilayer (BML), while y is the repeating number of CoPt (2 nm)/AlN (2 nm) bilayer in the BML) have been studied, which show strong perpendicular magnetic anisotropy. The perpendicular magnetic hysteresis loops exhibit multiple steps, which are attributed to the coercivity difference between CoPt TL and BML. The width of magnetization steps in the perpendicular magnetic hysteresis loops can be effectively controlled by adjusting the AlN interlayer thickness (x) and the repeating number (y). Our findings offer an alternative approach for the controlling coercivity in the formation of anti-parallel configuration of magnetization in the perpendicular magnetic tunneling junctions.
Laminated microfluidic system for small sample protein analysis
Authors: Saedinia Sara , Nastiuk Kent L. , Krolewski John J. , Li G. P. , Bachman Mark
Published: February 2014

We describe a technology based on lamination that allows for the production of highly integrated 3D devices suitable for performing a wide variety of microfluidic assays. This approach uses a suite of microfluidic coupons (“microfloupons”) that are intended to be stacked as needed to produce an assay of interest. Microfloupons may be manufactured in paper, plastic, gels, or other materials, in advance, by different manufacturers, then assembled by the assay designer as needed. To demonstrate this approach, we designed, assembled, and characterized a microfloupon device that performs sodium-dodecyl-sulfate polyacrylamide gel electrophoresis on a small sample of protein. This device allowed for the manipulation and transport of small amounts of protein sample, tight injection into a thin polyacrylamide gel, electrophoretic separation of the proteins into bands, and subsequent removal of the gel from the device for imaging and further analysis. The microfloupons are rugged enough to handle and can be easily aligned and laminated, allowing for a variety of different assays to be designed and configured by selecting appropriate microfloupons. This approach provides a convenient way to perform assays that have multiple steps, relieving the need to design highly sophisticated devices that incorporate all functions in a single unit, while still achieving the benefits of small sample size, automation, and high speed operation.
Electron microscopic evidence for a tribologically induced phase transformation as the origin of wear in diamond
Authors: Zhang Xinyi , Schneider Reinhard , Müller Erich , Mee Manuel , Meier Sven , Gumbsch Peter , Gerthsen Dagmar
Published: February 2014

Tribological testing of a coarse-grained diamond layer, deposited by plasma-enhanced chemical vapor deposition, was performed on a ring-on-ring tribometer with a diamond counterpart. The origin of the wear of diamond and of the low friction coefficient of 0.15 was studied by analyzing the microstructure of worn and unworn regions by transmission and scanning electron microscopy. In the worn regions, the formation of an amorphous carbon layer with a thickness below 100 nm is observed. Electron energy loss spectroscopy of the C-K ionization edge reveals the transition from sp3-hybridized C-atoms in crystalline diamond to a high fraction of sp2-hybridized C-atoms in the tribo-induced amorphous C-layer within a transition region of less than 5 nm thickness. The mechanically induced phase transformation from diamond to the amorphous phase is found to be highly anisotropic which is clearly seen at a grain boundary, where the thickness of the amorphous layer above the two differently oriented grains abruptly changes.
Single vortex core recording in a magnetic vortex lattice
Authors: Mitin D. , Nissen D. , Schädlich P. , Arekapudi S. S. P. K. , Albrecht M.
Published: February 2014

We investigated the reversal characteristics of magnetic vortex cores in a two dimensional assembly of magnetic vortices. The vortex lattice was created by film deposition of 30-nm-thick permalloy onto large arrays of self-assembled spherical SiO2-particles with a diameter of 330 nm. The vortex core reversal was investigated by employing a write/read tester. This device uses a state-of-the-art magnetic recording head of a hard disc drive, which allows imaging as well as applying a local magnetic field pulse to individual vortices. The successful writing and reading of individual vortex cores is demonstrated, including a switching map, which indicates the switching behavior dependent on the relative position of the field pulse with respect to the vortex core.
Magnetic and magnetoimpedance studies on controlled Joule annealed amorphous Co73Fe4.5Ni0.5Mn0.5Nb0.5Si4.2B16.8 alloy
Authors: Kumar Manna Subhendu , Srinivas V.
Published: February 2014

We report magnetic and magnetoimpedance (MI) properties of as-quenched and Joule annealed (with and without external magnetic field) amorphous Co73Fe4.5Ni0.5Mn0.5Nb0.5Si4.2B16.8 alloy composition. The Joule annealing in the presence of magnetic field induces not only surface microstructural changes but also favourable anisotropy. Dc magnetic measurements show controlled annealing enhances soft magnetic nature of the sample. Virgin ribbons show MS ∼ 125 emu/g with μr ∼ 104 and exhibit large MI ratio of ∼100% at 3 MHz frequency. This MI ratio was further enhanced to 152% on Joule annealing (current density 0.85 × 107 A/m2) in the presence of applied magnetic field of 500 Oe. The field dependence MI shows a double-peak feature in as-spun ribbons, which is significantly enhanced for field annealed (FA) samples. The enhancement in MI and magnetic field sensitivity (η) in FA amorphous ribbons is attributed to the development of nanograins on the surface layer that strengthens the transverse magnetic structure.
Magnetic and dielectric properties of one-dimensional array of S = 1/2 linear trimer system Na2Cu3Ge4O12
Authors: Yasui Yukio , Kawamura Yuji , Kobayashi Yoshiaki , Sato Masatoshi
Published: February 2014

Magnetic susceptibility χ, specific heat C, capacitance Cp, and 23Na-NMR measurements have been carried out on polycrystalline samples of quantum spin linear trimer system Na2Cu3Ge4O12, which has the one-dimensional array of Cu3O8 trimers formed of edge-sharing three CuO4 square planes. The exchange interactions between the Cu2+ (S = 1/2) spins have been determined by analyzing χ-T and C-T curves. By employing the isolated S = 1/2 Heisenberg trimer model above 70 K, the nearest-neighbor exchange couplings J1 and the second-neighbor one J2 in trimer have been evaluated to J1/kB = 30 ± 20 K (antiferromagnetic) and J2/kB = 340 ± 20 K. At low temperature region, two spins of the edge in the Cu3O8 trimers form a nonmagnetic singlet by strong antiferromagnetic interaction J2, and the spin left in the center of the Cu3O8 trimer forms one-dimensional chains by the exchange interaction J3 between the trimers. By employing the S = 1/2 uniform Heisenberg chain model below 70 K, we have evaluated to J3/kB = 18 ± 1 K. The mechanism of multiferroic behavior at Tc = 2 K is discussed.
Numerical study of Lamb waves band structure in one-dimensional phononic crystal slabs with the anti-symmetric boundary structure
Authors: Huang Pingping , Yao Yuanwei , Wu Fugen , Zhang Xin
Published: February 2014

This paper theoretically and numerically investigates the propagation of Lamb waves in a one-dimensional phononic crystal slab bordered with anti-symmetric boundary layers. The results show that the band structure of the anti-symmetric boundary phononic crystal is significantly different from those presented in the papers available. The eigenmodes displacement fields reveal that there is an essential distinction in the formation of the band gap between the anti-symmetric and the symmetric boundary model. On the other hand, the thickness of the boundary layers can remarkably change the width and the location of the band gaps. Furthermore, the variation of the phononic crystal band gaps and the band pinning elimination show the band gaps are sensitive to the degree of stagger of the boundary layers, and different band gap has a different response to the profile of the boundary. In other words, the topological distribution of the boundary layer has an influence on the band structures.
Enhanced optical bistability with film-coupled plasmonic nanocubes
Authors: Argyropoulos Christos , Ciracì Cristian , Smith David R.
Published: February 2014

Colloidally synthesized nanocubes strongly coupled to conducting films hold great promise for enhancing different nonlinear optical processes. They exhibit a robust and sensitive scattering response that can be easily controlled by their geometrical and material parameters. Strong local field enhancement is generated at the gap regions between the nanocubes and the metallic film. We show that strong optical bistability and all-optical switching behavior can be obtained by loading these nanogaps with Kerr nonlinear materials. Relatively low input intensities are required to obtain these nonlinear effects. The proposed design can lead to efficient, low-power, and ultrafast all-optical memories and scattering nanoswitches.
Reduction of critical field for magnetic and orbital-ordering phase transition in impurity-substituted Nd0.45Sr0.55MnO3 crystal
Authors: Izuchi Y. , Akaki M. , Akahoshi D. , Kuwahara H.
Published: February 2014

We have investigated the Mn-site substitution effect in Nd0.45Sr0.55MnO3 single crystal, which has an A-type layered antiferromagnetic (A-AFM) phase with the 3\documentclass[12pt]{minimal}\begin{document}$d_{x^2-y^2}$\end{document}dx2−y2-type orbital-order. Substitution of Fe or Ga for Mn-site suppresses both the A-AFM order and competing ferromagnetic (FM) correlation, whereas Cr substitution suppresses only the A-AFM order but reactivates the underlying FM correlation via double-exchange mechanism along the AFM coupled c-direction. In Nd0.45Sr0.55Mn0.95Cr0.05O3, the A-AFM state with the orbital-order is changed into the orbital-disordered three-dimensional FM metallic state by applying magnetic field of μ0H = 12 T, which is much smaller than that of the parent compound Nd0.45Sr0.55MnO3.
Spirulina (Spirulina platensis) algae supplementation increases microbial protein production and feed intake and decreases retention time of digesta in the rumen of cattle
Authors: Panjaitan T. , Quigley S. P. , McLennan S. R. , Swain A. J. , Poppi D. P.
Published: February 2014

Cattle consuming pastures low in protein have low liveweight gain due to low rumen degradable protein (RDP) supply and thus low microbial crude protein (MCP) production and efficiency of MCP production [EMCP, g MCP/kg digestible organic matter (DOM)]. Nitrogen supplements can increase MCP production and EMCP of cattle grazing low protein pastures. The objective of this study was to compare the effects of supplementation with a non-protein-N source (NPN), in this case urea and ammonium sulfate (US), with a single-cell algal protein source (Spirulina platensis), on intake, microbial protein supply and digestibility in cattle. Nine cannulated Bos indicus steers [initial liveweight 250.1 ± 10.86 (s.d.) kg] were fed Mitchell grass hay (Astrebla spp; 6.1 g N, 746 g NDF/kg DM) ad libitum and were supplied with increasing amounts of US (0, 6, 13, 19 and 33 g US DM/kg hay DM) or Spirulina 0, 0.5, 1.4, 2.5 and 6.1 g Spirulina DM/kg W.day in an incomplete Latin square design. The response of MCP production and EMCP to increasing amounts of the two supplements was different, with a greater response to Spirulina evident. The MCP production was predicted to peak at 140 and 568 g MCP/day (0.64 and 2.02 g MCP/kg W.day) for the US and Spirulina supplements, respectively. The highest measured EMCP were 92 and 166 g MCP/kg DOM for the US and Spirulina treatments at 170 and 290 g RDP/kg DOM, respectively, or a Spirulina intake of 5.7 g DM/kg W.day. Increasing RDP intake from US and Spirulina resulted in an increase in Mitchell grass hay intake and rumen NH3-N concentration and reduced the retention time of liquid and particulate markers and digesta DM, NDF and lignin in the rumen with greater changes due to Spirulina. Total DM intake peaked at a Spirulina supplement level of 4.6 g Spirulina DM/kg W.day with a 2.3-fold higher DOM intake than Control steers. Rumen NH3-N concentrations reached 128 and 264 mg NH3-N/L for the US and Spirulina treatments with a significant increase in the concentration of branched-chain fatty acids for the Spirulina treatment. The minimum retention time of liquid (Cr-EDTA; 23 and 13 h) and particulate (Yb; 34 and 22 h) markers in the rumen were significantly lower for Spirulina compared with US and lower than unsupplemented animals at 24 and 34 h for Cr-EDTA and Yb, respectively. Spirulina could be provided safely at much higher N intakes than NPN supplements. The results suggest that, at an equivalent RDP supply, Spirulina provided greater increases than US in MCP production, EMCP and feed intake of Bos indicus cattle consuming low protein forage and could also be fed safely at higher levels of N intake.
Physiological basis of salt stress tolerance in rice expressing the antiapoptotic gene SfIAP
Authors: Hoang Thi My Linh , Williams Brett , Khanna Harjeet , Dale James , Mundree Sagadevan G.
Published: February 2014

Programmed cell death-associated genes, especially antiapoptosis-related genes have been reported to confer tolerance to a wide range of biotic and abiotic stresses in dicotyledonous plants such as tobacco (Nicotiana tabacum L.) and tomato (Solanum lycopersicum L.). This is the first time the antiapoptotic gene SfIAP was transformed into a monocotyledonous representative: rice (Oryza sativa L.). Transgenic rice strains expressing SfIAP were generated by the Agrobacterium-mediated transformation method and rice embryogenic calli, and assessed for their ability to confer tolerance to salt stress at both the seedling and reproductive stages using a combination of molecular, agronomical, physiological and biochemical techniques. The results show that plants expressing SfIAP have higher salt tolerance levels in comparison to the wild-type and vector controls. By preventing cell death at the onset of salt stress and maintaining the cell membrane’s integrity, SfIAP transgenic rice plants can retain plant water status, ion homeostasis, photosynthetic efficiency and growth to combat salinity successfully.
Knockdown of regulator of G-protein signalling 2 (Rgs2) leads to abnormal early mouse embryo development in vitro
Authors: Zhu Yan , Jiang Ya-Hong , He Ya-Ping , Zhang Xuan , Sun Zhao-Gui , Jiang Man-Xi , Wang Jian
Published: February 2014

Regulator of G-protein signalling 2 (Rgs2) is involved in G-protein-mediated signalling by negatively regulating the activity of the G-protein α-subunit. In the present study, the expression patterns of Rgs2 in mouse ovarian tissues and early embryos were determined by semiquantitative reverse transcription–polymerase chain reaction, immunohistochemistry and immunofluorescent analyses. Rgs2 expression was observed in the ovarian tissues of adult female mice, with an almost equal expression levels during different stages of the oestrous cycle. Rgs2 was abundant in the cytoplasm, membrane, nuclei and spindles of intact polar bodies in mouse early embryos at different developmental stages from the zygote to blastocyst. The effect of Rgs2 knockdown on early embryonic development in vitro was examined by microinjecting Rgs2-specific short interfering (si) RNAs into mouse zygotes. Knockdown of endogenous Rgs2 expression led to abnormal embryonic development in vitro, with a considerable number of early embryos arrested at the 2- or 4-cell stage. Moreover, mRNA expression of three zygotic gene activation-related genes (i.e. Zscan4, Tcstv1 and MuERV-L) was decreased significantly in 2-cell arrested embryos. These results suggest that Rgs2 plays a critical role in early embryo development.
The syntax of modal polyfunctionality revisited
Authors: Hansen Bjorn
Published: February 2014

This paper deals with the semantics and the syntax of modal constructions from a cross-linguistic perspective. It focuses on the syntactic representation of modal polyfunctionality, usually understood as the semantic alternation between root and epistemic readings. This ambiguity is not an idiosyncratic feature of the Germanic languages, as it is also found in other non-related language families. In this contribution, the empirical base is broadened by discussing the data taken from Hansen and de Haan (2009), which covers all major languages spoken in Europe. I discuss the notion of modal polyfunctionality and give a first account of cross-linguistic morpho-syntactic variation among modal constructions in the languages of Europe. The hypothesis is forwarded that there is cross-linguistic evidence for the syntactic relevance of the distinction between epistemic-root polyfunctionality (EPI-ROOT) and alternations within root modality (ROOT). The relative semantic uniformity of modals contrasts with their structural diversity. It will be shown that modals in the languages of Europe vary with respect to two features: (i) the encoding of the subject and (ii) inflectional categories. It is shown that modal constructions are not restricted to canonical subjects, encoded in the default (nominative) case, but also allow for cases other than nominative, or null subjects. Thus, canonical subject constructions appear to be best suited to fully-fledged EPI-ROOT polyfunctionality, whereas quirky or null subjects tend to be restricted to alternations within the semantic domain ROOT. Categories such as the latter need not be marked on the modal itself, but can be assigned to a lexical verb or the copula – a fact which provides evidence for the claim that polyfunctionality is not restricted to ‘modal verbal status’. In the second part of the paper, the following question will be addressed: Which syntactic features are cross-linguistically connected to polyfunctionality? These chapters focus on (a) the distinction between verbs and auxiliaries in modal constructions, (b) raising vs. control status on the modal, and, (c) the coherence of modal verbal complexes. The subsequent analysis presents clear evidence for the tendency towards a loss of inflectional categories, but, on the other hand, does not lend itself to corroboration of the claim that modals form a syntactic category sui generis (cf. Reis 2001). The conclusion is drawn that the distinction raising vs. control is best suited to explain the syntactic prerequisites of polyfunctionality. It will be argued that modals with canonical subjects displaying full EPI-ROOT involve a raising structure, whereas modals with non-canonically case marked subjects displaying only ROOT alternations form control constructions (cf. Abraham 1989, 2001, 2002 on modals in Germanic).
Deontic or epistemic? habēre as a modal marker of future certainty in Macedonian
Authors: Mitkovska Liljana , Bužarovska Eleni
Published: February 2014

The Macedonian verb ima ‘have’, which is primarily used for possession and existence, can acquire various modal meanings in construction with the untensed da-clause. According to their semantic and syntactic properties, these constructions can be grouped into classes that represent different levels of grammaticalization. In this paper, we examine the most advanced grammaticalized constructions with inflected and uninflected ima, and we differentiate them on semantic grounds. The analysis focuses on uninflected ima, which exhibits a range of deontic and epistemic meanings which are of theoretical and typological significance. What is especially challenging is the meaning of future certainty that renders a future epistemic qualification. We propose that these meanings of uninflected ima cannot be understood properly without taking into account discourse factors.
Epistemic, evidential and attitudinal markers in clause-medial position in Cantonese
Authors: Yap Foong Ha , Chor Winnie
Published: February 2014

This paper examines two types of clause-medial stance markers in Cantonese.* We trace the evolution of these stance markers from their lexical origins as complement-taking psych verbs and directional verbs. Similar to English I think parentheticals, the evolution of the Cantonese psych verbs (e.g. gok3dak1 ‘feel/think’; paa3 ‘fear’; m4zi1 ‘don’t know’) involves ‘insubordination’ of the embedded complement clause. However, in Cantonese, subject ellipsis and topic constructions play an important role in the reanalysis of psych verbs into epistemic and negative attitudinal markers in clause-medial position.1 Directional verbs in Cantonese (e.g. faan1 ‘return’ and maai4 ‘approach’), on the other hand, develop into attitudinal particles via verbal complementation and a disjunctive strategy. Central to the development of both types of stance markers is the first person subject ngo5, whether explicitly or implicitly expressed, which makes the process of subjectification possible.
Modal particles in rationale clauses and related constructions
Authors: Grosz Patrick Georg
Published: February 2014

This paper discusses the connection between sentential modality (e.g. the modality introduced by a modal auxiliary such as may or must) and the force of an utterance. This connection is explored with a focus on the German particles ruhig/bloß/JA, which typically occur in modalized declaratives and in imperatives, indicating a connection between the two types of utterances. This paper poses the question of how to account for such particles in rationale clauses, which cannot be trivially analyzed as modalized declaratives or imperatives. I pursue a uniform analysis of ruhig/bloß/JA as ‘modal modifiers’ (in the spirit of Grosz 2010, 2011), which increase the strength of a modal utterance; I argue that rationale clauses (on a par with imperatives) contain a covert modal that is best characterized as an existential modal with a modal choice function, in the spirit of Rullmann et al. (2008).
Modal particles in causal clauses
Authors: Schenner Mathias , Sode Frank
Published: February 2014

It is well-known that modal particles are not only licensed in root clauses, but also in a proper subset of embedded clauses. However, most existing accounts are primarily concerned with syntactic licensing conditions of modal particles in embedded clauses, while their semantic aspects remain relatively unexplored. This article focuses on a particularly intriguing set of cases in which the commitment-weakening German modal particle wohl occurs in veridical contexts created by the causal connective weil, as in Er hat ein schlechtes Gewissen, weil er wohl gelogen hat. We argue that this combination gives rise to a rather complex interpretation that is unexpected given standard assumptions about modal particles and causal clauses, schematically ‘p and assume(speaker)(q) and (if q then cause(q)(p))’ for sentences of the form ‘p weil wohl q’, and we sketch a possible route for compositional interpretation of these constructions in a dynamic framework based on speaker commitments.
Enablement and possibility
Authors: Salkie Raphael
Published: February 2014

We need a better explanation of the differences in meaning and use between can and may. This paper proposes that the underlying semantics of all uses of can is enablement, in a precise sense derived from the philosophy of action, while may expresses metalinguistic possibility, linking a proposition with another domain of propositions. The widespread belief among linguists that modality involves possible worlds is wrong: neither “modality” nor “possible worlds” play a part in the analysis. Semantically, sentences containing can and may are typically incomplete, but the missing information is different in each case. Both involve impliciture (n.b. not implicature), a pervasive pragmatic process. The two words can and may thus have complex but divergent semantic properties, yet there is nothing unusual about their pragmatics. The analysis draws on Kent Bach’s work on semantics and pragmatics, which assumes a sharp conceptual divide between meaning and use.
Colloidal PbSe quantum dot-solution-filled liquid-core optical fiber for 1.55 μm telecommunication wavelengths
Authors: Zhang Lei , Zhang Yu , Kershaw Steve V , Zhao Yanhui , Wang Yu , Jiang Yongheng , Zhang Tieqiang , Yu William W , Gu Pengfei , Wang Yiding , Zhang Hanzhuang , Rogach Andrey L
Published: February 2014

We have studied the optical properties of PbSe colloidal quantum dot-solution filled hollow core multimode silica waveguides as a function of quantum dot-solution concentration, waveguide length, optical pump power and choice of organic solvent in order to establish the conditions to maximize near infrared spontaneous emission intensities. The optical performance was compared and showed good agreement with a simple three level system model for the quantum dots confined in an optical waveguide. Near infrared absorption-free solvent of tetrachlorethylene was confirmed to be a good candidate for the waveguide medium due to the enhancement of output intensity from the liquid-core fiber compared to the performance in toluene-based fiber. This approach demonstrates a useful method for early characterization of quantum dot materials in a waveguide test-bed with minimal material processing on the colloidal nanoparticles.
Deer Creek Farms: Tradition into the Future
Authors: Yeager Elizabeth A. , Stutzman Sarah A.
Published: February 2014

The Deer Creek Farms case study illustrates a family farm operation that is trying to identify how to transition the business to include the next generation. The family is currently growing corn, soybeans, and contract hogs. The family is faced with decisions to expand production in one or more of the current enterprises, exit out of one or more of the current enterprises, or diversify into additional enterprises. Each member of the family is given the task of proposing their vision of the farm's future. The examples illustrated through the Deer Creek Farms case study will assist agricultural producers as they monitor, identify, and manage strategic risk on their farms.
Supercomputing for the parallelization of whole genome analysis
Authors: Puckelwartz Megan J. , Pesce Lorenzo L. , Nelakuditi Viswateja , Dellefave-Castillo Lisa , Golbus Jessica R. , Day Sharlene M. , Cappola Thomas P. , Dorn Gerald W. , Foster Ian T. , McNally Elizabeth M.
Published: February 2014

Motivation: The declining cost of generating DNA sequence is promoting an increase in whole genome sequencing, especially as applied to the human genome. Whole genome analysis requires the alignment and comparison of raw sequence data, and results in a computational bottleneck because of limited ability to analyze multiple genomes simultaneously.

Results: We now adapted a Cray XE6 supercomputer to achieve the parallelization required for concurrent multiple genome analysis. This approach not only markedly speeds computational time but also results in increased usable sequence per genome. Relying on publically available software, the Cray XE6 has the capacity to align and call variants on 240 whole genomes in ∼50 h. Multisample variant calling is also accelerated.

Availability and implementation: The MegaSeq workflow is designed to harness the size and memory of the Cray XE6, housed at Argonne National Laboratory, for whole genome analysis in a platform designed to better match current and emerging sequencing volume.

Contact:  emcnally@uchicago.edu
BIMA V3: an aligner customized for mate pair library sequencing
Authors: Drucker Travis M. , Johnson Sarah H. , Murphy Stephen J. , Cradic Kendall W. , Therneau Terry M. , Vasmatzis George
Published: February 2014

Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate-pair read pairs to a reference genome is a challenging and time-consuming process for most next-generation sequencing alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.) and presence of structural variant breakpoints within reads increase mapping and alignment complexity. We describe an algorithm that is up to 20 times faster and 25% more accurate than popular next-generation sequencing alignment programs when processing mate pair sequencing.

Availability:  http://bioinformaticstools.mayo.edu/research/bima/

Contact:  vasm@mayo.edu or vasmatzis.george@mayo.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Spinoza and Descartes
Authors: Schmaltz Tad M.
Published: February 2014

This article considers the relation of Spinoza’s thought to the project in Descartes of providing new foundations for philosophy. The importance of this relation is indicated by the fact that Spinoza’s first published work is a reconstruction of portions of Descartes’s Principia Philosophiae. Following a consideration of this reconstruction that highlights the ways in which its views differ from Spinoza’s own, there is an examination of the manner in which Spinoza revises the foundational claims in Descartes concerning the nature of body as an extended thing, the nature of mind as a thinking thing, and the nature of God as infinite substance. Whereas Spinoza deviates in important ways from Descartes’s conception of extension and thought, there are some significant points of agreement with respect to Descartes’s doctrine of God’s creation of eternal truths.