bluuebunny/crossref_metadata_2025 huggingface dataset:
Pdx1 and USF transcription factors co-ordinately regulate Alx3 gene expression in pancreatic β-cells
Authors: Fernández-Pérez Antonio , Vallejo Mario
Published: July 2014

Alterations in transcription factors expressed in insulin-producing islet β-cells generate pancreatic dysfunction leading to diabetes. The homeodomain transcription factor Alx3 (aristaless-like homeobox 3) expressed in pancreatic islets participates in the regulated expression of several islet genes, and its deficiency in mice leads to islet cell apoptosis and glucose intolerance. In the present study, we investigated the mechanisms that regulate expression of Alx3 in pancreatic islets at the transcriptional level. We found that the Alx3 promoter contains at least eight putative regulatory elements with an E-box consensus sequence, three of which were determined to be functional and required for Alx3 promoter activity by mutational analysis in transfected MIN6 β-cells. We determined that these E-box elements are recognized by the basic helix–loop–helix transcription factors USF1 (upstream stimulatory factor 1) and USF2. We also identified a highly conserved A-box in the Alx3 promoter that is recognized by the islet-specific transcription factor Pdx1 (pancreatic and duodenal homeobox 1). Pdx1-mediated transactivation of the Alx3 promoter requires the integrity of the three functional E-boxes and the co-operation with USF transcription factors bound to them. The results from the present study indicate that Pdx1 contributes to the transcriptional transactivation of Alx3 in pancreatic β-cells by acting in co-ordination with USF1 and USF2.
A novel method for calculating the energy barriers for carbon diffusion in ferrite under heterogeneous stress
Authors: Tchitchekova Deyana S. , Morthomas Julien , Ribeiro Fabienne , Ducher Roland , Perez Michel
Published: July 2014

A novel method for accurate and efficient evaluation of the change in energy barriers for carbon diffusion in ferrite under heterogeneous stress is introduced. This method, called Linear Combination of Stress States, is based on the knowledge of the effects of simple stresses (uniaxial or shear) on these diffusion barriers. Then, it is assumed that the change in energy barriers under a complex stress can be expressed as a linear combination of these already known simple stress effects. The modifications of energy barriers by either uniaxial traction/compression and shear stress are determined by means of atomistic simulations with the Climbing Image-Nudge Elastic Band method and are stored as a set of functions. The results of this method are compared to the predictions of anisotropic elasticity theory. It is shown that, linear anisotropic elasticity fails to predict the correct energy barrier variation with stress (especially with shear stress) whereas the proposed method provides correct energy barrier variation for stresses up to ∼3 GPa. This study provides a basis for the development of multiscale models of diffusion under non-uniform stress.
High-frequency fluctuation measurements by far-infrared laser Faraday-effect polarimetry-interferometry and forward scattering system on MST
Authors: Ding W. X. , Lin L. , Duff J. R. , Brower D. L.
Published: July 2014

Magnetic fluctuation-induced transport driven by global tearing modes has been measured by Faraday-effect polarimetry and interferometry (phase measurements) in the MST reversed field pinch. However, the role of small-scale broadband magnetic and density turbulence in transport remains unknown. In order to investigate broadband magnetic turbulence, we plan to upgrade the existing detector system by using planar-diode fundamental waveguide mixers optimized for high sensitivity. Initial tests indicate these mixers have ×10 sensitivity improvement compared to currently employed corner-cube Schottky-diode mixers and ×5 lower noise. Compact mixer design will allow us to resolve the wavenumbers up to k ∼ 1–2 cm−1 for beam width w = 1.5 cm and 15 cm−1 for beam width w = 2 mm. The system can also be used to measure the scattered signal (amplitude measurement) induced by both plasma density and magnetic fluctuations.
Extending the applicability of the Tkatchenko-Scheffler dispersion correction via iterative Hirshfeld partitioning
Authors: Bučko Tomáš , Lebègue Sébastien , Ángyán János G. , Hafner Jürgen
Published: July 2014

Recently we have demonstrated that the applicability of the Tkatchenko-Scheffler (TS) method for calculating dispersion corrections to density-functional theory can be extended to ionic systems if the Hirshfeld method for estimating effective volumes and charges of atoms in molecules or solids (AIM’s) is replaced by its iterative variant [T. Bučko, S. Lebègue, J. Hafner, and J. Ángyán, J. Chem. Theory Comput. 9, 4293 (2013)]. The standard Hirshfeld method uses neutral atoms as a reference, whereas in the iterative Hirshfeld (HI) scheme the fractionally charged atomic reference states are determined self-consistently. We show that the HI method predicts more realistic AIM charges and that the TS/HI approach leads to polarizabilities and C6 dispersion coefficients in ionic or partially ionic systems which are, as expected, larger for anions than for cations (in contrast to the conventional TS method). For crystalline materials, the new algorithm predicts polarizabilities per unit cell in better agreement with the values derived from the Clausius-Mosotti equation. The applicability of the TS/HI method has been tested for a wide variety of molecular and solid-state systems. It is demonstrated that for systems dominated by covalent interactions and/or dispersion forces the TS/HI method leads to the same results as the conventional TS approach. The difference between the TS/HI and TS approaches increases with increasing ionicity. A detailed comparison is presented for isoelectronic series of octet compounds, layered crystals, complex intermetallic compounds, and hydrides, and for crystals built of molecules or containing molecular anions. It is demonstrated that only the TS/HI method leads to accurate results for systems where both electrostatic and dispersion interactions are important, as illustrated for Li-intercalated graphite and for molecular adsorption on the surfaces in ionic solids and in the cavities of zeolites.
Numerical study of transition to supersonic flows in the edge plasma
Authors: Goswami Rajiv , Artaud Jean-François , Imbeaux Frédéric , Kaw Predhiman
Published: July 2014

The plasma scrape-off layer (SOL) in a tokamak is characterized by ion flow down a long narrow flux tube terminating on a solid surface. The ion flow velocity along a magnetic field line can be equal to or greater than sonic at the entrance of a Debye sheath or upstream in the presheath. This paper presents a numerical study of the transition between subsonic and supersonics flows. A quasineutral one-dimensional (1D) fluid code has been used for modeling of plasma transport in the SOL along magnetic field lines, both in steady state and under transient conditions. The model uses coupled equations for continuity, momentum, and energy balance with ionization, radiation, charge exchange, and recombination processes. The recycled neutrals are described in the diffusion approximation. Standard Bohm sheath criterion is used as boundary conditions at the material surface. Three conditions conducive for the generation of supersonic flows in SOL plasmas have been explored. It is found that in steady state high (attached) and low (detached) divertor temperatures cases, the role of particle, momentum, and energy loss is critical. For attached case, the appearance of shock waves in the divertor region if the incoming plasma flow is supersonic and its effect on impurity retention is presented. In the third case, plasma expansion along the magnetic field can yield time-dependent supersonic solutions in the quasineutral rarefaction wave. Such situations can arise in the parallel transport of intermittent structures such as blobs and edge localized mode filaments along field lines.
Comparison of x-ray absorption spectra between water and ice: New ice data with low pre-edge absorption cross-section
Authors: Sellberg Jonas A. , Kaya Sarp , Segtnan Vegard H. , Chen Chen , Tyliszczak Tolek , Ogasawara Hirohito , Nordlund Dennis , Pettersson Lars G. M. , Nilsson Anders
Published: July 2014

The effect of crystal growth conditions on the O K-edge x-ray absorption spectra of ice is investigated through detailed analysis of the spectral features. The amount of ice defects is found to be minimized on hydrophobic surfaces, such as BaF2(111), with low concentration of nucleation centers. This is manifested through a reduction of the absorption cross-section at 535 eV, which is associated with distorted hydrogen bonds. Furthermore, a connection is made between the observed increase in spectral intensity between 544 and 548 eV and high-symmetry points in the electronic band structure, suggesting a more extended hydrogen-bond network as compared to ices prepared differently. The spectral differences for various ice preparations are compared to the temperature dependence of spectra of liquid water upon supercooling. A double-peak feature in the absorption cross-section between 540 and 543 eV is identified as a characteristic of the crystalline phase. The connection to the interpretation of the liquid phase O K-edge x-ray absorption spectrum is extensively discussed.
Perturbative many-body expansion for electrostatic energy and field for system of polarizable charged spherical ions in a dielectric medium
Authors: Freed Karl F.
Published: July 2014

An analytical solution for the electrostatic energy and potential for a system of charged, polarizable spheres in a dielectric medium is developed from a multiple scattering expansion that is equivalent to a formal solution to Poisson's equation for the system. The leading contributions emerge in the form of effective two-, three-, and four-body interactions that are explicit analytical functions of the sphere positions, charges, and internal dielectric constants and the external dielectric constant, thereby also enabling analytical computation of the electrostatic forces on the ions. Tests of successive terms demonstrate their rapid convergence. Similar methods can be used to evaluate higher order contributions and the expansion for the electrostatic field. The results will prove far more efficient for MD and MC simulations with spherical particles than current approximate methods that require the computation of surface polarization charge distributions but that apply also for systems with complex geometries.
Calculation of the vibrational excited states of malonaldehyde and their tunneling splittings with the multi-configuration time-dependent Hartree method
Authors: Schröder Markus , Meyer Hans-Dieter
Published: July 2014

We report energies and tunneling splittings of vibrational excited states of malonaldehyde which have been obtained using full dimensional quantum mechanical calculations. To this end we employed the multi configuration time-dependent Hartree method. The results have been obtained using a recently published potential energy surface [Y. Wang, B. J. Braams, J. M. Bowman, S. Carter, and D. P. Tew, J. Chem. Phys. 128, 224314 (2008)] which has been brought into a suitable form by a modified version of the n-mode representation which was used with two different arrangements of coordinates. The relevant terms of the expansion have been identified with a Metropolis algorithm and a diffusion Monte-Carlo technique, respectively.
Development of 2D soft X-ray measurement system in the large helical device
Authors: Takemura Y. , Ohdachi S. , Watanabe K. Y. , Du X. D.
Published: July 2014

A fast two-dimensional soft X-ray camera using silicon photo diode array is being developed in order to investigate high frequency MHD instability with high mode number. The advantage of the adopted diode is a large sensor area of 10 mm × 10 mm and small diode capacitance which enable us to measure signals with the short response time. The characteristic of the prototype is summarized as follows: Channel number is 6 × 8 = 48, detection range 1∼10 keV, the spatial resolution 128 mm at the plasma location, and frequency range DC∼100 kHz. Synthetic image of the prototype in the Large Helical Device is estimated by using perturbation model of MHD mode.
Veselago lens by photonic hyper-crystals
Authors: Huang Zun , Narimanov Evgenii E.
Published: July 2014

Based on the recent concept of the photonic hyper-crystal—an artificial optical medium that combines the properties of hyperbolic materials and photonic crystals, we present the imaging system functioning as a Veselago lens. This planar lens shows a nearly constant negative refractive index with substantially reduced image aberrations, and can find potential applications in photolithography and hot-spots detection of silicon-based integrated circuits.
Percolation thresholds for polydisperse circular disks: A lattice-based exploration
Authors: Chatterjee Avik P.
Published: July 2014

The percolation threshold for polydisperse systems of (i) isotropically oriented, and (ii) perfectly aligned, circular disks is calculated within an analogy to a lattice model. Our results are expressed in terms of moments of the distribution function over the disk radii, and they closely resemble findings obtained from an integral equation approach. The threshold is found to be quite sensitive to polydispersity in the disk radii and, for monodisperse systems, to approach a plateau for large values of the aspect ratio (thickness to diameter ratio). A similar plateau is found for disks with perfectly nematic orientational order, for which the percolation threshold always exceeds that for identical systems of disks that are oriented isotropically.
X-ray polarization splitting by a single crystal evaluated with synchrotron x-rays
Authors: Pereira N. R. , Presura R. , Wallace M. , Kastengren A.
Published: July 2014

In hexagonal crystals such as quartz, an asymmetric Bragg reflection from two equivalent internal crystal planes can separate unpolarized x-rays into two linearly polarized components. The perfectly polarized and tunable x-rays from a synchrotron are ideal to evaluate polarization spitting in detail. One unanticipated feature is that additional reflections from the crystal affect the diffraction intensity of the two polarized components, an effect that is unlikely to matter in polarization spectroscopy of radiating plasmas for which the crystal is intended.
Investigation of magnetic properties of Fe3O4 nanoparticles using temperature dependent magnetic hyperthermia in ferrofluids
Authors: Nemala H. , Thakur J. S. , Naik V. M. , Vaishnava P. P. , Lawes G. , Naik R.
Published: July 2014

Rate of heat generated by magnetic nanoparticles in a ferrofluid is affected by their magnetic properties, temperature, and viscosity of the carrier liquid. We have investigated temperature dependent magnetic hyperthermia in ferrofluids, consisting of dextran coated superparamagnetic Fe3O4 nanoparticles, subjected to external magnetic fields of various frequencies (188–375 kHz) and amplitudes (140–235 Oe). Transmission electron microscopy measurements show that the nanoparticles are polydispersed with a mean diameter of 13.8 ± 3.1 nm. The fitting of experimental dc magnetization data to a standard Langevin function incorporating particle size distribution yields a mean diameter of 10.6 ± 1.2 nm, and a reduced saturation magnetization (∼65 emu/g) compared to the bulk value of Fe3O4 (∼95 emu/g). This is due to the presence of a finite surface layer (∼1 nm thickness) of non-aligned spins surrounding the ferromagnetically aligned Fe3O4 core. We found the specific absorption rate, measured as power absorbed per gram of iron oxide nanoparticles, decreases monotonically with increasing temperature for all values of magnetic field and frequency. Using the size distribution of magnetic nanoparticles estimated from the magnetization measurements, we have fitted the specific absorption rate versus temperature data using a linear response theory and relaxation dissipation mechanisms to determine the value of magnetic anisotropy constant (28 ± 2 kJ/m3) of Fe3O4 nanoparticles.
A polarization-independent broadband terahertz absorber
Authors: Shi Cheng , Zang XiaoFei , Wang YiQiao , Chen Lin , Cai Bin , Zhu YiMing
Published: July 2014

A highly efficient broadband terahertz absorber is designed, fabricated, and experimentally as well as theoretically evaluated. The absorber comprises a heavily doped silicon substrate and a well-designed two-dimensional grating. Due to the destructive interference of waves and diffraction, the absorber can achieve over 95% absorption in a broad frequency range from 1 to 2 THz and for angles of incidence from 0° to 60°. Such a terahertz absorber is also polarization-independent due to its symmetrical structure. This omnidirectional and broadband absorber have potential applications in anti-reflection coatings, imaging systems, and so on.
Electrocaloric characterization of a poly(vinylidene fluoride-trifluoroethylene-chlorofluoroethylene) terpolymer by infrared imaging
Authors: Guo Dongzhi , Gao Jinsheng , Yu Ying-Ju , Santhanam Suresh , Fedder Gary K. , McGaughey Alan J. H. , Yao S. C.
Published: July 2014

The electrocaloric effect in thin films of a poly(vinylidene fluoride-trifluoroethylene chlorofluoroethylene) terpolymer (62.6/29.4/8 mol. %, 11–12 μm thick) is directly measured by infrared imaging at ambient conditions. The adiabatic temperature change is estimated to be 5.2 K for an applied electric field of 90 V/μm. The temperature change is independent of the operating frequency in the range of 0.03–0.3 Hz and is stable over a testing period of 30 min. Application of this terpolymer is promising for micro-scale refrigeration.
Permanent magnet with MgB2 bulk superconductor
Authors: Yamamoto Akiyasu , Ishihara Atsushi , Tomita Masaru , Kishio Kohji
Published: July 2014

Superconductors with persistent zero-resistance currents serve as permanent magnets for high-field applications requiring a strong and stable magnetic field, such as magnetic resonance imaging. The recent global helium shortage has quickened research into high-temperature superconductors (HTSs)—materials that can be used without conventional liquid-helium cooling to 4.2 K. Herein, we demonstrate that 40-K-class metallic HTS magnesium diboride (MgB2) makes an excellent permanent bulk magnet, maintaining 3 T at 20 K for 1 week with an extremely high stability (<0.1 ppm/h). The magnetic field trapped in this magnet is uniformly distributed, as for single-crystalline neodymium-iron-boron. Magnetic hysteresis loop of the MgB2 permanent bulk magnet was detrmined. Because MgB2 is a simple-binary-line compound that does not contain rare-earth metals, polycrystalline bulk material can be industrially fabricated at low cost and with high yield to serve as strong magnets that are compatible with conventional compact cryocoolers, making MgB2 bulks promising for the next generation of Tesla-class permanent-magnet applications.
Strain-balanced InGaN/GaN multiple quantum wells
Authors: Van Den Broeck D. M. , Bharrat D. , Hosalli A. M. , El-Masry N. A. , Bedair S. M.
Published: July 2014

InGaN/GaN multiple quantum well (MQW) structures suffer from a high amount of compressive strain in the InGaN wells and the accompanied piezoelectric field resulting in both a blue shift in emission and a reduction of emission intensity. We report the growth of InxGa1−xN/GaN “strain-balanced” multiple quantum wells (SBMQWs) grown on thick InyGa1−yN templates for x > y by metal organic chemical vapor deposition. SBMQWs consist of alternating layers of InxGa1−xN wells and GaN barriers under compressive and tensile stress, respectively, which have been lattice matched to a thick InyGa1−yN template. Growth of the InyGa1−yN template is also detailed in order to achieve thick, relaxed InyGa1−yN grown on GaN without the presence of V-grooves. When compared to conventional InxGa1−xN/GaN MQWs grown on GaN, the SBMQW structures exhibit longer wavelength emission and higher emission intensity for the same InN mole fraction due to a reduction in the well strain and piezoelectric field. By matching the average lattice constant of the MQW active region to the lattice constant of the InyGa1−yN template, essentially an infinite number of periods can be grown using the SBMQW growth method without relaxation-related effects. SBMQWs can be utilized to achieve longer wavelength emission in light emitting diodes without the use of excess indium and can be advantageous in addressing the “green gap.”
A sensitive film structure improvement of reduced graphene oxide based resistive gas sensors
Authors: Zhou Yong , Xie GuangZhong , Xie Tao , Yuan Huan , Tai HuiLing , Jiang YaDong , Chen Zhi
Published: July 2014

This study was focused on how to improve the gas sensing properties of resistive gas sensors based on reduced graphene oxide. Sol-airbrush technology was utilized to prepare reduced graphene oxide films using porous zinc oxide films as supporting materials mainly for carbon dioxide sensing applications. The proposed film structure improved the sensitivity and the response/recovery speed of the sensors compared to those of the conventional ones and alleviated the restrictions of sensors' performance to the film thickness. In addition, the fabrication technology is relatively simple and has potential for mass production in industry. The improvement in the sensitivity and the response/recovery speed is helpful for fast detection of toxic gases or vapors in environmental and industrial applications.
Multi-region relaxed magnetohydrodynamics with anisotropy and flow
Authors: Dennis G. R. , Hudson S. R. , Dewar R. L. , Hole M. J.
Published: July 2014

We present an extension of the multi-region relaxed magnetohydrodynamics (MRxMHD) equilibrium model that includes pressure anisotropy and general plasma flows. This anisotropic extension to our previous isotropic model is motivated by Sun and Finn's model of relaxed anisotropic magnetohydrodynamic equilibria. We prove that as the number of plasma regions becomes infinite, our anisotropic extension of MRxMHD reduces to anisotropic ideal MHD with flow. The continuously nested flux surface limit of our MRxMHD model is the first variational principle for anisotropic plasma equilibria with general flow fields.
Highly focused and efficient terahertz radiation generation by photo-mixing of lasers in plasma in the presence of magnetic field
Authors: Malik Anil K. , Singh Kunwar Pal , Sajal V.
Published: July 2014

A mechanism of efficient and highly focused terahertz (THz) radiation generation by photo-mixing of top-hat like lasers with frequencies ω1, ω2 and wave numbers k1, k2 in pre-formed rippled density (corrugated) plasma is proposed. In this mechanism, intensity variation of lasers offers nonlinear ponderomotive force at frequency ω′=ω1−ω2 and wave number k′=k1−k2 which couples with density ripples in the plasma and leads to a strong nonlinear oscillatory current that resonantly excites highly focused and intense THz radiation at frequency ωUH=(ωp2+ωc2) (where ωc is electron cyclotron frequency). The efficiency of emitted THz radiation of the order of 15% is obtained under optimum conditions. It is observed that focus and intensity of emitted radiation can be controlled by selecting a proper profile index of the lasers, ripple parameters, and tuning of external magnetic field.
Nonpolar III-nitride vertical-cavity surface emitting lasers with a polarization ratio of 100% fabricated using photoelectrochemical etching
Authors: Holder C. O. , Leonard J. T. , Farrell R. M. , Cohen D. A. , Yonkee B. , Speck J. S. , DenBaars S. P. , Nakamura S. , Feezell D. F.
Published: July 2014

Photoelectrochemical (PEC) band gap selective undercut etching is discussed as an alternative technique to chemical-mechanical polishing and laser-lift off for substrate removal for III-nitride vertical-cavity surface-emitting lasers (VCSELs). A top-down PEC etch is also described, which offers the ability to epitaxially define an etch-stop layer, thereby achieving a high degree of cavity length control. The temperature-dependent lasing characteristics of m-plane VCSELs fabricated using PEC etching techniques are analyzed. Measurements of multiple VCSELs from the same wafer yielded lasing emission polarized along the a-direction with a polarization ratio of 100%, indicating that the entire array was uniformly polarized.
Magnetization reversal in perpendicularly magnetized L1 FePd/FePt heterostructures
Authors: Ma L. , Gilbert D. A. , Neu V. , Schäfer R. , Zheng J. G. , Yan X. Q. , Shi Z. , Liu Kai , Zhou S. M.
Published: July 2014

The magnetization reversal process is investigated in perpendicular spring magnets of epitaxial L10 FePd/FePt (24 nm) thin films with varying FePd thickness. For thin FePd layers, the reversal is initiated by the nucleation of reversed bubble domains and is then mainly accomplished by the depinning and lateral movement of domain walls. For thick FePd layers, the magnetization reversal is predominantly governed by the nucleation process rather than wall motion, resulting in an increased density of bubble domains at more negative magnetic fields. The switching field is reduced significantly with increasing FePd thickness and exchange springs are formed locally due to a tilted magnetization in the FePd. These results arise from the interplay between differently strong perpendicular magnetic anisotropies in FePd and FePt and from layer dependent structural modifications, which is important for high density magnetic recording media.
A micropillar array for sample concentration via in-plane evaporation
Authors: Choi Jae-Woo , Hosseini Hashemi Seyyed Mohammad , Erickson David , Psaltis Demetri
Published: July 2014

We present a method to perform sample concentration within a lab-on-a-chip using a microfluidic structure which controls the liquid-gas interface through a micropillar array fabricated in polydimethylsiloxane between microfluidic channels. The microstructure confines the liquid flow and a thermal gradient is used to drive evaporation at the liquid-gas-interface. The evaporation occurs in-plane to the microfluidic device, allowing for precise control of the ambient environment. This method is demonstrated with a sample containing 1 μm, 100 nm fluorescent beads and SYTO-9 labelled Escherichia coli bacteria. Over 100 s, the fluorescent beads and bacteria are concentrated by a factor of 10.
Tuning a microsphere whispering-gallery-mode sensor for extreme thermal stability
Authors: Zhi Y. , Meldrum A.
Published: July 2014

The reactive sensing application of optical microspheres can be plagued by local temperature fluctuations. Fluctuations due to laser heating or ambient changes in the lab environment cause resonance shifts that appear as noise or an underlying drift in the sensor data. Here, we show that thermal fluctuations can be exactly compensated in virtually any local medium (i.e., “analyte”) by the application of a high-index coating on the surface of the microsphere. The coating precisely controls the extent of the field penetration into the surroundings in such a way that the thermal shifts associated with the three layers (the glass sphere, the coating, and the exterior medium) can be exactly balanced. The conditions required for thermal stability were investigated theoretically; on the basis of these calculations a real sphere was then synthesized that showed excellent stability for aqueous solutions.
Modulation of mixed-phase titania photoluminescence by oxygen adsorption
Authors: Pallotti D. , Orabona E. , Amoruso S. , Maddalena P. , Lettieri S.
Published: July 2014

We investigate the effect of oxygen (O2) adsorption on photoluminescence properties of mixed-phase titania nanoparticle films deposited by femtosecond pulsed laser deposition, aiming to assess preliminary conclusions about the feasibility of opto-chemical sensing based on titania. We evidence that O2 produces opposite responses in rutile and anatase photoluminescence efficiency, highlighting interesting potentialities for future double-parametric optical sensing based on titania. The results evidence an important role of lattice oxygen atoms, suggesting that the standard Schottky barrier mechanism driving the response toward gas species in most used metal-oxide sensors (e.g., tin dioxide) is not the only active mechanism in titania.
Genetic improvement of subterranean clover (Trifolium subterraneum L.). 2. Breeding for disease and pest resistance
Authors: Nichols P. G. H. , Jones R. A. C. , Ridsdill-Smith T. J. , Barbetti M. J.
Published: July 2014

Subterranean clover (Trifolium subterraneum L.) is the most widely sown pasture legume in southern Australia and resistance to important diseases and pests has been a major plant-breeding objective. Kabatiella caulivora, the cause of clover scorch, is the most important foliar fungal pathogen, and several cultivars have been developed with resistance to both known races. Screening of advanced breeding lines has been conducted to prevent release of cultivars with high susceptibility to other important fungal foliar disease pathogens, including rust (Uromyces trifolii-repentis), powdery mildew (Oidium sp.), cercospora (Cercospora zebrina) and common leaf spot (Pseudopeziza trifolii). Several oomycete and fungal species cause root rots of subterranean clover, including Phytophthora clandestina, Pythium irregulare, Aphanomyces trifolii, Fusarium avenaceum and Rhizoctonia solani. Most breeding efforts have been devoted to resistance to P. clandestina, but the existence of different races has confounded selection. The most economically important virus diseases in subterranean clover pastures are Subterranean clover mottle virus and Bean yellow mosaic virus, while Subterranean clover stunt virus, Subterranean clover red leaf virus (local synonym for Soybean dwarf virus), Cucumber mosaic virus, Alfalfa mosaic virus, Clover yellow vein virus, Beet western yellows virus and Bean leaf roll virus also cause losses. Genotypic differences for resistance have been found to several of these fungal, oomycete and viral pathogens, highlighting the potential to develop cultivars with improved resistance. The most important pests of subterranean clover are redlegged earth mite (RLEM) (Halotydeus destructor), blue oat mite (Penthaleus major), blue-green aphid (Acyrthosiphon kondoi) and lucerne flea (Sminthurus viridis). New cultivars have been bred with increased RLEM cotyledon resistance, but limited selection has been conducted for resistance to other pests. Screening for disease and pest resistance has largely ceased, but recent molecular biology advances in subterranean clover provide a new platform for development of future cultivars with multiple resistances to important diseases and pests. However, this can only be realised if skills in pasture plant pathology, entomology, pre-breeding and plant breeding are maintained and adequately resourced. In particular, supporting phenotypic disease and pest resistance studies and understanding their significance is critical to enable molecular technology investments achieve practical outcomes and deliver subterranean clover cultivars with sufficient pathogen and pest resistance to ensure productive pastures across southern Australia.
Harmonization of initial estimates of shale gas life cycle greenhouse gas emissions for electric power generation
Authors: Heath Garvin A. , O’Donoughue Patrick , Arent Douglas J. , Bazilian Morgan
Published: July 2014

Significance

Previously published life cycle assessments (LCAs) of greenhouse gas emissions from the production and use of shale gas have come to widely varying conclusions about both the magnitude of emissions and its comparison with conventionally produced natural gas and coal for electricity generation. We harmonize estimates from this literature to establish more consistently derived and robust summary of the current state of knowledge. Whereas median estimates for both gas types appear less than half that of coal, alternative assumptions may lead to emissions approaching best-performing coal units, with implications for climate change mitigation strategies.
Control of axon–axon attraction by Semaphorin reverse signaling
Authors: Hsieh Hsiao-Han , Chang Wen-Tzu , Yu Li , Rao Yong
Published: July 2014

Significance

Bidirectional signaling between ligand and receptor facilitates cell–cell communication. Recent studies show that members of the well-known Semaphorin family proteins can mediate both forward and reverse signaling in regulating neural network formation. In this study, we identify new components of the Semaphorin reverse signaling pathway and reveal a novel mechanism by which Semaphorin reverse signaling promotes axon–axon attraction in patterning neuronal circuitry during development.
Sequence-resolved free energy profiles of stress-bearing vimentin intermediate filaments
Authors: Ramm Beatrice , Stigler Johannes , Hinczewski Michael , Thirumalai D. , Herrmann Harald , Woehlke Günther , Rief Matthias
Published: July 2014

Significance

Intermediate filaments (IFs) are an essential part of the cytoskeleton of metazoan cells, responsible for the cell’s shape and motility. To exert their mechanical function, IF dimers undergo a complex assembly into long filaments. The dimer ends are thought to mediate assembly. Mutations in these regions are associated with various diseases. We use single-molecule force spectroscopy by optical tweezers to mechanically open the C-terminal part of the dimer of the IF vimentin. Using deconvolution, a specialized analytic method, we can directly assess the stability of the C-terminal dimer end. Relating this stability to the amino acid sequence and structural features of the dimer, we shed light on the early assembly and mechanical properties of IFs.
Prolactin prevents hepatocellular carcinoma by restricting innate immune activation of c-Myc in mice
Authors: Hartwell Hadley J. , Petrosky Keiko Y. , Fox James G. , Horseman Nelson D. , Rogers Arlin B.
Published: July 2014

Significance

Hormonally active women are better protected from the primary liver cancer hepatocellular carcinoma (HCC) than men. In rodent models, the pituitary gland governs sexually dimorphic HCC risk. We found that the estrogen-responsive pituitary hormone prolactin (PRL) inhibits HCC by binding liver short-form prolactin receptors, resulting in accelerated degradation of a multimolecular “trafasome” involved in tumor-promoting innate immune signaling and preventing activation of the HCC-associated gene c-Myc. Mouse models confirmed sex-dependent HCC regulation upstream of c-Myc and a requirement for PRL but not estrogen in female tumor resistance. Importantly, a preclinical trial in mice showed that pharmacologic PRL mobilization using the human drug domperidone protected males from HCC. PRL-targeted therapy may help prevent liver cancer in high-risk men and women.
Side-chain conformation at the selectivity filter shapes the permeation free-energy landscape of an ion channel
Authors: Harpole Tyler J. , Grosman Claudio
Published: July 2014

Significance

Our mutagenesis work on the ring of glutamates in the charge-selectivity filter region of the muscle nicotinic acetylcholine receptor led us to propose that the rate at which ions permeate through the open channel depends not only on the number of these glutamates, but also on the conformation of their side chains. Because our inferences were made on the basis of electrophysiological observations, however, we decided to test the plausibility of these ideas using computer simulations. Remarkably, the simulations gave ample credence to all aspects of our proposal and allowed us to gain insight into the effect of specific glutamate rotamers on single-channel conductance.
Impact of DNA
3′
pp
5′
G capping on repair reactions at DNA 3′ ends
Authors: Das Ushati , Chauleau Mathieu , Ordonez Heather , Shuman Stewart
Published: July 2014

Significance

When DNA breakage results in a 3′-PO
4
terminus, the end is considered “dirty” because it cannot prime repair synthesis by DNA polymerases or sealing by classic DNA ligases. This paper shows how the noncanonical ligase RtcB can evade the dirty end problem by transferring GMP to the DNA 3′-PO
4
to form a DNA
3′
pp
5′
G cap. DNA capping blocks 3′ end-resection and healing, while permitting DNA synthesis from the cap guanosine–3′-OH primer by polymerases. Cap-primed synthesis embeds a pyrophosphate linkage in DNA. A 3′ decapping activity inherent in the disease-associated repair enzyme aprataxin suggests that DNA capping is a dynamic process.
Pathway of binding of the intrinsically disordered mitochondrial inhibitor protein to F
1
-ATPase
Authors: Bason John V. , Montgomery Martin G. , Leslie Andrew G. W. , Walker John E.
Published: July 2014

Significance

ATP, the fuel of biology, is produced by a molecular machine with a rotary action inside the mitochondria of living cells. Rotation is driven by a proton motive force (a voltage) across the inner membranes of the organelle generated from the controlled oxidation of sugars and fats in food-stuffs. If the cell were to encounter anoxic conditions, the rotary machine would use the energy stored in ATP and reverse its rotation. To prevent this wastage, reversal, but not forward rotation, is prevented by an intrinsically unfolded inhibitor protein, IF
1
, which inserts itself in the machine and stops reverse rotation. The article describes how this intrinsically disordered protein gains α-helical structure during the process of insertion into the machine.
Culpability across borders: print media of the DSK affair from an SFL perspective
Authors: Tjondro Michelle
Published: July 2014

This article explores the interactions between culture, linguistic choices and hard news journalistic practices, focusing on the Dominique Strauss-Kahn (DSK) affair of 2011 as the basis for a comparative analysis across three cultures: France, America and Guinea. The present study is motivated by the growing application of linguistic approaches to media studies and cross-cultural research, whose findings affirm the position that language is a resource capable of articulating and reproducing beliefs, judgments and even ideologies about social realities. Through the lens of systemic functional linguistics, patterns of linguistic choices that vary across the French and English language corpus are identified and then analysed with reference to the key discourses generated by the DSK affair. The results demonstrate the value of grammatical description in unveiling cultural, societal and individual ideologies that ordinarily have limited scope for expression in the hard news genre. Consequently, these findings suggest a tension between the presupposed neutrality of the legal process and the power of the media’s rhetoric in its capacity as an additional yet covert trial participant.
18-HEPE, an n-3 fatty acid metabolite released by macrophages, prevents pressure overload–induced maladaptive cardiac remodeling
Authors: Endo Jin , Sano Motoaki , Isobe Yosuke , Fukuda Keiichi , Kang Jing X. , Arai Hiroyuki , Arita Makoto
Published: July 2014

N-3 polyunsaturated fatty acids (PUFAs) have potential cardiovascular benefit, although the mechanisms underlying this effect remain poorly understood. Fat-1 transgenic mice expressing Caenorhabditis elegans n-3 fatty acid desaturase, which is capable of producing n-3 PUFAs from n-6 PUFAs, exhibited resistance to pressure overload–induced inflammation and fibrosis, as well as reduced cardiac function. Lipidomic analysis revealed selective enrichment of eicosapentaenoic acid (EPA) in fat-1 transgenic bone marrow (BM) cells and EPA-metabolite 18-hydroxyeicosapentaenoic acid (18-HEPE) in fat-1 transgenic macrophages. BM transplantation experiments revealed that fat-1 transgenic BM cells, but not fat-1 transgenic cardiac cells, contributed to the antiremodeling effect and that the 18-HEPE–rich milieu in the fat-1 transgenic heart was generated by BM-derived cells, most likely macrophages. 18-HEPE inhibited macrophage-mediated proinflammatory activation of cardiac fibroblasts in culture, and in vivo administration of 18-HEPE reproduced the fat-1 mice phenotype, including resistance to pressure overload–induced maladaptive cardiac remodeling.
Acid sphingomyelinase modulates the autophagic process by controlling lysosomal biogenesis in Alzheimer’s disease
Authors: Lee Jong Kil , Jin Hee Kyung , Park Min Hee , Kim Bo-ra , Lee Phil Hyu , Nakauchi Hiromitsu , Carter Janet E. , He Xingxuan , Schuchman Edward H. , Bae Jae-sung
Published: July 2014

In Alzheimer’s disease (AD), abnormal sphingolipid metabolism has been reported, although the pathogenic consequences of these changes have not been fully characterized. We show that acid sphingomyelinase (ASM) is increased in fibroblasts, brain, and/or plasma from patients with AD and in AD mice, leading to defective autophagic degradation due to lysosomal depletion. Partial genetic inhibition of ASM (ASM+/−) in a mouse model of familial AD (FAD; amyloid precursor protein [APP]/presenilin 1 [PS1]) ameliorated the autophagocytic defect by restoring lysosomal biogenesis, resulting in improved AD clinical and pathological findings, including reduction of amyloid-β (Aβ) deposition and improvement of memory impairment. Similar effects were noted after pharmacologic restoration of ASM to the normal range in APP/PS1 mice. Autophagic dysfunction in neurons derived from FAD patient induced pluripotent stem cells (iPSCs) was restored by partial ASM inhibition. Overall, these results reveal a novel mechanism of ASM pathogenesis in AD that leads to defective autophagy due to impaired lysosomal biogenesis and suggests that partial ASM inhibition is a potential new therapeutic intervention for the disease.
Understanding the release efficiency of Atlantic cod (Gadus morhua) from trawls with a square mesh panel: effects of panel area, panel position, and stimulation of escape response
Authors: Herrmann Bent , Wienbeck Harald , Karlsen Junita Diana , Stepputtis Daniel , Dahm Erdmann , Moderhak Waldemar
Published: July 2014

Based on size selectivity data for more than 25 000 cod (Gadus morhua) collected during experimental trawl fishing with six different codends, all of which included a square mesh panel, we investigated the effect on cod-release efficiency based on the size of the square mesh panel area, position of the square mesh panel, and stimulation of the escape response. Based on the results, we were able to explain why the BACOMA codend, applied in the Baltic Sea cod directed trawl fishery, releases juvenile cod efficiently, whereas other designs, including a square mesh panel with similar mesh size, are less efficient. Our main findings reveal that the release efficiency of the square mesh panel in the BACOMA codend depends largely on the overlap of the square mesh panel and the catch-accumulation zone in the codend, where cod do not have the option of just drifting further back in the trawl when proximate to the panel. On the contrary, the reduction in panel size by 50% did not significantly affect the release efficiency when the panel overlapped with the catch-accumulation zone. It was possible to stimulate an escape response for cod to achieve a release through a square mesh panel positioned away from the catch-accumulation zone. Our findings demonstrated that this release was as efficient as for a panel mounted in the catch-accumulation zone of the codend. Devices that stimulate behaviour may improve the release efficiency of cod through square mesh panels in other fisheries where this is a problem.
Capitalism
Authors: Robotham Donald
Published: July 2014

The study of capitalism covers a wide range of issues from the economic to the civilizational, which can easily overwhelm the scholar. For the purposes of clarity, capitalism is best defined as an economic system based on private ownership of the means of production and in which goods and services are freely exchanged by means of the market mechanism. It can be contrasted to various models of “state socialism” in which the means of production are collectively owned either through the state or in a cooperative relationship at the plant level and in which economic production and exchange are centrally planned and controlled. It is also to be distinguished from “market socialism,” which is a hybrid economic system in which critical areas of the economy, especially finance and core production functions, are collectively owned by the state but a large range of consumer enterprises are privatized, allowing market exchange to play a major role in economic transactions albeit within a framework of selective central planning and administrative oversight and regulation. The outstanding case of a capitalist economy today is the United States; the classical case of “state socialism” was the Soviet Union; and the best current example of “market socialism” is the Chinese economy. Given the vital issues of human development, political freedom, and ideology that are involved, these distinctions are highly controversial and contested. For example, debate is ongoing as to whether China is to be understood as a market socialist economy or simply a capitalist economy with a veneer of socialist rhetoric and an authoritarian political structure. Notwithstanding these debates, which cannot be avoided, the distinctions made above offer a useful point of departure to embark on the study of capitalism in an organized and logically coherent fashion. While focusing on the core economic aspects, this article attempts to cover the central cultural issues that would most interest anthropologists. It discusses the critical “peasant question” that occupied anthropological debates in the 1970s; the relationship between capitalism, development, and neoliberal globalization as well as the problem of capitalism and alienation, race, and the increasingly important study of place and space. Finally, toward the end, selections of some of the main studies that address the critical issue of money and the alternatives to capitalism are brought to the reader’s attention.
Fatal Acanthamoeba Encephalitis in a Patient With a Total Artificial Heart (Syncardia) Device
Authors: Tan Susanna K. , Gajurel Kiran , Tung Christie , Albers Gregory , Deresinski Stan , Montoya Jose G. , Sheikh Ahmad Y. , Banerjee Dipanjan , Ha Richard
Published: July 2014

Acanthamoeba encephalitis is an uncommon but often fatal infection complication. Here we report the first case of Acanthamoeba encephalitis in a patient with a Total Artificial Heart device.
Varicella Zoster Virus Pneumonitis and Brainstem Encephalitis Without Skin Rash in an Immunocompetent Adult
Authors: Nandhagopal Ramachandiran , Khmeleva Nelly , Jayakrishnan B. , White Teresa , Al Azri Faisal , George Jojy , Heintzman Anna , Al Zeedy Khalfan , Rorke-Adams Lucy , Gujjar Arunodaya R. , Schmid D. Scott , Al-Asmi Abdullah , Nagel Maria A. , Jacob Poovathoor Chacko , Gilden Don
Published: July 2014

Varicella zoster virus (VZV) pneumonitis and brainstem encephalitis developed in an immunocompetent adult without rash. Chest computed tomography exhibited nodularity; lung biopsy revealed multinucleated giant cells, Cowdry A inclusions, VZV antigen, and DNA. Varicella zoster virus central nervous system disease was verified by cerebrospinal fluid (CSF) anti-VZV IgG antibody with reduced serum/CSF ratios.