bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-focusing of a Hermite-cosh Gaussian laser beam in a magnetoplasma with ramp density profile
Authors: Nanda Vikas , Kant Niti , Wani Manzoor Ahmad
Published: November 2013

The early and strong self-focusing of a Hermite-cosh-Gaussian laser beam in magnetoplasma in the presence of density ramp has been observed. Focusing and de-focusing nature of the Hermite-cosh-Gaussian laser beam with decentered parameter and magnetic field has been studied, and strong self-focusing is reported. It is investigated that decentered parameter "b" plays a significant role for the self-focusing of the laser beam and is very sensitive as in case of extraordinary mode. For mode indices, m = 0, 1, 2,andb = 4.00, 3.14,and2.05, strong self-focusing is observed. Similarly in case of ordinary mode, for m = 0, 1, 2andb = 4.00, 3.14, 2.049, respectively, strong self-focusing is reported. Further, it is seen that extraordinary mode is more prominent toward self-focusing rather than ordinary mode of propagation. For mode indices  m = 0, 1,and2, diffraction term becomes more dominant over nonlinear term for decentered parameter b=0. For selective higher values of decentered parameter in case of mode indices m=0, 1,and2, self-focusing effect becomes strong for extraordinary mode. Also increase in the value of magnetic field enhances the self-focusing ability of the laser beam, which is very useful in the applications like the generation of inertial fusion energy driven by lasers, laser driven accelerators, and x-ray lasers.
Enhanced light scattering in Si nanostructures produced by pulsed laser irradiation
Authors: Sberna P. M. , Scapellato G. G. , Piluso N. , Boninelli S. , Miritello M. , Crupi I. , Bruno E. , Privitera V. , Simone F. , Mirabella S.
Published: November 2013

An innovative method for Si nanostructures (NS) fabrication is proposed, through nanosecond laser irradiation (λ = 532 nm) of thin Si film (120 nm) on quartz. Varying the laser energy fluences (425–1130 mJ/cm2) distinct morphologies of Si NS appear, going from interconnected structures to isolated clusters. Film breaking occurs through a laser-induced dewetting process. Raman scattering is enhanced in all the obtained Si NS, with the largest enhancement in interconnected Si structures, pointing out an increased trapping of light due to multiple scattering. The reported method is fast, scalable and cheap, and can be applied for light management in photovoltaics.
Heavily p-type doped chemical vapor deposition graphene field-effect transistor with current saturation
Authors: Peng Song-ang , Jin Zhi , Ma Peng , Yu Guang-hui , Shi Jing-yuan , Zhang Da-yong , Chen Jiao , Liu Xin-yu , Ye Tian-chun
Published: November 2013

Current saturation in graphene field-effect transistor (GFET) is of significant importance to improve the maximum oscillation frequency (fmax). We investigated the direct current (dc) and radio frequency (rf) characteristics of a heavily p-type doped GFET based on chemical vapor deposition grown material. The drain current saturation is found in our device. It cannot be explained by the “pinch-off” effect associated with ambipolar transport, but can be attributed to nonlinear channel conductance and velocity saturation in unipolar channel. This study promotes understanding the behaviors of heavily doped GFETs and their radio frequency applications.
Improving the quality factor of polycrystalline Si thin-film micromechanical resonators by metal-induced lateral crystallization using biomineralized Ni nanoparticles
Authors: Kumagai Shinya , Tomikawa Takashi , Ogawa Shohei , Yamashita Ichiro , Uraoka Yukiharu , Sasaki Minoru
Published: November 2013

We employed metal-induced lateral crystallization (MILC), using Ni nanoparticles synthesized within cage-shaped protein molecules, to crystallize an amorphous Si film into a polycrystalline film. This process allowed us to choose the crystallization sites of the polycrystalline silicon (poly-Si) film and enlarged the average grain size. We fabricated cantilever resonators from the poly-Si film to characterize them and extract quality factors. The reference resonator, fabricated without MILC, had a quality factor of 12 100, while the resonator crystallized along the axial direction had a quality factor of 26 200. Two-fold increase was achieved by tuning the crystal structure of the poly-Si film.
The Hamiltonian structure of a coupled system derived from a supersymmetric breaking of super Korteweg-de Vries equations
Authors: Restuccia A. , Sotomayor A.
Published: November 2013

A supersymmetric breaking procedure for N = 1 super Korteweg-de Vries (KdV), using a Clifford algebra, is implemented. Dirac's method for the determination of constraints is used to obtain the Hamiltonian structure, via a Lagrangian, for the resulting solitonic system of coupled KdV type system. It is shown that the Hamiltonian obtained by this procedure is bounded from below and in that sense represents a model which is physically admissible.
A Kramers-Kronig integral relation turned into a simple convolution operation and its application to dielectric measurements
Authors: Dias C. J.
Published: November 2013

This paper proposes that the conduction-free imaginary-part of dielectric constant may be obtained from a convolution between its real-part on a logarithmic scale of frequency and the hyperbolic cosecant function. This equation is, in fact, one of the Kramers-Kronig relations and is deduced from the relationships that relate a distribution of relaxation frequencies both to the real-part and to the conduction-free imaginary-part of the dielectric constant. This simple result has a large practical interest as it allows, for instance, checking for the presence of conductivity on experimental data.
Role of positive ions on the surface production of negative ions in a fusion plasma reactor type negative ion source—Insights from a three dimensional particle-in-cell Monte Carlo collisions model
Authors: Fubiani G. , Boeuf J. P.
Published: November 2013

Results from a 3D self-consistent Particle-In-Cell Monte Carlo Collisions (PIC MCC) model of a high power fusion-type negative ion source are presented for the first time. The model is used to calculate the plasma characteristics of the ITER prototype BATMAN ion source developed in Garching. Special emphasis is put on the production of negative ions on the plasma grid surface. The question of the relative roles of the impact of neutral hydrogen atoms and positive ions on the cesiated grid surface has attracted much attention recently and the 3D PIC MCC model is used to address this question. The results show that the production of negative ions by positive ion impact on the plasma grid is small with respect to the production by atomic hydrogen or deuterium bombardment (less than 10%).
Relativistic plasma expansion with Maxwell-Ju¨ttner distribution
Authors: Huang Yongsheng , Wang Naiyan , Tang Xiuzhang , Shi Yijin
Published: November 2013

A self-similar analytical solution is proposed to describe the relativistic ion acceleration with the local Maxwell-Ju¨ttner relativistic distribution electrons. It is an alternative to the existing static model [M. Passoni and M. Lontano, Phys. Rev. Lett. 101, 115001 (2008)], which exploits a limited solution for the acceleration potential. With our model, the potential is finite naturally and has an upper limitation proportional to the square root of the electron temperature. The divergent potential in the non-relativistic case is the linear items of the Taylor expansion of that obtained relativistic one here. The energy distribution of ions and the dependence of the ion momentum on the acceleration time are obtained analytically. Maximum ion energy has an upper limitation decided by the finite potential difference. In the ultra-relativistic region, the ion energy at the ion front is proportional to t4/5 and the energy of the ions behind the ion front is proportional to t2/3 since the field there is shielded by the ions beyond them and the field at the ion front is the most intense.
Arbitrary amplitude magnetosonic solitary and shock structures in spin quantum plasma
Authors: Sahu Biswajit , Sinha Anjana , Roychoudhury Rajkumar , Khan Manoranjan
Published: November 2013

A nonlinear analysis is carried out for the arbitrary amplitude magnetosonic solitary and shock structures in spin quantum plasmas. A quantum magnetohydrodynamic model is used to describe the magnetosonic quantum plasma with the Bohm potential and the pressure like spin force for electrons. Analytical calculations are used to simplify the basic equations, which are then studied numerically. It is shown that the magnetic diffusivity is responsible for dissipation, which causes the shock-like structures rather than the soliton structures. Additionally, wave speed, Zeeman energy, and Bohm potential are found to have significant impact on the shock wave structures.
On the electrodynamic model of ultra-relativistic laser-plasma interactions caused by radiation reaction effects
Authors: Bashinov A. V. , Kim A. V.
Published: November 2013

A simple electrodynamic model is developed to define plasma-field structures in self-consistent ultra-relativistic laser-plasma interactions when the radiation reaction effects come into play. An exact analysis of a circularly polarized laser interacting with plasmas is presented. We define fundamental notions, such as nonlinear dielectric permittivity, ponderomotive and dissipative forces acting in a plasma. Plasma-field structures arising during the ultra-relativisitc interactions are also calculated. Based on these solutions, we show that about 50% of laser energy can be converted into gamma-rays in the optimal conditions of laser-foil interaction.
Simulation and mitigation of the magneto-Rayleigh-Taylor instabilities in Z-pinch gas discharge extreme ultraviolet plasma radiation sources
Authors: Huang B. , Tomizuka T. , Xie B. , Sakai Y. , Zhu Q. , Song I. , Okino A. , Xiao F. , Watanabe M. , Hotta E.
Published: November 2013

The development and use of a single-fluid two-temperature approximated 2-D Magneto-Hydrodynamics code is reported. Z-pinch dynamics and the evolution of Magneto-Rayleigh-Taylor (MRT) instabilities in a gas jet type Extreme Ultraviolet (EUV) source are investigated with this code. The implosion and stagnation processes of the Z-pinch dynamics and the influence of initial perturbations (single mode, multi- mode, and random seeds) on MRT instability are discussed in detail. In the case of single mode seeds, the simulation shows that the growth rates for mm-scale wavelengths up to 4 mm are between 0.05 and 0.065 ns−1. For multi-mode seeds, the mode coupling effect leads to a series of other harmonics, and complicates MRT instability evolution. For perturbation by random seeds, the modes evolve to longer wavelengths and finally converge to a mm-scale wavelength approximately 1 mm. MRT instabilities can also alter the pinch stagnation state and lead to temperature and density fluctuations along the Z axis, which eventually affects the homogeneity of the EUV radiation output. Finally, the simulation results are related to experimental results to discuss the mitigations of MRT instability.
Influence of finite radial geometry on the growth rate of ion-channel free electron laser
Authors: Bahmani Mohammad , Hasanbeigi Ali , Hamzehpour Hossein
Published: November 2013

The influence of finite radial geometry on the instability of a tenuous relativistic electron beam propagating in an ion-channel in a waveguide is investigated. The instability analysis is based on the linearized Vlasov-Maxwell equations for the perturbation about a self-consistent beam equilibrium. With the help of characteristic method the dispersion relation for the TE-mode is derived and analyzed through the numerical solutions. It is found that the positioning of the beam radius Rb relative to the waveguide radius Rc, and the ion-channel frequency can have a large influence on the maximum growth rate and corresponding wave number.
GaN nanorod light emitting diodes with suspended graphene transparent electrodes grown by rapid chemical vapor deposition
Authors: Xu Kun , Xu Chen , Xie Yiyang , Deng Jun , Zhu Yanxu , Guo Weiling , Mao Mingming , Xun Meng , Chen Maoxing , Zheng Lei , Sun Jie
Published: November 2013

Ordered and dense GaN light emitting nanorods are studied with polycrystalline graphene grown by rapid chemical vapor deposition as suspended transparent electrodes. As the substitute of indium tin oxide, the graphene avoids complex processing to fill up the gaps between nanorods and subsequent surface flattening and offers high conductivity to improve the carrier injection. The as-fabricated devices have 32% improvement in light output power compared to conventional planar GaN-graphene diodes. The suspended graphene remains electrically stable up to 300 °C in air. The graphene can be obtained at low cost and high efficiency, indicating its high potential in future applications.
X-ray induced mobility of molecular oxygen at extreme conditions
Authors: Pravica Michael , Popov Dmitry , Sinogeikin Stanislav , Sneed Daniel , Guardala Griffin , Smith Quinlan
Published: November 2013

We report an in situ Raman study of KClO4 irradiated with x-rays in a diamond anvil cell. Decomposition via KClO4 + hv → KCl + 2O2 was monitored via the O2 vibron at 2 GPa, 6 GPa, and 9 GPa. For all pressures, the vibron grew in intensity and then diminished after successive irradiation suggesting that O2 was diffusing away from the irradiated region. Surprisingly, the diffusion rate accelerated with pressure increase, indicating that the nonhydrostatic pressure gradient was likely driving molecular diffusion of oxygen. At 9 GPa, the vibron bifurcated suggesting that O2 exists as two forms: interstitial and bulk solid. This method can be employed to study molecular diffusion under extreme conditions.
Spectral broadening in Brillouin imaging
Authors: Antonacci Giuseppe , Foreman Matthew R. , Paterson Carl , Török Peter
Published: November 2013

Brillouin microscopy is an emerging imaging modality that provides fundamental information about mechanical properties of media in a non-contact manner. To date, low numerical aperture (NA) optics have been used, due to noticeable angular broadening of the Brillouin spectrum at higher NAs. In this work, we investigate theoretically and experimentally the dependence of spectral broadening effects in Brillouin imaging on system NA, for both 90° and 180° scattering geometries. Lineshape deformations and broadening are found to be minimised in a backscattering geometry, hence paving the way for high resolution in-vivo mechanical imaging.
Ruminal pH and whole-tract digestibility in dairy cows consuming fresh cut herbage plus concentrates and conserved forage fed either separately or as a partial mixed ration
Authors: Greenwood J. S. , Auldist M. J. , Marett L. C. , Hannah M. C. , Jacobs J. L. , Wales W. J.
Published: November 2013

The objective of this experiment was to compare ruminal pH and whole-tract digestibility in cows consuming fresh cut herbage plus concentrates and silage or hay fed either separately or as a partial mixed ration (PMR). Fourteen rumen-fistulated Holstein-Friesian cows that had calved in late winter were housed in metabolism stalls for 9-day experiments in spring (97 days in milk (DIM)) and autumn (237 DIM). All cows were offered 8 kg dry matter (DM)/day of fresh cut perennial ryegrass (Lolium perenne L.) herbage, provided in two equal portions after each milking. Seven cows were assigned to each of two diets: (i) Control: 8.8 kg DM/cow.day milled wheat grain in two equal portions at milking, plus 3.2 kg DM/cow.day perennial ryegrass silage, with all cows receiving the silage portion of their diet after their grain but before their fresh herbage at the afternoon milking; and (ii) PMR: 12 kg DM/cow.day of a PMR containing similar ME as the Control supplements, but comprising maize grain, maize silage, wheat grain, lucerne hay (spring) and pasture silage (autumn). Intake and faecal output was measured on 5 days during each experiment, and ruminal pH was measured every 2 h for a 24-h period. Degradability of wheat and maize grain was measured using standard in sacco techniques. In both experiments, cows fed PMR had higher ruminal fluid pH than Control cows for at least part of the day. Apparent whole-tract digestibilities of DM, organic matter, nitrogen, neutral detergent fibre and starch were greater for Control than PMR cows in spring and not different in autumn (except starch). Ruminal pH was increased by feeding a maize-based PMR but this was not associated with increased whole-tract digestibility. We conclude that the ruminal pH in the Control cows was not low enough for long enough to compromise digestion, or that there was compensatory post-ruminal digestion.
Biological effect of tannins from different vegetal origin on microbial and fermentation traits in vitro
Authors: Rodríguez R. , de la Fuente G. , Gómez S. , Fondevila M.
Published: November 2013

The biological effect of tannins (proportion of the response in different parameters when tannins were inactivated with polyethylene glycol, PEG) as an easy, rapid way to estimate the magnitude of their effect on rumen microbial fermentation, was estimated in vitro for the tropical browse legumes Albizia lebbekoides, Acacia cornigera and Leucaena leucocephala, which differ in their phenolic and tannin content. Samples were incubated in rumen fluid for 24 h in four runs. The inactivation by PEG of tannins from A. lebbekoides increased gas production from 1.62- to 2.83-fold, with this biological effect increasing up to 8 h incubation, then being maintained and increasing after 16 h. In A. cornigera and L. leucocephala, the magnitude of the improvement of gas production was lower (from 1.1- to 1.32-fold and from 1.29- to 1.56-fold) and constant. The inclusion of PEG increased total volatile fatty acids (VFA) concentration (P = 0.019), reduced the molar proportion of acetate (P < 0.001) and increased that of butyrate (P < 0.001) and branched-chain VFA (P < 0.001). Microbial protein mass in A. lebbekoides increased with PEG in a higher extent (P < 0.001) than in L. leucocephala, but it was reduced in A. cornigera. No biological effect was observed on the efficiency of microbial protein synthesis when it was related to VFA concentration (P > 0.10), but when related to the gas produced it was lowest with A. lebbekoides (P = 0.023). The biological effect of tannins, either in total extent or along the incubation period differed according to their origin. Irrespective of their amount or chemical nature, the biological effect gives a direct idea of how tannins affect both the extent and pattern of forages fermentation.
The effect of peri-conceptual grazing of live pasture on fetal numbers in unsynchronised ewes
Authors: Robertson S. M. , King B. J. , Allworth M. B. , Rummery J. , Friend M. A.
Published: November 2013

Methods of increasing the number of lambs born per ewe that avoid the use of pharmaceutical methods of oestrus synchronisation but which require a short period of increased nutrition are desirable. Four separate experiments evaluated whether peri-conceptual grazing of lucerne, compared with senescent herbage or other live herbage, increased fetal numbers in unsynchronised ewes. Merino ewes that grazed lucerne pasture for 7 days before joining and for the first 7 days of a 5–6-week joining produced up to 21 extra (P < 0.05) fetuses per 100 ewes joined, compared with ewes grazing cereal stubble with minimal live herbage (Experiment 2). In Experiments 1, 3 and 4, Merino or First Cross ewes grazing either cereal stubbles or phalaris pasture with as little as 200 kg DM/ha of live herbage produced a similar (P > 0.05) number of fetuses per ewe joined as those grazing on lucerne, either because this quantity of live feed was sufficient to increase fetal numbers, or because, for Experiment 3, First Cross ewes may not have responded at the commencement of the breeding season. It is concluded that grazing live pasture for 7 days before joining and for the first 7 days of joining during the breeding season can substantially increase fetal numbers in unsynchronised ewes compared with ewes grazing stubbles containing no live herbage. The response appears to occur on a range of plant species, and a small quantity of live herbage can elicit a response. Grazing lucerne in the peri-conceptual period did not increase (P > 0.05) the proportion of non-pregnant ewes. Further studies are required to determine how early in the breeding season ewes with a distinct breeding season will respond to nutritional manipulation.
Molecular cloning, expression analysis and developmental changes in ovarian follicles of goose 3β-hydroxysteroid dehydrogenase 1
Authors: Zhang Yingying , Liu Hehe , Yang Mingjun , Hu Shengqiang , Li Liang , Wang Jiwen
Published: November 2013

The enzyme 3β-hydroxysteroid dehydrogenase/isomerase1 (3βHSD1) can catalyse the conversion of pregnenolone to progesterone in the △4-3-ketosteroid metabolic pathway. The aim of the present study was to clone 3βHSD1 and to determine whether this enzyme in the follicular wall has an effect on yolk progesterone in geese (Anser cygnoides). A putative coding sequence of 3βHSD1, which was 1134 nucleotides in length, was successfully obtained by using reverse transcription polymerase chain reaction (RT–PCR). A comparison of the deduced amino acid sequence with chicken, quail, zebra finch, cattle, horse, pig, human and mouse 3βHSD1 showed 89.7%, 88.4%, 87.3%, 55.6%, 54.0%, 53.5%, 55.3% and 52.9% similarity, respectively. The detection of 3βHSD1 mRNA levels in several tissues by quantitative real-time PCR showed that the highest level of 3βHSD1 was in the adrenal gland, followed by the ovary, which indicated that the gene we obtained was the adrenal gland/gonad-specific one. We measured the level of 3βHSD1 mRNA in the follicular wall and determined the concentration of progesterone in the yolk of these ovarian follicles; the concentration of progesterone in the yolk had a pattern of expression similar to that of 3βHSD1 in the follicular wall during follicular development. This result suggests that the expression of 3βHSD1 in the follicular wall may be a main factor that contributes to the accumulation of yolk progesterone.
Phosphorus supply level affects the regulation of phosphorus uptake by different arbuscular mycorrhizal fungal species in a highly P-efficient backcross maize line
Authors: Zheng Chaoyuan , Zhang Junling , Li Xiaolin
Published: November 2013

Arbuscular mycorrhizal (AM) fungi are known to facilitate effective acquisition of phosphorus (P) by host plants in low P soils. However, the contribution of mycorrhizal traits to high P-use efficiency in modern-bred maize genotypes is still not clear. In the present study one backcross maize inbred line 224 (bred for high P-use efficiency) was used as the host plant associated with AM fungal species (Rhizophagus irregularis or Glomus mosseae) grown at a range of soil P treatments (10, 20, 30, 40, 50, 100 mg P kg–1, Experiment 1) or foliar P applications (0, 0.025%, 0.5% m/v, Experiment 2). The experiments were to test the hypothesis whether the change point of the mycorrhizal growth and P responsiveness of 224, as well as the expression of ZEAma;Pht1;6 was at or near the optimal P supply level. In addition, different AM inoculants might differ in regulating P uptake of the host. Our results indicated that inbred line 224 was highly responsive to mycorrhizal inoculation. In Experiment 1, root colonisation rate, hyphal length density and alkaline phosphatase increased with the increase of soil P supply level. However, the mycorrhizal growth response (MGR) and P accumulation in shoot (MPR) were greatly affected by soil P supply level and varied between the two fungal species. Maize plants exhibited higher MGR and MPR at lower P supply when inoculated with R. irregularis, and at intermediate P supply when inoculated with G. mosseae. In Experiment 2, shoot P uptake was significantly increased by foliar P supply and inoculation, whereas shoot growth was significantly affected by P supply and the interaction. The expression of the AM-inducible Pi transporter gene ZEAma;Pht1;6 was neither significantly affected by soil (except at 100 mg P kg–1, Experiment 1) or foliar P supply level, nor by fungal species. Root P uptake efficiency (RPUE) was generally greatly increased by mycorrhizal colonisation at all P supply levels in both experiments, and significant correlations were observed between mycorrhizal variables and RPUE in Experiment 1. Our results indicate that the formation of mycorrhizal association could increase RPUE and thus may be partly attributed to high P-use efficiency of inbred line 224. The different responsiveness of mycorrhizal fungi to soil-available P implies the importance for the development of precision strategies to optimise the potential function of AM fungi under different P fertilisation management regime in agricultural soils.
Influence of sperm fertilising concentration, sperm selection method and sperm capacitation procedure on the incidence of numerical chromosomal abnormalities in IVF early bovine embryos
Authors: Demyda-Peyrás Sebastián , Dorado Jesús , Hidalgo Manuel , Moreno-Millán Miguel
Published: November 2013

The occurrence of numerical chromosomal aberrations, widely described as a major cause of mortality in in vitro-produced (IVP) embryos, has been linked to several factors. In the present study we investigated the effect of sperm fertilising concentration and semen handling (sperm selection and capacitation) before IVF on the rate of numerical chromosomal abnormalities in bovine embryos. In all, 466 IVP cattle embryos were karyotyped throughout three sequential experiments, analysing the effects of sperm fertilising concentration (0.1, 1.0 or 10 × 106 spermatozoa mL–1), selection method (unselected or Percoll-selected spermatozoa) and capacitation medium (bovine serum albumin (BSA), heparin or their combination). The percentage of normal (diploid) and aberrant (haploid, polyploid or aneuploid) embryos was noted in each experiment. The rate of numerical chromosomal abnormalities was mainly affected by sperm fertilising concentration (P < 0.01) and, to a lesser extent, by the sperm capacitation medium (P < 0.05). Polyploidy and haploidy rates were only affected by sperm fertilising concentration (P < 0.05). Interestingly, the sperm selection technique used in the present study did not reduce the incidence of chromosome abnormalities in IVP cattle embryos (P > 0.05). Finally, aneuploidy rates were not affected during the experiments (P > 0.05), which suggests that they are not related to sperm-related factors. On the basis of these results, we conclude that sperm fertilising concentration is the ‘paternal’ key factor that affects the rate of numerical chromosomal abnormalities in IVP bovine embryos. By making small adjustments to fertilising protocols, the rate of cytogenetically aberrant embryos can be markedly reduced.
Characterising weather patterns associated with fire in a seasonally dry tropical forest in southern India
Authors: Mondal Nandita , Sukumar Raman
Published: November 2013

Anthropogenic fires in seasonally dry tropical forests are a regular occurrence during the dry season. Forest managers in India, who presently follow a fire suppression policy in such forests, would benefit from a system of assessing the potential risk to fire on a particular day. We examined the relationship between weather variables (seasonal rainfall, relative humidity, temperature) and days of fire during the dry seasons of 2004–2010, based on MODIS fire incident data in the seasonally dry tropical forests of Mudumalai in the Western Ghats, southern India. Logistic regression analysis showed that high probabilities of a fire day, indicating successful ignition of litter and grass fuel on the forest floor, were associated with low levels of early dry season rainfall, low daily average relative humidity and high daily average temperatures. These weather conditions are representative of low moisture levels of fine fuels, suggesting that the occurrence of fire is moderated by environmental conditions that reduce the flammability of fine fuels in the dry tropics. We propose a quantitative framework for assessing risk of a fire day to assist forest managers in anticipating fire occurrences in this seasonally dry tropical forest, and possibly for those across South Asia.
Memory and synaptic deficits in
Hip14/DHHC17
knockout mice
Authors: Milnerwood Austen J. , Parsons Matthew P. , Young Fiona B. , Singaraja Roshni R. , Franciosi Sonia , Volta Mattia , Bergeron Sabrina , Hayden Michael R. , Raymond Lynn A.
Published: November 2013

Significance

Palmitoylation can influence the subcellular localization of various synaptic proteins; this process is therefore increasingly recognized as an important regulator of basal synaptic communication as well as activity-dependent synaptic plasticity. Despite the fact that in vitro experiments indicate that many synaptic proteins can be palmitoylated by more than one palmitoyl acyltransferase (PAT), the enzymes responsible for palmitoylation, we describe in this paper various synaptic, plastic, and cognitive consequences that result from constitutive loss of a single PAT, namely Hip14/DHHC17. This reveals an important functional role for this PAT that cannot be compensated for by other existing PATs.
Genome-scale metabolic reconstructions of multiple
Escherichia coli
strains highlight strain-specific adaptations to nutritional environments
Authors: Monk Jonathan M. , Charusanti Pep , Aziz Ramy K. , Lerman Joshua A. , Premyodhin Ned , Orth Jeffrey D. , Feist Adam M. , Palsson Bernhard Ø.
Published: November 2013

Significance

Multiple
Escherichia coli
genome sequences have recently been made available by advances in DNA sequencing. Analysis of these genomes has demonstrated that the fraction of genes common to all
E. coli
strains in the species represents a small fraction of the entire
E. coli
gene pool. This observation raises the question: what is a strain and what is a species? In this study, genome-scale metabolic reconstructions of multiple
E. coli
strains are used to reconstruct the metabolic network for an entire species and its strain-specific variants. The models are used to determine functional differences between strains and define the
E. coli
species based on common metabolic capabilities. Individual strains were differentiated based on niche-specific growth capabilities.
ORAI1 calcium channel orchestrates skin homeostasis
Authors: Vandenberghe Matthieu , Raphaël Maylis , Lehen’kyi V’yacheslav , Gordienko Dmitri , Hastie Ryan , Oddos Thierry , Rao Anjana , Hogan Patrick G. , Skryma Roman , Prevarskaya Natalia
Published: November 2013

Significance

The epidermis of the skin is composed of keratinocytes that are organized in several layers. Basal cells divide and produce cells moving outwards the epidermis while undergoing the process of terminal differentiation, crucial for the barrier function of the skin. Calcium is an indispensible ion for differentiation, and calcium channels are of primary importance. Unexpectedly, we discovered that the Orai1 calcium channel is mainly expressed in the basal layer, functioning to negatively control differentiation. The Orai1 channel supplies calcium to sustain proliferation and, in particular, to drive migration of keratinocytes, both processes being the feature of basal keratinocytes.
Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution
Authors: Smyshlyaev Georgy , Voigt Franka , Blinov Alexander , Barabas Orsolya , Novikova Olga
Published: November 2013

Significance

Transposons are jumping genes that constitute a sizeable fraction of eukaryotic genomes. They drive genome evolution and can cause genetic diseases and cancer. Although transposons were first discovered in plants and much of our knowledge about them stems from plants, the most abundant human transposon, L1, has barely been investigated in plants. In this study, we identify plant L1 retrotransposons from a variety of plant genomes and show that, similar to viruses, they evolved in a modular fashion by gaining and losing various protein-coding domains. Moreover, we find that plant L1s carry an active Archaea-like ribonuclease H (RNH) domain, suggesting that they shuttle RNH between plants, bacteria, and Archaea.
Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages
Authors: de Mendoza Alex , Sebé-Pedrós Arnau , Šestak Martin Sebastijan , Matejčić Marija , Torruella Guifré , Domazet-Lošo Tomislav , Ruiz-Trillo Iñaki
Published: November 2013

Significance

Independent transitions to multicellularity in eukaryotes involved the evolution of complex transcriptional regulation toolkits to control cell differentiation. By using comparative genomics, we show that plants and animals required richer transcriptional machineries compared with other eukaryotic multicellular lineages. We suggest this is due to their orchestrated embryonic development. Moreover, our analysis of transcription factor (TF) expression patterns during the development of animals reveal links between TF evolution, species ontogeny, and the phylotypic stage.
Internalizing MHC class II–peptide complexes are ubiquitinated in early endosomes and targeted for lysosomal degradation
Authors: Furuta Kazuyuki , Walseng Even , Roche Paul A.
Published: November 2013

Significance

Antigen-presenting cells (APCs) function as the sentinels of the immune system by ingesting foreign pathogens, generating peptide fragments of these pathogens in endo-/lysosomes, where the peptides bind to MHC class II molecules, and expressing these peptide–MHC class II complexes (pMHC-II) on the APC surface. Antigen-specific CD4 T cells scan APC surfaces for appropriate pMHC-II, and, if not recognized by T cells, pMHC-II are degraded. We now show that internalizing pMHC-II are targeted for degradation by ubiquitination by the E3 ligase March-I in early endosomes. The “arrive at the surface, internalize from the surface, become ubiquitinated, then die” life cycle for pMHC-II ensures that APCs have ample opportunity to present a wide variety of foreign antigens to the immune system.
Constitutively active UVR8 photoreceptor variant in
Arabidopsis
Authors: Heijde Marc , Binkert Melanie , Yin Ruohe , Ares-Orpel Florence , Rizzini Luca , Van De Slijke Eveline , Persiau Geert , Nolf Jonah , Gevaert Kris , De Jaeger Geert , Ulm Roman
Published: November 2013

Significance

Sunlight is an essential environmental factor for photosynthetic plants and ultimately for life on Earth, which is sustained through plants as fundamental source of food. However, plants have a love/hate relationship with sunlight and must be protected from potentially harmful UV-B radiation. The UV-B photoreceptor UVR8 is of great importance in mounting UV-protective responses and thus for survival in sunlight. Based on our understanding of UVR8 signaling, we have engineered a UVR8 variant that is constitutively active in transgenic plants. The generation of a constitutively active photoreceptor variant is an important step in understanding the molecular signaling mechanism and may hold opportunities for crop improvement.
Unsteady penetration of a target by a liquid jet
Authors: Uth Tobias , Deshpande Vikram S.
Published: November 2013

Significance

It is widely acknowledged that a projectile impacting a ceramic target may erode on the surface of the target without substantial penetration for a significant amount of time and then suddenly start to penetrate. This phenomenon, commonly referred to as dwell, although known for four decades, remains largely unexplained. We demonstrate that dwell also occurs for a gel-like target material impacted by a water jet due to an increase in the force exerted by the jet on the target. The force increase is a fluid–structure interaction effect and traced to flow reversal of the jet caused by the progressive deformation of the jet–target interface. This effect is expected to occur in situations such as water-jet cutting and needleless injection.
Atmospheric deposition of methanol over the Atlantic Ocean
Authors: Yang Mingxi , Nightingale Philip D. , Beale Rachael , Liss Peter S. , Blomquist Byron , Fairall Christopher
Published: November 2013

Significance

Transport of gases between the ocean and the atmosphere has profound implications for our environment and the Earth’s climate. An example of this transport is the oceanic uptake of carbon dioxide, which has buffered us from a higher concentration of this greenhouse gas in the atmosphere while also causing ocean acidification. Here we describe the first direct measurements of air–sea methanol transfer. Atmospheric methanol, a ubiquitous and abundant organic gas of primarily terrestrial origin, is observed to be transported over thousands of kilometers and deposited over the ocean, where it is likely consumed by marine microbes. We quantify the rate of methanol deposition and examine the governing processes near the air–sea interface.
ABCC6 prevents ectopic mineralization seen in pseudoxanthoma elasticum by inducing cellular nucleotide release
Authors: Jansen Robert S. , Küçükosmanoğlu Aslı , de Haas Marcel , Sapthu Sunny , Otero Jon Andoni , Hegman Ilse E. M. , Bergen Arthur A. B. , Gorgels Theo G. M. F. , Borst P. , van de Wetering Koen
Published: November 2013

Significance

Pseudoxanthoma elasticum (PXE) is a heritable disease characterized by mineralization of the skin, eyes, and arteries, for which no effective treatment exists. PXE is caused by inactivating mutations in the gene encoding the transporter ABCC6. PXE is a metabolic disease caused by the absence of an unknown factor in the circulation. Our study indicates that the factor that normally prevents PXE is pyrophosphate, which is provided to the circulation in the form of nucleoside triphosphates via an ABCC6-dependent mechanism. Our findings provide leads for the treatment of this intractable disease.
Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins
Authors: Heaton Nicholas S. , Sachs David , Chen Chi-Jene , Hai Rong , Palese Peter
Published: November 2013

Significance

Influenza A virus is characterized by a large host range and rapid antigenic drift—features not common to many viruses. To begin to understand the molecular basis behind these features, we performed genome-wide mutagenesis to gauge the relative flexibility of the viral genome. We found that only two small regions in the genome (the hemagglutinin head domain and nonstructural protein 1) were highly tolerant to transposon-based insertional mutation. We believe that this analysis highlights an evolutionary strategy of influenza A virus: maintain highly plastic domains in proteins required for rapid host adaptation. This finding may help explain why influenza viruses possess certain traits not common to all RNA viruses.
A Multicenter Case-Case Control Study for Risk Factors and Outcomes of Extensively Drug-ResistantAcinetobacter baumanniiBacteremia
Authors: Ng Tat Ming , Teng Christine B. , Lye David C. , Apisarnthanarak Anucha
Published: November 2013

Objective.

Extensively drug resistant (XDR)Acinetobacter baumanniiinfections are increasing. Knowledge of risk factors can help to prevent these infections.

Methods.

We designed a 1: 1: 1 case-case-control study to identify risk factors for XDRA. baumanniibacteremia in Singapore and Thailand. Case group 1 was defined as having infection due to XDRA. baumannii, and case group 2 was defined as having infection due to non-XDRA. baumannii. The control group comprised patients with blood cultures obtained to determine possible infection.

Results.

There were 93 patients in each group. Pitt bacteremia score (adjusted odds ratio [aOR], 2.570 [95% confidence interval (CI), 1.528–4.322]), central venous catheters (CVCs; aOR, 12.644 [95% CI, 2.143–74.620]), use of carbapenems (aOR, 54.391 [95% CI, 3.869–764.674]), and piperacillin-tazobactam (aOR, 55.035 [95% CI, 4.803–630.613]) were independently associated with XDRA. baumanniibacteremia. In case group 2, Pitt bacteremia score (aOR, 1.667 [95% CI, 1.265–2.196]) and third-generation cephalosporins (aOR, 2.965 [95% CI, 1.224–7.182]) were independently associated with non-XDRA. baumanniibacteremia. Concurrent infections (aOR, 3.527 [95% CI, 1.479–8.411]), cancer (aOR, 3.172 [95% CI, 1.135–8.865]), and respiratory source (aOR, 2.690 [95% CI, 1.160–6.239]) were associated with an increased risk of 30-day mortality. Survivors received more active empirical therapy (16.7% vs 9.6%;P= .157), had fewer cases of XDR bacteremia (45.8% vs 52.6%;P= .452), and received higher median definitive polymyxin B doses (840,000 units vs 700,000 units;P= .339)

Conclusions.

Use of CVC and broad spectrum antibiotics were unique risk factors of XDRA. baumanniibacteremia. Effective antimicrobial stewardship together with use of a CVC bundle may reduce the incidence of these infections. Risk factors of acquisition and mortality may help identify patients for early initiation of polymyxin B therapy.
Contamination of Healthcare Workers' Hands with Clostridium difficile Spores after Caring for Patients with C. difficile Infection
Authors: Landelle C. , Verachten M. , Legrand P. , Girou E. , Barbut F. , Buisson C. Brun
Published: November 2013

Objective.

We determined the percentage of healthcare workers' (HCWs') hands contaminated with Clostridium difficile spores after caring for patients with C. difficile infection (CDI) and risk factors associated with contamination.

Design.

Prospective study.

Setting.

A French university hospital.

Methods.

We compared the hand contamination rate among HCWs caring for patients with CDI (exposed group; n = 66) with that among an unexposed group (n = 44). Spores of C. difficile were recovered from the hands of HCWs after rubbing their fingers and palms in alcohol shortly after patient care. Associations between hand contamination and HCW category, type (patient or environment), and risk level (high or low risk) of HCW contacts and their respective duration as well as use of gloves were analyzed by bivariate and multivariate analysis.

Results.

C. difficile spores were detected on 24% of HCWs' hands in the exposed group and on 0% in the unexposed group (P < .001). In the exposed group, logistic regression, which adjusted for high-risk contact (ie, exposure to fecal soiling), contact with the environment, and contact with or without use of gloves, revealed that high-risk contact (adjusted odds ratio [aOR] per 1 contact increment, 2.78; 95% confidence interval [CI], 1.42–5.45; P = .003) and at least 1 contact without use of gloves (aOR, 6.26; 95% CI, 1.27–30.78; P = .02) were independently associated with HCW hand contamination by C. difficile spores.

Conclusions.

Nearly one-quarter of HCWs have hands contaminated with C. difficile spores after routine care of patients with CDI. Hand contamination is positively associated with exposure to fecal soiling and lack of glove use.
Optimality of CKP-inequality in the critical case
Authors: Gao Fuchang
Published: November 2013

It is proved that the CKP inequality
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartRoot log upper N left-parenthesis cov left-parenthesis upper T right-parenthesis comma 2 epsilon right-parenthesis EndRoot precedes-above-single-line-equals StartFraction 1 Over epsilon EndFraction integral Subscript epsilon slash 2 Superscript normal infinity Baseline StartRoot log upper N left-parenthesis upper T comma r right-parenthesis EndRoot d r">

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is optimal in the critical case
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.
Structural determinants of DNA recognition by plant MADS-domain transcription factors
Authors: Muiño Jose M. , Smaczniak Cezary , Angenent Gerco C. , Kaufmann Kerstin , van Dijk Aalt D.J.
Published: November 2013

Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.
Cyclobacterium xiamenense sp. nov., isolated from aggregates of Chlorella autotrophica, and emended description of the genus Cyclobacterium
Authors: Chen Zhangran , Yang Luxi , Li Yi , Lai Qiliang , Zhang Huajun , Wei Jun , Zhou Yanyan , Lei Xueqian , Zheng Wei , Tian Yun , Xiong Xiaojing , Zheng Tianling
Published: November 2013

A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain KD51T, forming colonies coloured pink by carotenoid pigments, was isolated from aggregates of the alga Chlorella autotrophica collected from the coastal sea off the city of Xiamen, Fujian Province, China. 16S rRNA gene sequence comparison showed that strain KD51T was a member of the genus

Cyclobacterium

, forming a distinct lineage with

Cyclobacterium lianum

HY9T. The 16S rRNA gene sequence similarity between strain KD51T and the type strains of species of the genus

Cyclobacterium

ranged from 92.1 % to 95.2 %. Growth occurred at 4–40 °C (optimum, 28 °C), in the presence of 3–9 % NaCl (optimum, 3–5 %) and at pH 6–10 (optimum, pH 7.5). The dominant fatty acids (>20 %) of strain KD51T were iso-C15 : 0 (32.2 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c; 22.2 %). The DNA G+C content was 41.7 mol% and the only respiratory quinone was menaquinone-7. On the basis of phenotypic data and phylogenetic inference, strain KD51T represents a novel species of the genus

Cyclobacterium

, for which the name Cyclobacterium xiamenense sp. nov. is proposed. The type strain is KD51T ( = CGMCC 1.12432T = KCTC 32253T). An emended description of the genus

Cyclobacterium

is also proposed.