bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of static carrier screening on the energy relaxation of electrons in polar-semiconductor multiple-quantum-well superlattices
Authors: Feng Y. , Lin S. , Green M. , Conibeer G.
Published: January 2013

An electro-static model has been formalized to analyze the effect of carrier screening on the energy relaxation of electrons in polar-semiconductor multiple-quantum-well superlattices. The screened polar potential in this structure has been obtained in terms of its 0th order and 1st order Fourier components. The 1st order correction gives a further reduction of the coupling strength due to the uneven spatial distribution of carriers, and it heavily depends on the relative bi-layer thickness compared to the Debye screening length. The reductions of electron energy relaxation in In0.25GaAs/GaAsP0.33 multiple-quantum-well superlattices have been numerically analyzed yielding conclusions which agree with the recent experiments. The model provides a quantified approach to optimize the structure configuration in terms of the carrier cooling rate, allowing the multiple-quantum-well superlattice to be an ideal absorber candidate for realizing the hot carrier solar cell.
Direct current plasma jet at atmospheric pressure operating in nitrogen and air
Authors: Deng X. L. , Nikiforov A. Yu. , Vanraes P. , Leys Ch.
Published: January 2013

An atmospheric pressure direct current (DC) plasma jet is investigated in N2 and dry air in terms of plasma properties and generation of active species in the active zone and the afterglow. The influence of working gases and the discharge current on plasma parameters and afterglow properties are studied. The electrical diagnostics show that discharge can be sustained in two different operating modes, depending on the current range: a self-pulsing regime at low current and a glow regime at high current. The gas temperature and the N2 vibrational temperature in the active zone of the jet and in the afterglow are determined by means of emission spectroscopy, based on fitting spectra of N2 second positive system (C3Π-B3Π) and the Boltzmann plot method, respectively. The spectra and temperature differences between the N2 and the air plasma jet are presented and analyzed. Space-resolved ozone and nitric oxide density measurements are carried out in the afterglow of the jet. The density of ozone, which is formed in the afterglow of nitrogen plasma jet, is quantitatively detected by an ozone monitor. The density of nitric oxide, which is generated only in the air plasma jet, is determined by means of mass-spectroscopy techniques.
Effective potential energy curves of the ground electronic state of CH+
Authors: Sauer Stephan P. A. , Špirko Vladimír
Published: January 2013

This study presents effective (mass-dependent) potential energy curves for the methylidyne cation, which reproduce highly accurately all the available spectral data and allow for evaluation of reliable ro-vibrational wavefunctions of the probed isotopomers. The ro-vibrational wavefunctions are then used to average ab initio calculated radial functions of the rotational g-factor and spin-rotation constants yielding rotational and vibrational matrix elements of these properties for specific ro-vibrational states or transition moments for all isotopomers. The results can be of use in answering open questions concerning the formation/destruction of CH+ in the interstellar medium and in the assignment of Zeeman or hyperfine splittings in rotational spectra of CH+.
Multi-stack InAs/InGaAs sub-monolayer quantum dots infrared photodetectors
Authors: Kim J. O. , Sengupta S. , Barve A. V. , Sharma Y. D. , Adhikary S. , Lee S. J. , Noh S. K. , Allen M. S. , Allen J. W. , Chakrabarti S. , Krishna S.
Published: January 2013

We report on the design and performance of multi-stack InAs/InGaAs sub-monolayer (SML) quantum dots (QD) based infrared photodetectors (SML-QDIP). SML-QDIPs are grown with the number of stacks varied from 2 to 6. From detailed radiometric characterization, it is determined that the sample with 4 SML stacks has the best performance. The s-to-p (s/p) polarized spectral response ratio of this device is measured to be 21.7%, which is significantly higher than conventional Stranski-Krastanov quantum dots (∼13%) and quantum wells (∼2.8%). This result makes the SML-QDIP an attractive candidate in applications that require normal incidence.
Influence of the oxide aperture radius on the mode spectra of (Al,Ga)As vertical microcavities with electrically excited InP quantum dots
Authors: Weidenfeld S. , Schulz W.-M. , Kessler C. A. , Reischle M. , Eichfelder M. , Wiesner M. , Jetter M. , Michler P.
Published: January 2013

In this letter, we report about mode characteristics of microcavity lasers with red-emitting InP quantum dots. The mode spectra and the quality factor of devices with different oxide aperture sizes are analyzed. The lateral mode confinement in the electrical devices is defined via oxide apertures. We found a good agreement between a simple analytical modeling of the mode structure and measurements, which allows to adjust the design of future devices. The quality factors show an analogous behavior as etched micropillars. The enhanced intensity of the higher order modes compared to the fundamental mode can be explained with the current density distribution within the device favoring higher order modes.
Four-electrode impedance spectrometer for investigation of solid ion conductors
Authors: Kežionis A. , Butvilas P. , Šalkus T. , Kazlauskas S. , Petrulionis D. , Žukauskas T. , Kazakevičius E. , Orliukas A. F.
Published: January 2013

An impedance spectrometer capable of accurately measuring solid ion conducting sample impedance spectra by two- or four-electrode methods in either time or frequency domain has been built. The four-electrode measurement mode is implemented by constructing a differential amplifier with a very high input impedance and common mode rejection ratio over a wide frequency range. All of the measurements can be performed in frequencies ranging from 10 Hz to 2 MHz and sample temperatures up to 800 K. The working principle of the spectrometer as well as its technical parameters and accuracy estimation are presented in this paper. The advantage of four-electrode over two-electrode measurement mode is shown by an example of Ce0.9Gd0.1O1.95 solid electrolyte ceramic impedance measurements.
Observation of symmetrically decay of A1(longitudinal optical) mode in free-standing GaN bulk single crystal from Li3N flux method
Authors: Zhang X. H. , Zhao C. L. , Han J. C. , Wang Y. , Jian J. K. , Wang G. , Zhang Z. H. , Li H. , Wang W. J. , Song Y. T. , Liu Y. , Bao H. Q. , Chen X. L. , Song B.
Published: January 2013

We report Raman analysis of A1(LO) (longitudinal optical) and E2(high) phonon lifetimes in a bulk GaN single crystal and their temperature dependence from 77 K to 770 K. Both the A1(LO) and E2(high) phonons in GaN were observed decaying primarily into two phonons of equal energy [Klemens model, P. G. Klemens, Phys. Rev. 148, 845 (1966)]. This is a rare example of a high-quality free-standing GaN bulk single crystal displaying abnormal A1(LO) phonon decay. These results will have significant impact on designing and understanding of GaN-based high-speed, high-power electric devices.
Strange hardness characteristic of hydrogenated diamond-like carbon thin film by plasma enhanced chemical vapor deposition process
Authors: Dwivedi Neeraj , Kumar Sushil , Malik Hitendra K.
Published: January 2013

By creating nanostructures and controlling the hydrogen content and sp3/sp2 bonding ratio, we report the formation of very hard (35.8 GPa) hydrogenated diamond-like carbon film at a self-bias of −100 V using simple radio frequency-plasma enhanced chemical vapor deposition process. When the self-bias is varied and modifications such as incorporation of nitrogen and Ag interlayer are executed, the mechanical properties of such films, however, got altered that are correlated well with the structural changes investigated using various spectroscopic and microscopic techniques.
Large-area ultraviolet GaN-based photonic quasicrystal laser with high-efficiency green color emission of semipolar {10-11} In0.3Ga0.7N/GaN multiple quantum wells
Authors: Chen Cheng-Chang , Chiu Ching-Hsueh , Chang Shih-Pang , Shih M. H. , Kuo Ming-Yen , Huang Ji-Kai , Kuo Hao-Chung , Chen Shih-Pu , Lee Li-Ling , Jeng Ming-Shan
Published: January 2013

In this study, a multi-color emission was observed from the large-area GaN-based photonic quasicrystal (PQC) nanopillar laser. The GaN PQC nanostructure was fabricated on an n-GaN layer by using nanoimprint lithographic technology. The regrown InGaN/GaN multiple quantum wells (MQWs) formed a nanopyramid structure on top of the PQC nanopillars. A lasing action was observed at ultraviolet wavelengths with a low threshold power density of 24 mJ/cm2, and a green color emission from InGaN/GaN MQWs was also achieved simultaneously.
GaN/AlGaN waveguide quantum cascade photodetectors at λ ≈ 1.55 μm with enhanced responsivity and ∼40 GHz frequency bandwidth
Authors: Sakr S. , Crozat P. , Gacemi D. , Kotsar Y. , Pesach A. , Quach P. , Isac N. , Tchernycheva M. , Vivien L. , Bahir G. , Monroy E. , Julien F. H.
Published: January 2013

We report on ultrafast GaN/AlGaN waveguide quantum cascade detectors with a peak detection wavelength of 1.5 μm. Mesa devices with a size of 7 × 7 and 10 × 10 μm2 have been fabricated with radio-frequency impedance-matched access lines. A strong enhancement of the responsivity is reported by illuminating the waveguide facet, with respect to illumination of the top surface. The room temperature responsivity is estimated to be higher than 9.5 ± 2 and 7.8 ± 2 mA/W, while the −3dB frequency response is extracted to be 42 and 37.4 GHz for 7 × 7 and 10 × 10 μm2 devices, respectively.
High-quality InP nanoneedles grown on silicon
Authors: Ren Fan , Wei Ng Kar , Li Kun , Sun Hao , Chang-Hasnain Connie J.
Published: January 2013

In this letter, we report the growth of self-assembled, catalyst-free InP nanoneedles on Si substrate by low-temperature metal-organic chemical vapor deposition. With a characteristic core-shell growth mode, the nanostructure size is scalable with growth time, and InP/InGaAs/InP double-heterostructure is demonstrated. Single crystalline wurtzite InP nanoneedles essentially free of stacking faults and polytypism are achieved. The internal quantum efficiency of as-grown unpassivated InP nanoneedles can reach as high as 15% at room temperature. Laser oscillation is realized from single InP nanoneedle under optical pump. These promising results reveal the potential of integrating InP nanoneedle optoelectronic devices with traditional silicon.
Highly efficient fluorescence detection using a simplified hollow core microstructured optical fiber
Authors: Li Zhi-Li , Zhou Wen-Yuan , Liu Yan-Ge , Ye Qing , Ma Yue , Wei Hui-Feng , Tian Jian-Guo
Published: January 2013

A high efficiency fluorescence measurement technology based on a simplified hollow-core microstructured optical fiber (SHMOF) and a charge-coupled device (CCD) lateral side detection approach is demonstrated. By selective injection of dye solutions into the hollow core, the input laser beam is transferred between the hollow core and the liquid core of the SHMOF, resulting in strong fluorescence stimulation. By using a CCD to detect fluorescence on the fiber's lateral side, highlighted sensitivity with dye concentrations down to 1 pM is achieved. It also provides a practical way to detect multiple signals simultaneously and distinguish between them in space.
On the interplay of point defects and Cd in non-polar ZnCdO films
Authors: Zubiaga A. , Reurings F. , Tuomisto F. , Plazaola F. , García J. A. , Kuznetsov A. Yu. , Egger W. , Zúñiga-Pérez J. , Muñoz-Sanjosé V.
Published: January 2013

Non-polar ZnCdO films, grown over m- and r-sapphire with a Cd concentration ranging between 0.8% and 5%, have been studied by means of slow positron annihilation spectroscopy (PAS) combined with chemical depth profiling by secondary ion mass spectroscopy and Rutherford back-scattering. Vacancy clusters and Zn vacancies with concentrations up to 1017 cm−3 and 1018 cm−3, respectively, have been measured inside the films. Secondary ion mass spectroscopy results show that most Cd stays inside the ZnCdO film but the diffused atoms can penetrate up to 1.3 μm inside the ZnO buffer. PAS results give an insight to the structure of the meta-stable ZnCdO above the thermodynamical solubility limit of 2%. A correlation between the concentration of vacancy clusters and Cd has been measured. The concentration of Zn vacancies is one order of magnitude larger than in as-grown non-polar ZnO films and the vacancy cluster are, at least partly, created by the aggregation of smaller Zn vacancy related defects. The Zn vacancy related defects and the vacancy clusters accumulate around the Cd atoms as a way to release the strain induced by the substitutional CdZn in the ZnO crystal.
Oxygen vacancy migration in compressively strained SrTiO3
Authors: Al-Hamadany Raied , Goss J. P. , Briddon P. R. , Mojarad Shahin A. , Al-Hadidi Meaad , O'Neill A. G. , Rayson M. J.
Published: January 2013

The intrinsic properties of strontium titanate render it promising in applications such as gate dielectrics and capacitors. However, there is growing evidence that oxygen vacancies significantly impact upon its use, with the diffusion and deep donor level of the oxygen vacancy leading to electrical leakage. Where grown epitaxially on a lattice mismatched substrate, SrTiO3 undergoes bi-axial strain, altering its crystal structure and electronic properties. In this paper, we present the results of first-principles simulations to evaluate the impact of strain in a (001) plane upon the migration of oxygen vacancies. We show that in the range of strains consistent with common substrate materials, diffusion energies in different directions are significantly affected, and for high values of strain may be altered by as much as a factor of two. The resulting diffusion anisotropy is expected to impact upon the rate at which oxygen vacancies are injected into the films under bias, a critical factor in the leakage and resistive switching seen in this material.
Molecular dynamic simulation of diamond/silicon interfacial thermal conductance
Authors: Khosravian N. , Samani M. K. , Loh G. C. , Chen G. C. K. , Baillargeat D. , Tay B. K.
Published: January 2013

Non-equilibrium molecular dynamic simulation was employed to investigate the interfacial thermal conductance between diamond and silicon substrate. The interfacial thermal conductance was computed based on Fourier's law. The simulation was done at different temperature ranges and results show that the interfacial thermal conductance between diamond-silicon is proportional to temperature and increases with temperature even above Debye temperature of silicon. Enhancement of thermal boundary conductance with temperature is attributed to inelastic phonon-phonon scattering at the interface. The system size dependence of interfacial thermal conductance was also examined. We found that thermal transport is a function of the system size when the size of system is smaller than the phonon mean free path and increases with the size of structure. We also simulated the effect of interface defect on phonon scattering and subsequently thermal conductance. The results also show that interface defect enhances acoustic phonon scattering which results in reduction of thermal boundary conductance. Our findings provide accurate and valuable information on phonon transport in diamond-silicon structure.
Role of carrier density and disorder on anisotropic charge transport in polypyrrole
Authors: Varade Vaibhav , Anjaneyulu P. , Suchand Sangeeth C. S. , Ramesh K. P. , Menon Reghu
Published: January 2013

Polypyrrole (PPy) has been synthesized electrochemically on platinum substrate by varying synthesis temperature and dopant concentration. The charge transport in PPy has been investigated as a function of temperature for both in-plane and out-of-plane geometry in a wide temperature range of 5 K–300 K. The charge transport showed strong anisotropy and various mechanisms were used to explain the transport. The conductivity ratio, σr = σ(300 K)/σ(5 K) is calculated for each sample to quantify the relative disorder. At all the temperatures, the conductivity values for in-plane transport are found to be more for PPy synthesized at lower temperature, while the behavior is found to be different for out-of-plane transport. The carrier density is found to play a crucial role in case of in-plane transport. An effort has been made to correlate charge transport to morphology by analyzing temperature and frequency dependence of conductivity. Charge transport in lateral direction is found to be dominated by hopping whereas tunneling mechanisms are dominated in vertical direction. Parameters such as density of states at the Fermi level [N(EF)], average hopping distance (R), and average hopping energy (W) have been estimated for each samples in both geometry.
Ethanol-enriched low-pressure chemical vapor deposition ZnO bilayers: Properties and growth—A potential electrode for thin film solar cells
Authors: Messerschmidt Daniel , Nicolay Sylvain , Ding Laura , Bugnon Gregory , Meillaud Fanny , Eberhardt Jens , Ballif Christophe
Published: January 2013

Ethanol is used as a precursor during the growth of zinc oxide (ZnO) by low-pressure chemical vapor deposition (LPCVD). By adding ethanol, the surface of the deposited ZnO layer is flattened and its roughness is decreased about sevenfold. The layers become increasingly stressed and their resistivity grows significantly. We propose an explanation for the observed behavior based on the catalytic decomposition of ethanol at the ZnO surface and on the growth of selected crystal planes. By using ethanol for the last 10% of the total ZnO layer growth only, sheet resistance is maintained and roughness is slightly decreased. Our results indicate that such LPCVD ZnO bilayers could be a promising method to modify the ZnO surface morphology before cell deposition, thus, providing an alternative to argon plasma treatment, which is typically reported to improve solar cell parameters such as open-circuit voltage and fill factor.
High power continuous wave microwave test bench at 4.6 GHz for experimental advanced superconducting tokamak
Authors: Ma Wendong , Hu Huaichuan , Shan Jiafang , Xu Handong , Wang Mao , Wu Zege , Zhu Liang
Published: January 2013

The lower hybrid current drive (LHCD) is an effective approach for auxiliary heating and non-inductive current drive in the experimental advanced superconducting tokamak. The 6 MW/4.6 GHz LHCD system is being designed and installed with twenty-four 250 KW/4.6 GHz high power klystron amplifiers. The test bench operating at 250 KW/4.6 GHz in continuous wave mode has been set up, which can test and train microwave components for the 6 MW/4.6 GHz LHCD system. In this paper, the system architecture and software of the microwave test bench are presented. Moreover, the test results of these klystrons and microwave units are described here in detail. The long term operation of the test bench and improved performance of all microwave component samples indicated that the related technologies on test bench can be applied in the large scale LHCD systems.
Toroidal magnetized plasma device with sheared magnetic field lines using an internal ring conductor
Authors: Pierre Th.
Published: January 2013

In a new toroidal laboratory plasma device including a poloidal magnetic field created by an internal circular conductor, the confinement efficiency of the magnetized plasma and the turbulence level are studied in different situations. The plasma density is greatly enhanced when a sufficiently large poloidal magnetic field is established. Moreover, the instabilities and the turbulence usually found in toroidal devices without sheared magnetic field lines are suppressed by the finite rotational transform. The particle confinement time is estimated from the measurement of the plasma decay time. It is compared to the Bohm diffusion time and to the value predicted by different diffusion models, in particular neoclassical diffusion involving trapped particles.
Radiation damage in heteroepitaxial BaTiO3 thin films on SrTiO3 under Ne ion irradiation
Authors: Bi Z. , Uberuaga B. P. , Vernon L. J. , Fu E. , Wang Y. , Li N. , Wang H. , Misra A. , Jia Q. X.
Published: January 2013

The microstructure evolution of heteroepitaxial BaTiO3 (BTO) thin films grown on single crystal (001) SrTiO3 (STO) under Ne irradiation at room temperature was systematically investigated with special attention given to the behavior at the BTO/STO interface. Cross sectional transmission electron microscope investigations reveal that amorphization occurs at the top BTO film region. BTO grains in the dimensions of 10–20 nm survived the irradiation damage and maintained their original crystal orientation. Other irradiation-induced defects such as dislocation loops and defect clusters were observed only at the portion of the BTO thin film near the interface, but not at the STO side of the bilayer. Atomic calculations find that the energetics of defects are very similar on each side of the BTO/STO interface, suggesting that the interface will not significantly modify radiation damage evolution in this system, in agreement with the experimental observations. These results support the hypothesis we presented in previous work about the role of coherent interfaces on radiation damage evolution.
Communication: One third: A new recipe for the PBE0 paradigm
Authors: Guido Ciro A. , Brémond Eric , Adamo Carlo , Cortona Pietro
Published: January 2013

We analyze the performances of the parameter-free hybrid density functional PBE0-1/3 obtained combining the PBE generalized-gradient functional with a predefined amount of exact exchange of 1/3, as recently discussed by Cortona [J. Chem. Phys. 136, 086101 (2012)10.1063/1.3690462]. The numerical results that we have obtained for various properties, such as atomization energies (G2-148 dataset), weak interactions (NCB31 dataset), hydrogen-bond length optimizations, and dissociation energies (HB10 dataset), and vertical excitation energies, show an increased performance of PBE0-1/3 with respect to the widely used PBE0. We therefore propose to use one third as the mixing coefficient for the PBE-based hybrid functional.
The effect of light soaking on crystalline silicon surface passivation by atomic layer deposited Al2O3
Authors: Liao Baochen , Stangl Rolf , Mueller Thomas , Lin Fen , Bhatia Charanjit S. , Hoex Bram
Published: January 2013

The effect of light soaking of crystalline silicon wafer lifetime samples surface passivated by thermal atomic layer deposited (ALD) Al2O3 is investigated in this paper. Contrary to other passivation materials used in solar cell applications (i.e., SiO2, SiNx), using thermal ALD Al2O3, an increase in effective carrier lifetime after light soaking under standard testing conditions is observed for both p-type (∼45%) and n-type (∼60%) FZ c-Si lifetime samples. After light soaking and storing the samples in a dark and dry environment, the effective lifetime decreases again and practically returns to the value before light soaking. The rate of lifetime decrease after light soaking is significantly slower than the rate of lifetime increase by light soaking. To investigate the underlying mechanism, corona charge experiments are carried out on p-type c-Si samples before and after light soaking. The results indicate that the negative fixed charge density Qf present in the Al2O3 films increases due to the light soaking, which results in an improved field-effect passivation. Numerical calculations also confirm that the improved field-effect passivation is the main contributor for the increased effective lifetime after light soaking. To further understand the light soaking phenomenon, a kinetic model—a charge trapping/de-trapping model—is proposed to explain the time dependent behavior of the lifetime increase/decrease observed under/after light soaking. The trap model fits the experimental results very well. The observed light enhanced passivation for ALD Al2O3 passivated c-Si is of technological relevance, because solar cell devices operate under illumination, thus an increase in solar cell efficiency due to light soaking can be expected.
Signature of magnetization dynamics in spin-transfer-driven nanopillars with tilted easy axis
Authors: Zhang Hong , Lin Weiwei , Mangin Stéphane , Zhang Zongzhi , Liu Yaowen
Published: January 2013

Special spin-transfer-driven magnetic behaviors can take place in a spin valve nanopillar with perpendicular anisotropy due to reduced symmetry of easy axis. Micromagnetic simulation demonstrates a dip in the average magnetization curve, which corresponds to the experimentally observed undulation of dc resistance. The dip is a signature of spin-transfer-driven reversable magnetic process with slightly tilted easy axis in the free layer. This featured magnetization dynamics includes non-uniform magnetization precession and multi-mode propagating spin waves, which are attributed to the competition among tilted magnetic anisotropy, magnetic field, and spin transfer torque.
Effects of excitation laser wavelength on Ly-α and He-α line emission from nitrogen plasmas
Authors: Harilal S. S. , Miloshevsky G. V. , Sizyuk T. , Hassanein A.
Published: January 2013

Laser-produced nitrogen plasmas emitting radiation at 2.48 nm (Ly-α) and 2.88 nm (He-α) are considered potential efficient sources for water-window (WW) microscopy. The atomic and optical properties of nitrogen plasma and influence of the laser wavelength on the line emission in the WW range are investigated. It is found that the optimal temperatures for maximum emission from Ly-α and He-α spectral lines are 40-60 eV and 80-100 eV, respectively. The WW line emission and the conversion efficiency (CE) are estimated for three distinct Nd:YAG laser wavelengths (1064 nm, 532 nm, and 266 nm). The calculated CEs are compared with experimentally observed CE values. It is found that 1064 nm wavelength provides the highest CE from laser to Ly-α and He-α radiation.
Laser-driven collimated tens-GeV monoenergetic protons from mass-limited target plus preformed channel
Authors: Zheng F. L. , Wu S. Z. , Wu H. C. , Zhou C. T. , Cai H. B. , Yu M. Y. , Tajima T. , Yan X. Q. , He X. T.
Published: January 2013

Proton acceleration by ultra-intense laser pulse irradiating a target with cross-section smaller than the laser spot size and connected to a parabolic density channel is investigated. The target splits the laser into two parallel propagating parts, which snowplow the back-side plasma electrons along their paths, creating two adjacent parallel wakes and an intense return current in the gap between them. The radiation-pressure pre-accelerated target protons trapped in the wake fields now undergo acceleration as well as collimation by the quasistatic wake electrostatic and magnetic fields. Particle-in-cell simulations show that stable long-distance acceleration can be realized, and a 30 fs monoenergetic ion beam of >10 GeV peak energy and <2° divergence can be produced by a circularly polarized laser pulse at an intensity of about 1022 W/cm2.
Collisional effects on the generation of fast electrons in fast ignition scheme
Authors: Wang Wei-wu , Cai Hong-bo , Jia Qing , Zhu Shao-ping
Published: January 2013

The effects of collision on the generation and transportation of fast electrons produced by ultra-intense laser pulse in overdense plasma for densities ranging from below to 400 times critical density are investigated by collisional particle-in-cell code. It is found that a relatively stable state of fast electron energy flux exists in the simulations, where collision contributes to increasing the production of fast electrons. The unexpected increase of production is attributed to the efficient local heating of the thermal electrons, which results in higher thermal pressure and less steepened interface. Therefore, fast electrons can be effectively accelerated through 2ω oscillation from J×B force in the collisional case, while it is suppressed in the collisionless case because of the highly steepened plasma density. The collisional effects on the transportation of fast electrons in the solid target are also discussed.
CePa: an R package for finding significant pathways weighted by multiple network centralities
Authors: Gu Zuguang , Wang Jin
Published: January 2013

Summary: CePa is an R package aiming to find significant pathways through network topology information. The package has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centralities are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. CePa has been evaluated with high performance on real-world data, and it can provide more information directly related to current biological problems.

Availability: CePa is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/CePa/

Contact:  jwang@nju.edu.cn

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Pregnancy and treatment outcome in a patient with left ventricular non‐compaction
Authors: Sawant Rahul D. , Freeman Leisa J. , Stanley Katherine P.S. , McKelvey Alistair
Published: January 2013

Left ventricular non‐compaction (LVNC) is a rare form of cardiomyopathy. This case reviews a woman with familial LVNC (EF 45%, NYHA class I, evidence of non‐sustained ventricular tachycardia pre‐pregnancy) who had significant decompensation with heart failure in the third trimester that required early delivery. Deterioration in symptoms and LV function 7 days after delivery required further hospitalization and aggressive treatment. Suppression of lactation with bromocriptine, together with standard heart failure management, has allowed recovery and return to full activities and work. Acknowledged adverse risk factors in LVNC are considered, and pre‐pregnancy risk assessment is reviewed. There is no specific treatment for LVNC in pregnancy besides the usual management of dilated cardiomyopathy. This is the ninth case report of LVNC in pregnancy reported in the literature.
Common genetic variants of the natriuretic peptide gene locus are not associated with heart failure risk in participants in the EPIC‐Norfolk study
Authors: Pfister Roman , Luben Robert N. , Khaw Kay‐Tee , Wareham Nick J.
Published: January 2013

Aims

BNP has important effects on haemodynamics and myocardial remodelling which are protective from development and progression of heart failure. The aim of this study was to examine whether three common genetic variants (rs198389, rs5068, and rs198358) within or adjacent to the BNP gene locus which were shown to be associated with BNP blood levels are associated with risk of heart failure in the pospective population‐based EPIC‐Norfolk cohort.

Methods and results

The hazard ratio on heart failure was calculated in 23 192 participants in the EPIC‐Norfolk study with Cox proportional regression analyses. During a mean follow‐up of 12.6 years, 1673 (7.2%) participants had a heart failure event. There was no significant association between genotypes of rs198389, rs5068, and rs198358 and heart failure risk. Results did not differ materially in analyses stratified by hypertension, obesity, and coronary heart disease.

Conclusions

Common genetic variants reported to be associated with BNP levels were not associated with a relevant risk of heart failure in our population‐based cohort. However, we cannot exclude a small association with risk of heart failure or an association with individual subtypes of the heart failure syndrome.
Long-term changes in coastal zoobenthos in the northern Baltic Sea: the role of abiotic environmental factors
Authors: Rousi Heta , Laine Ari O. , Peltonen Heikki , Kangas Pentti , Andersin Ann-Britt , Rissanen Jouko , Sandberg-Kilpi Eva , Bonsdorff Erik
Published: January 2013

Rousi, H., Laine, A. O., Peltonen, H., Kangas, P., Andersin, A-B., Rissanen, J., Sandberg-Kilpi, E., and Bonsdorff, E. 2013. Long-term changes in coastal zoobenthos in the northern Baltic Sea: the role of abiotic environmental factors – ICES Journal of Marine Science, 70: 440–451. We investigated site-specific changes in a coastal zoobenthic community during 1964–2007 in the northern Baltic Sea. Multivariate analysis indicated that the community structure had changed. The amphipods Monoporeia affinis and Pontoporeia femorata decreased drastically in the late 1970s–early 1980s, and by the early 1990s P. femorata vanished and M. affinis abundance was low. The decline of M. affinis and P. femorata was followed by an increase of the bivalve Macoma balthica and the arrival of the polychaete genus Marenzelleria in the 1990s. Trend analyses showed a rising trend for near-bottom temperature from the late 1960s. There was a significant decline in salinity during the early 1980s, which stabilized during the early 1990s. A negative trend was observed for oxygen concentration during the entire study period. There were interannual variations in the phosphorus and nitrogen concentrations, and a step-like increase in phosphorus concentration at the beginning of the 21st century. The correlations of temperature, salinity, oxygen, total phosphorus and nitrogen with zoobenthic communities were examined using Constrained Correspondence Analysis. Temperature was the most highly correlated explanatory variable for the benthic species. The study highlights the importance of long-term data sets in assessing the state and ecological processes of zoobenthic systems.
Installing kelp forests/seaweed beds for mitigation and adaptation against global warming: Korean Project Overview
Authors: Chung Ik Kyo , Oak Jung Hyun , Lee Jin Ae , Shin Jong Ahm , Kim Jong Gyu , Park Kwang-Seok
Published: January 2013

Chung, I. K., Oak, J. H., Lee, J. A., Shin, J. A., Kim, J. G., and Park, K.-S. 2013. Installing kelp forests/seaweed beds for mitigation and adaptation against global warming: Korean Project Overview. – ICES Journal of Marine Science, 70: 1038–1044. Seaweed beds can serve as a significant carbon dioxide (CO2) sink while also satisfying global needs for food, fodder, fuel, and pharmaceutical products. The goal of our Korean Project has been to develop new baseline and monitoring methodologies for mitigation and adaptation within the context of climate change. Using innovative research approaches, we have established the Coastal CO2 Removal Belt (CCRB), which comprises both natural and man-made plant communities in the coastal region of southern Korea. Implemented on various spatial–temporal scales, this scheme promotes the removal of CO2 via marine forests. For example, when populated with the perennial brown alga Ecklonia, a pilot CCRB farm can draw down ∼10 t of CO2 per ha per year. This success is manifested by an increment in biomass accumulations and a decrease in the amount of dissolved inorganic carbon in the water column.
Mesorhizobium

sangaii sp. nov., isolated from the root nodules of Astragalus luteolus and Astragalus ernestii
Authors: Zhou Shen , Li Qiongfang , Jiang Huaming , Lindström Kristina , Zhang Xiaoping
Published: January 2013

Our previous published data indicated that the two rhizobial strains SCAU7T and SCAU27, which were isolated from the root nodules of Astragalus luteolus and Astragalus ernestii respectively, in Sichuan Province, China, might be novel species of the genus

Mesorhizobium

. Their exact taxonomic position was determined in the present study by using polyphasic approaches. Comparative analysis of nearly full-length 16S rRNA gene sequences showed that these strains belonged to the genus

Mesorhizobium

, with

Mesorhizobium ciceri

USDA 3383T,

Mesorhizobium loti

NZP 2213T,

Mesorhizobium shangrilense

CCBAU 65327T and

Mesorhizobium australicum

WSM2073T as the closest neighbours (>99 % 16S rRNA gene sequence similarity). Phylogenies of the housekeeping genes atpD and recA confirmed their distinct position, showing low similarity with respect to those of

M. loti

LMG 6125T (96.5 % and 92.3 % similarity respectively),

M. ciceri

USDA 3383T (96.8 % and 93.3 % similarity, respectively),

M. shangrilense

CCBAU 65327T (96.5 % and 92.7 % similarity, respectively) and

M. australicum

WSM2073T (95.4 % and 90.6 % similarity, respectively). The DNA–DNA relatedness values between strain SCAU7T and strain SCAU27 were 83.0 %, showing that they belong to the same species. The DNA–DNA relatedness values of SCAU7T with

M. loti

NZP 2213T,

M. ciceri

USDA 3383T and

M. shangrilense

CCBAU 65327T were 41.1 %, 48.8 % and 23.4 %, respectively, clearly indicating that strain SCAU7T represents a novel species. A series of phenotypic and genotypic tests and comparison of cellular fatty acids indicated that the novel group of isolates was distinct from previously described species. Therefore, we propose that strains SCAU7T and SCAU27 represent a novel species of the genus

Mesorhizobium

,

Mesorhizobium

sangaii sp. nov., with strain SCAU7T ( = HAMBI 3318T = ACCC 13218T) as the type strain.
Reclassification of
[Glaciecola] lipolytica

and [

Aestuariibacter] litoralis

in Aliiglaciecola gen. nov., as Aliiglaciecola lipolytica comb. nov. and Aliiglaciecola litoralis comb. nov., respectively
Authors: Jean Wen Dar , Hsu Cheng Yu , Huang Ssu-Po , Chen Jwo-Sheng , Lin Saulwood , Su Mong-Huai , Shieh Wung Yang
Published: January 2013

Following phylogenetic analysis based on 16S rRNA gene sequences, together with DNA G+C contents and differential chemotaxonomic and physiological characteristics, a new genus with the name Aliiglaciecola gen. nov. is proposed to more appropriately accommodate two recognized species of the genera

Glaciecola

and

Aestuariibacter

. Accordingly,
[Glaciecola] lipolytica

and [

Aestuariibacter] litoralis

should be reassigned to the novel genus as Aliiglaciecola lipolytica comb. nov. (type strain, E3T = JCM 15139T = CGMCC 1.7001T) and Aliiglaciecola litoralis comb. nov. (type strain, KMM 3894T = JCM 15896T = NRIC 0754T), respectively. Aliiglaciecola lipolytica is proposed as the type species of this new genus. Physiologically, the combined characteristics of positive reactions for nitrate reduction and growth at 4 °C and 36 °C distinguish the new genus from the genera

Aestuariibacter

and

Glaciecola

by one to three traits. Moreover, the new genus is also distinguished from the genus

Glaciecola

by the fatty acid profile and distinguished from the genus

Aestuariibacter

by the differences of major isoprenoid quinone (MK-7 vs Q-8) and DNA G+C content (40.8–43.0 mol% vs 48.0–54.0 mol%).
Cohnella

formosensis sp. nov., a xylanolytic bacterium isolated from the rhizosphere of Medicago sativa L
Authors: Hameed Asif , Hung Mei-Hua , Lin Shih-Yao , Hsu Yi-Han , Liu You-Cheng , Shahina Mariyam , Lai Wei-An , Huang Hsin-Chieh , Young Li-Sen , Young Chiu-Chung
Published: January 2013

A Gram-positive, spore-forming, aerobic, rod-shaped, xylanolytic bacterium designated strain CC-Alfalfa-35T was isolated from the rhizosphere of Medicago sativa L. in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain CC-Alfalfa-35T was affiliated to the genus

Cohnella

. Strain CC-Alfalfa-35T shared 95.3 % pairwise 16S rRNA gene sequence similarity to the type strain of the type species of the genus

Cohnella

(

Cohnella thermotolerans

DSM 17683T) besides showing a similarity of 97.4–93.6 % with other recognized species of the genus

Cohnella

. The DNA–DNA hybridization value between CC-Alfalfa-35T and

Cohnella thailandensis

KCTC 22296T was 37.7 %±1.7 % (reciprocal value, 55.7 %±3.0 %). Predominant cellular fatty acids were iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile constituted diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysyl-phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. The major respiratory quinone was MK-7 and the DNA G+C content was 58.3 mol%. Strain CC-Alfalfa-35T contained meso-diaminopimelic acid as the major diamino acid in the cell-wall peptidoglycan. Based on the polar lipid and fatty acid profiles, which were in line with those of

C. thermotolerans

DSM 17683T, coupled with additional distinguishing genotypic, phenotypic and chemotaxonomic features, strain CC-Alfalfa-35T is proposed to represent a novel species within the genus

Cohnella

, for which the name

Cohnella

formosensis sp. nov. is proposed. The type strain is CC-Alfalfa-35T ( = JCM 18405T = BCRC 80428T).
Mucilaginibacter

sabulilitoris sp. nov., isolated from marine sand in a firth
Authors: Kang Chul-Hyung , Jung Yong-Taek , Yoon Jung-Hoon
Published: January 2013

A Gram-stain-negative, non-spore-forming, strictly aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, designated SMS-12T, was isolated from marine sand in a firth on the western coast of South Korea. Strain SMS-12T grew optimally at 25 °C, at pH 7.0–7.5 and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SMS-12T fell within the clade comprising species of the genus

Mucilaginibacter

, forming a coherent cluster with the type strain of

Mucilaginibacter lappiensis

, with which it exhibited the highest 16S rRNA gene sequence similarity value of 97.5 %. Levels of sequence similarity to the type strains of the other species of the genus

Mucilaginibacter

and the other species used in the phylogenetic analysis were 93.3–96.4 % and <91.5 %, respectively. Strain SMS-12T contained MK-7 as the predominant menaquinone, and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified aminophospholipid; sphingolipids were present. The DNA G+C content was 41.8 mol% and the mean DNA–DNA relatedness with

M. lappiensis

KACC 14978T was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SMS-12T is separate from other species of the genus

Mucilaginibacter

. On the basis of the data presented, strain SMS-12T is considered to represent a novel species of the genus

Mucilaginibacter

, for which the name

Mucilaginibacter

sabulilitoris sp. nov. is proposed. The type strain is SMS-12T ( = KCTC 32111T = CCUG 62214T).
Cryobacterium

levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice
Authors: Liu Qing , Liu Hongcan , Zhang Jianli , Zhou Yuguang , Xin Yuhua
Published: January 2013

In this study, two psychrophilic bacterial strains were isolated from the China No. 1 glacier in Xinjiang, north-west China. Cells were Gram-positive rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belonged to the genus

Cryobacterium

. Phylogenetic analysis showed that they clustered together and are most closely related to

Cryobacterium luteum

CGMCC 1.11210T,

Cryobacterium flavum

CGMCC 1.11215T,

Cryobacterium psychrophilum

CGMCC 1.4292T,

Cryobacterium psychrotolerans

CGMCC 1.5382T and

Cryobacterium roopkundense

CGMCC 1.10672T. The major cellular fatty acids of the novel strains were anteiso-C15 : 0, anteiso-C15 : 1 A, iso-C16 : 0 and iso-C15 : 0. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid in the cell membrane. The results of DNA–DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strains Hh34T and Hh28 from related species. However, their high DNA–DNA relatedness showed that they belong to the same novel species. Strain Hh34T ( = NBRC 107883T = CGMCC 1.11211T) was selected as the type strain to represent this novel species, for which the name

Cryobacterium

levicorallinum sp. nov. is proposed.
Chryseobacterium

kwangjuense sp. nov., isolated from pepper (Capsicum annuum L.) root
Authors: Sang Mee Kyung , Kim Hye-Sook , Myung Inn-Shik , Ryu Choong-Min , Kim Beom Seok , Kim Ki Deok
Published: January 2013

The yellow-pigmented, Gram-stain-negative, rod-shaped bacterium KJ1R5T was isolated from the root of a pepper plant grown in a field in Kwangju, Korea. Strain KJ1R5T was characterized by physiological, biochemical, and molecular genetic analyses. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KJ1R5T was most closely related to members of the genus

Chryseobacterium

, and that the strain exhibited the highest similarities with type strains of

Chryseobacterium vrystaatense

(97.0 %) and

Chryseobacterium rhizosphaerae

(97.1 %). DNA–DNA hybridization reassociation values between strain KJ1R5T and type strains of

C. vrystaatense

KACC 11675T and

C. rhizosphaerae

KACC 14918T were 46.9 and 38.4 %, respectively. The DNA G+C content of KJ1R5T is 40.2 mol%. The predominant respiratory quinone of KJ1R5T was menaquinone MK-6; major cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 1ω9c, and iso-C17 : 0 3-OH. On the basis of these phenotypic and genotypic characteristics, the strain significantly differed from representative strains belonging to the genus

Chryseobacterium

. Thus, we propose that strain KJ1R5T represents a novel species of the genus

Chryseobacterium

, named

Chryseobacterium

kwangjuense sp. nov. The type strain is KJ1R5T ( = KACC 13029T = JCM 15904T).
Gramella

aestuarii sp. nov., isolated from a tidal flat, and emended description of

Gramella echinicola
Authors: Jeong Sang Hyeon , Jin Hyun Mi , Jeon Che Ok
Published: January 2013

A Gram-staining-negative, yellow-pigmented, strictly aerobic bacterial strain motile by gliding, designated BS12T, was isolated from a tidal flat at Boseong, Korea. Cells were moderately halotolerant, catalase- and oxidase-positive rods. Growth was observed at 5–40 °C (optimum, 25 °C), at pH 5.5–9.0 (optimum, pH 7.0–7.5) and in the presence of 1–11 % (w/v) NaCl (optimum, 2–4 %). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and anteiso-C15 : 0. The polar lipid pattern comprised phosphatidylethanolamine, four unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 42.3 mol% and the only respiratory quinone was menaquinone 6. Phylogenetic inference based on 16S rRNA gene sequences showed that strain BS12T formed a tight phyletic lineage with members of the genus

Gramella

. Strain BS12T was most closely related to ‘

Gramella

jeungdoensis’ HMD3159 with sequence similarity of 97.5 %, but the DNA–DNA relatedness value between the two strains was only 22.1±2.2 %. On the basis of phenotypic and molecular features, strain BS12T was shown to represent a novel species of the genus

Gramella

, for which the name

Gramella

aestuarii sp. nov. is proposed. The type strain is BS12T ( = KACC 16188T = JCM 17790T). An emended description of

Gramella echinicola

is also proposed.