bluuebunny/crossref_metadata_2025 huggingface dataset:
Static and dynamic magnetic properties of epitaxial Fe1.7Ge thin films grown on Ge(111)
Authors: Belmeguenai M. , Berling D. , Garreau G. , Chérif S. M. , Faurie D. , Seiler W. , Moch P.
Published: February 2012

We have studied the magnetic properties of thin epitaxial hexagonal Fe1.7Ge films grown on Ge(111) substrates by molecular beam epitaxy. For all samples, X-ray diffraction revealed an excellent epitaxy of the Fe1.7Ge films, with crystallographic [112¯0] and [11¯00] axes lying in the sample plane. The static magnetic properties were studied by Magneto-Optical Kerr Effect (MOKE) at room temperature. The dynamic magnetic properties at room temperature were investigated by Micro-Strip Ferromagnetic Resonance (MS-FMR). The frequency dependence of the spectra versus the orientation of the applied in-plane magnetic field shows that the contribution of the in-plane anisotropy to the magnetic energy density consists in two distinct terms exhibiting a twofold and a sixfold symmetry, respectively. The amplitude of the sixfold anisotropy constant is an increasing function of the film thickness. The observed angular dependence of the MOKE reduced remanent magnetization is described using a coherent rotation model. A good agreement is observed between the in-plane anisotropy values derived from MS-FMR and those obtained with MOKE Transverse Bias Initial Inverse Susceptibility and Torque data.
Hysteresis and relaxation in granular permanent magnets
Authors: Skomski Ralph , Balamurugan B. , George Tom A. , Chipara Mircea , Wei Xiao-Hui , Shield Jeff E. , Sellmyer D. J.
Published: February 2012

Some nontrivial aspects of the magnetic and structural characterization of hard-magnetic nanoparticles are investigated. Dilute ensembles are well-described by mean-field theory, although there is an asymmetry between exchange and magnetostatic interaction fields. Corrections to the mean-field approximation are caused by cooperative effects and have the character of Onsager reaction fields, which are much stronger in micromagnetism than in atomic-scale magnetism. The slow dynamics of zero-field-cooled (ZFC) magnetization curves is strongly affected by the particles′ magnetic anisotropy, which reduces the corresponding energy-barrier height from 25 to 19.1 kBT.
Annealing effects on superconductivity and magnetism in Fe1+yTe1−xSx single crystals
Authors: Zhang Z. T. , Yang Z. R. , Li L. , Pi L. , Tan S. , Zhang Y. H.
Published: February 2012

The annealing effects on superconductivity and magnetism in Fe1 + yTe1−xSx single crystals have been investigated. It is found that the superconductivity is improved not only by annealing in air but also by annealing in vacuum or argon. In addition, even for a low S content sample with long-range magnetic order, the superconductivity is also obviously improved by air annealing. These are inconsistent with the previous results of other groups. In the air annealing case, energy dispersive x-ray spectrometer analyses and heat capacity results show that oxygen is incorporated into the system and the long-range magnetic order is partially suppressed. In contrast, for vacuum or argon annealing, no change of composition is detected and no other ions are incorporated, and the enhancement of superconductivity clearly indicates that the modulation of the microstructure plays an important role in the annealing effect on superconductivity and magnetism.
Dynamic hysteresis modeling of silicon steel having nonuniform magnetic property
Authors: Mitsuoka R. , Mifune T. , Matsuo T.
Published: February 2012

Finite-element eddy-current analysis is combined with the play model to represent the AC hysteretic properties of a silicon steel sheet. The dependence of the anomaly factor on the excitation frequency is discussed. The finite element analysis with a constant anomaly factor overestimates the iron loss relative to the result obtained from classical eddy-current theory because of the nonlinearity of magnetization. The nonuniform magnetic property along the thickness direction is examined, and a dynamic anomaly factor is then introduced to directly represent the frequency dependence. The alternating magnetic properties simulated by the proposed model agree well with measured properties.
Physics research and technology developments of electron string ion sources
Authors: Donets D. E. , Donets E. E. , Honma T. , Noda K. , Ramzdorf A. Yu. , Salnikov V. V. , Shutov V. B. , Donets E. D.
Published: February 2012

The most recent experimental information on electron string phenomenon, such as two step transition to electron string state, stability of e-strings in condition of electron energy recuperation, are described. The new technology developments of electron string ion sources (ESIS) include pulse injection of gaseous species in e-string and its efficient conversion to ion beams, slow ion extraction, ion–ion cooling of heavy ions with CH4 coolant, and a progress in the construction of the new Joint Institute for Nuclear Research ESIS with 6 T solenoid are briefly considered.
Characteristic of a triple-cathode vacuum arc plasma source
Authors: Xiang W. , Li M. , Chen L.
Published: February 2012

In order to generate a better ion beam, a triple-cathode vacuum arc plasma source has been developed. Three plasma generators in the vacuum arc plasma source are equally located on a circle. Each generator initiated by means of a high-voltage breakdown between the cathode and the anode could be operated separately or simultaneously. The arc plasma expands from the cathode spot region in vacuum. In order to study the behaviors of expanding plasma plume generated in the vacuum arc plasma source, a Langmuir probe array is employed to measure the saturated ion current of the vacuum arc plasma source. The time-dependence profiles of the saturated current density of the triple vacuum arc plasma source operated separately and simultaneously are given. Furthermore, the plasma characteristic of this vacuum arc plasma source is also presented in the paper.
Charge transport in two different conductive polymer and semiconducting quantum dot nanocomposite systems
Authors: Biswas Sushmita , Li Yang , Stroscio Michael A. , Dutta Mitra
Published: February 2012

Charge transport mechanisms have been investigated in two different nanocomposite structures made of conductive polymers embedded with II-VI semiconducting quantum dots. Photoluminescence data indicated charge transport in the two systems. Higher photocurrents observed in the poly(3-hexylthiophene-2,5-diyl) polymer-based heterostructure in comparison with the poly(2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylenevinylene) polymer-based heterostructure have been analyzed with hole and electron conduction. For larger concentrations of quantum dots, both electron transport through nanocrystals and hole transport through polymer become relevant. Based on the electron tunneling mechanism, current voltage characteristics are modeled for a double barrier quantum well device formed by semiconducting quantum dots and polymer molecules.
Physical principles of the preglow effect and scaling of its basic parameters for electron cyclotron resonance sources of multicharged ions
Authors: Skalyga V. , Izotov I. , Zorin V. , Sidorov A.
Published: February 2012

A study of pulsed mode operation of modern ECR ion sources has clearly demonstrated the reality of an unexpected transient current peak, occurring at the very beginning of the plasma breakdown. This regime was named the preglow, as an explicit reference to the afterglow occurring at the microwave pulse end. After the transient preglow peak, the plasma regime relaxes to the classical steady state one. During last three years, a lot of experimental data together with first theoretical interpretations were published. The present paper is a continuation of previous investigations by the authors and contains full description of the preglow effect physical principles. Analysis of preglow parameters dependences on properties of microwave radiation used for plasma heating is presented. Some kind of preglow scaling for ECRIS is proposed.
Electromagnetically induced transparency with quantum interferometry
Authors: Bhattacharjee Anindita , Dastidar Krishna Rai
Published: February 2012

We have shown that electromagnetically induced transparency can be achieved by control-probe interferometry using two delayed phase-locked ultrashort pulses. Two vibrational wavepackets on the excited state, excited by two delayed phase-locked ultrashort pulses, interfere constructively or destructively leading to enhancement or suppression of absorption to a selective set of vibrational levels. Depending on the phase difference and the delay between the pulses with same carrier frequency, one can design different transparency windows between absorption peaks at consecutive even(odd) vibrational levels by eliminating absorption at odd(even) vibrational levels. We have shown that by switching the phase difference of two delayed femtosecond pulses, one can switch to complete elimination of absorption from enhanced absorption to a particular set of vibrational levels in the excited state. Thus, switching of transparency through window between odd vibrational levels to that between even vibrational levels is possible. By properly choosing the temporal width and the carrier frequency of the pulses, lossless transmission of complete or bands of frequencies of the pulses can be achieved through these transparency windows. Hence, designing of single- or multi-mode transparency windows in NaH molecule is feasible by control-probe quantum interferometry.
Regularized path integrals and anomalies: U(1) chiral gauge theory
Authors: Kopper Christoph , Lévêque Benjamin
Published: February 2012

We analyze the origin of the Adler–Bell–Jackiw anomaly of chiral U(1) gauge theory within the framework of regularized path integrals. Momentum or position space regulators allow for mathematically well-defined path integrals but violate local gauge symmetry. It is known how (nonanomalous) gauge symmetry can be recovered in the renormalized theory in this case [Kopper, C. and Müller, V. F., “Renormalization of spontaneously broken SU(2) Yang-Mills theory with flow equations,” Rev. Math. Phys. 21, 781 (2009)]10.1142/S0129055X0900375X. Here we analyze U(1) chiral gauge theory to show how the appearance of anomalies manifests itself in such a context. We show that the three-photon amplitude leads to a violation of the Slavnov-Taylor identities which cannot be restored on taking the UV limit in the renormalized theory. We point out that this fact is related to the nonanalyticity of this amplitude in the infrared region.
Enhanced performance of resonant sub-terahertz detection in a plasmonic cavity
Authors: Dyer G. C. , Preu S. , Aizin G. R. , Mikalopas J. , Grine A. D. , Reno J. L. , Hensley J. M. , Vinh N. Q. , Gossard A. C. , Sherwin M. S. , Allen S. J. , Shaner E. A.
Published: February 2012

A multi-gate high electron mobility transistor coupled to a log-periodic antenna was engineered to detect sub-terahertz radiation through resonant excitation of plasmon modes in the channel. The device was integrated with a silicon hyper-hemispherical lens in order to enhance radiation collection and eliminate parasitic substrate modes. The continuous detector response spectrum from 185 GHz to 380 GHz indicates the presence of distinct collective plasmonic cavity modes resulting from the quantization of the plasmon wavevector. In a bolometric detection mode, a noise equivalent power of less than 50 pW/Hz1/2 and a responsivity exceeding 100 kV/W have been measured at 11.5 K.
Interfacial chemistry in an InAs/GaSb superlattice studied by pulsed laser atom probe tomography
Authors: Müller M. , Gault B. , Field M. , Sullivan G. J. , Smith G. D. W. , Grovenor C. R. M.
Published: February 2012

Pulsed laser atom probe tomography was employed to study the interfacial chemistry in an InAs/GaSb superlattice nanostructure. The InAs-on-GaSb anion sublattice interface was found to be wider than the GaSb-on-InAs interface, in good agreement with previous electron microscopy studies. Hetero-nuclear group-V cluster ions at the InAs-on-GaSb interface as detected by atom probe are indicative of a strong As for Sb exchange reaction when InAs is grown onto GaSb.
Enhanced electron field emission from plasma-nitrogenated carbon nanotips
Authors: Wang B. B. , Cheng Q. J. , Zhong X. X. , Wang Y. Q. , Chen Y. A. , Ostrikov K.
Published: February 2012

Nitrogenated carbon nanotips (NCNTPs) are synthesized by plasma-enhanced hot filament chemical vapor deposition from the hydrogen, methane, and nitrogen gas mixtures with different flow rate ratios of hydrogen to nitrogen. The morphological, structural, compositional, and electron field emission (EFE) properties of the NCNTPs were investigated by field emission scanning electron microscopy, Raman spectroscopy, x ray photoelectron spectroscopy, and EFE high-vacuum system. It is shown that the NCNTPs deposited at an intermediate flow rate ratio of hydrogen to nitrogen feature the best size/shape and pattern uniformity, the highest nanotip density, the highest nitrogen concentration, as well as the best electron field emission performance. Several factors that come into play along with the nitrogen incorporation, such as the combined effect of the plasma sputtering and etching, the transition of sp3 carbon clusters to sp2 carbon clusters, the increase of the size of the sp2 clusters, as well as the reduction of the work function, have been examined to interpret these experimental findings. Our results are highly relevant to the development of the next generation electron field emitters, flat panel displays, atomic force microscope probes, and several other advanced applications.
A unified model for unipolar resistive random access memory
Authors: Lee Kwangseok , Jang Jung-Shik , Kwon Yongwoo , Lee Keun-Ho , Park Young-Kwan , Young Choi Woo
Published: February 2012

A unified model for resistive random access memory has been proposed for the accurate prediction of forming, reset, and set operations. Unlike conventional random circuit breaker network model, the unified model can simulate realistic cell structures with higher accuracy.
DNA-cisplatin binding mechanism peculiarities studied with single molecule stretching experiments
Authors: Crisafuli F. A. P. , Cesconetto E. C. , Ramos E. B. , Rocha M. S.
Published: February 2012

We propose a method to determine the DNA-cisplatin binding mechanism peculiarities by monitoring the mechanical properties of these complexes. To accomplish this task, we have performed single molecule stretching experiments by using optical tweezers, from which the persistence and contour lengths of the complexes can be promptly measured. The persistence length of the complexes as a function of the drug total concentration in the sample was used to deduce the binding data, from which we show that cisplatin binds cooperatively to the DNA molecule, a point which so far has not been stressed in binding equilibrium studies of this ligand.
Tuning the nonlinear response of coupled split-ring resonators
Authors: Hannam Kirsty E. , Powell David A. , Shadrivov Ilya V. , Kivshar Yuri S.
Published: February 2012

We introduce the concept of controlling the nonlinear response of the metamaterial by altering its internal structure. We experimentally demonstrate tuning of the nonlinear response of two coupled split-ring resonators by changing their mutual position. This effect is achieved through modification of the structure of the coupled resonant modes and their interaction with the incident field. By offsetting the resonators we control the maximum currents through the nonlinear elements, which affect the nonlinear response of the system.
Controlling extraordinary transmission characteristics of metal hole arrays with spoof surface plasmons
Authors: Miyamaru Fumiaki , Kamijyo Mototsugu , Hanaoka Naoki , Takeda Mitsuo W.
Published: February 2012

We experimentally controlled the spectral characteristics of the extraordinary transmissions observed in metal hole arrays by analogy with spoof surface plasmon-polaritons (spoof SPPs). We constructed doubly periodic metal hole arrays. The larger and smaller periodic holes are for inducing extraordinary transmissions and modifying the spoof SPPs’ characteristics, respectively. Introducing the smaller holes that surround the larger hole arrays can modify the dispersion curve of the surface waves excited on a structured metal surface analogous to the spoof SPP model, and consequently, the extraordinary transmission peak will show a redshift.
Direct detection of magnon spin transport by the inverse spin Hall effect
Authors: Chumak A. V. , Serga A. A. , Jungfleisch M. B. , Neb R. , Bozhko D. A. , Tiberkevich V. S. , Hillebrands B.
Published: February 2012

Conversion of traveling magnons into an electron carried spin current is demonstrated in a time resolved experiment using a spatially separated inductive spin-wave source and an inverse spin Hall effect (ISHE) detector. A spin-wave packet is excited in a yttrium-iron garnet waveguide by a microwave signal and is detected 3 mm apart by an attached platinum layer as a delayed ISHE voltage pulse. The delay appears due to the finite spin-wave group velocity and proves the magnon spin transport. The experiment suggests the utilization of spin waves for the information transfer over macroscopic distances in spintronic devices and circuits.
Diabetes-related major lower limb amputation in Far North Queensland, 1998 - 2008
Authors: O'Rourke Sharon R. , Steffen Christina M. , Raulli Alexandra , Tulip Fiona J.
Published: February 2012

Objective. To report on the accuracy of reports of diabetes-related major amputations, rates per 100 000 people and trends over the 10-year period from 1998–99 to 2007–08 in Far North Queensland. Methods. Three data sources were cross-checked. Poisson regression was used to calculate the percentage change in trends in diabetes amputation hospitalisations over the period. Results. There was a discrepancy of 6 (3.7%) in 161 cases over 10 years. The number of diabetes-related hospitalisations for major lower limb amputation did not show a significant trend during this period, with an annual percentage change of –0.32%, P = 0.915. Conclusion. Amputation data in Far North Queensland were accurate. There was a modest reduction in the hospitalisation rate for major lower limb amputation over the 10-year period, demonstrating the need for improvements in the organisation of care. What is known about the topic? Diabetic foot complications resulting in amputation are recognised internationally as a costly, major health problem. Limited data are available in the Australian context, especially for regional high risk populations. What does this paper add? Accurate data on an Australian Institute of Health and Welfare recommended indicator, namely major amputations in people with diabetes. Confirmation of the accuracy of the data, enables benchmarking for future improvements. What are the implications for practitioners? A focus on major amputations is a useful indicator of the quality and safety of care for people with diabetes.
Stabilising the aged care workforce: an analysis of worker retention and intention
Authors: Howe Anna L. , King Debra S. , Ellis Julie M. , Wells Yvonne D. , Wei Zhang , Teshuva Karen A.
Published: February 2012

Concerns about the capacity of the aged care industry to attract and retain a workforce with the skills required to deliver high quality care are widespread, but poor conceptualisation of the problem can result in strategies to address turnover being poorly targeted. A census of residential and community aged care services conducted by the National Institute of Labour Studies (NILS) in 2007 provided a comprehensive empirical account of the workforce, and estimated turnover on the basis of retention: that is, the proportion of the workforce who had been in their job for 1 year or less. This paper adds the dimension of intention: that is, workers’ expectations as to whether in 1 year’s time, they would still be working in the same aged care service. The dual driver model that takes both retention and intention into account was applied in further analysis of the 2007 NILS data. Investigation of relationships between workforce instability and 13 variables covering worker attributes, organisational attributes and structural attributes of the industry demonstrated the usefulness of the dual driver model for reconceptualising and analysing stability and, in turn, refining strategies to address turnover.

What is known about the topic?
Widespread concerns about turnover in the aged care workforce are based on estimates of 25% turnover per annum in both residential and community care workforces reported by NILS in 2007. This rate is low compared to US reports averaging ~50%.

What does this paper add?
Application of the dual-driver model to the analysis of 13 variables covering worker, organisational and structural attributes clarifies the nature of instability and shows that drivers affecting retention and workers’ intentions to stay or leave the job operate differently in the residential and community care workforces.

What are the implications for practitioners?
Those involved in workforce management and policy development in aged care should give more attention to identifying and realising workers’ intentions to stay, addressing factors affecting retention, and developing more refined strategies to address instability rather than focusing primarily on recruitment.
Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin
Authors: Zakeri Bijan , Fierer Jacob O. , Celik Emrah , Chittock Emily C. , Schwarz-Linek Ulrich , Moy Vincent T. , Howarth Mark
Published: February 2012

Protein interactions with peptides generally have low thermodynamic and mechanical stability.
Streptococcus pyogenes
fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.
Government Insurance Program Design, Incentive Effects, and Technology Adoption: The Case of Skip‐Row Crop Insurance
Authors: Woodard Joshua D. , Pavlista Alexander D. , Schnitkey Gary D. , Burgener Paul A. , Ward Kimberley A.
Published: February 2012

Can the availability of poorly‐designed government insurance alter technology adoption decisions? A theoretical model of technology adoption and insurance incentive effects for a high‐ and low‐risk technology is developed and explored empirically using a unique dataset of skip‐row agronomic trial data. A multivariate nonparametric resampling technique is developed, which augments the trial data with a larger dataset of conventional yields to improve estimation efficiency. Skip‐row adoption is found to increase mean yields and reduce risk in areas prone to drought. RMA insurance rules have incentive‐distorting impacts which disincentivize skip‐row adoption.
Evading invaders: the effectiveness of a behavioral response acquired through lifetime exposure
Authors: Freidenfelds N. A. , Robbins T. R. , Langkilde T.
Published: February 2012

Understanding the mechanisms driving adaptations to survive agonistic interactions, and their function, provides insight into how native species adapt to aggressive invaders, a growing global threat. We staged encounters between native fence lizards (Sceloporus undulatus) and red imported fire ants (Solenopsis invicta) on and off the ant mound (nest) to examine the effectiveness of lizard antipredator behavior through ontogeny while focusing on the impact of lifetime and evolutionary exposure to this invasive threat. We used field-caught and lab-reared lizards from a fire ant–invaded and an uninvaded site. In ∼90% of cases, fire ants found lizards within 12 min in natural lizard habitat. Lizards that performed rapid twitches of their body and/or fled after initial encounter with a fire ant scout reduced their risk of having additional fire ants recruit to the attack. The majority of lizards that had been exposed to fire ants within their lifetime (field-caught lizards from the invaded site) behaviorally responded to attack, whereas relatively few lizards that were naïve to fire ants (all lab-reared lizards and field-caught lizards from the uninvaded site) responded. Because fewer adult lizards responded to fire ants than juveniles, they were recruited to by additional attacking ants significantly more than were juveniles. Our data suggest that the higher percentage of responsive adults within invaded populations is the result of within-lifetime selection acting against unresponsive adults, and/or lifetime exposure to fire ants triggering the retention of this juvenile behavior into adulthood, rather than selection acting on a heritable trait across generations.
Unipro UGENE: a unified bioinformatics toolkit
Authors: Okonechnikov Konstantin , Golosova Olga , Fursov Mikhail ,   the UGENE team
Published: February 2012

Summary: Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality.

Availability and implementation: UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.

Contact:  ugene@unipro.ru

Supplementary information:  Supplementary data are available at Bioinformatics online.
A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data
Authors: Chen Zhongxue , Liu Qingzhong , Nadarajah Saralees
Published: February 2012

Motivation: As an epigenetic alteration, DNA methylation plays an important role in epigenetic controls of gene transcription. Recent advances in genome-wide scan of DNA methylation provide great opportunities in studying the impact of DNA methylation on many human diseases including various types of cancer. Due to the unique feature of this type of data, applicable statistical methods are limited and new sophisticated approaches are desirable.

Results: In this article, we propose a new statistical test to detect differentially methylated loci for case control methylation data generated by Illumina arrays. This new method utilizes the important finding that DNA methylation is highly correlated with age. The proposed method estimates the overall P-value by combining the P-values from independent individual tests each for one age group. Through real data application and simulation study, we show that the proposed test is robust and usually more powerful than other methods.

Contact:  Zhongxue.Chen@uth.tmc.edu
Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels
Authors: Schulz Marcel H. , Zerbino Daniel R. , Vingron Martin , Birney Ewan
Published: February 2012

Motivation: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values.

Results: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.

Availability and implementation: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/

Contact:  dzerbino@ucsc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
SiteComp: a server for ligand binding site analysis in protein structures
Authors: Lin Yingjie , Yoo Seungyeul , Sanchez Roberto
Published: February 2012

Motivation: Computational characterization of ligand-binding sites in proteins provides preliminary information for functional annotation, protein design and ligand optimization. SiteComp implements binding site analysis for comparison of binding sites, evaluation of residue contribution to binding sites and identification of sub-sites with distinct molecular interaction properties.

Availability and implementation: The SiteComp server and tutorials are freely available at http://sitecomp.sanchezlab.org

Contact:  roberto@sanchezlab.org; roberto.sanchez@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment
Authors: Huang Hanwen , Lu Xiaosun , Liu Yufeng , Haaland Perry , Marron J.S.
Published: February 2012

Summary: R/DWD is an extensible package for classification. It is built based on a recently developed powerful classification method called distance weighted discrimination (DWD). DWD is related to, and has been shown to be superior to, the support vector machine in situations that are fundamental to bioinformatics, such as very high dimensional data. DWD has proven to be very useful for several fundamental bioinformatics tasks, including classification, data visualization and removal of biases, such as batch effects. Earlier DWD implementations, however, relied on Matlab, which is not free and requires a license. The major contribution of the R/DWD package is an implementation that is completely in R and thus can be used without any requirements for licensing or software purchase. In addition, R/DWD also provides efficient solvers for second-order-cone-programming and quadratic programming.

Availability and implementation: The package is freely available from cran.r-project.org.

Contact:  hanwen.huang@uth.tmc.edu; Perry_Haaland@bd.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bdellovibrio exovorus sp. nov., a novel predator of Caulobacter crescentus
Authors: Koval Susan F. , Hynes Sandra H. , Flannagan Ronald S. , Pasternak Zohar , Davidov Yaacov , Jurkevitch Edouard
Published: February 2012

The life cycle, prey range and taxonomic status of aBdellovibrio-like organism, strain JSST, were studied. Strain JSSTwas isolated from sewage in London, Ontario, Canada, in enrichment culture withCaulobacter crescentusprey cells. During predation, this strain remained attached to the outside of a stalkedC. crescentuscell. No periplasmic growth stage was observed and no bdelloplast was formed. The stalked cells ofC. crescentusretained their shape and, after predation, were devoid of cytoplasmic content, as shown by transmission electron microscopy. A periplasmic growth stage has been a definitive character in the description of members of the generaBdellovibrio,Bacteriovorax,BacteriolyticumandPeredibacter. This is the first description of an epibiotic predator in this group of prokaryotic predators. The G+C content of the genomic DNA of strain JSSTwas 46.1 mol%. 16S rRNA gene sequence analysis showed that this strain was related toBdellovibrio bacteriovorusstrains HD100T, 109J, 114 and 127 (90–93 % similarity). Phylogenetic analysis based on 16S rRNA gene sequences grouped strain JSSTwith theBdellovibriocluster, but at a distance from otherBdellovibrioisolates. On the basis of features of the life cycle and phylogenetic data, it was concluded that strain JSSTmerits classification as the type strain of a novel species, for which the nameBdellovibrio exovorussp. nov. is proposed (type strain JSST = ATCC BAA-2330T = DSM 25223T).
Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA
Authors: Khil Pavel P. , Smagulova Fatima , Brick Kevin M. , Camerini-Otero R. Daniel , Petukhova Galina V.
Published: February 2012

Meiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. DSBs can be directly mapped using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Nevertheless, the genome-wide mapping of recombination hotspots in mammals is still a challenge due to the low frequency of recombination, high heterogeneity of the germ cell population, and the relatively low efficiency of ChIP. To overcome these limitations we have developed a novel method—single-stranded DNA (ssDNA) sequencing (SSDS)—that specifically detects protein-bound single-stranded DNA at DSB ends. SSDS comprises a computational framework for the specific detection of ssDNA-derived reads in a sequencing library and a new library preparation procedure for the enrichment of fragments originating from ssDNA. The use of our technique reduces the nonspecific double-stranded DNA (dsDNA) background >10-fold. Our method can be extended to other systems where the identification of ssDNA or DSBs is desired.
Identifying key trends in sales – from a training perspective
Authors: Little Bob
Published: February 2012

Purpose

This paper aims to describe key issues at macro and micro levels which impact – and affect – sales training activities and facilitation for “successful selling” in the contemporary economic climate.

Design/methodology/approach

This paper reports presentations from key speakers at the Institute of Sales & Marketing's Successful Selling conference.

Findings

At the macro level, a number of crises are impacting on the economy and, thus, successful selling. However, there is still the opportunity to compete for market share, via brand differentiation. At the micro level, customers must see sellers as “trusted advisors”; successful selling depends on “connecting” with customers' values; ethical selling is important not just in helping people to be successful salespeople but also in helping society to have confidence in its sales professionals, thus enabling buyers to buy with confidence; traditional sales models are becoming superseded by “internet research, internal discussion and the preparation of shortlists, then a decision followed by contacting the vendor”. “E‐selling” is becoming increasingly important, so sellers must have personal branding, create an internet footprint, and engage with social media.

Practical implications

This paper reveals key issues in sales so L&D professionals can commission, develop, deliver and/or facilitate appropriate activities and resources to develop the sales skills needed for success in the next ten years.

Originality/value

Armed with knowledge of the modern trends in successful selling, L&D professionals can source and resource sales‐related training activities to turn their salespeople into star performers in contemporary markets and enable their organisations to maintain/increase their competitive advantage.
Social discovery tools: extending the principle of user convenience
Authors: Spiteri Louise F.
Published: February 2012

Purpose

New social discovery systems have social‐type Web 2.0 features that allow users to enhance the content of bibliographic records by adding their own tags, ratings, and reviews. One of the primary underlying principles of cataloguing is that catalogue records be designed with the user in mind, i.e. user convenience. The purpose of this paper is to explore the relationship between the principle of user convenience and social discovery systems.

Design/methodology/approach

A review of the literature and codes of ethics of associations of information professions was undertaken to examine: the ethical dimensions of creating catalogue records to reflect user convenience, the relationship between culture and user convenience, and how social discovery tools can facilitate the creation of interactive and flexible catalogue records that reflect the culture(s) and needs of the library communities in which they exist.

Findings

Social discovery systems can address the primary barriers to creating catalogue records that meet user convenience: determining and reflecting the needs and cultural warrant of the users, and maintaining the quality and integrity of the catalogue records.

Practical implications

Social discovery systems can serve as a bridge between cataloguers' desire to create accurate catalogue records that conform to accepted cataloguing standards, and their ethical imperative to ensure that these records meet the needs of the clients.

Originality/value

The findings of this study pave the way for further research into how user‐contributed metadata allow clients to express their needs and cultural warrant and to interact with one another and library staff.
The influence of honing process parameters on surface quality, productivity, cutting angle and coefficients of friction
Authors: Vrac Damir S. , Sidjanin Leposava P. , Kovac Pavel P. , Balos Sebastian S.
Published: February 2012

Purpose

The purpose of this paper is to explore the influence of tool kinematics parameters on surface roughness, productivity and cutting angle for grey cast iron cylinder liners machined by normal honing.

Design/methodology/approach

For experimental investigation, a long stroke honing system was used. Diamond and SiC tools were used, for pre‐ and finishing, respectively. The values of cutting parameters were varied within the following limits: cutting speed vs=0.931‐1.11 m/s; specific pressure of pre‐honing process pd=1.0‐1.4 N/mm2 and specific pressure of finishing honing process pz=0.2‐0.5 N/mm2. The analysis of dispersion was conducted for determining the mathematical model for cutting parameter influence on surface roughness and productivity.

Findings

Dispersion analysis proved that the most influential parameters on maximum roughness depth are cutting speed for D181 tool and specific pressure of finishing honing for D151 tool. The most influential parameter on productivity in the honing process with D181 and D151 tool is cutting speed.

Originality/value

The paper gives new information related to the normal honing optimization process. Normal honing offers the highest surface quality which is achieved by a low speed machining. However, that means also a relatively low productivity, demanding a thorough process optimization. Furthermore, normal honing is usually done by ECH pre‐honing and mechanical finishing honing, but in this paper, all‐mechanical honing was used for the same result, at a lower lost.
The effect of hexagonal boron nitride additive on the effectiveness of grease‐based lubrication of a steel surface
Authors: Pawlak Zenon , Kałdoński Tadeusz , Lisewski Michal , Urbaniak Wieslaw , Oloyede Adekunle
Published: February 2012

Purpose

The purpose of this paper is to study the sliding and the vibrating fretting tests mechanism of h‐BN micro‐particles when used as a lubricating grease‐2 additive.

Design/methodology/approach

The fretting tests were conducted on steel/steel contacts using both vibrating fretting apparatus and the shaft‐sleeve slide fitted tester. The wear scars were characterized with profilometry. The tribological properties of grease‐2 compounded with h‐BN additive were also compared to those obtained for the commercial product Militec‐4.

Findings

The experiment showed significant differences between the results obtained from the vibrating fretting and the shaft‐sleeve sliding fitted tests. Adding h‐BN to the lubricant leads to a better performance in the shaft‐sleeve slide regime than in the steel/steel vibrating test condition.

Originality/value

The results of the experimental studies demonstrate the potential of h‐BN as an additive for preventing fretting sliding, and can very useful for further application of compound grease‐2 with h‐BN additive in industrial equipment.
Tribological properties of polytetrafluoroethylene as additive in titanium complex grease
Authors: Jiguo Chen
Published: February 2012

Purpose

The purpose of this paper is to study, analyze and present the lubricating mechanism and tribological properties of two types of oil‐based titanium complex grease containing Polytetrafluoroethylene (PTFE).

Design/methodology/approach

Two types of oil‐based sebacic acid/stearic acid titanium complex greases containing PTFE additive were synthesized using 3 L reaction vessel, and the base oils including neopentyl polyol ester and mixed oil of 650SN and neopentyl polyol (1:1.8). Friction‐reduction, antiwear, and load‐carrying properties of greases were evaluated using a four‐ball tester, and their dropping point and penetration were characterized using relevant ASTM standards. Morphologies of wear scar and chemical states of typical elements on worn surfaces were characterized by means of scanning electron microscope and X‐ray photoelectron spectroscopy, respectively.

Findings

Tribological results show that titanium complex grease containing PTFE had better friction‐reduction and antiwear properties than base grease. However, PTFE could not improve the load‐carrying capacity of base grease. Moreover, a synergistic effect between deposited film and adsorptive film contributes to good tribological properties of titanium complex grease.

Practical implications

Such a very useful lubricating material could be used in industrial applications including steel plants, power plants, packaging, and fertilizer industries.

Originality/value

The lubricating mechanism of titanium complex grease containing PTFE was proposed by tribochemical analysis of worn surfaces. The mechanism should become the direction of the theoretical and applied research of grease in the future.
Enhancing employee outcomes
Authors: San Lam Cheok , O'Higgins Eleanor R.E.
Published: February 2012

Purpose

The purpose of this paper is to examine the interrelated influences of managers' emotional intelligence, leadership styles and employee outcomes. In particular, this study aims to explore the potential mediating effects of managers' transformational leadership style on the relationships between managers' emotional intelligence and employee outcomes of: employee performance, job satisfaction, organisational commitment and job stress.

Design/methodology/approach

The study was conducted in two large organisations in Shanghai, China, on a sample of 323 participants, including both managers and subordinate employees. Emotional intelligence was measured by using the Wong Emotional Intelligence Scale (WEIS), and leadership style, using the Multifactor Leadership Questionnaire (MLQ‐5x Short).

Findings

The results showed that managers' transformational leadership style fully mediates the relationship between managers' emotional intelligence and employee job satisfaction. However, no mediating effect of managers' transformational leadership style is found on the relationship between managers' emotional intelligence and employee performance, organizational commitment and job stress.

Originality/value

The results of this study contribute to current insights about the interrelationships on managers' emotional intelligence, leadership style and employee outcomes, showing that the power of managers' emotional intelligence on job satisfaction must be expressed through a third mediating variable, transformational leadership.
A structuralist perspective on economic growth in China and India: anticipating the end game
Authors: Babones Salvatore J.
Published: February 2012

Purpose

The purpose of this paper is to examine a much‐overlooked aspect of the rise of China: when will it end? Obviously, the Chinese economy will not grow at an annual rate of 10 percent forever. At some point Chinese growth will stabilize. When is of vast importance for the political, economic, and ecological future of the world.

Design/methodology/approach

Data from the World Development Indicators database are used to benchmark the recent economic growth of China (and India) to the long‐term trajectory of Brazil. A structuralist approach derived from world‐systems analysis predicts that Chinese growth will stabilize once China reaches an equilibrium income level characteristic of the semiperiphery of the world‐economy.

Findings

Based on recent trends, the structuralist perspective suggests that China's extraordinary rate of economic growth will fall back to global norms after 2020. China is unlikely to reach US or EU levels of total national income before mid‐century.

Research limitations/implications

The research presented here is highly speculative. The data are of very poor quality and the assumptions are quite heroic. That said, the China 2020 prediction is relatively robust to variations in data and assumptions.

Social implications

The rise of China is unlikely to have much impact on the structure of the modern world economy or the continuation of US hegemony for the foreseeable future, and its impact on greenhouse gas emissions may be less than anticipated.

Originality/value

This study will hopefully open a debate about planning for the end game of rapid Chinese economic growth.