bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling current-induced magnetization switching in Heusler alloy Co2FeAl-based spin-valve nanopillar
Authors: Huang H. B. , Ma X. Q. , Liu Z. H. , Zhao C. P. , Chen L. Q.
Published: April 2014

We investigated the current-induced magnetization switching in a Heusler alloy Co2FeAl-based spin-valve nanopillar by using micromagnetic simulations. We demonstrated that the elimination of the intermediate state is originally resulted from the decease of effective magnetic anisotropy constant. The magnetization switching can be achieved at a small current density of 1.0 × 104 A/cm2 by increasing the demagnetization factors of x and y axes. Based on our simulation, we found magnetic anisotropy and demagnetization energies have different contributions to the magnetization switching.
Observational constraints of stellar collapse: Diagnostic probes of nature's extreme matter experiment
Authors: Fryer Chris L. , Even Wesley , Grefenstette Brian W. , Wong Tsing-Wai
Published: April 2014

Supernovae are Nature's high-energy, high density laboratory experiments, reaching densities in excess of nuclear densities and temperatures above 10 MeV. Astronomers have built up a suite of diagnostics to study these supernovae. If we can utilize these diagnostics, and tie them together with a theoretical understanding of supernova physics, we can use these cosmic explosions to study the nature of matter at these extreme densities and temperatures. Capitalizing on these diagnostics will require understanding a wide range of additional physics. Here we review the diagnostics and the physics neeeded to use them to learn about the supernova engine, and ultimate nuclear physics.
Ellipsometry characterization of polycrystalline ZnO layers with the modeling of carrier concentration gradient: Effects of grain boundary, humidity, and surface texture
Authors: Sago Keisuke , Kuramochi Hideto , Iigusa Hitoshi , Utsumi Kentaro , Fujiwara Hiroyuki
Published: April 2014

Spectroscopic ellipsometry (SE) has been applied to study the effects of grain boundary, humidity, and surface texture on the carrier transport properties of Al-doped ZnO layers fabricated by dc and rf magnetron sputtering. In the SE analysis, the variation in the free carrier absorption toward the growth direction, induced by the ZnO grain growth on foreign substrates, has been modeled explicitly by adopting a multilayer model in which the optical carrier concentration (Nopt) varies continuously with a constant optical mobility (μopt). The effect of the grain boundary has been studied by comparing μopt with Hall mobility (μHall). The change in μHall/μopt indicates a sharp structural transition of the ZnO polycrystalline layer at a thickness of d ∼ 500 nm, which correlates very well with the structure confirmed by transmission electron microscopy. In particular, below the transition thickness, the formation of the high density grain boundary leads to the reduction in the μHall/μopt ratio as well as Nopt. As a result, we find that the thickness dependence of the carrier transport properties is almost completely governed by the grain boundary formation. On the other hand, when the ZnO layer is exposed to wet air at 85 °C, μHall reduces drastically with a minor variation of μopt due to the enhanced grain boundary scattering. We have also characterized textured ZnO:Al layers prepared by HCl wet etching by SE. The analysis revealed that the near-surface carrier concentration increases slightly after the etching. We demonstrate that the SE technique can be applied to distinguish various rough textured structures (size ∼ 1 μm) of the ZnO layers prepared by the HCl etching.
Magnetic properties and local microstructures in Zn-doped YMnO3
Authors: Zhang A. M. , Zhou G. T. , Zheng L. , Wu X. S.
Published: April 2014

The hole doping effect on the magnetic properties of multiferroic YMn1−xZnxO3 was studied through investigating the local microstructures. Polycrystalline YMn1−xZnxO3 samples with x ranging from 0 to 0.22 are synthesized by solid-state reaction method. The x-ray diffraction patterns reveal that YMn1−xZnxO3 samples with low Zn2+ doping concentration (x < 0.1) maintain single phase which show hexagonal structure with space group of P63cm. The temperature dependence of magnetization presents that the magnetic moment at low temperature and the FM transition temperature increase with increasing the doping concentration of Zn2+. Meanwhile, ferromagnetism induced by Zn2+ doping is found to become stronger. EXAFS analysis reveals the in-plane Mn-OP bond length decreases while the out-of-plane Mn-OA bond length keeps almost constant. The weak FM order is ascribed to order-to-disorder effect resulting from the diluted exchange interaction among Mn3+ ions and double-exchange interaction between the mixed valence-state of Mn3+ and Mn4+ by hole doping of Zn2+.
Perpendicular magnetic anisotropy and magnetization of L1 FePt/FeCo bilayer films
Authors: Wang Bochong , Oomiya Hiroyuki , Arakawa Akira , Hasegawa Takashi , Ishio Shunji
Published: April 2014

Fe40Co60 epitaxial thin films are prepared on L10 ordered Fe60Pt40 underlayer by ultrahigh vacuum multiple dc-sputtering systems. Magnetic properties of the Fe60Pt40 (10 nm)/Fe40Co60 (t nm) bilayer films are investigated. When the FeCo thickness is less than 3 nm, the easy magnetization axis of FePt/FeCo bilayer film is perpendicular to the film plane. Compared with FePt/Fe and FePt/Co films, FePt/FeCo bilayer films possess not only higher anisotropy field Hk but also larger magnetic anisotropy energy Ku, which may be due to the perpendicular magnetic anisotropy yielded by the tetragonal distorted FeCo layer on FePt, while the magnetic easy axes of Fe and Co layers lie in the film plane. Meanwhile, saturation magnetization of FePt/FeCo film increases reasonably because of the high Ms value of FeCo component. These results indicate that the FePt/FeCo bilayer films which possess both large magnetic anisotropy energy Ku and high saturation magnetization Ms have great potential for using as the magnetic recording media, and also give a clue to develop a new type of permanent magnet without rare-earth metals.
Water shells of diamond nanoparticles in colloidal solutions
Authors: Batsanov Stepan S. , Lesnikov Evgeny V. , Dan'kin Dimitry A. , Balakhanov Dimitry M.
Published: April 2014

The refractive index of colloidal particles formed by nanodiamond in water (average diameters of 106, 122, and 854 nm) was measured by Fabry-Perot interferometry as n = 1.78, 1.74, and 1.79, respectively, which suggests the molar ratio of water to carbon within these particles of 0.16:1, and the effective thickness of interfacial (nano) water shells around a 5 nm diamond particle of 0.48(5) nm. Structural implications of this are discussed.
Enhanced 2.7 μm emission from Er3+ doped oxyfluoride tellurite glasses for a diode-pump mid-infrared laser
Authors: Zhang F. F. , Zhang W. J. , Yuan J. , Chen D. D. , Qian Q. , Zhang Q. Y.
Published: April 2014

The influence of fluoride and shielding gas (O2 or Ar) on the physical and spectroscopic properties of Er3+ doped TeO2-ZnO-ZnF2 glass system is investigated. The larger electronegativity of F than O accounts for the gradual decrease of refractive index, density, and J-O parameters with increasing ZnF2. An analysis on Fourier transform infrared transmission spectra reveals that the absorption coefficient of OH− around 3 μm as low as 0.247 cm−1 can be achieved when 30 mol% ZnF2 containing sample is treated with Ar gas during glass melting process. The reduction of OH− groups combined with the low multiphonon relaxation rate (207 s−1) contributes to the enhanced emissions at 1.5 and 2.7 μm, along with prolonged lifetimes of 4I11/2 and 4I13/2 levels. A high branching ratio (17.95%) corresponding to the Er3+: 4I11/2 → 4I13/2 transition, the large absorption and emission cross section (0.44 × 10−20 cm2 and 0.45 × 10−20 cm2), and good gain cross section demonstrate that oxyfluoride tellurite glass could be a promising material for a diode-pump 2.7 μm fiber laser.
Thermal conductivity of silicene from first-principles
Authors: Xie Han , Hu Ming , Bao Hua
Published: April 2014

Silicene, as a graphene-like two-dimensional material, now receives exceptional attention of a wide community of scientists and engineers beyond graphene. Despite extensive study on its electric property, little research has been done to accurately calculate the phonon transport of silicene so far. In this paper, thermal conductivity of monolayer silicene is predicted from first-principles method. At 300 K, the thermal conductivity of monolayer silicene is found to be 9.4 W/mK and much smaller than bulk silicon. The contributions from in-plane and out-of-plane vibrations to thermal conductivity are quantified, and the out-of-plane vibration contributes less than 10% of the overall thermal conductivity, which is different from the results of the similar studies on graphene. The difference is explained by the presence of small buckling, which breaks the reflectional symmetry of the structure. The flexural modes are thus not purely out-of-plane vibration and have strong scattering with other modes.
Influence of globulin subunit composition of soybean proteins on silken tofu quality. 1. Effect of growing location and 11SA4 and 7Sα’ deficiency
Authors: Yang Aijun , James Andrew T.
Published: April 2014

Growing location and genotypes are known to affect the subunit composition of the major storage proteins of soybeans, β-conglycinin (7S globulins) and glycinin (11S globulins), which have been associated with tofu quality. In this study, we examined 16 soybean genotypes grown at two locations in Queensland, Australia, for the influence of globulin subunit composition, growing location and genotype × growing location interaction on seed, soymilk and silken tofu properties. These genotypes comprised four groups: with all globulin subunits, without 11SA4, without 7Sα’, or without 11SA4 and 7Sα’. There were significant differences in the major protein subunits among the genotypes and the four groups and between locations. Significant genotypic and location differences were also observed in the properties of the seed, soymilk and silken tofu. There were no significant genotype × location interactions. The group without 11SA4 had less 11S and more 7S globulins, resulting in the lowest 11S/7S ratio. The silken tofu from this group had firmer texture and less water loss than the group containing all globulin subunits. The results suggested that genotypes of differing globulin subunit composition may produce tofu with different qualities and the effect of globulin subunit composition on tofu quality could be affected by growing location and the absence of certain globulin subunits.
Effects of vitrification on the expression of pluripotency, apoptotic and stress genes in in vitro-produced porcine blastocysts
Authors: Castillo-Martín Miriam , Yeste Marc , Pericuesta Eva , Morató Roser , Gutiérrez-Adán Alfonso , Bonet Sergi
Published: April 2014

The aims of the present study were to: (1) evaluate the effect of vitrification and warming on quality parameters and expression levels of pluripotency, apoptotic and stress genes in in vitro-produced (IVP) porcine blastocysts; and (ii) determine the correlation between these parameters. To this end, total cell number, DNA fragmentation, peroxide levels and the relative transcript abundance of BCL-2 associated X protein (BAX), BCL2-like 1 (BCL2L1), heat shock protein 70 (HSPA1A), POU class 5 homeobox 1 (POU5F1), superoxide dismutase 1 (SOD1) and superoxide dismutase 2 (SOD2) were analysed in fresh and vitrified IVP blastocysts. The results suggest that vitrification procedures have no effect on total cell number and gene expression of BAX, BCL2L1, SOD1 and SOD2 or the BAX : BCL2L1 ratio. Nevertheless, a significant increase in DNA fragmentation (2.9 ± 0.4% vs 11.9 ± 2.0%) and peroxide levels (80.4 ± 2.6 vs 97.2 ± 3.1) were seen in vitrified compared with Day 7 fresh blastocysts. In addition, after blastocyst vitrification, relative transcript abundance was downregulated for POU5F1 and upregulated for HSPA1A. Finally, there was a significant correlation of POU5F1 and HSPA1A with DNA fragmentation (POU5F1, r = –0.561; HSPA1A, r = 0.604) and peroxide levels (POU5F1, r = –0.590; HSPA1A, r = 0.621). In conclusion, under the conditions of the present study, vitrification and warming of IVP porcine blastocysts resulted in altered expression of POU5F1 and HSPA1A, but had no effect on BAX, BCL2L1, SOD1 and SOD2 expression.
A comparison of stocking methods for beef production in northern Australia: pasture and soil surface condition responses
Authors: Hall Trevor J. , McIvor John G. , Reid David J. , Jones Paul , MacLeod Neil D. , McDonald Cam K. , Smith David R.
Published: April 2014

Historical stocking methods of continuous, season-long grazing of pastures with little account of growing conditions have caused some degradation within grazed landscapes in northern Australia. Alternative stocking methods have been implemented to address this degradation and raise the productivity and profitability of the principal livestock, cattle. Because information comparing stocking methods is limited, an evaluation was undertaken to quantify the effects of stocking methods on pastures, soils and grazing capacity. The approach was to monitor existing stocking methods on nine commercial beef properties in north and south Queensland. Environments included native and exotic pastures and eucalypt (lighter soil) and brigalow (heavier soil) land types. Breeding and growing cattle were grazed under each method. The owners/managers, formally trained in pasture and grazing management, made all management decisions affecting the study sites. Three stocking methods were compared: continuous (with rest), extensive rotation and intensive rotation (commonly referred to as ‘cell grazing’). There were two or three stocking methods examined on each property: in total 21 methods (seven continuous, six extensive rotations and eight intensive rotations) were monitored over 74 paddocks, between 2006 and 2009. Pasture and soil surface measurements were made in the autumns of 2006, 2007 and 2009, while the paddock grazing was analysed from property records for the period from 2006 to 2009. The first 2 years had drought conditions (rainfall average 3.4 decile) but were followed by 2 years of above-average rainfall. There were no consistent differences between stocking methods across all sites over the 4 years for herbage mass, plant species composition, total and litter cover, or landscape function analysis (LFA) indices. There were large responses to rainfall in the last 2 years with mean herbage mass in the autumn increasing from 1970 kg DM ha–1 in 2006–07 to 3830 kg DM ha–1 in 2009. Over the same period, ground and litter cover and LFA indices increased. Across all sites and 4 years, mean grazing capacity was similar for the three stocking methods. There were, however, significant differences in grazing capacity between stocking methods at four sites but these differences were not consistent between stocking methods or sites. Both the continuous and intensive rotation methods supported the highest average annual grazing capacity at different sites. The results suggest that cattle producers can obtain similar ecological responses and carry similar numbers of livestock under any of the three stocking methods.
An agronomic test to manage phosphorus environmental risk from pastures with good grazing management
Authors: Hart M. R. , Cornish P. S.
Published: March 2014

Management of phosphorus (P) environmental risk has been hampered by the lack of widely applicable threshold values for the soil properties that determine concentrations of P in runoff. This paper simplified the task of developing threshold values by restricting land-use to pastures and by using a single methodology based on simulated rainfall across 38 field sites (76 plots) that included a range of land-use intensities, and soils that varied widely in lithology and soil properties. An ‘adjusted’ soil-test P was determined from the measured Colwell-P minus the threshold P for agronomic response, which was estimated from P-buffering index (PBI). Concentrations of total P (TP) in runoff rose exponentially with rising ‘adjusted’ soil-test P, although only with pastures with high groundcover (r2 = 0.87), or if plots were protected from erosion with a cover of shade-cloth (r2 = 0.70). Concentrations of TP in runoff were low (<0.5 mg L–1) where adjusted Colwell-P was less than zero, which on this scale is the threshold for agronomic response. Similar results were found for dissolved reactive P (DRP) in runoff, although for plots with soil P below the agronomic threshold, the concentrations of DRP were lower than for TP. We conclude that Colwell-P and soil PBI together provide a widely applicable test for environmental P risk from pastures with good ground cover. The same threshold values may be used for both agronomic and environmental purposes.
Dimerization of mammalian kinesin-3 motors results in superprocessive motion
Authors: Soppina Virupakshi , Norris Stephen R. , Dizaji Aslan S. , Kortus Matt , Veatch Sarah , Peckham Michelle , Verhey Kristen J.
Published: April 2014

Significance

The kinesin-3 family is one of the largest among the kinesin superfamily and its members play important roles in a variety of cellular functions ranging from intracellular transport to mitosis. Defects in kinesin-3 transport have been implicated in a variety of neurodegenerative, developmental, and cancer diseases, yet the molecular mechanisms of kinesin-3 regulation and cargo transport are largely unknown. We show that kinesin-3 motors undergo cargo-mediated dimerization to transport cellular cargoes. We also show that dimerization results in kinesin-3 motors that are fast and superprocessive. Such high processivity has not been observed for any other motor protein and suggests that kinesin-3 motors are evolutionarily adapted to serve as the marathon runners of the cellular world.
Hydration kinetics and 10‐km outdoor running performance following 75% versus 150% between bout fluid replacement
Authors: Davis Brett Alan , Thigpen Lauren Kellet , Hornsby Jared Heath , Green James Matthew , Coates Thomas Elliot , O'Neal Eric Kyle
Published: April 2014

Current American College of Sports Medicine (ACSM) guidelines recommend replacing 150% of sweat losses between training bouts separated by ≤12 hours, but little evidence exists concerning the implications of this strategy for runners. Participants (n = 13) in this study replaced 75% (1637 ± 372 mL) or 150% (3099 ± 850 mL) of sweat losses following an outdoor evening run (∼75 minutes; Wet‐bulb‐globe temperature (WBGT) = ∼27°C) and consumed a standardised evening meal and breakfast before completing an outdoor (WBGT = ∼23°C) 10‐km time‐trial the following morning. Urine was collected between runs and urine specific gravity (USG) was assessed pre‐run. Significant differences were found in pre‐run body mass (75% = 69.6 ± 9.2; 150% = 70.1 ± 9.3 kg; P = 0.02) and USG (75% = 1.026 ± 0.005; 150% = 1.014 ± 0.007; P < 0.001). Heart rate during 10‐km run (168 ± 14 versus 168 ± 12 beats min−1) and post‐run intestinal temperature (39.08 ± 0.52 versus 39.00 ± 0.70 °C) did not differ for 75% and 150%, respectively, despite an ∼3% performance improvement (75% = 47.28 ± 6.64; 150% = 45.93 ± 6.04 minutes; P = 0.001) due to a faster pace in the second half of the run with 150% replacement. Session rate of perceived exertion (RPE) was lower (P = 0.02) during 150% (7.5 ± 1.3) versus 75% (8.4 ± 0.9). Reluctant drinkers potentially hinder training quality between evening and morning runs in the heat, but copious urine production and difficulty in consuming recommended fluid volumes suggest fluid replacement <150% may be more ideal.
About the unidirectionality of interference: Insight from the musical Stroop effect
Authors: Grégoire Laurent , Perruchet Pierre , Poulin-Charronnat Bénédicte
Published: April 2014

The asymmetry of interference in a Stroop task usually refers to the well-documented result that incongruent colour words slow colour naming (Stroop effect) but incongruent colours do not slow colour word reading (no reverse Stroop effect). A few other studies have suggested that, more generally, a reverse Stroop effect can be occasionally observed but at the expense of the Stroop effect itself, as if interference was inherently unidirectional, from the stronger to the weaker of the two competing processes. We describe here a situation conducive to a pervasive mutual interference effect. Musicians were exposed to congruent and incongruent note name/note position patterns, and they were asked either to read the word while ignoring the location of the note within the staff, or to name the note while ignoring the note name written inside the note picture. Most of the participants exhibited interference in the two tasks. Overall, this result pattern runs against the still prevalent model of the Stroop phenomenon [Cohen, J. D., Dunbar, K., & McClelland, J. L. (1990). On the control of automatic processes: A parallel distributed processing account of the Stroop effect. Psychological Review, 97(3), 332–361]. However, further analyses lend support to one of the key tenets of the model, namely that the pattern of interference depends on the relative strength of the two competing pathways. The reasons for the impressive differences between the results collected in the present study and in the standard colour–word (or picture–word) paradigms are also examined. We suggest that these differences reveal the importance of stimulus–response contingency in the formation of automatisms.
Measuring effects of voluntary attention: A comparison among predictive arrow, colour, and number cues
Authors: Olk Bettina , Tsankova Elena , Petca A. Raisa , Wilhelm Adalbert F. X.
Published: April 2014

The Posner cueing paradigm is one of the most widely used paradigms in attention research. Importantly, when employing it, it is critical to understand which type of orienting a cue triggers. It has been suggested that large effects elicited by predictive arrow cues reflect an interaction of involuntary and voluntary orienting. This conclusion is based on comparisons of cueing effects of predictive arrows, nonpredictive arrows (involuntary orienting), and predictive numbers (voluntary orienting). Experiment 1 investigated whether this conclusion is restricted to comparisons with number cues and showed similar results to those of previous studies, but now for comparisons to predictive colour cues, indicating that the earlier conclusion can be generalized. Experiment 2 assessed whether the size of a cueing effect is related to the ease of deriving direction information from a cue, based on the rationale that effects for arrows may be larger, because it may be easier to process direction information given by symbols such as arrows than that given by other cues. Indeed, direction information is derived faster and more accurately from arrows than from colour and number cues in a direction judgement task, and cueing effects are larger for arrows than for the other cues. Importantly though, performance in the two tasks is not correlated. Hence, the large cueing effects of arrows are not a result of the ease of information processing, but of the types of orienting that the arrows elicit.
Crop Insurance Savings Accounts: A Viable Alternative to Crop Insurance?
Authors: Colson Gregory , Ramirez Octavio A. , Fu Shengfei
Published: April 2014

This research explores the viability of an alternative design for crop insurance based upon farmer‐owned savings accounts that are regulated, monitored, and marginally assisted by the government. Such accounts could be an effective risk management tool for many farmers and could operate without major government subsidization. Relative to the current program, the proposed design should exhibit minimal moral hazard and adverse selection problems, and since farm‐level risk does not have to be priced, the proposed design eliminates the premium rating difficulties that weaken actuarial soundness and trigger the need for substantial external subsidies. In addition, administrative costs should be considerably lower.
PRADA: pipeline for RNA sequencing data analysis
Authors: Torres-García Wandaliz , Zheng Siyuan , Sivachenko Andrey , Vegesna Rahulsimham , Wang Qianghu , Yao Rong , Berger Michael F. , Weinstein John N. , Getz Gad , Verhaak Roel G.W.
Published: April 2014

Summary:  Technological advances in high-throughput sequencing necessitate improved computational tools for processing and analyzing large-scale datasets in a systematic automated manner. For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification. PRADA uses a dual-mapping strategy that increases sensitivity and refines the analytical endpoints. PRADA has been used extensively and successfully in the glioblastoma and renal clear cell projects of The Cancer Genome Atlas program.

Availability and implementation:   http://sourceforge.net/projects/prada/

Contact:   gadgetz@broadinstitute.org or rverhaak@mdanderson.org

Supplementary information:   Supplementary data are available at Bioinformatics online.
An Enabling Act
Authors: Chalkias Spyridon , Doweiko John P. , Eliopoulos George M.
Published: April 2014

Infection with human T-lymphotropic virus type 1 (HTLV-1) can be associated with hematologic malignancy, inflammatory syndromes, or infectious complications. Herein, we bring attention to HTLV-1 infection complications as we discuss a case of disseminated cryptococcosis in a patient with HTLV-1-associated T cell lymphoma.
Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy
Authors: Srinivas A. , Sasikala Ch. , Ramana Ch. V.
Published: April 2014

A Gram-stain-negative, rod-shaped, phototrophic bacterium, strain JA793T, was isolated from rhizosphere soil of paddy. The strain was capable of growing phototrophically and chemotrophically. Bacteriochlorophyll-a and carotenoids of the spirilloxanthin series were present as photosynthetic pigments. The major fatty acid of strain JA793T was C18 : 1ω7c/C18 : 1ω6c (>65.7 %), with minor amounts of C16 : 0, C16 : 1ω7c/C16 : 1ω6c, C20 : 2ω6,9c, C16 : 0 3-OH, C14 : 0 and C18 : 0 also present. Ubiquinone-10 and rhodoquinone-10 were present as primary quinones. Phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were the major polar lipids, while minor amounts of amino lipids and unidentified lipids were also present. The G+C content of genomic DNA of strain JA793T was 68.7 mol%. 16S rRNA gene-based EzTaxon-e blast search analysis of strain JA793T indicated highest sequence similarity with members of the genus

Rhodoplanes

in the family

Hyphomicrobiaceae

of the class

Alphaproteobacteria

. Strain JA793T had high sequence similarity with

Rhodoplanes elegans

AS130T (98.6 %),

Rhodoplanes roseus

941T (98 %),

Rhodoplanes pokkaliisoli

JA415T (97.5 %) and

Rhodoplanes piscinae

JA266T (97.3 %) and other members of the genus

Rhodoplanes

(<97 %). However, strain JA266T was related by <59 % (based on DNA–DNA hybridization) to

Rhodoplanes elegans

DSM 11907T ( = AS130T),

Rhodoplanes roseus

DSM 5909T ( = 941T),

Rhodoplanes pokkaliisoli

JA415T and

Rhodoplanes piscinae

JA266T. The genomic information was well supported by phenotypic and chemotaxonomic data to classify strain JA793T as a representative of a novel species in the genus

Rhodoplanes

, for which the name Rhodoplanes oryzae sp. nov. is proposed. The type strain is JA793T ( = NBRC 109406T = KCTC 15260T).
Aminoglycoside inhibition of Staphylococcus aureus biofilm formation is nutrient dependent
Authors: Henry-Stanley Michelle J. , Hess Donavon J. , Wells Carol L.
Published: April 2014

Biofilms represent microbial communities, encased in a self-produced matrix or extracellular polymeric substance. Microbial biofilms are likely responsible for a large proportion of clinically significant infections and the multicellular nature of biofilm existence has been repeatedly associated with antibiotic resistance. Classicalin vitroantibiotic-susceptibility testing utilizes artificial growth media and planktonic microbes, but this method may not account for the variability inherent in environments subject to biofilm growthin vivo. Experiments were designed to test the hypothesis that nutrient concentration can modulate the antibiotic susceptibility ofStaphylococcus aureusbiofilms. DevelopingS. aureusbiofilms initiated on surgical sutures, and in selected experiments planktonic cultures, were incubated for 16 h in 66 % tryptic soy broth, 0.2 % glucose (1× TSBg), supplemented with bactericidal concentrations of gentamicin, streptomycin, ampicillin or vancomycin. In parallel experiments, antibiotics were added to growth medium diluted one-third (1/3× TSBg) or concentrated threefold (3× TSBg). Following incubation, viable bacteria were enumerated from planktonic cultures or suture sonicates, and biofilm biomass was assayed using spectrophotometry. Interestingly, bactericidal concentrations of gentamicin (5 µg gentamicin ml−1) and streptomycin (32 µg streptomycin ml−1) inhibited biofilm formation in samples incubated in 1/3× or 1× TSBg, but not in samples incubated in 3× TSBg. The nutrient dependence of aminoglycoside susceptibility is not only associated with biofilm formation, as planktonic cultures incubated in 3× TSBg in the presence of gentamicin also showed antibiotic resistance. These findings appeared specific for aminoglycosides because biofilm formation was inhibited in all three growth media supplemented with bactericidal concentrations of the cell wall-active antibiotics, ampicillin and vancomycin. Additional experiments showed that the ability of 3× TSBg to overcome the antibacterial effects of gentamicin was associated with decreased uptake of gentamicin byS. aureus. Uptake is known to be decreased at low pH, and the kinetic change in pH of growth medium from biofilms incubated in 5 µg gentamicin ml−1in the presence of 3× TSBg was decreased when compared with pH determinations from biofilms formed in 1/3× or 1× TSBg. These studies underscore the importance of environmental factors, including nutrient concentration and pH, on the antibiotic susceptibility ofS. aureusplanktonic and biofilm bacteria.
Shortening the unstructured, interdomain region of the non-structural protein NS1 of an avian H1N1 influenza virus increases its replication and pathogenicity in chickens
Authors: Trapp Sascha , Soubieux Denis , Marty Hélène , Esnault Evelyne , Hoffmann Thomas W. , Chandenier Margaux , Lion Adrien , Kut Emmanuel , Quéré Pascale , Larcher Thibaut , Ledevin Mireille , Munier Sandie , Naffakh Nadia , Marc Daniel
Published: April 2014

Currently circulating H5N1 influenza viruses have undergone a complex evolution since the appearance of their progenitor A/Goose/Guangdong/1/96 in 1996. After the eradication of the H5N1 viruses that emerged in Hong Kong in 1997 (HK/97 viruses), new genotypes of H5N1 viruses emerged in the same region in 2000 that were more pathogenic for both chickens and mice than HK/97 viruses. These, as well as virtually all highly pathogenic H5N1 viruses since 2000, harbour a deletion of aa 80–84 in the unstructured region of the non-structural (NS) protein NS1 linking its RNA-binding domain to its effector domain. NS segments harbouring this mutation have since been found in non-H5N1 viruses and we asked whether this 5 aa deletion could have a general effect not limited to the NS1 of H5N1 viruses. We genetically engineered this deletion in the NS segment of a duck-origin avian H1N1 virus, and compared the in vivo and in vitro properties of the WT and NSdel8084 viruses. In experimentally infected chickens, the NSdel8084 virus showed both an increased replication potential and an increased pathogenicity. This in vivo phenotype was correlated with a higher replicative efficiency in vitro, both in embryonated eggs and in a chicken lung epithelial cell line. Our data demonstrated that the increased replicative potential conferred by this small deletion was a general feature not restricted to NS1 from H5N1 viruses and suggested that viruses acquiring this mutation may be selected positively in the future.
Numerous new mitogenomic sequences and multiple new environmental DNA markers for invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) populations in North America
Authors: Lance Richard F. , Farrington Heather L. , Edwards Christine E. , Guan Xin , Carr Matthew R. , Baerwaldt Kelly
Published: March 2014

Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American waterways. Recently, environmental DNA (eDNA), the use of species-specific genetic assays to detect the DNA of a particular species in a water sample, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American waterways. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with other common and closely related species to identify potential eDNA markers. We then field-tested these genetic markers for species-specificity and sensitivity in environmental samples. Newly developed markers performed well in field trials, had low false positive rates and had comparable sensitivity compared to current markers. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp, and can be used to improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species.
Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA
Authors: Ramakrishna Suresh , Kwaku Dad Abu-Bonsrah , Beloor Jagadish , Gopalappa Ramu , Lee Sang-Kyung , Kim Hyongbum
Published: April 2014

RNA-guided endonucleases (RGENs) derived from the CRISPR/Cas system represent an efficient tool for genome editing. RGENs consist of two components: Cas9 protein and guide RNA. Plasmid-mediated delivery of these components into cells can result in uncontrolled integration of the plasmid sequence into the host genome, and unwanted immune responses and potential safety problems that can be caused by the bacterial sequences. Furthermore, this delivery method requires transfection tools. Here we show that simple treatment with cell-penetrating peptide (CPP)–conjugated recombinant Cas9 protein and CPP-complexed guide RNAs leads to endogenous gene disruptions in human cell lines. The Cas9 protein was conjugated to CPP via a thioether bond, whereas the guide RNA was complexed with CPP, forming condensed, positively charged nanoparticles. Simultaneous and sequential treatment of human cells, including embryonic stem cells, dermal fibroblasts, HEK293T cells, HeLa cells, and embryonic carcinoma cells, with the modified Cas9 and guide RNA, leads to efficient gene disruptions with reduced off-target mutations relative to plasmid transfections, resulting in the generation of clones containing RGEN-induced mutations. Our CPP-mediated RGEN delivery process provides a plasmid-free and additional transfection reagent–free method to use this tool with reduced off-target effects. We envision that our method will facilitate RGEN-directed genome editing.
The Redox Potential of the Plastoquinone Pool of the Cyanobacterium Synechocystis Species Strain PCC 6803 Is under Strict Homeostatic Control
Authors: Schuurmans R. Milou , Schuurmans J. Merijn , Bekker Martijn , Kromkamp Jacco C. , Matthijs Hans C.P. , Hellingwerf Klaas J.
Published: April 2014

A method is presented for rapid extraction of the total plastoquinone (PQ) pool from Synechocystis sp. strain PCC 6803 cells that preserves the in vivo plastoquinol (PQH2) to -PQ ratio. Cells were rapidly transferred into ice-cold organic solvent for instantaneous extraction of the cellular PQ plus PQH2 content. After high-performance liquid chromatography fractionation of the organic phase extract, the PQH2 content was quantitatively determined via its fluorescence emission at 330 nm. The in-cell PQH2-PQ ratio then followed from comparison of the PQH2 signal in samples as collected and in an identical sample after complete reduction with sodium borohydride. Prior to PQH2 extraction, cells from steady-state chemostat cultures were exposed to a wide range of physiological conditions, including high/low availability of inorganic carbon, and various actinic illumination conditions. Well-characterized electron-transfer inhibitors were used to generate a reduced or an oxidized PQ pool for reference. The in vivo redox state of the PQ pool was correlated with the results of pulse-amplitude modulation-based chlorophyll a fluorescence emission measurements, oxygen exchange rates, and 77 K fluorescence emission spectra. Our results show that the redox state of the PQ pool of Synechocystis sp. strain PCC 6803 is subject to strict homeostatic control (i.e. regulated between narrow limits), in contrast to the more dynamic chlorophyll a fluorescence signal.
Internalizing cross-cultural sensitivity: reflective journals of migrant students
Authors: Starr-Glass David
Published: April 2014

Purpose

– This article, which is exploratory in nature, considers the experiences of migrant students enrolled in the transnational degree program of an accredited American college located in the Czech Republic. Migrant students have considerable experience in negotiating the different national cultures of their college and of the new country in which they live. Students, participating in a Cross-culture Management course, were asked to maintain reflective journals in which they recorded their experiences of national culture difference. The purpose was to encourage consideration, reflection, and the growing internalization of cross-cultural appreciation and negotiation.

Design/methodology/approach

– Participants were asked to maintain reflective journals during the semester, in which they identified and considered critical incidents and defining issues in their cross-cultural experiences. Journals were analyzed from an inductive phenomenological perspective with no preconceived imposition of structure, although participants had been informed that the root-metaphor of the journal should be that of “journeys”. Ten emergent themes were identified and a number of these, which seemed to impact national culture adaptation, are discussed. In an attempt to retain the authentic voice of participants, verbatim quotations are reproduced in some detail.

Findings

– The emergent themes identified give insight into the range of national cultural complexities that these migrant students confronted. Sharing these issues with those who have less national culture experience might increase their understanding of the adaption process. More importantly, the journal increased reflection, prompted deeper sensemaking, and allowed participants to articulate their experiences. Making explicit their own cultural adaption problems may also be beneficial for these participants.

Originality/value

– Cross-culture education has often taken a didactic approach that emphasized teaching and learning. The reflective journal focuses on an experiential approach to making sense of cultural experience. From a learner perspective, the use of a reflective journal stimulates reflection and contributes to resolution. From an instructor perspective, journals provide valuable insight into issues significant in a developing awareness of a national culture. Journals also provide an unrecognized insight into the personal experiences of international and transnational students that may have implications in their general learning and broader education.
Proverbial wisdom – a “serious” international business game
Authors: E. Witte Anne , Daly Peter
Published: April 2014

Purpose

– This paper aims to describe a proverb game where the themes of work and money introduce participants to world perspectives on handling social transactions and establishing “fair play” between people.

Design/methodology/approach

– Students are involved in a “serious game” where they work in international groups to piece together parts of a linguistic puzzle drawing on the language competencies of the group. They exchange viewpoints about “fair play”. This experiential learning opportunity introduces an ethics and cross-cultural framework into the curriculum.

Findings

– The game has been used to “break the ice” at the start of international business programs and allow exchange students greater opportunity to become involved in problem solving activities.

Practical implications

– In three versions, the authors have tested over three academic years, the proverb game has allowed the participants to reach the objectives: become involved with international classmates, co-produce cultural knowledge with peers (an alternative to a teacher-driven seminar on culture), develop awareness of cultural self, study world values through proverbs, and examine the importance of rule-based behavior and fair play.

Originality/value

– To the authors' knowledge, there are no “language” games suitable for the international business classroom whose purpose is actually ethical.
Flexibility i-deals: how much is ideal?
Authors: R. Vidyarthi Prajya , Chaudhry Anjali , Anand Smriti , C. Liden Robert
Published: April 2014

Purpose

– This paper aimed to explore the relationship between flexibility i-deals and employee attitudes. The authors developed theory and tested a non-linear model between i-deals and perceived organizational support (POS), and career satisfaction.

Design/methodology/approach

– Hierarchical linear modeling using multisource data collected in a field study from 207 employees and 39 managers supported the hypotheses.

Findings

– Consistent with the proposed non-linear model, low and high levels of flexibility i-deals were associated with high POS and career satisfaction. At moderate levels of i-deals, employee attitudes were lower.

Research limitations/implications

– Though non-linear relationships are unlikely to result from multi source common method data, the cross-sectional study design limits the authors from claiming causality between the variables of interest. This study is an important step towards elucidating the complex nature of relationship between flexibility i-deals and employee outcomes.

Practical implications

– Organizations must heed the needs of employees who seek accommodations in their work schedule. However, organizations should be cognizant of the associated implications at different levels of flexibility granted.

Social implications

– I-deals partly satisfied employees' need for affiliation by strengthening their emotional bonds with the organization (i.e. POS). I-deals also enhanced employees' career satisfaction which is an important component of self-actualization. By meeting employees' higher order needs i-deals have the potential to create a workplace that provides overall wellbeing rather than just a living.

Originality/value

– This is the first study to investigate non-linear relationships between flexibility i-deals and employee attitudes.
The impact of impression management over time
Authors: C. Bolino Mark , C. Klotz Anthony , Daniels Denise
Published: April 2014

Purpose

– The purpose of these studies was to investigate how the repeated use of impression management (IM) tactics is related to supervisor perceptions in newly formed supervisor-subordinate dyads.

Design/methodology/approach

– Two studies were conducted – a lab study in which participants evaluated a confederate who performed an accounting task while using different types of IM across five trials, and a field study examining the IM tactics of new employees and their supervisors' ratings of likability and performance at two points in time.

Findings

– In the lab study, the repeated use of ingratiation had an increasingly positive effect on performance ratings, whereas repeated apologies had an increasingly negative effect on evaluations of performance. The influence of IM tactics on ratings of subordinate likability did not change with repeated use. In the field study, subordinates' use of apologies and justifications was more strongly associated with supervisor evaluations of likability and performance in earlier stages of their relationship.

Practical implications

– Employees need to be mindful that IM tactics may vary in their effectiveness depending on the timing and frequency of their use. Furthermore, supervisors should consider the initial influence that IM has on their ability to objectively evaluate new subordinates.

Originality/value

– This research is unique in that it examined how the repeated use of both assertive (i.e. ingratiation and self-promotion) and defensive (i.e. apologies and justifications) IM tactics are related to both evaluations of likability and performance ratings at multiple points in time.
The effect of multiple host species on a keystone parasitic plant and its aphid herbivores
Authors: Rowntree Jennifer K. , Fisher Barham David , Stewart Alan J. A. , Hartley Sue E.
Published: April 2014

The exploitation of shared resources by diverse organisms underpins the structure of ecological communities. Hemiparasitic plants and the insect herbivores feeding on them both rely, directly and indirectly, on the resources supplied by the parasite's host plant. Therefore, the identity and number of host plant species providing these resources is likely to be critical for parasite and herbivore performance.

We tested the effect of single and multiple host species on the biomass of the generalist parasitic plant Rhinanthus minor and the abundance of its aphid (Aphis gossypii) herbivores.

Parasite biomass was proportional to the number of haustorial connections to host roots and was determined by host species identity rather than host functional group. Host species identity was also an important influence on aphid population size, and parasites attached to Lotus corniculatus experienced a considerable reduction in aphid herbivory.

The effects on the parasite attaching to multiple hosts depended on the combination of species present. However, host mixtures generally benefitted aphids by diluting the negative effects of particular host species.

Our findings suggest that the specificity of host attachment alters the impact of this keystone parasitic plant on its own herbivores and, potentially, on the wider plant and herbivore community.