bluuebunny/crossref_metadata_2025 huggingface dataset:
Fully packaged millimetre‐wave dielectric waveguide with multimodal excitation
Authors: Dolatsha N. , Saiz N. , Arbabian A.
Published: August 2015

A millimetre‐wave interconnect on a very low‐cost plastic waveguide is proposed for applications in terabit per second wireline links. Simultaneous utilisation of the two fundamental and polarisation‐orthogonal degenerate Ex11 and Ey11 waveguide modes doubles the capacity of a single line without sacrificing robustness or adding implementation cost and complexity. A prototype of the structure has been fabricated in high‐density polyethylene (HDPE) fed with dipole/slot coupling structures on Rogers RO6006, and operates at frequencies of about 75 GHz with an aggregate 3 dB bandwidth exceeding 60 GHz.
Continuous‐wave lasing at 100°C in 1.3 µm quantum dot microdisk diode laser
Authors: Kryzhanovskaya N.V. , Moiseev E.I. , Kudashova Yu. V. , Zubov F.I. , Lipovskii A.A. , Kulagina M.M. , Troshkov S.I. , Zadiranov Yu. M. , Livshits D.A. , Maximov M.V. , Zhukov A.E.
Published: August 2015

A 31 µm in diameter microdisk laser with an InAs/InGaAs quantum dot active region has been tested in the continuous‐wave regime at elevated temperatures. Lasing is achieved up to 100°C with a threshold current of 13.8 mA. The emission spectrum demonstrates single‐mode lasing at 1304 nm with a side mode suppression ratio of 24 dB and a dominant mode linewidth of 35 pm.
Proactive spectrum handoff protocol for cognitive radio ad hoc network and analytical evaluation
Authors: Mehrnoush Morteza , Fathi Reza , Vakili Vahid T.
Published: August 2015

Spectrum handoff in cognitive radio technology has been emerged as a new method for improving performance of the cognitive radio networks. The authors propose a proactive spectrum handoff protocol based on a single rendezvous (SRV) coordination scheme without common control channel. This protocol utilises a multi‐user greedy channel selection method to select the best channel based on minimum service time for the secondary users to achieve a higher aggregate throughput. The authors proposed a novel theoretical analysis to evaluate the aggregate throughput of the secondary users in the proposed protocol. It uses Markov Chain to model the distributed channel selection scheme. The simulation results show the proposed protocol increases the throughput up to 38.7% in comparison with the study by Song and Xie, for 12 secondary users in the network with transmission rates of primary and secondary users equal to 5 (pkt/s) and 500 (pkt/s), respectively.
Directional transport of water droplets on superhydrophobic aluminium alloy surface
Authors: Yang Xiaolong , Liu Xin , Li Juan , Huang Shuai , Song Jinlong , Xu Wenji
Published: August 2015

The directional transport of water droplets has great potential applications in biochemical analysis. An aluminium (Al) alloy surface with a contact angle (CA) of 154° and a sliding angle of about 3.5° was prepared by the electrochemical etching method, which is eco‐friendly and economic. An arc path line with a radius of 50 mm and a width of 400 μm was created on the superhydrophobic surface by means of lithography. CAs of water droplets on the lines exhibit anisotropy and 50 μl water droplets could slide exactly along the created line when the substrate was tilted to about 7°. The anisotropic wettability and mechanism of water droplets transport on the surface was investigated. The surface still has great water transport capability after 8 months, indicating that the water transport property of the patterned surface is stable and persistent. This method combines electrochemical etching and lithography; it is universal and economical, and could be used to build patterns on various substrates to realise the directional transport of water droplets.
Time domain DNP with the NOVEL sequence
Authors: Can T. V. , Walish J. J. , Swager T. M. , Griffin R. G.
Published: August 2015

We present results of a pulsed dynamic nuclear polarization (DNP) study at 0.35 T (9.7 GHz/14.7 MHz for electron/1H Larmor frequency) using a lab frame-rotating frame cross polarization experiment that employs electron spin locking fields that match the 1H nuclear Larmor frequency, the so called NOVEL (nuclear orientation via electron spin locking) condition. We apply the method to a series of DNP samples including a single crystal of diphenyl nitroxide (DPNO) doped benzophenone (BzP), 1,3-bisdiphenylene-2-phenylallyl (BDPA) doped polystyrene (PS), and sulfonated-BDPA (SA-BDPA) doped glycerol/water glassy matrices. The optimal Hartman-Hahn matching condition is achieved when the nutation frequency of the electron matches the Larmor frequency of the proton, ω1S = ω0I, together with possible higher order matching conditions at lower efficiencies. The magnetization transfer from electron to protons occurs on the time scale of ∼100 ns, consistent with the electron-proton couplings on the order of 1-10 MHz in these samples. In a fully protonated single crystal DPNO/BzP, at 270 K, we obtained a maximum signal enhancement of ε = 165 and the corresponding gain in sensitivity of εT1/TB1/2=230 due to the reduction in the buildup time under DNP. In a sample of partially deuterated PS doped with BDPA, we obtained an enhancement of 323 which is a factor of ∼3.2 higher compared to the protonated version of the same sample and accounts for 49% of the theoretical limit. For the SA-BDPA doped glycerol/water glassy matrix at 80 K, the sample condition used in most applications of DNP in nuclear magnetic resonance, we also observed a significant enhancement. Our findings demonstrate that pulsed DNP via the NOVEL sequence is highly efficient and can potentially surpass continuous wave DNP mechanisms such as the solid effect and cross effect which scale unfavorably with increasing magnetic field. Furthermore, pulsed DNP is also a promising avenue for DNP at high temperature.
Design, development, and results from a charge-collector diagnostic for a toroidal electron plasma experiment
Authors: Pahari Sambaran , Lachhvani Lavkesh , Bajpai Manu , Rathod Karan , Yeole Yogesh , Chattopadhyay P. K.
Published: August 2015

A suitable charge-collector has been designed and developed to estimate charge-content of electron plasmas in a Small Aspect Ratio Toroidal Experiment in a C-shaped trap (SMARTEX-C). The electrons are periodically injected and held in the trap with the aid of electrostatic end-fields and a toroidal magnetic field. After a preset “hold” time, the trapped charges are dumped onto a grounded collector (by gating it). As the charges flow along the magnetic field lines onto the collector, the integrated current gives the charge-content of the plasma at the instant of dump. In designing such a charge collector, several challenges peculiar to the geometry of the trap and the nature of the plasma had to be addressed. Instantaneous charge measurements synchronised with the E × B drift of the plasma, along with fast transit times of electrons to the collector (few 100 ns or less) (due to the low aspect ratio of the trap) essentially require fast gating of the collector. The resulting large capacitive transients alongside low charge content (few nC) of such plasmas further lead to increasing demands on response and sensitivity of the collector. Complete cancellation of such transients is shown to be possible, in principle, by including the return path in our measurement circuit but the “non-neutrality” of the plasma acts as a further impediment. Ultimately, appropriate shielding and measurement circuits allow us to (re)distribute the capacitance and delineate the paths of these currents, leading to effective cancellation of transients and marked improvement in sensitivity. Improved charge-collector has thus been used to successfully estimate the time evolution of total charge of the confined electron plasma in SMARTEX-C.
Computational study of ridge states in GaAs nanopillars
Authors: Yu Ted H. , Ratsch Christian
Published: August 2015

Semiconductor nanopillars have unique geometries that make them very promising materials for a variety of devices. In order to improve their performance, we need to understand how they are affected by ridge states that lie on the six corners of the nanopillar hexagon. Although the GaAs nanopillars are primarily zinc blende (ABC), stacking faults of wurtzite (AB) stacking occur. We use density-functional theory to study stacking faults using one-dimensional periodic geometries that have a combination of zinc blende and wurtzite stacking. In contrast to perfect zinc blende nanopillars, energetically favorable midgap ridge states created by stacking faults are found in these geometries using density-functional theory. The calculated band diagrams and densities of state help us to understand how these midgap states lead to a reduced mobility and carrier localization. We also study how sulfur passivation affects and potentially improves the performance by modifying the ridges.
Reduction groups and related integrable difference systems of nonlinear Schrödinger type
Authors: Konstantinou-Rizos S. , Mikhailov A. V. , Xenitidis P.
Published: August 2015

We extend the reduction group method to the Lax-Darboux schemes associated with nonlinear Schrödinger type equations. We consider all possible finite reduction groups and construct corresponding Lax operators, Darboux transformations, hierarchies of integrable differential-difference equations, integrable partial difference systems, and associated scalar partial difference equations.
Infrared imaging diagnostics for intense pulsed electron beam
Authors: Yu Xiao , Shen Jie , Qu Miao , Liu Wenbin , Zhong Haowen , Zhang Jie , Yan Sha , Zhang Gaolong , Le Xiaoyun
Published: August 2015

Infrared imaging diagnostic method for two-dimensional calorimetric diagnostics has been developed for intense pulsed electron beam (IPEB). By using a 100-μm-thick tungsten film as the infrared heat sink for IPEB, the emitting uniformity of the electron source can be analyzed to evaluate the efficiency and stability of the diode system. Two-dimensional axisymmetric finite element method heat transfer simulation, combined with Monte Carlo calculation, was performed for error estimation and optimization of the method. The test of the method was finished with IPEB generated by explosive emission electron diode with pulse duration (FWHM) of 80 ns, electron energy up to 450 keV, and a total beam current of over 1 kA. The results showed that it is possible to measure the cross-sectional energy density distribution of IPEB with energy sensitivity of 0.1 J/cm2 and spatial resolution of 1 mm. The technical details, such as irradiation protection of bremsstrahlung γ photons and the functional extensibility of the method were discussed in this work.
The effect of driven electron-phonon coupling on the electronic conductance of a polar nanowire
Authors: Mardaani Mohammad , Rabani Hassan , Esmaili Esmat , Shariati Ashrafalsadat
Published: August 2015

A semi-classical model is proposed to explore the effect of electron-phonon coupling on the coherent electronic transport of a polar chain which is confined between two rigid leads in the presence of an external electric field. To this end, we construct the model by means of Green's function technique within the nearest neighbor tight-binding and harmonic approximations. For a time-periodic electric field, the atomic displacements from the equilibrium positions are obtained precisely. The result is then used to compute the electronic transport properties of the chain within the Peierls-type model. The numerical results indicate that the conductance of the system shows interesting behavior in some special frequencies. For each special frequency, there is an electronic quasi-state in which the scattering of electrons by vibrating atoms reaches maximum. The system electronic conductance decreases dramatically at the strong electron-phonon couplings and low electron energies. In the presence of damping forces, the electron-phonon interaction has a less significant effect on the conductance.
Shear-flow trapped-ion-mode interaction revisited. II. Intermittent transport associated with low-frequency zonal flow dynamics
Authors: Ghizzo A. , Palermo F.
Published: August 2015

We address the mechanisms underlying low-frequency zonal flow generation in turbulent system and the associated intermittent regime of ion-temperature-gradient (ITG) turbulence. This model is in connection with the recent observation of quasi periodic zonal flow oscillation at a frequency close to 2 kHz, at the low-high transition, observed in the ASDEX Upgrade [Conway et al., Phys. Rev. Lett. 106, 065001 (2011)] and EAST tokamak [Xu et al., Phys. Rev. Lett 107, 125001 (2011)]. Turbulent bursts caused by the coupling of Kelvin-Helmholtz (KH) driven shear flows with trapped ion modes (TIMs) were investigated by means of reduced gyrokinetic simulations. It was found that ITG turbulence can be regulated by low-frequency meso-scale zonal flows driven by resonant collisionless trapped ion modes (CTIMs), through parametric-type scattering, a process in competition with the usual KH instability.
Magnetic coupling in ferromagnetic semiconductor (Ga,Mn)As/(Al,Ga,Mn)As bilayers
Authors: Wang M. , Wadley P. , Campion R. P. , Rushforth A. W. , Edmonds K. W. , Gallagher B. L. , Charlton T. R. , Kinane C. J. , Langridge S.
Published: August 2015

We report on a study of ferromagnetic semiconductor (Ga,Mn)As/(Al,Ga,Mn)As bilayers using magnetometry and polarized neutron reflectivity (PNR). From depth-resolved characterization of the magnetic structure obtained by PNR, we concluded that the (Ga,Mn)As and (Al,Ga,Mn)As layers have in-plane and perpendicular-to-plane magnetic easy axes, respectively, with weak interlayer coupling. Therefore, the layer magnetizations align perpendicular to each other under low magnetic fields and parallel at high fields.
Determination of oxygen diffusion kinetics during thin film ruthenium oxidation
Authors: Coloma Ribera R. , van de Kruijs R. W. E. , Yakshin A. E. , Bijkerk F.
Published: August 2015

In situ X-ray reflectivity was used to reveal oxygen diffusion kinetics for thermal oxidation of polycrystalline ruthenium thin films and accurate determination of activation energies for this process. Diffusion rates in nanometer thin RuO2 films were found to show Arrhenius behaviour. However, a gradual decrease in diffusion rates was observed with oxide growth, with the activation energy increasing from about 2.1 to 2.4 eV. Further exploration of the Arrhenius pre-exponential factor for diffusion process revealed that oxidation of polycrystalline ruthenium joins the class of materials that obey the Meyer-Neldel rule.
Live-streaming: Time-lapse video evidence of novel streamer formation mechanism and varying viscosity
Authors: Parvinzadeh Gashti Mazeyar , Bellavance Julien , Kroukamp Otini , Wolfaardt Gideon , Taghavi Seyed Mohammad , Greener Jesse
Published: August 2015

Time-lapse videos of growing biofilms were analyzed using a background subtraction method, which removed camouflaging effects from the heterogeneous field of view to reveal evidence of streamer formation from optically dense biofilm segments. In addition, quantitative measurements of biofilm velocity and optical density, combined with mathematical modeling, demonstrated that streamer formation occurred from mature, high-viscosity biofilms. We propose a streamer formation mechanism by sudden partial detachment, as opposed to continuous elongation as observed in other microfluidic studies. Additionally, streamer formation occurred in straight microchannels, as opposed to serpentine or pseudo-porous channels, as previously reported.
Bound state solutions of Dirac equation with repulsive scalar linear potential
Authors: Tezuka Hirokazu
Published: August 2015

It is shown that the Dirac equation has bound-state solutions for a repulsive scalar linear potential. Analytical solutions exist when there exist certain quantitative relations between the strength constant a of the linear potential and the mass m of the particle, as shown in a previous case that examines the attractive scalar linear potential. The energies of the bound states and relations between a and m are the same as those of attractive potential except for the sign of a.
A study of the temperature dependence of the local ferroelectric properties of c-axis oriented Bi6Ti3Fe2O18 Aurivillius phase thin films: Illustrating the potential of a novel lead-free perovskite material for high density memory applications
Authors: Faraz Ahmad , Deepak Nitin , Schmidt Michael , Pemble Martyn E. , Keeney Lynette
Published: August 2015

The ability to control the growth, texture and orientation of self-nanostructured lead-free Aurivillius phase thin films can in principle, greatly improve their ferroelectric properties, since in these materials the polarization direction is dependent on crystallite orientation. Here, we report the growth of c-plane oriented Bi6Ti3Fe2O18 (B6TFO) functional oxide Aurivillius phase thin films on c-plane sapphire substrates by liquid injection chemical vapour deposition (LI-CVD). Microstructural analysis reveals that B6TFO thin films annealed at 850°C are highly crystalline, well textured (Lotgering factor of 0.962) and single phase. Typical Aurivillius plate-like morphology with an average film thickness of 110nm and roughness 24nm was observed. The potential of B6TFO for use as a material in lead-free piezoelectric and ferroelectric data storage applications was explored by investigating local electromechanical (piezoelectric) and ferroelectric properties at the nano-scale. Vertical and lateral piezoresponse force microscopy (PFM) reveals stronger in-plane polarization due to the controlled growth of the a-axis oriented grains lying in the plane of the B6TFO films. Switching spectroscopy PFM (SS-PFM) hysteresis loops obtained at higher temperatures (up to 200°C) and at room temperature reveal a clear ferroelectric signature with only minor changes in piezoresponse observed with increasing temperature. Ferroelectric domain patterns were written at 200°C using PFM lithography. Hysteresis loops generated inside the poled regions at room and higher temperatures show a significant increase in piezoresponse due to alignment of the c-axis polarization components under the external electric field. No observable change in written domain patterns was observed after 20hrs of PFM scanning at 200°C, confirming that B6TFO retains polarization over this finite period of time. These studies demonstrate the potential of B6TFO thin films for use in piezoelectric applications at elevated temperatures and for use in non-volatile ferroelectric memory applications.
Raman scattering study of temperature induced phase transition in [C8H10NO]2 [ZnCl4]
Authors: Fersi M. Amine , Chaabane I. , Gargouri M. , Bulou Alain
Published: August 2015

The Raman spectra of bis (4-acetylanilinium) tetrachloridozincate single crystals were studied in the range of 100-3500 cm−1 as a function of temperature of 298 K to 398 K. The bands mainly associated with the internal modes of the ZnCl4 anions only undergo weak changes. However, the strong evolutions of wavenumbers, widths and intensities of many lines associated with the organic cations are observed with discontinuities in the vicinity of the phase transition at 351 K. A phase transition at Tc = 351K was observed and characterized by the differential scanning calorimetry (DSC). The most important changes are observed for two lines at 3197.13 cm−1 and 3167.10 cm−1 (at room temperature) issued from asymmetric and symmetric stretching vibrations of (C-H) band and (NH3) group, respectively. The spectral characteristics of these lines are analyzed and consistently described in the framework of an order–disorder model for the phase transition.
Beyond the ocean: contamination of freshwater ecosystems with (micro-)plastic particles
Authors: Dris Rachid , Imhof Hannes , Sanchez Wilfried , Gasperi Johnny , Galgani François , Tassin Bruno , Laforsch Christian
Published: August 2015

Environmental context Microplastics in freshwater ecosystems are an increasingly important environmental issue, with the few available studies suggesting high contamination worldwide. Reliable data on concentrations, fluxes and polymer types in continental aquatic environments, including urban water systems, are needed. High environmental and ecological risk polymers and associated or adsorbed chemicals have to be identified, as well as their effects on both organisms and ecosystems. Abstract Massive accumulation of plastic particles has been reported for marine ecosystems around the world, posing a risk to the biota. Freshwater ecosystems have received less attention despite most plastic litter being produced onshore and introduced into marine environments by rivers. Some studies not only report the presence of microplastics in freshwater ecosystems, but show that contamination is as severe as in the oceans. In continental waters, microplastics have been observed in both sediments (predominantly lake shores but also riverbanks) and water samples (predominantly surface water of lakes and rivers). This review highlights recent findings and discusses open questions, focussing on the methodology of assessing this contaminant in freshwater ecosystems. In this context, method harmonisation is needed in order to obtain comparable data from different environmental compartments and sites. This includes sampling strategies (at spatial and temporal scales), sample treatment (taking into consideration high levels of organic matter and suspended solids) and reliable analytical methods to identify microplastics.
The complex factors that contribute to Clostridium difficile infection
Authors: Mackin Kate E , Lyras Dena
Published: August 2015

Over the past decade Clostridium difficile has emerged as a serious public health issue, causing both hospital-based epidemics and community-associated disease. The most commonly recognised cause of antibiotic-associated diarrhoea in the human population, C. difficile was initially seen as a nuisance pathogen causing limited disease in the hospital setting. However, the emergence of ‘hypervirulent' strain types, associated with an increase in both morbidity and mortality, has made it a pathogen of great concern worldwide. Infection with C. difficile is also being increasingly documented in animals, with suggestions that animals destined for human consumption may provide a reservoir for disease. The use of antibiotics is considered the main risk factor for the development of human infection; however, many other factors such as strain type, patient age, and host immune response all contribute to disease caused by C. difficile.
Community-acquired Clostridium difficile infection and Australian food animals
Authors: Squire Michele M , Knight Daniel R , Riley Thomas V
Published: August 2015

Clostridium difficile is an anaerobic Gram positive spore-forming bacterium, the leading cause of infectious diarrhoea (C. difficile infection; CDI) in hospitalised humans. The assumption that CDI is primarily a hospital-acquired infection is being questioned. Community-acquired CDI (CA-CDI) is increasing1 particularly in groups previously considered at low risk2,3. In Australia, CA-CDI rates doubled during 2011 and increased by 24% between 2011 and 20124. Two potentially high-risk practices in Australian food animal husbandry may present a risk for CA-CDI: slaughtering of neonatal animals for food, and effluent recycling to agriculture.
Spatio-temporal variability of the surf-zone fauna of two Ecuadorian sandy beaches
Authors: Marin Jarrin Jose R. , Miño Quezada Sandra L. , Dominguez-Granda Luis E. , Guartatanga Argudo Sonnia M. , de Grunauer Maria del Pilar Cornejó R.
Published: August 2015

Temperate and subtropical sandy beach surf zones present diverse and abundant fauna that are important in local food webs. However, dynamics of these fauna have been poorly studied in tropical areas. The aims of the present study were to describe the small swimming surf-zone fauna (~1–5mm in length) of two Ecuadorian sandy beaches, determine whether this fauna varies with beach, season or tide, and explore the environmental factors correlated with faunal variability. Beaches were sampled in wet and dry seasons during high, mid- and low tide (2001–2002) by using a hyperbenthic sledge. Beaches were inhabited by an abundant and diverse fauna (>1200 individuals per 100m2 and >30 taxa), where most individuals were in their early life stages (65%), and the dominant taxa included mysid shrimp (>40% of individuals) and fish and crab larvae (>25 taxa). Composition of groups that are present during their entire life or only early life stages varied most strongly between beaches, potentially because of differences in wave exposure and the influence of an adjacent river, and between seasons with changes in coastal oceanic currents. These results suggest that despite the environmental stability often portrayed for tropical environments, Ecuadorian surf-zone fauna are spatially and temporally variable.
Population dynamics of a high-latitude coral Alveopora japonica Eguchi from Jeju Island, off the southern coast of Korea
Authors: Vieira Christophe , Keshavmurthy Shashank , Ju Se-Jong , Hyeong Kiseong , Seo Inah , Kang Chang-Keun , Hong Hyun-Ki , Chen Chaolun Allen , Choi Kwang-Sik
Published: August 2015

Although coral reefs are facing severe challenges from a variety of natural and anthropogenic stresses, there is anecdotal evidence that the high-latitude coral species Alveopora japonica Eguchi, 1968, has increased its population over the past two decades around Jeju Island, off the southern coast of Korea. The present study provides the first ecological data on this species. Alveopora japonica is opportunistically occupying the empty space left vacant following the recent kelp-forest decline. Colony abundance, age- and size-frequency distributions, lifespan, growth rates and biological characteristics such as surface area, weight and volume of two A. japonica populations in Jeju Island were investigated. Alveopora japonica around Jeju Island is characterised by a mean colony size of 30cm2, a slow growth rate (4.8mm year–1), and a short lifespan of 12–13 years, as determined by X-radiographic measurements. Alveopora japonica presented a dense population of 120 colonies m–2 on average. Population-age and -size structures at both sites reflected a healthy status and indicated a local stability, with a stationary size structure allowing population maintenance over time. The present study provided data to develop population-dynamics models to predict the potential outcomes of A. japonica populations to alternative management scenarios in Jeju Island.
Influence of oceanic fronts on mesozooplankton abundance and grazing during spring in the south-western Atlantic
Authors: Lopes Rubens M. , Marcolin Catarina R. , Brandini Frederico P.
Published: August 2015

We investigated the influence of oceanic fronts on mesozooplankton distribution and grazing activity in the south-west Atlantic. Sampling was conducted during late spring 1993 along a north–south transect between subtropical waters off Brazil and Antarctic waters. Mesozooplankton abundance and biomass were ~10-fold higher in the Subtropical Confluence Zone (SCZ) and in the Antarctic Polar Front (APF) relative to subtropical and subantarctic waters beyond the influence of those frontal systems. Mesozooplankton was dominated by calanoid and cyclopoid copepods. Community ingestion rates ranged between 0.1 and 0.3mg chlorophyll-a m–2day–1 in interfrontal areas, increasing to 2.0 and 9.0mg chlorophyll-a m–2day–1 in the APF and SCZ respectively. Mesozooplankton grazing removed up to 40% of the total chlorophyll stock in the SCZ, and 22% in the APF, on a daily basis. These estimates suggest that mesozooplankton exert a significant grazing impact on phytoplankton over much of the frontal areas studied. Recent investigations have shown that the geographic position of oceanic fronts and plankton biomass maxima in the study area have remained basically the same from the time of our sampling effort to date, meaning that our results apply to present conditions.
Demersal chondrichthyans in the western Mediterranean: assemblages and biological parameters of their main species
Authors: Ramírez-Amaro Sergio , Ordines Francesc , Terrasa Bàrbara , Esteban Antonio , García Cristina , Guijarro Beatriz , Massutí Enric
Published: August 2015

The composition and structure of demersal chondrichthyan assemblages and the biological parameters of their main species were compared in four geographical subareas (GSAs) established by the General Fisheries Commission for the Mediterranean in the western Mediterranean:northern Alboran Sea (GSA01) and Alboran Island (GSA02), Balearic Islands (GSA05) and northern Spain (GSA06), with the first two being considered jointly. Data were obtained from 199 hauls undertaken from May to June 2013 during the Spanish International Bottom Trawl Survey in the Mediterranean (MEDITS). Twenty-five different chondrichthyan species were caught in all GSAs: seven were common to all areas, five appeared only in GSA01, nine appeared only in GSA05 and one appeared only in GSA06. Analysis of community structure (clusters, multidimensional scaling, analysis of similitude) revealed two assemblages related to depth, with very similar bathymetric ranges in all GSAs, namely continental shelf (from 41 to 252m) and slope (from 284 to 813m). The highest diversity, biomass and abundance values on the shelf and slope assemblages were recorded in GSA05 and GSA01 respectively. These results highlight the effects of the distinct fishing and oceanographic parameters related to the GSAs. Generally, the biological parameters of the most important species did not show differences between GSAs, which could suggest the existence of a single population in the western Mediterranean.
Slow-release boron fertilisers: co-granulation of boron sources with mono-ammonium phosphate (MAP)
Authors: Abat Margaret , Degryse Fien , Baird Roslyn , McLaughlin Michael J.
Published: August 2015

The application of pure boron (B) fertilisers, independent of other macronutrients, is impractical due to the increased cost of dual handling and spreading. Bulk blending of B with other micronutrients is also an unattractive option as the relatively low rates of B required results in poor nutrient distribution in the field. Co-granulating B with other macronutrients such as mono-ammonium phosphate (MAP) may overcome these problems. Five B sources (boron phosphate (BPO4) synthesised at 500 and 800°C for 1 h, colemanite, ulexite and borax) were co-granulated with MAP to targeted B contents of 0.5, 1.0 and 2.0%. The co-granulated BPO4 had lower water solubility than co-granulated colemanite, ulexite and borax. Boron released from co-granulated borax, ulexite and colemanite was remarkably greater than co-granulated BPO4 products. Over a 4-week soil incubation period with weekly leaching of one pore volume of water, the cumulative B release from co-granulated ulexite, borax and colemanite was 97, 75 and 58%, respectively, but only 16 and 4% for the co-granulated BPO4 synthesised at 500 and 800°C, respectively. Co-granulated BPO4 products have potential as a high quality fertiliser to increase crop yield with slow B release.
Anaerobic biosynthesis of the lower ligand of vitamin B
12
Authors: Hazra Amrita B. , Han Andrew W. , Mehta Angad P. , Mok Kenny C. , Osadchiy Vadim , Begley Tadhg P. , Taga Michiko E.
Published: August 2015

Significance

Vitamin B
12
is required by humans and a variety of other organisms for diverse metabolic processes, but is produced only by a subset of microorganisms. The anaerobic biosynthesis of the “lower ligand” of B
12
, 5,6-dimethylbenzimidazole (DMB), is the only unknown component of the B
12
biosynthetic pathway. We report the identification of the
bzaABCDE
genes that are necessary and sufficient for the anaerobic biosynthesis of DMB. We have characterized the role of each of the
bza
genes and identified three intermediates in the pathway. This finding not only completes the B
12
biosynthesis pathway but also enables the sequence-based prediction of cobamides synthesized by anaerobic microorganisms.
Epidermal growth factor–stimulated Akt phosphorylation requires clathrin or ErbB2 but not receptor endocytosis
Authors: Garay Camilo , Judge Gurjeet , Lucarelli Stefanie , Bautista Stephen , Pandey Rohan , Singh Tanveer , Antonescu Costin N.
Published: August 2015

Epidermal growth factor (EGF) binding to its receptor (EGFR) activates several signaling intermediates, including Akt, leading to control of cell survival and metabolism. Concomitantly, ligand-bound EGFR is incorporated into clathrin-coated pits—membrane structures containing clathrin and other proteins—eventually leading to receptor internalization. Whether clathrin might regulate EGFR signaling at the plasma membrane before vesicle scission is poorly understood. We compared the effect of clathrin perturbation (preventing formation of, or receptor recruitment to, clathrin structures) to that of dynamin2 (allowing formation of clathrin structures but preventing EGFR internalization) under conditions in which EGFR endocytosis is clathrin dependent. Clathrin perturbation by siRNA gene silencing, with the clathrin inhibitor pitstop2, or knocksideways silencing inhibited EGF-simulated Gab1 and Akt phosphorylation in ARPE-19 cells. In contrast, perturbation of dynamin2 with inhibitors or by siRNA gene silencing did not affect EGF-stimulated Gab1 or Akt phosphorylation. EGF stimulation enriched Gab1 and phospho-Gab1 within clathrin structures. ARPE-19 cells have low ErbB2 expression, and overexpression and knockdown experiments revealed that robust ErbB2 expression bypassed the requirement for clathrin for EGF-stimulated Akt phosphorylation. Thus clathrin scaffolds may represent unique plasma membrane signaling microdomains required for signaling by certain receptors, a function that can be separated from vesicle formation.
Phosphorylation-dependent inhibition of Cdc42 GEF Gef1 by 14-3-3 protein Rad24 spatially regulates Cdc42 GTPase activity and oscillatory dynamics during cell morphogenesis
Authors: Das Maitreyi , Nuñez Illyce , Rodriguez Marbelys , Wiley David J. , Rodriguez Juan , Sarkeshik Ali , Yates John R. , Buchwald Peter , Verde Fulvia
Published: August 2015

Active Cdc42 GTPase, a key regulator of cell polarity, displays oscillatory dynamics that are anticorrelated at the two cell tips in fission yeast. Anticorrelation suggests competition for active Cdc42 or for its effectors. Here we show how 14-3-3 protein Rad24 associates with Cdc42 guanine exchange factor (GEF) Gef1, limiting Gef1 availability to promote Cdc42 activation. Phosphorylation of Gef1 by conserved NDR kinase Orb6 promotes Gef1 binding to Rad24. Loss of Rad24–Gef1 interaction increases Gef1 protein localization and Cdc42 activation at the cell tips and reduces the anticorrelation of active Cdc42 oscillations. Increased Cdc42 activation promotes precocious bipolar growth activation, bypassing the normal requirement for an intact microtubule cytoskeleton and for microtubule-dependent polarity landmark Tea4-PP1. Further, increased Cdc42 activation by Gef1 widens cell diameter and alters tip curvature, countering the effects of Cdc42 GTPase-activating protein Rga4. The respective levels of Gef1 and Rga4 proteins at the membrane define dynamically the growing area at each cell tip. Our findings show how the 14-3-3 protein Rad24 modulates the availability of Cdc42 GEF Gef1, a homologue of mammalian Cdc42 GEF DNMBP/TUBA, to spatially control Cdc42 GTPase activity and promote cell polarization and cell shape emergence.
The nucleoporin ALADIN regulates Aurora A localization to ensure robust mitotic spindle formation
Authors: Carvalhal Sara , Ribeiro Susana Abreu , Arocena Miguel , Kasciukovic Taciana , Temme Achim , Koehler Katrin , Huebner Angela , Griffis Eric R.
Published: August 2015

The formation of the mitotic spindle is a complex process that requires massive cellular reorganization. Regulation by mitotic kinases controls this entire process. One of these mitotic controllers is Aurora A kinase, which is itself highly regulated. In this study, we show that the nuclear pore protein ALADIN is a novel spatial regulator of Aurora A. Without ALADIN, Aurora A spreads from centrosomes onto spindle microtubules, which affects the distribution of a subset of microtubule regulators and slows spindle assembly and chromosome alignment. ALADIN interacts with inactive Aurora A and is recruited to the spindle pole after Aurora A inhibition. Of interest, mutations in ALADIN cause triple A syndrome. We find that some of the mitotic phenotypes that we observe after ALADIN depletion also occur in cells from triple A syndrome patients, which raises the possibility that mitotic errors may underlie part of the etiology of this syndrome.
ASSIsT: an automatic SNP scoring tool for in- and outbreeding species
Authors: Di Guardo Mario , Micheletti Diego , Bianco Luca , Koehorst-van Putten Herma J. J. , Longhi Sara , Costa Fabrizio , Aranzana Maria J. , Velasco Riccardo , Arús Pere , Troggio Michela , van de Weg Eric W.
Published: August 2015

ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker–trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.

Availability and implementation: The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/.

Contact:  eric.vandeweg@wur.nl
ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy
Authors: Bystry Vojtech , Agathangelidis Andreas , Bikos Vasilis , Sutton Lesley Ann , Baliakas Panagiotis , Hadzidimitriou Anastasia , Stamatopoulos Kostas , Darzentas Nikos
Published: August 2015

Motivation: An ever-increasing body of evidence supports the importance of B cell receptor immunoglobulin (BcR IG) sequence restriction, alias stereotypy, in chronic lymphocytic leukemia (CLL). This phenomenon accounts for ∼30% of studied cases, one in eight of which belong to major subsets, and extends beyond restricted sequence patterns to shared biologic and clinical characteristics and, generally, outcome. Thus, the robust assignment of new cases to major CLL subsets is a critical, and yet unmet, requirement.

Results: We introduce a novel application, ARResT/AssignSubsets, which enables the robust assignment of BcR IG sequences from CLL patients to major stereotyped subsets. ARResT/AssignSubsets uniquely combines expert immunogenetic sequence annotation from IMGT/V-QUEST with curation to safeguard quality, statistical modeling of sequence features from more than 7500 CLL patients, and results from multiple perspectives to allow for both objective and subjective assessment. We validated our approach on the learning set, and evaluated its real-world applicability on a new representative dataset comprising 459 sequences from a single institution.

Availability and implementation: ARResT/AssignSubsets is freely available on the web at http://bat.infspire.org/arrest/assignsubsets/

Contact:  nikos.darzentas@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA)
Authors: Taruttis Franziska , Spang Rainer , Engelmann Julia C.
Published: August 2015

Motivation: We address the following question: Does inhibition of the expression of a gene X in a cellular assay affect the expression of another gene Y? Rather than inhibiting gene X experimentally, we aim at answering this question computationally using as the only input observational gene expression data. Recently, a new statistical algorithm called Intervention calculus when the Directed acyclic graph is Absent (IDA), has been proposed for this problem. For several biological systems, IDA has been shown to outcompete regression-based methods with respect to the number of true positives versus the number of false positives for the top 5000 predicted effects. Further improvements in the performance of IDA have been realized by stability selection, a resampling method wrapped around IDA that enhances the discovery of true causal effects. Nevertheless, the rate of false positive and false negative predictions is still unsatisfactorily high.

Results: We introduce a new resampling approach for causal discovery called accumulation IDA (aIDA). We show that aIDA improves the performance of causal discoveries compared to existing variants of IDA on both simulated and real yeast data. The higher reliability of top causal effect predictions achieved by aIDA promises to increase the rate of success of wet lab intervention experiments for functional studies.

Availability and implementation: R code for aIDA is available in the Supplementary material.

Contact:  franziska.taruttis@ur.de, julia.engelmann@ur.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management
Authors: Pak Theodore R. , Kasarskis Andrew
Published: August 2015

Recent reviews have examined the extent to which routine next-generation sequencing (NGS) on clinical specimens will improve the capabilities of clinical microbiology laboratories in the short term, but do not explore integrating NGS with clinical data from electronic medical records (EMRs), immune profiling data, and other rich datasets to create multiscale predictive models. This review introduces a range of “omics” and patient data sources relevant to managing infections and proposes 3 potentially disruptive applications for these data in the clinical workflow. The combined threats of healthcare-associated infections and multidrug-resistant organisms may be addressed by multiscale analysis of NGS and EMR data that is ideally updated and refined over time within each healthcare organization. Such data and analysis should form the cornerstone of future learning health systems for infectious disease.
Remembering to Forget Richard de Fournival's
Bestiaire d'amour
in Italy: The Case of Pierpont Morgan MS 459
Authors: Zingesser Eliza
Published: August 2015

This article focuses on the prologue to the expanded version of Richard de Fournival's
Bestiaire d'amour
contained in a manuscript of Italian origin: New York, Pierpont Morgan MS 459. Its aim is to shed light on the cultural antagonism on the part of the prologue author towards the authorial version of Richard's
Bestiaire
. While the prologue author alludes to the authorial
Bestiaire
and even devotes a biographical sketch to its author in the form of a
vida
, I show that the prologue author nevertheless definitively ‘authorizes’ for posterity the francophone Italian continuation, which is retrospectively framed as the sole authentic version of the
Bestiaire
. The
vida
, for its part, does more to condemn Richard to oblivion than to memorialize him. This new, expanded version of the
Bestiaire
is in turn authenticated through cultural markers of ‘Frenchness’, even though the prologue author subtly indicates his own non-French status. The logic of the prologue is thus ambivalent: it both draws attention to the genuine version of the
Bestiaire
and ensures that it is perceived as insignificant; both memorializes Richard as an author and relegates him to oblivion; both heaps on markers of Frenchness and indicates its position of cultural remove.
Self-Control and Uncontrollable Passion in Stendhal's Theory of Love
Authors: Gill Miranda
Published: August 2015

This article explores Stendhal's understanding of self-control and willpower (and their loss) through a close reading of
De l'amour
. Although recent criticism has tended to dismiss the author's scientific claims for the text, Stendhal addresses aspects of self-control also discussed in recent research in the cognitive and behavioural sciences. Bringing both these accounts and the cultural histories of emotion and gender into dialogue with Stendhal's text, the article identifies a key conceptual tension. Firstly, Stendhal asserts that passionate love is an almost entirely uncontrollable phenomenon. While this view draws on the ancient topos of ‘love as illness’, Stendhal also analyses issues such as self-deception, boredom, gambling, reverie, and temperament to help explain the limits of conscious volition in love. Secondly, he simultaneously suggests that love is impossible without self-control, for reasons related to the temporal dynamics of love and the honour ethic, although self-control has quite different cultural meanings for nineteenth-century male and female subjects. The article concludes that, for Stendhal, self-control is like a ladder without which love cannot develop but which must ultimately be discarded. The dialectic of control and the loss of control also highlights tensions between the honour ethic and the still influential code of sensibility.
Measuring line-of-sight-dependent Fourier-space clustering using FFTs
Authors: Bianchi Davide , Gil-Marín Héctor , Ruggeri Rossana , Percival Will J.
Published: August 2015

Observed galaxy clustering exhibits local transverse statistical isotropy around the line of sight (LOS). The variation of the LOS across a galaxy survey complicates the measurement of the observed clustering as a function of the angle to the LOS, as fast Fourier transforms (FFTs) based on Cartesian grids, cannot individually allow for this. Recent advances in methodology for calculating LOS-dependent clustering in Fourier space include the realization that power spectrum LOS-dependent moments can be constructed from sums over galaxies, based on approximating the LOS to each pair of galaxies by the LOS to one of them. We show that we can implement this method using multiple FFTs, each measuring the LOS-weighted clustering along different axes. The Nlog N nature of FFTs means that the computational speed-up is a factor of >1000 compared with summing over galaxies. This development should be beneficial for future projects such as DESI and Euclid which will provide an order of magnitude more galaxies than current surveys.
The extreme ultraviolet spectrum of the kinetically dominated quasar 3C 270.1
Authors: Punsly Brian , Marziani Paola
Published: August 2015

Only a handful of quasars have been identified as kinetically dominated, their long-term time-averaged jet power, $\overline{Q}$, exceeds the bolometric thermal emission, Lbol, associated with the accretion flow. This Letter presents the first extreme ultraviolet (EUV) spectrum of a kinetically dominated quasar, 3C 270.1. The EUV continuum flux density of 3C 270.1 is very steep, $F_{\nu } \sim \nu ^{-\alpha _{{\rm EUV}}}$, αEUV = 2.98 ± 0.15. This value is consistent with the correlation of $\overline{Q}/L_{{\rm bol}}$ and αEUV found in previous studies of the EUV continuum of quasars, the EUV deficit of radio loud quasars. Curiously, although ultraviolet broad absorption line (BAL) troughs in quasar spectra are anticorrelated with $\overline{Q}$, 3C 270.1 has been considered a BAL quasar based on an SDSS spectrum. This claim is examined in terms of the EUV spectrum of O vi and the highest resolution C iv spectrum in the archival data and the SDSS spectrum. First, from [O iii]4959,5007 (IR) observations and the UV spectral lines, it is concluded that the correct redshift for 3C 270.1 is 1.5266. It is then found that the standard measure of broad absorption, BALnicity = 0, for Mg ii 2800, C iv 1549 and O vi 1032 in all epochs.