bluuebunny/crossref_metadata_2025 huggingface dataset:
Tracing low‐temperature fluid flow on ridge flanks with sedimentary uranium distribution
Authors: Mills R. A. , Dunk R. M.
Published: August 2010

The uranium content of sediments and pore fluids along a ridge axis to ridge flank transect perpendicular to the southern East‐Pacific Rise is used to assess the impact of low‐temperature fluid flow on U distribution. Two distinct regions are identified: (1) a young crustal site (0.36 Ma crust) where significant solid phase U enrichments occur and (2) the ridge flank (1.9–4.6 Ma crust) with uniform U association with hydrothermal Fe oxide phases in the solid phases. Upward advection and diffusion of cool, U‐depleted basement fluids occurs at many coring sites. At the 0.36 Ma site the oxic basal‐fluids strip the plume derived sediment of the excess U, effectively migrating the U upwards through the sediment into the overlying water column. At the ridge flank sites the pore fluid advection rates are highest at bathymetric/basement highs and advection velocities of up to 7.5 mm yr−1 are inferred from the pore fluid profiles. These estimates are consistent with previous calculations based on fluoride pore fluid distributions. The basal‐fluid U depletions are in the range 10–70% relative to seawater depending on temperature and redox state. Low‐temperature uptake of U during basalt alteration is a significant sink from seawater in the global seawater U budget (6.7–29 Mmol yr−1). Pore fluid U content is a sensitive tracer of extremely low‐temperature (<5°C) and low‐velocity (<10 mm yr−1) advection through ridge flank systems and the basal sediment U/Fe ratio is potentially a useful proxy for basement alteration history where low ratios indicate extensive oxic alteration of basal‐sediments during fluid flow.
Variation of Saturn's UV aurora with SKR phase
Authors: Nichols J. D. , Cecconi B. , Clarke J. T. , Cowley S. W. H. , Gérard J.‐C. , Grocott A. , Grodent D. , Lamy L. , Zarka P.
Published: August 2010

It is well known that a wide range of kronian magnetospheric phenomena, including the Saturn kilometric radiation (SKR), exhibit oscillations near the planetary rotation period. However, although the SKR is believed to be generated by unstable auroral electrons, no connection has been established to date between diurnal SKR modulations and UV auroral power. We use an empirical SKR phase determined from Cassini observations to order the ‘quiet time’ total emitted UV auroral power as observed by the Hubble Space Telescope in programs during the interval 2005–2009. Our results indicate that both the northern and southern UV powers are dependent on SKR phase, varying diurnally by factors of ∼3. We also show that the UV variation originates principally from the morning half of the oval, consistent with previous observations of the SKR sources.
The innate immune system and diabetes mellitus: the relevance of periodontitis? A hypothesis
Authors: Lazenby Martin G. , Crook Martin A.
Published: August 2010

About a decade ago, a hypothesis was proposed suggesting that the innate immune system, including acute-phase reactants, contribute to the development of T2DM [Type 2 DM (diabetes mellitus)] and the metabolic syndrome. In this model, it was hypothesized that the innate immune system modulates the effects of many factors, including genes, fetal programming, nutrition and aging, upon the later development of metabolic problems associated with insulin resistance. In this present article, we expand this hypothesis by looking at the involvement of periodontitis in DM and its complications. Periodontitis is a common inflammatory process involving the innate immune system and is associated with DM. We will also illustrate how dental disease is important in patients with DM and could be implicated in various diabetic complications.
Mechanism for improvement of n-channel metal-oxide-semiconductor transistors by tensile stress
Authors: Yang Peizhen , Lau W. S. , Lai Seow Wei , Lo V. L. , Toh L. F. , Wang Jacob , Siah S. Y. , Chan L.
Published: August 2010

This paper investigates the physics behind the overall on-current (Ion) improvement of n-channel metal-oxide-semiconductor (NMOS) transistors by uniaxial tensile stress. The strain-induced change in subthreshold off-current (Ioff) is related to the following strain-induced effects: (i) mobility enhancement, (ii) reduction in the saturation threshold voltage (Vth,sat), and (iii) improvement in subthreshold swing (Sts). By selecting transistors whose Ioff is less sensitive to the statistical variation in gate length, we studied the effects of process-induced tensile stress on Ion and Ioff of NMOS transistors. We found that both externally applied tensile stress and process-induced tensile stress led to a bigger percentage increase in subthreshold Ioff compared to the percentage increase in Ion. Our explanation is that the increase in Ioff is mainly due to an increase in mobility and a decrease in Vth,sat by tensile stress. The improvement of subthreshold swing by tensile stress can lead to a decrease in subthreshold Ioff; for the time being, this seems to be a relatively minor effect. Since the subthreshold Ioff is more sensitive to change in Vth,sat than Ion, the increase in subthreshold Ioff can be removed by a slight adjustment in Vth,sat without too much effect on Ion such that tensile stress can bring about an overall Ion improvement in NMOS transistors despite increase in both Ion and Ioff by tensile stress.
Fracture behaviors induced by electromagnetic force in a long cylindrical superconductor
Authors: Zeng Jun , Zhou You-He , Yong Hua-Dong
Published: August 2010

In the present work, the crack problem of a long cylindrical superconductor with a center crack is investigated. The Bean and Kim model of critical state are considered, and the stress intensity factors are calculated for zero-field cooling (ZFC) and field cooling (FC) magnetization processes, respectively. Based on the finite element method, the variation laws of the stress intensity factors for different magnetic field are obtained first. As the applied field decreases, the stress intensity factors increase quickly first, and then decrease gradually after they reach a peak value. Subsequently, for every length of the crack, the maximum of the stress intensity factor is calculated. Numerical results obtained show that, the FC activation process has more significant influence on the stress intensity factors than the ZFC activation process. Finally, the results obtained from Bean model and Kim model are compared. When the dimensionless parameter p is lesser, the results in two different critical state models are equal almost. Generally speaking, all of the results are useful for understanding the critical state model and the fracture mechanism of high-temperature superconductors.
Remarkable enhancement in crystalline perfection, second harmonic generation efficiency, optical transparency, and laser damage threshold in potassium dihydrogen phosphate crystals by L-threonine doping
Authors: Kushwaha S. K. , Shakir Mohd. , Maurya K. K. , Shah A. L. , Wahab M. A. , Bhagavannarayana G.
Published: August 2010

Effect of L-threonine (LT) doping on crystalline perfection, second harmonic generation (SHG) efficiency, optical transparency, and laser damage threshold (LDT) in potassium dihydrogen phosphate (KDP) crystals grown by slow evaporation solution technique (SEST) has been investigated. The influence of doping on growth rate and morphology of the grown crystals has also been studied. Powder x-ray diffraction data confirms the crystal structure of KDP and shows a systematic variation in intensity of diffraction peaks in correlation with morphology due to varying LT concentration. No extra phase formation was observed which is further confirmed by Fourier transform Raman (FT-Raman) studies. High-resolution x-ray diffraction curves indicate that crystalline perfection has been improved to a great extent at low concentrations with a maximum perfection at 1 mol % doping. At higher concentrations (5 to 10 mol %), it is slightly reduced due to excess incorporation of dopants at the interstitial sites of the crystalline matrix. LDT has been increased considerably with increase in doping concentration, whereas SHG efficiency was found to be maximum at 1 mol % in correlation with crystalline. The optical transparency for doped crystals has been increased as compared to that of pure KDP with a maximum value at 1 mol % doping.
Size based separation of microparticles using a dielectrophoretic activated system
Authors: Khoshmanesh Khashayar , Zhang Chen , Nahavandi Saeid , Tovar-Lopez Francisco J. , Baratchi Sara , Mitchell Arnan , Kalantar-zadeh Kourosh
Published: August 2010

This work describes the separation of polystyrene microparticles suspended in deionized (DI) water according to their dimensions using a dielectrophoretic (DEP) system. The DEP system utilizes curved microelectrodes integrated into a microfluidic system. Microparticles of 1, 6, and 15 μm are applied to the system and their response to the DEP field is studied at different frequencies of 100, 200, and 20 MHz. The microelectrodes act as a DEP barrier for 15 μm particles and retain them at all frequencies whereas the response of 1 and 6 μm particles depend strongly on the applied frequency. At 100 kHz, both particles are trapped by the microelectrodes. However, at 200 kHz, the 1 μm particles are trapped by the microelectrodes while the 6 μm particles are pushed toward the sidewalls. Finally, at 20 MHz, both particles are pushed toward the sidewalls. The experiments show the tunable performance of the system to sort the microparticles of various dimensions in microfluidic systems.
Defect engineering of the electrochemical characteristics of carbon nanotube varieties
Authors: Hoefer Mark A. , Bandaru Prabhakar R.
Published: August 2010

The electrochemical behavior of carbon nanotubes (CNTs) containing both intrinsic and extrinsically introduced defects has been investigated through the study of bamboo and hollow multiwalled CNT morphologies. The controlled addition of argon ions was used for varying the charge and type of extrinsic defects. It was indicated from Raman spectroscopy and voltammetry that the electrocatalytic response of hollow type CNTs could be tailored more significantly, compared to bamboo type CNTs which have innately high reactive site densities and are less amenable to modification. An in-plane correlation length parameter was used to understand the variation of the defect density as a function of argon ion irradiation. The work has implications in the design of nanotube based chemical sensors, facilitated through the introduction of suitable reactive sites.
Effective thermal conductivity of polycrystalline materials with randomly oriented superlattice grains
Authors: Yang Fan , Ikeda Teruyuki , Snyder G. Jeffrey , Dames Chris
Published: August 2010

A model has been established for the effective thermal conductivity of a bulk polycrystal made of randomly oriented superlattice grains with anisotropic thermal conductivity. The in-plane and cross-plane thermal conductivities of each superlattice grain are combined using an analytical averaging rule that is verified using finite element methods. The superlattice conductivities are calculated using frequency dependent solutions of the Boltzmann transport equation, which capture greater thermal conductivity reductions as compared to the simpler gray medium approximation. The model is applied to a PbTe/Sb2Te3 nanobulk material to investigate the effects of period, specularity, and temperature. The calculations show that the effective thermal conductivity of the polycrystal is most sensitive to the in-plane conductivity of each superlattice grain, which is generally four to five times larger than the cross-plane conductivity of a grain. The model is compared to experimental measurements of the same system for periods ranging from 287 to 1590 nm and temperatures from 300 to 500 K. The comparison suggests that the effective specularity increases with increasing annealing temperature and shows that these samples are in a mixed regime where both Umklapp and boundary scattering are important.
Asymmetric hysteresis loops and smearing of the dielectric anomaly at the transition temperature due to space charges in ferroelectric thin films
Authors: Misirlioglu I. B. , Okatan M. B. , Alpay S. P.
Published: August 2010

Ferroelectric thin films often exhibit a displacement of the polarization versus the electric field hysteresis loops, particularly along the electric field axis. This shift is typically attributed to structural and electronic asymmetry of the film-electrode interfaces, asymmetric surface fields, as well as space charge regions. In this study, we analyze the effect of a spatial, continuous distribution of space charge on the hysteresis response and phase transition characteristics of epitaxial (001) PbZr0.3Ti0.7O3 thin films sandwiched between metallic electrodes on (001) SrTiO3 substrate. Using a nonlinear thermodynamic model, we compute numerically the internal electrical fields and polarizations for several different space charge distributions both in the presence of a triangular external electric field and as a function of temperature at zero applied field. We show that space charge accumulated near the metal-ferroelectric interfaces can dramatically displace the hysteresis along the electric field axis such that the otherwise symmetric coercive fields EC− and EC+ in a bulk ferroelectric related to each other through |EC−|=EC+ may shift depending on the space charge concentration in such a manner that both EC−,EC+>0 or EC−,EC+<0. This gives rise to a very strong imprint. Our findings reveal that the presence of space charges in ferroelectric thin films results in significant changes in the phase transition characteristics, including a reduction in the phase transition temperature, smearing of the transition over a temperature range instead of a sharp dielectric anomaly at the bulk Curie temperature, and a reduction in the dielectric response compared to defect-free ferroelectrics of the same composition.
A perfectly matched layer applied to a reactive scattering problem
Authors: Nissen Anna , Karlsson Hans O. , Kreiss Gunilla
Published: August 2010

The perfectly matched layer (PML) technique is applied to a reactive scattering problem for accurate domain truncation. A two-dimensional model for dissociative adsorbtion and associative desorption of H2 from a flat surface is considered, using a finite difference spatial discretization and the Arnoldi method for time-propagation. We compare the performance of the PML to that of a monomial complex absorbing potential, a transmission-free complex absorbing potential, and to exterior complex scaling. In particular, the reflection properties due to the numerical treatment are investigated. We conclude that the PML is accurate and efficient, especially if high accuracy is of significance. Moreover, we demonstrate that the errors from the PML can be controlled at a desired accuracy, enabling efficient numerical simulations.
Superlow friction of titanium/silicon codoped hydrogenated amorphous carbon film in the ambient air
Authors: Jiang Jinlong , Hao Junying , Wang Peng , Liu Weimin
Published: August 2010

Titanium/silicon codoped hydrogenated carbon film was deposited on the n-Si (100) substrates by reactive magnetron sputtering Ti80Si20 target in a mixture of argon and methane. Microstructure of the film was investigated using x-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, Raman spectroscopy, and attenuated total reflectance Fourier transform infrared spectroscopy. The investigations have revealed that the film has an amorphous structure and consists of high sp2 hybridized carbon atoms and bonding hydrogen atoms. The mechanical and tribological properties were evaluated using a nanoindentor and a ball-on-disk tribometer, respectively. The film exhibits hardness of 9.6 GPa, high elastic recovery of 73.0% and high H/E ratio of 0.156. Most significant, the superlow friction (μ<0.01) and special low wear rate (2.4×10−7 mm3 N−1 m−1) was observed in ambient air with 40% relative humidity. Combining the results of scanning electron microscopy and Raman analyses of the worn surface, it is concluded that some mechanisms, e.g., transfer films, friction-induced graphitization, hydrogen-terminated carbon surface, tribochemical reaction, etc., could be together responsible for this superlow friction in the ambient air.
Plasmon assisted single photon emission of CdSe/CdS nanocrystals deposited on random gold film
Authors: Mallek-Zouari I. , Buil S. , Quélin X. , Mahler B. , Dubertret B. , Hermier J.-P.
Published: August 2010

We have investigated the modifications of the fluorescence properties of single CdSe/CdS nanocrystals deposited close to a semicontinuous gold film. We report a reduction by a factor of ten of the monoexcitonic state decay rate. Due to the structure of the plasmon resonances, the decay depends on the nanocrystal position. Through the detailed study of the collection efficiency, we show that a large fraction of the plasmons are converted in far field single photons. These results demonstrate the great interest of plasmonic devices to control the single photon emission of colloidal nanocrystals.
Tunable electron counting statistics in a single-molecule magnet
Authors: Xue Hai-Bin , Nie Y.-H. , Li Z.-J. , Liang J.-Q.
Published: August 2010

Based on an efficient particle-number-resolved quantum master equation, we study the full counting statistics of electron transport through a single-molecule magnet (SMM) weakly coupled to two metallic electrodes. It is demonstrated that the internal level structure of the SMM and the left-right asymmetry of the SMM-electrode coupling play a crucial role in the super-Poissonian statistics of electron transport. In particular, above the sequential tunneling threshold the shot noise depends not only on the gate voltage by which the internal level structure of the SMM can be tuned but also on the left-right asymmetry of the SMM-electrode coupling. Moreover, it was found that the temperature dependence of super-Poissonian shot noise also depends on the left-right asymmetry of the SMM-electrode coupling. The occurrence-mechanism of super-Poissonian shot noise can be qualitatively attributed to the competition between fast and slow transport channels.
Differential reflection spectroscopy of a single quantum dot strongly coupled to a photonic crystal cavity
Authors: Kim Erik D. , Majumdar Arka , Kim Hyochul , Petroff Pierre , Vučković Jelena
Published: August 2010

We demonstrate the use of periodically modulated Coulomb shifts in quantum dot (QD) transition energies to obtain differential reflection spectra of a photonic crystal nanocavity containing strongly coupled dots. Measured spectra isolate the change in the empty cavity optical reflectivity spectrum due to the presence of each dot. This technique permits the probing of coupled QD-cavity systems possessing cavity modes of arbitrary polarization, making it attractive for use in both cavity quantum electrodynamics studies and quantum information applications.
A dielectrophoretic chip with a roughened metal surface for on-chip surface-enhanced Raman scattering analysis of bacteria
Authors: Cheng I-Fang , Lin Chi-Chang , Lin Dong-Yi , Chang Hsien-Chang
Published: August 2010

We present an analysis of the results of in situ surface-enhanced Raman scattering (SERS) of bacteria using a microfluidic chip capable of continuously sorting and concentrating bacteria via three-dimensional dielectrophoresis (DEP). Microchannels were made by sandwiching DEP microelectrodes between two glass slides. Avoiding the use of a metal nanoparticle suspension, a roughened metal surface is integrated into the DEP-based microfluidic chip for on-chip SERS detection of bacteria. On the upper surface of the slide, a roughened metal shelter was settled in front of the DEP concentrator to enhance Raman scattering. Similarly, an electrode-patterned bottom layer fabricated on a thin cover-slip was used to reduce fluorescence noise from the glass substrate. Gram positive (Staphylococcus aureus) and Gram negative (Pseudomonas aeruginosa) bacteria were effectively distinguished in the SERS spectral data. Staphylococcus aureus (concentration of 106 CFU/ml) was continuously separated and concentrated via DEP out of a sample of blood cells. At a flow rate of 1 μl/min, the bacteria were highly concentrated at the roughened surface and ready for on-chip SERS analysis within 3 min. The SERS data were successfully amplified by one order of magnitude and analyzed within a few minutes, resulting in the detection of signature peaks of the respective bacteria.
Propagation of energetic electrons in a hollow plasma fiber
Authors: Zhou C. T. , Chew L. Y. , He X. T.
Published: August 2010

Transport of energetic electrons in a hollow plasma fiber is investigated. The high-current electron beam induces in the fiber strong radial electric fields and azimuthal magnetic fields on the inner and outer surfaces of the hollow fiber. The hot electrons are pushed out by the surface magnetic field and returned into the fiber by the sheath electric field. Imbalance of the latter fields can drive chaotic oscillations of electrons around the fiber wall. Intense thin return-current layers inside both the inner and outer wall surfaces are observed. This enhances local joule heating around both surfaces by the return current.
Quantitative determination of anisotropic magnetoelectric coupling in BiFeO3–CoFe2O4 nanostructures
Authors: Oh Yoon Seok , Crane S. , Zheng H. , Chu Y. H. , Ramesh R. , Kim Kee Hoon
Published: August 2010

The transverse and longitudinal magnetoelectric susceptibilities (MES) were quantitatively determined for (001) heteroepitaxial BiFeO3–CoFe2O4 nanostructures. Both of these MES values were sharply enhanced at magnetic fields below 6 kOe and revealed asymmetric line shapes with respect to the dc magnetic field, demonstrating the strain-induced magnetoelectric effect. The maximum transverse MES, which reached as high as ∼60 mV/cm Oe, was about five times larger than the longitudinal MES. This observation signifies that transverse magnetostriction of the CoFe2O4 nanopillars is enhanced more than the bulk value due to preferred magnetic domain alignment along the [001] direction coming from compressive, heteroepitaxial strain.
Indium incorporation and optical transitions in InGaN bulk materials and quantum wells with arbitrary polarity
Authors: Durnev M. V. , Omelchenko A. V. , Yakovlev E. V. , Evstratov I. Yu. , Karpov S. Yu.
Published: August 2010

Indium incorporation into strained InGaN coherently grown on a GaN substrate with arbitrary polarity is simulated using a simplified epitaxy model. The InGaN composition is predicted as a function of C-axis inclination angle. Effect of strain originated from the lattice mismatch on optical transitions in the bulk InGaN and quantum wells is examined with account of both complex valence band structure and polarization charges induced at the InGaN/GaN interfaces. A higher indium incorporation on nonpolar and semipolar planes, as compared to the ordinary C-plane, is found to not necessarily result in a longer emission wavelength.
Refractive index dynamics of quantum dot based waveguide electroabsorbers
Authors: Piwonski Tomasz , Pulka Jaroslaw , Viktorov Evgeny A. , Huyet Guillaume , Houlihan John
Published: August 2010

The refractive index dynamics of InAs/GaAs quantum dot based waveguide absorbers is studied using heterodyne pump-probe measurements. Absorption reduction due to the pump can be accompanied by either positive or negative refractive index changes depending on the wavelength used. This change in sign of the phase amplitude coupling can be understood by considering the atomlike nature of the quantum dot transitions involved.
Vertical low-voltage oxide transistors gated by microporous SiO2/LiCl composite solid electrolyte with enhanced electric-double-layer capacitance
Authors: Jiang Jie , Sun Jia , Zhou Bin , Lu Aixia , Wan Qing
Published: August 2010

Vertical low-voltage indium-tin oxide field-effect transistors (FETs) gated by microporous SiO2-based solid electrolyte are fabricated at room temperature. Our results indicate that Li ions can enhance the electric-double-layer capacitance of the microporous SiO2 solid electrolyte and reduce the operation voltage of the vertical FETs from 1.5 to 0.8 V. Such vertical low-voltage FETs exhibited a good performance with a high current output (∼1.0 A/cm2), a low subthreshold swing (<80 mV/decade), and a large on-off ratio (>106), respectively. An operation mechanism which provides a better insight into the oxide-based vertical FETs is discussed.
Silicon impurity-induced layer disordering of AlGaN/AlN superlattices
Authors: Wierer J. J. , Allerman A. A. , Li Q.
Published: August 2010

Impurity-induced layer disordering is demonstrated in Al0.1Ga0.9N/AlN superlattices grown by metal-organic vapor phase epitaxy. During growth at temperatures as low as 885 °C and under post growth annealing at 1000 °C in N2 the heterointerfaces of Si-doped (Si concentration >8×1019 cm−3) superlattices exhibit layer disordering (intermixing) while the unintentionally doped superlattices remain stable. Shifts in the intersubband energy transitions and scanning transmission electron microscope images showing changes in the layer abruptness are used to verify layer disordering due to Si diffusion in Al0.1Ga0.9N/AlN superlattices.
Soil microbial respiration responses to changing temperature and substrate availability in fertile grassland
Authors: Uchida Yoshitaka , Clough Timothy J. , Kelliher Francis M. , Sherlock Robert R.
Published: August 2010

A relationship between soil respiration rate (Rs) and temperature (Ts), has been understood to be predicated on carbon (C) substrate availability. However, unlike Ts, C availability in soils is not a state variable that can be readily measured. The C in soils has come from plants, so the C supply rate can be affected by the weather and nutrient supply. We studied a fertile soil beneath pasture, measuring Rs across a temperate – climate range of Ts. Our objectives were to: (1) quantify the synchrony of diurnal changes in Ts and Rs beneath pasture under conditions favourable for plants, (2) quantify responses of microbial respiration (Rm) to the removal of plants and depletion of C supply over time at various Ts, and (3) determine if Rm was related to water-soluble (WSC, 20°C) and hot-water-soluble C (HWSC, 80°C) contents. At a grassland site, Rs increased with Ts as predicted by an Arrhenius type relationship. Sampled soil was incubated at 3°, 9°, and 24°C and Rm was measured over 14 days. In addition soil samples were pre-incubated at 3° or 9°C for both 5 and 14 days, then incubated at 24°C for 1 day and Rm was measured. On day 2, Rm was less than predicted at 24° and 9°C, respectively, suggesting a C availability limitation. The time courses of Rm, revealed that at 24°C, Rm utilised C that was not utilised at lower Ts, indicating that evidently recalcitrant C was available to microbes at a warmer temperature. The responses of Rm at 24°C after the pre-incubation treatments were identical for the 3°C and 9°C pre-incubation treatments, although significantly more C was respired during pre-incubation at 9°C. The WSC and HWSC contents were unaffected by Ts, so did not provide useful measures of the C substrate available for Rm.
Identification of a Nuclear Export Signal in the Catalytic Subunit of AMP-activated Protein Kinase
Authors: Kazgan Nevzat , Williams Tyisha , Forsberg Lawrence J. , Brenman Jay E.
Published: August 2010

The metabolic regulator AMP-activated protein kinase (AMPK) maintains cellular homeostasis through regulation of proteins involved in energy-producing and -consuming pathways. Although AMPK phosphorylation targets include cytoplasmic and nuclear proteins, the precise mechanisms that regulate AMPK localization, and thus its access to these substrates, are unclear. We identify highly conserved carboxy-terminal hydrophobic amino acids that function as a leptomycin B–sensitive, CRM1-dependent nuclear export sequence (NES) in the AMPK catalytic subunit (AMPKα). When this sequence is modified AMPKα shows increased nuclear localization via a Ran-dependent import pathway. Cytoplasmic localization can be restored by substituting well-defined snurportin-1 or protein kinase A inhibitor (PKIA) CRM1-binding NESs into AMPKα. We demonstrate a functional requirement in vivo for the AMPKα carboxy-terminal NES, as transgenic Drosophila expressing AMPKα lacking this NES fail to rescue lethality of AMPKα null mutant flies and show decreased activation loop phosphorylation under heat-shock stress. Sequestered to the nucleus, this truncated protein shows highly reduced phosphorylation at the key Thr172 activation residue, suggesting that AMPK activation predominantly occurs in the cytoplasm under unstressed conditions. Thus, modulation of CRM1-mediated export of AMPKα via its C-terminal NES provides an additional mechanism for cells to use in the regulation of AMPK activity and localization.
Vestigial Is Required during Late-Stage Muscle Differentiation inDrosophila melanogaster Embryos
Authors: Deng Hua , Bell John B. , Simmonds Andrew J.
Published: August 2010

The somatic muscles of Drosophila develop in a complex pattern that is repeated in each embryonic hemi-segment. During early development, progenitor cells fuse to form a syncytial muscle, which further differentiates via expression of muscle-specific factors that induce specific responses to external signals to regulate late-stage processes such as migration and attachment. Initial communication between somatic muscles and the epidermal tendon cells is critical for both of these processes. However, later establishment of attachments between longitudinal muscles at the segmental borders is largely independent of the muscle–epidermal attachment signals, and relatively little is known about how this event is regulated. Using a combination of null mutations and a truncated version of Sd that binds Vg but not DNA, we show that Vestigial (Vg) is required in ventral longitudinal muscles to induce formation of stable intermuscular attachments. In several muscles, this activity may be independent of Sd. Furthermore, the cell-specific differentiation events induced by Vg in two cells fated to form attachments are coordinated by Drosophila epidermal growth factor signaling. Thus, Vg is a key factor to induce specific changes in ventral longitudinal muscles 1–4 identity and is required for these cells to be competent to form stable intermuscular attachments with each other.
SPRINT: side-chain prediction inference toolbox for multistate protein design
Authors: Fromer Menachem , Yanover Chen , Harel Amir , Shachar Ori , Weiss Yair , Linial Michal
Published: August 2010

Summary: SPRINT is a software package that performs computational multistate protein design using state-of-the-art inference on probabilistic graphical models. The input to SPRINT is a list of protein structures, the rotamers modeled for each structure and the pre-calculated rotamer energies. Probabilistic inference is performed using the belief propagation or A* algorithms, and dead-end elimination can be applied as pre-processing. The output can either be a list of amino acid sequences simultaneously compatible with these structures, or probabilistic amino acid profiles compatible with the structures. In addition, higher order (e.g. pairwise) amino acid probabilities can also be predicted. Finally, SPRINT also has a module for protein side-chain prediction and single-state design.

Availability: The full C++ source code for SPRINT can be freely downloaded from http://www.protonet.cs.huji.ac.il/sprint

Contact:  fromer@cs.huji.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Length of delay in seeking medical care by patients with heart failure symptoms and the role of symptom‐related factors: a narrative review
Authors: Gravely‐Witte Shannon , Jurgens Corrine Y. , Tamim Hala , Grace Sherry L.
Published: August 2010

Aims

The delay in seeking timely medical care by patients with acute coronary syndrome and stroke is well established. Less is known about the delay in patients with heart failure (HF). Reducing the delay in seeking care and the early initiation of treatment is associated with improved outcomes in patients with HF. The purpose of this narrative review was to describe the length of the delay in seeking care for HF symptoms and identify symptom‐related factors that contribute to the delay in seeking medical care.

Methods and results

A literature search was conducted to identify English language studies that (i) describe the length of care‐seeking delay for HF symptoms and/or (ii) identify symptom‐related factors that contribute to delay in seeking medical care. The results of this review demonstrate that upon hospital admission patients report wide variations in median symptom time course from 2 h to 7 days from the onset of symptoms to hospital admission. The ability of patients to recognize, interpret, and appraise HF symptoms has been demonstrated to be limited. Symptom characteristics such as dyspnoea, oedema, orthopnoea, higher somatic awareness, higher symptom distress, nocturnal symptom onset, and the pattern of symptom onset were related to longer delay in care‐seeking for HF symptoms. Furthermore, cognitive responses to HF may also play an important role in symptom appraisal.

Conclusion

Delays in seeking care for HF symptoms have been shown to range from hours to days from symptom onset to hospital admission. Healthcare professionals should therefore be more vigilant in identifying high‐risk individuals and educating them about the warning signs of HF. Moreover, access to outpatient chronic disease management programmes may have the potential to reduce these delays.
Life-history traits of the giant squid Architeuthis dux revealed from stable isotope signatures recorded in beaks
Authors: Guerra Ángel , Rodríguez-Navarro Alejandro B. , González Ángel F. , Romanek Chris S. , Álvarez-Lloret Pedro , Pierce Graham J.
Published: August 2010

Guerra, Á., Rodríguez-Navarro, A. B., González, Á. F., Romanek, C. S., Álvarez-Lloret, P., and Pierce, G. J. 2010. Life-history traits of the giant squid Architeuthis dux revealed from stable isotope signatures recorded in beaks. – ICES Journal of Marine Science, 67: 1425–1431. Carbon and nitrogen isotope profiles constructed from the upper beaks of four giant squid Architeuthis dux from the Bay of Biscay and Namibian waters provided a time-integrated record of their diet. Values of δ15N ranged from 5.5 to 13.4‰ and of δ13C from −14.4 to −17.8‰. Nitrogen isotope profiles differed significantly in shape among the four animals analysed, but δ15N increased along each profile, with lowest values around the rostral tip. The difference between the lowest and the highest δ15N values was ∼5.8‰, slightly less than a two-level difference between the trophic position of small and large A. dux. The increase in δ13C values was not as pronounced as for the δ15N profiles, but the changes suggest an ontogenetic shift in diet early in life from smaller prey of relatively low trophic status to larger prey of higher status. Fluctuations in δ13C values observed near the rostral tip may be associated with a greater intrinsic variability in the carbon isotope composition of relatively small prey, and/or transient migratory behaviour early in life. The relative stability of the δ13C profiles over the remainder of their lifespan is consistent with the hypothesis that adult giant squid inhabit relatively small, well-defined, and productive areas, where food resources have a constant carbon isotope composition.
Ontogenic changes in diel vertical migration patterns compared with known allometric changes in three mesopelagic squid species suggest an expanded definition of a paralarva
Authors: Shea Elizabeth K. , Vecchione Michael
Published: August 2010

Shea, E. K., and Vecchione, M. 2010. Ontogenic changes in diel vertical migration patterns compared with known allometric changes in three mesopelagic squid species suggest an expanded definition of a paralarva. – ICES Journal of Marine Science, 67: 1436–1443. Planktonic and newly hatched cephalopods are routinely called paralarvae. Currently, the onset of diel vertical migration (DVM) marks the end of the paralarval phase, although changes in ontogenic growth trajectories may also be used. Patterns of DVM are reported for the first time for three poorly understood mesopelagic squid species. Discrete-depth samples taken during the Amsterdam Mid North Atlantic Plankton Expeditions (AMNAPE) of 1980–1983 are used to examine the timing of ecological and morphological changes in Chtenopteryx sicula, Mastigoteuthis magna, and Brachioteuthis sp. 3. DVM patterns are species-specific, and ontogenic changes in DVM coincide with allometric changes in the arm, fin, and funnel characters of C. sicula at 7 mm mantle length. Mastigoteuthis magna is not concentrated in the upper 250 m of the water column during the day, and no clear DVM pattern is found in Brachioteuthis sp. 3, meaning that the endpoint of the paralarval phase cannot be defined ecologically in these species. Other ecological transformations, e.g. changes in prey-capture ability, are therefore explored as alternatives to DVM. The pad-shaped club and long neck are proposed as visual markers of the end of the paralarval phase of C. sicula and Brachioteuthis sp. 3, respectively.
Plasmodesmata: Gateways to Local and Systemic Virus Infection
Authors: Benitez-Alfonso Yoselin , Faulkner Christine , Ritzenthaler Christophe , Maule Andrew J.
Published: August 2010

As channels that provide cell-to-cell connectivity, plasmodesmata are central to the local and systemic spread of viruses in plants. This review discusses the current state of knowledge of the structure and function of these channels and the ways in which viruses bring about functional changes that allow macromolecular trafficking to occur. Despite the passing of two decades since the first identification of a viral movement protein that mediates these changes, our understanding of the relevant molecular mechanisms remains in its infancy. However, viral movement proteins provide valuable tools for the modification of plasmodesmata and will continue to assist in the dissection of plasmodesmal properties in relation to their core roles in cell-to-cell communication.
Age-Related Resistance of Nicotiana benthamiana Against Hemibiotrophic Pathogen Phytophthora infestans Requires Both Ethylene- and Salicylic Acid–Mediated Signaling Pathways
Authors: Shibata Yusuke , Kawakita Kazuhito , Takemoto Daigo
Published: August 2010

Phytophthora infestans, the agent of late blight disease of potato, is a hemibiotrophic pathogen with biotrophic action during early infection and necrotrophic in the later stage of colonization. Mature Nicotiana benthamiana was resistant to P. infestans, whereas relatively young plants were susceptible to this pathogen. Young plants became resistant following a pretreatment with acibenzolar-S-methyl, a functional analog of salicylic acid (SA), indicating that susceptibility of young plants is due to a lack of induction of SA signaling. Further analysis with virus-induced gene silencing indicated that NbICS1 and NbEIN2, the genes for SA biosynthesis and ethylene (ET) signaling, respectively, are required for the resistance of mature N. benthamiana against P. infestans. Furthermore, these genes are required for the production of reactive oxygen species (ROS) induced by treatment of the INF1 elicitor. In NbICS1-silenced plants, cell death induced by either INF1 or necrosis-inducing protein NPP1.1 was significantly accelerated. Expression of genes for phytoalexin (capsidiol) biosynthesis, NbEAS and NbEAH, were regulated by ET, and gene silencing of either of them compromised resistance of N. benthamiana to P. infestans. Together, these results suggest that resistance of N. benthamiana against hemibiotrophic P. infestans requires both SA-regulated appropriate induction of cell death and ET-induced production of phytoalexin.
RBOHF2 of Barley Is Required for Normal Development of Penetration Resistance to the Parasitic Fungus Blumeria graminis f. sp. hordei
Authors: Proels Reinhard K. , Oberhollenzer Kathrin , Pathuri Indira Priyadarshini , Hensel Götz , Kumlehn Jochen , Hückelhoven Ralph
Published: August 2010

Plant respiratory burst oxidase homologs are prominent sources of reactive oxygen species (ROS) in signal transduction and in interaction with microbes. However, the function of respiratory burst oxidase homologue (RBOH) genes in interaction with microbes might differ for certain plant and pathogen species. We produced transgenic barley knock down (KD) for the HvRBOHF2 isoform of NADPH oxidases. Young HvRBOHF2 KD shoots did not show obvious morphological alterations from the wild type but adult HvRBOHF2 KD plants developed fewer tillers, were less fertile, and showed spontaneous cell death in leaf mesophyll. Additionally, HvRBOHF2 KD plants were unable to contain wound-induced cell death. Before developmental failure became obvious, young HvRBOHF2 KD seedlings were much more susceptible to penetration by the biotrophic powdery mildew fungus Blumeria graminis f. sp. hordei. Strikingly, the B. graminis f. sp. hordei-induced cell-wall-associated oxidative burst was not substantially attenuated in HvRBOHF2 KD plants but enhanced susceptibility apparently influenced the subcellular site of hydrogen peroxide accumulation. Taken together, misexpression of HvRBOHF2 caused failure of barley to normally develop penetration resistance to B. graminis f. sp. hordei and to control leaf cell death.
Rhodococcus fascians Impacts Plant Development Through the Dynamic Fas-Mediated Production of a Cytokinin Mix
Authors: Pertry Ine , Václavíková Katerina , Gemrotová Markéta , Spíchal Lukáš , Galuszka Petr , Depuydt Stephen , Temmerman Wim , Stes Elisabeth , De Keyser Annick , Riefler Michael , Biondi Stefania , Novák Ondrej , Schmülling Thomas , Strnad Miroslav , Tarkowski Petr , Holsters Marcelle , Vereecke Danny
Published: August 2010

The phytopathogenic actinomycete Rhodococcus fascians D188 relies mainly on the linear plasmid-encoded fas operon for its virulence. The bacteria secrete six cytokinin bases that synergistically redirect the developmental program of the plant to stimulate proliferation of young shoot tissue, thus establishing a leafy gall as a niche. A yeast-based cytokinin bioassay combined with cytokinin profiling of bacterial mutants revealed that the fas operon is essential for the enhanced production of isopentenyladenine, trans-zeatin, cis-zeatin, and the 2-methylthio derivatives of the zeatins. Cytokinin metabolite data and the demonstration of the enzymatic activities of FasD (isopentenyltransferase), FasE (cytokinin oxidase/dehydrogenase), and FasF (phosphoribohydrolase) led us to propose a pathway for the production of the cytokinin spectrum. Further evaluation of the pathogenicity of different fas mutants and of fas gene expression and cytokinin signal transduction upon infection implied that the secretion of the cytokinin mix is a highly dynamic process, with the consecutive production of a tom initiation wave followed by a maintenance flow.
Transcription of Two Blue Copper-Binding Protein Isogenes Is Highly Correlated with Arbuscular Mycorrhizal Development in Medicago truncatula
Authors: Parádi István , van Tuinen Diederik , Morandi Dominique , Ochatt Sergio , Robert Franck , Jacas Louis , Dumas-Gaudot Eliane
Published: August 2010

Expression profiling of two paralogous arbuscular mycorrhizal (AM)-specific blue copper-binding gene (MtBcp1a and MtBcp1b) isoforms was performed by real-time quantitative polymerase chain reaction in wild-type Medicago truncatula Jemalong 5 (J5) during the mycorrhizal development with Glomus intraradices for up to 7 weeks. Time-course analysis in J5 showed that expression of both MtBcp1 genes increased continuously and correlated strongly with the colonization intensity and arbuscule content. MtPT4, selected as a reference gene of the functional plant-fungus association, showed a weaker correlation to mycorrhizal development. In a second experiment, a range of mycorrhizal mutants of the wild-type J5 was assessed. Strictly AM-penetration-defective TRV25-C and TRV25-D (dmi3, Mtsym13), hypomycorrhizal TR25 and TR89 (dmi2, Mtsym2) mutants, and a hypermycorrhizal mutant TRV17 (sunn, Mtsym12) were compared with J5 3 and 7 weeks after inoculation. No MtBcp1 transcripts were detected in the mutants blocked at the appressoria stage. Conversely, TR25, TR89, and J5 showed a gradual increase of the expression of both MtBcp1 genes in 3- and 7-week-old plants, similar to the increase in colonization intensity and arbuscule abundance. The strong correlation between the expression level of AM-specific blue copper-binding protein-encoding genes and AM colonization may imply a basic role in symbiotic functioning for these genes, which may serve as new molecular markers of arbuscule development in M. truncatula.
BAX INHIBITOR-1 Is Required for Full Susceptibility of Barley to Powdery Mildew
Authors: Eichmann Ruth , Bischof Melanie , Weis Corina , Shaw Jane , Lacomme Christophe , Schweizer Patrick , Duchkov Dimitar , Hensel Götz , Kumlehn Jochen , Hückelhoven Ralph
Published: August 2010

BAX INHIBITOR-1 (BI-1) is one of the few proteins known to have cross-kingdom conserved functions in negative control of programmed cell death. Additionally, barley BI-1 (HvBI-1) suppresses defense responses and basal resistance to the powdery mildew fungus Blumeria graminis f. sp. hordei and enhances resistance to cell death–provoking fungi when overexpressed in barley. Downregulation of HvBI-1 by transient-induced gene silencing or virus-induced gene silencing limited susceptibility to B. graminis f. sp. hordei, suggesting that HvBI-1 is a susceptibility factor toward powdery mildew. Transient silencing of BI-1 did not limit supersusceptibility induced by overexpression of MLO. Transgenic barley plants harboring an HvBI-1 RNA interference (RNAi) construct displayed lower levels of HvBI-1 transcripts and were less susceptible to powdery mildew than wild-type plants. At the cellular level, HvBI-1 RNAi plants had enhanced resistance to penetration by B. graminis f. sp. hordei. These data support a function of BI-1 in modulating cell-wall-associated defense and in establishing full compatibility of B. graminis f. sp. hordei with barley.
Plant species richness, identity and productivity differentially influence key groups of microbes in grassland soils of contrasting fertility
Authors: De Deyn Gerlinde B. , Quirk Helen , Bardgett Richard D.
Published: August 2010

The abundance of microbes in soil is thought to be strongly influenced by plant productivity rather than by plant species richness
per se
. However, whether this holds true for different microbial groups and under different soil conditions is unresolved. We tested how plant species richness, identity and biomass influence the abundances of arbuscular mycorrhizal fungi (AMF), saprophytic bacteria and fungi, and actinomycetes, in model plant communities in soil of low and high fertility using phospholipid fatty acid analysis. Abundances of saprophytic fungi and bacteria were driven by larger plant biomass in high diversity treatments. In contrast, increased AMF abundance with larger plant species richness was not explained by plant biomass, but responded to plant species identity and was stimulated by
Anthoxantum odoratum
. Our results indicate that the abundance of saprophytic soil microbes is influenced more by resource quantity, as driven by plant production, while AMF respond more strongly to resource composition, driven by variation in plant species richness and identity. This suggests that AMF abundance in soil is more sensitive to changes in plant species diversity
per se
and plant species composition than are abundances of saprophytic microbes.