bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduction of the Germano-identity error in the dynamic Smagorinsky model
Authors: Park Noma , Mahesh Krishnan
Published: June 2009

We revisit the Germano-identity error in the dynamic modeling procedure in the sense that the current modeling procedure to obtain the dynamic coefficient may not truly minimize the error in the mean and global sense. A “corrector step” to the conventional dynamic Smagorinsky model is proposed to obtain a corrected eddy viscosity which further reduces the error. The change in resolved velocity due to the coefficient variation as well as nonlocal nature of the filter and flow unsteadiness is accounted for by a simplified suboptimal control formalism without resorting to the adjoint equations. The objective function chosen is the Germano-identity error integrated over the entire computational volume and pathline. In order to determine corrected eddy viscosity, the Fréchet derivative of the objective function is directly evaluated by a finite-differencing formula in an efficient predictor-corrector-type framework. The proposed model is applied to decaying isotropic turbulence and turbulent channel flow at various Reynolds numbers and resolutions to obtain noticeable reduction in the Germano-identity error and significantly improved flow statistics. From channel flow large-eddy simulation, it is shown that conventional dynamic model underestimates subgrid scale eddy viscosity when the resolution gets coarse, and this underestimation is responsible for increased anisotropy of predicted Reynolds stress. The proposed model raises both the overall and near-wall subgrid scale eddy viscosity to reduce exaggerated Reynolds stress anisotropy and yield significantly improved flow statistics.
Capturing light pulses into a pair of coupled photonic crystal cavities
Authors: Otey Clayton R. , Povinelli Michelle L. , Fan Shanhui
Published: June 2009

We describe finite-difference time-domain simulations of a two-dimensional photonic crystal implementation of a two-resonator system capable of capturing light pulses from a waveguide. As much as 99.61% of incident pulse energy is captured in simulations. The release of near-perfect Gaussian pulses is also demonstrated.
A realistic modeling of fluid infiltration in thin fibrous sheets
Authors: Jaganathan Sudhakar , Tafreshi Hooman Vahedi , Pourdeyhimi Behnam
Published: June 2009

In this paper, a modeling study is presented to simulate the fluid infiltration in fibrous media. The Richards’ equation of two-phase flow in porous media is used here to model the fluid absorption in unsaturated/partially saturated fibrous thin sheets. The required consecutive equations, relative permeability, and capillary pressure as functions of medium’s saturation are obtained via fiber-level modeling and a long-column experiment, respectively. Our relative permeability calculations are based on solving the Stokes flow equations in partially saturated three-dimensional domains obtained by imaging the sheets’ microstructures. The Richards’ equation, together with the above consecutive correlations, is solved for fibrous media inclined with different angles. Simulation results are obtained for three different cases of upward, horizontal, and downward infiltrations. We also compared our numerical results with those of our long-column experiment and observed a good agreement. Moreover, we establish empirical coefficients for the semianalytical correlations previously proposed in the literature for the case of horizontal and downward infiltrations in thin fibrous sheets.
Spin-driven structural effects in alkali doped H4e clusters from quantum calculations
Authors: Bovino S. , Coccia E. , Bodo E. , Lopez-Durán D. , Gianturco F. A.
Published: June 2009

In this paper, we carry out variational Monte Carlo and diffusion Monte Carlo (DMC) calculations for Li2(Σ1g+)(H4e)N and Li2(Σ3u+)(H4e)N with N up to 30 and discuss in detail the results of our computations. After a comparison between our DMC energies with the “exact” discrete variable representation values for the species with one H4e, in order to test the quality of our computations at 0 K, we analyze the structural features of the whole range of doped clusters. We find that both species reside on the droplet surface, but that their orientation is spin driven, i.e., the singlet molecule is perpendicular and the triplet one is parallel to the droplet’s surface. We have also computed quantum vibrational relaxation rates for both dimers in collision with a single H4e and we find them to differ by orders of magnitude at the estimated surface temperature. Our results therefore confirm the findings from a great number of experimental data present in the current literature and provide one of the first attempts at giving an accurate, fully quantum picture for the nanoscopic properties of alkali dimers in H4e clusters.
A conditional sampling-based method for noise and resolution corrections for scalar dissipation rate measurements
Authors: Cai Jian , Tong Chenning
Published: June 2009

A conditional sampling-based method for correcting noise and resolution effects for scalar dissipation rate measurements is developed. Noise and resolution effects on the measured dissipation rate have opposite trends, making their separation and accurate corrections difficult. A major task in dissipation rate correction, therefore, is to isolate each effect. The conditional-sampling method presented in this work uses instantaneous local scalar mean and variance as conditioning variables, and is based in part on Kolmogorov’s refined similarity hypotheses. It ensures selection of instantaneous fully resolved local scalar fields, which are analyzed to determine the measurement noise. Noise correction is applied to potentially under-resolved local scalar fields, also selected using the conditional-sampling procedure, effectively separating the effects of noise from those of resolution. The error function is used as a model for the potentially under-resolved local scalar fields to evaluate their dissipation length scales and to make corrections for the dissipation rate. The present method uses local instead of spectral analyses; therefore, can be applied to the mean scalar dissipation rate conditional on the scalar values. An application of the method to temperature dissipation rate in a slightly heated turbulent jet shows excellent results, validating the method. The method can also be applied to other challenge situations, such as turbulent flames.
Determining optimum tilt angles of photovoltaic panels at typical north-tropical latitudes
Authors: Calabrò Emanuele
Published: June 2009

An application of renewable energy technology is the installation of photovoltaic systems that generate power without emitting pollutants and requiring no fuel. Solar radiation varies with geographic latitude, season, and time of day due to the various sun positions in the sky. Hence, the problem of designing the optimal tilt angle and the orientation of a solar panel arises for maximizing solar radiation collection at a fixed latitude. An approach of employing sky radiance models for determining optimal tilt angle values of solar collectors with respect to a set of geographic latitudes was conducted by using a data archive of the daily global solar radiation collected by the Italian Institute of ENEA. The results provided a set of tilt angles for winter months that enables a solar panel to absorb the maximum amount of global solar radiation and another set of smaller tilt angle values for summer months, as well. The great difference between these two sets suggested to us to plan semifixed solar panels whose tilt angle can be changed twice a year. The relative gain in solar radiation collectable should not be negligible, as shown in Sec. III.
Broad M-band multi-keV x-ray emission from plasmas created by short laser pulses
Authors: Harmand M. , Dorchies F. , Peyrusse O. , Descamps D. , Fourment C. , Hulin S. , Petit S. , Santos J. J.
Published: June 2009

The investigation of the broad M-band x-ray emission from high-Z plasmas created by a laser, with a 30 fs to 3 ps pulse duration and achieving 1015–17 W/cm2 on target, is reported. Experimental emission spectra are measured in the energy range from 1.50 to 1.75 keV and discussed as potential backlighting x-ray sources for time-resolved x-ray absorption spectroscopy studies. They are compared with theoretical nonlocal thermodynamic equilibrium calculations of x-ray emission.
Understanding the dispersion of coaxial plasmonic structures through a connection with the planar metal-insulator-metal geometry
Authors: Catrysse Peter B. , Fan Shanhui
Published: June 2009

We elucidate the dispersion behavior of deep-subwavelength propagating modes in coaxial plasmonic structures by making an explicit connection with the planar metal-insulator-metal geometry. We provide an intuitive picture that allows for a qualitative understanding and a quantitative prediction of the entire dispersion behavior, which includes the number of modes at every frequency, the modal propagation constants, the propagation losses, and the cutoff frequencies of propagating modes supported by these technologically important structures. We validate our analytical approach by comparing its predictions to first-principles finite-difference frequency-domain simulations.
Substrate-dependent interface composition and charge transport in films for organic photovoltaics
Authors: Germack David S. , Chan Calvin K. , Hamadani Behrang H. , Richter Lee J. , Fischer Daniel A. , Gundlach David J. , DeLongchamp Dean M.
Published: June 2009

The buried interface composition of polymer-fullerene blends is found by near-edge x-ray absorption fine structure spectroscopy to depend on the surface energy of the substrate upon which they are cast. The interface composition determines the type of charge transport measured with thin film transistors. These results have implications for organic photovoltaics device design and the use of transistors to evaluate bulk mobility in blends.
Charging and discharging of graphene in ambient conditions studied with scanning probe microscopy
Authors: Verdaguer A. , Cardellach M. , Segura J. J. , Sacha G. M. , Moser J. , Zdrojek M. , Bachtold A. , Fraxedas J.
Published: June 2009

By means of scanning probe microscopy we are able to inject charges in isolated graphene sheets deposited on SiO2/Si wafers and characterize the discharge induced by water in controlled ambient conditions. Contact potential differences between the graphene surface and the probe tip, measured by Kelvin probe microscopy, show a linear relationship with the tip bias during charge injection. The discharge depends on relative humidity and decays exponentially with time constants of the order of tens of minutes. We propose that graphene discharges through the water film adsorbed on the SiO2 surface.
Fourier transform microwave spectroscopy of CH2CFO
Authors: Watanabe Akihiro , Sumiyoshi Yoshihiro , Endo Yasuki
Published: June 2009

Rotational spectra of the CH2CFO radical in the A2″ ground state with resolved fine and hyperfine structures have been observed for the first time by Fourier transform microwave spectroscopy. Rotational transitions are analyzed using the ordinary rigid asymmetric top Hamiltonian for doublet species with three nuclear spins. Seventeen molecular constants including the fine and hyperfine coupling constants have been determined. The CH2CFO radical is confirmed to be a planer molecule in the ground electronic state since it has a small positive inertial defect. From the hyperfine coupling constants of protons, the unpaired electron density on the CH2 carbon atom is estimated to be about 85%. Thus, the formylmethyl-type resonance form (ĊH2CF=O) is a dominant structure in the ground electronic state, and fluorine substitution has negligible effect on the C–C–O π conjugate system.
Comment on “Effects of charged dust particles on nonlinear ion acoustic solitary waves in a relativistic plasma” [Phys. Plasmas 16, 043701 (2009)]
Authors: Verheest Frank , Hellberg Manfred A.
Published: June 2009

The claim by Choi et al. [C.-R. Choi, D.-Y. Lee, Y.-H. Kim, and N. C. Lee, Phys. Plasmas 16, 043701 (2009)] that different solitary wave types (humps, dips, and kinks) can be combined in one smooth profile is completely erroneous and contravenes generic rules for pseudopotential treatments.
Nonadiabatic small polaron tunneling conduction in reduced Cr-doped SrTiO3−δ thin films
Authors: Phan Bach Thang , Lee Jaichan
Published: June 2009

We investigated the electrical conduction and dielectric relaxation of reduced Cr-doped SrTiO3−δ thin films. The electrical conduction behavior indicates the formation of small polarons in oxygen deficient Cr-doped SrTiO3−δ thin films. The associated dielectric relaxation further indicates nonadiabatic small polaron tunneling conduction. A strong electron-phonon interaction is identified based on the large polaron coupling constant, α≈28(α⪢4).
Controlling the field distribution in waveguides with transformation optics
Authors: Wang Zhiyu , Luo Yu , Cui Wanzhao , Ma Wei , Peng Liang , Huangfu Jiangtao , Chen Hongsheng , Ran Lixin
Published: June 2009

Artificially designed transformation medium offers great opportunity to control the field distributions inside a waveguide. By rigorously solving Maxwell’s equations in cylindrical and rectangular waveguides, we show that filling waveguides with properly designed transformation medium with a space gradient can reduce the electric field at boundary to zero. Full-wave finite element modeling is also performed to confirm this point. This property can be used to reduce the probability of multipactor discharge at the surface of conductor inside a waveguide.
One-dimensional contact mode interdigitated center of pressure sensor
Authors: Xu Tian-Bing , Guerreiro Nelson , Hubbard James , Kang Jin Ho , Park Cheol , Harrison Joycelyn
Published: June 2009

A one-dimensional contact mode interdigitated center of pressure sensor (CMIPS) has been developed. The experimental study demonstrated that the CMIPS has the capability to measure the overall pressure as well as the center of pressure in one dimension simultaneously. A theoretical model for the CMIPS is established here based on the equivalent circuit of the configuration of the CMIPS as well as the material properties of the sensor. The experimental results match well with theoretical modeling predictions. A system mapped with two or more pieces of the CMIPS can be used to obtain information from the pressure distribution in multidimensions.
Laser triggered single streamer in a pin-to-pin coplanar dielectric barrier discharge
Authors: Ambrico P. F. , Ambrico M. , Šimek M. , Colaianni A. , Dilecce G. , De Benedictis S.
Published: June 2009

The effect of laser light interaction with alumina surface of a single filament coplanar dielectric barrier discharge has been investigated. It has been found that for laser photon energy lower than the pure alumina photoelectron emission threshold, the laser beam was effective in triggering single streamer discharge below regular ignition voltage threshold. This work demonstrates that triggering of the filamentary discharge occurs due to the laser induced extraction of electrons originally trapped by the plasma radiation at the dielectric surface; the trap energy levels lower than the dielectric band gap explain the easier electron detrapping due to incident laser photons.
N
2
(
A
Σ
u
+
3
)
time evolution in N2 atmospheric pressure surface dielectric barrier discharge driven by ac voltage under modulated regime
Authors: Ambrico P. F. , Šimek M. , Dilecce G. , De Benedictis S.
Published: June 2009

The relaxation of N2(AΣu+3) metastable in N2 ac (5 KHz and 7 KVpp) surface dielectric barrier discharge driven under pulse modulated regime, TON=5 ms and TOFF=20 ms, at atmospheric pressure has been investigated. N2(A) has been detected by optical-optical double resonance laser induced fluorescence in a space layer (space afterglow) at 1 mm above the discharge electrode. The time evolution clearly shows that in the space afterglow layer N2(A) builds up and decay in millisecond time scale and does not vary in the voltage cycle.
Temperature stabilization of optofluidic photonic crystal cavities
Authors: Karnutsch Christian , Smith Cameron L. C. , Graham Alexandra , Tomljenovic-Hanic Snjezana , McPhedran Ross , Eggleton Benjamin J. , O’Faolain Liam , Krauss Thomas F. , Xiao Sanshui , Mortensen N. Asger
Published: June 2009

We present a principle for the temperature stabilization of photonic crystal (PhC) cavities based on optofluidics. We introduce an analytic method enabling a specific mode of a cavity to be made wavelength insensitive to changes in ambient temperature. Using this analysis, we experimentally demonstrate a PhC cavity with a quality factor of Q≈15 000 that exhibits a temperature-independent resonance. Temperature-stable cavities constitute a major building block in the development of a large suite of applications from high-sensitivity sensor systems for chemical and biomedical applications to microlasers, optical filters, and switches.
Reliable thin film encapsulation for organic light emitting diodes grown by low-temperature atomic layer deposition
Authors: Meyer J. , Schneidenbach D. , Winkler T. , Hamwi S. , Weimann T. , Hinze P. , Ammermann S. , Johannes H.-H. , Riedl T. , Kowalsky W.
Published: June 2009

We report on highly efficient gas diffusion barriers for organic light emitting diodes (OLEDs). Nanolaminate (NL) structures composed of alternating Al2O3 and ZrO2 sublayers grown by atomic layer deposition at 80 °C are used to realize long-term stable OLED devices. While the brightness of phosphorescent p-i-n OLEDs sealed by a single Al2O3 layer drops to 85% of the initial luminance of 1000 cd/m2 after 1000 h of continuous operation, OLEDs encapsulated with the NL retain more than 95% of their brightness. An extrapolated device lifetime substantially in excess of 10 000 h can be achieved, clearly proving the suitability of the NLs as highly dense and reliable thin film encapsulation of sensitive organic electronic devices.
Non-Stick Sugars: Synthesis of Difluorosugar Fluorides as Potential Glycosidase Inactivators
Authors: Rempel Brian P. , Withers Stephen G.
Published: June 2009

Four new difluorosugar fluorides, 2-deoxy-2,5-difluoro-α-l-idopyranosyl fluoride, 1,5-difluoro-d-glucopyranosyl fluoride, 1,5-difluoro-l-idopyranosyl fluoride, and 2-deoxy-1,2-difluoro-d-glucopyranosyl fluoride, were synthesized from known precursors by a radical bromination/fluoride displacement sequence, followed by deprotection. The compounds were tested as time-dependent inactivators of the β-glucosidase from Agrobacterium sp. (Abg, EC 3.2.1.21) and, while they were shown to bind to the enzyme active site as reversible competitive inhibitors, the only time-dependent inactivation observed was traced to the presence of an extremely small amount (<0.1%) of a highly reactive contaminating impurity.
Two new rare species and a new hybrid in Eucalyptus series Tetrapterae (Myrtaceae) from southern coastal Western Australia
Authors: Hopper Stephen D. , McQuoid Nathan K.
Published: June 2009

Three new rare taxa allied to the conspicuous, common four-winged mallee (Eucalyptus tetraptera Turcz.) are described. E. sweedmaniana is a large-leaved and prostrate coastal mallee known only from Mount Arid, Western Australia. E. brandiana, a non-lignotuberous mallet, occupies spongolite hilltops and escarpments near the Fitzgerald River Inlet in Fitzgerald River National Park, Western Australia. A single hybrid mallet, E. arborella × brandiana, is described from the type locality of E. brandiana. Both new species and the new hybrid show potential for horticultural use, given their compact habit, large leaves and conspicuous red floral hypanthia and fruits. E. arborella × brandiana and E. brandiana are particularly at risk, being highly localised endemics that are killed by fire.
Functional and genetic evidence that the Mal/TIRAP allele variant 180L has been selected by providing protection against septic shock
Authors: Ferwerda Bart , Alonso Santos , Banahan Kathy , McCall Matthew B. B. , Giamarellos-Bourboulis Evangelos J. , Ramakers Bart P. , Mouktaroudi Maria , Fain Pamela R. , Izagirre Neskuts , Syafruddin Din , Cristea Tudor , Mockenhaupt Frank P. , Troye-Blomberg Marita , Kumpf Oliver , Maiga Boubacar , Dolo Amagana , Doumbo Ogobara , Sundaresan Santhosh , Bedu-Addo George , van Crevel Reinout , Hamann Lutz , Oh Djin-Ye , Schumann Ralf R. , Joosten Leo A. B. , de la Rúa Concepcion , Sauerwein Robert , Drenth Joost P. H. , Kullberg Bart-Jan , van der Ven André J. A. M. , Hill Adrian V. , Pickkers Peter , van der Meer Jos W. M. , O'Neill Luke A. J. , Netea Mihai G.
Published: June 2009

Adequate responses by our innate immune system toward invading pathogens were of vital importance for surviving infections, especially before the antibiotic era. Recently, a polymorphism in Mal (Ser180Leu,
TIRAP
rs8177374), an important adaptor protein downstream of the Toll-like receptor (TLR) 2 and 4 pathways, has been described to provide protection against a broad range of infectious pathogens. We assessed the functional effects of this polymorphism in human experimental endotoxemia, and we demonstrate that individuals bearing the
TIRAP
180L allele display an increased, innate immune response to TLR4 and TLR2 ligands, but not to TLR9 stimulation. This phenotype has been related to an increased resistance to infection. However, an overshoot in the release of proinflammatory cytokines by
TIRAP
180L homozygous individuals suggests a scenario of balanced evolution. We have also investigated the worldwide distribution of the Ser180Leu polymorphism in 14 populations around the globe to correlate the genetic makeup of
TIRAP
with the local infectious pressures. Based on the immunological, clinical, and genetic data, we propose that this mutation might have been selected in West Eurasia during the early settlement of this region after the out-of-Africa migration of modern
Homo sapiens
. This combination of functional and genetic data provides unique insights to our understanding of the pathogenesis of sepsis.
SUN1 and SUN2 play critical but partially redundant roles in anchoring nuclei in skeletal muscle cells in mice
Authors: Lei Kai , Zhang Xiaochang , Ding Xu , Guo Xue , Chen Muyun , Zhu Binggen , Xu Tian , Zhuang Yuan , Xu Rener , Han Min
Published: June 2009

How the nuclei in mammalian skeletal muscle fibers properly position themselves relative to the cell body is an interesting and important cell biology question. In the syncytial skeletal muscle cells, more than 100 nuclei are evenly distributed at the periphery of each cell, with 3–8 nuclei anchored beneath the neuromuscular junction (NMJ). Our previous studies revealed that the KASH domain–containing Syne-1/Nesprin-1 protein plays an essential role in anchoring both synaptic and nonsynaptic myonuclei in mice. SUN domain–containing proteins (SUN proteins) have been shown to interact with KASH domain–containing proteins (KASH proteins) at the nuclear envelope (NE), but their roles in nuclear positioning in mice are unknown. Here we show that the synaptic nuclear anchorage is partially perturbed in
Sun1
, but not in
Sun2
, knockout mice. Disruption of 3 or all 4
Sun1
/
2
wild-type alleles revealed a gene dosage effect on synaptic nuclear anchorage. The organization of nonsynaptic nuclei is disrupted in
Sun1
/
2
double-knockout (DKO) mice as well. We further show that the localization of Syne-1 to the NE of muscle cells is disrupted in
Sun1
/
2
DKO mice. These results clearly indicate that SUN1 and SUN2 function critically in skeletal muscle cells for Syne-1 localization at the NE, which is essential for proper myonuclear positioning.
Does vegetation prevent wave erosion of salt marsh edges?
Authors: Feagin R. A. , Lozada-Bernard S. M. , Ravens T. M. , Möller I. , Yeager K. M. , Baird A. H.
Published: June 2009

This study challenges the paradigm that salt marsh plants prevent lateral wave-induced erosion along wetland edges by binding soil with live roots and clarifies the role of vegetation in protecting the coast. In both laboratory flume studies and controlled field experiments, we show that common salt marsh plants do not significantly mitigate the total amount of erosion along a wetland edge. We found that the soil type is the primary variable that influences the lateral erosion rate and although plants do not directly reduce wetland edge erosion, they may do so indirectly via modification of soil parameters. We conclude that coastal vegetation is best-suited to modify and control sedimentary dynamics in response to gradual phenomena like sea-level rise or tidal forces, but is less well-suited to resist punctuated disturbances at the seaward margin of salt marshes, specifically breaking waves.
Connexin 43 and plakophilin-2 as a protein complex that regulates blood–testis barrier dynamics
Authors: Li Michelle W. M. , Mruk Dolores D. , Lee Will M. , Cheng C. Yan
Published: June 2009

The blood–testis barrier (BTB) formed by adjacent Sertoli cells is composed of coexisting tight junction (TJ), basal ectoplasmic specialization (ES), and desmosome-like junction. Desmosome-like junctions display structural features of desmosome and gap junctions, but its function at the BTB remains unknown. Herein, we demonstrate that connexin 43 (Cx43), a gap junction integral membrane protein, structurally interacts with desmosomal protein plakophilin-2 (PKP2), basal ES proteins N-cadherin and β-catenin, and signaling molecule c-Src, but not with the TJ proteins occludin and ZO-1 in the seminiferous epithelium of adult rats. The localization of Cx43 in the seminiferous epithelium during (
i
) the normal epithelial cycle of spermatogenesis and (
ii
) anchoring junction restructuring at the Sertoli–spermatid interface induced by adjudin which mimics junction restructuring events during spermatogenesis have suggested that Cx43 is involved in cell adhesion. The knockdown of Cx43 by RNAi technique using specific siRNA duplexes was performed in primary Sertoli cell cultures with an established TJ permeability barrier that mimicked the BTB in vivo. This knockdown of Cx43 affected neither the TJ barrier function nor the steady-state levels of junction proteins of TJ, basal ES, and desmosome-like junction. However, after the knockdown of both Cx43 and PKP2, the Sertoli cell TJ barrier function was perturbed transiently. This perturbation was concomitant with a mislocalization of occludin and ZO-1 from the cell–cell interface. In summary, Cx43 and PKP2 form a protein complex within the desmosome-like junction to regulate cell adhesion at the BTB, partly through its effects on the occludin/ZO-1 complex, so as to facilitate the transit of primary preleptotene spermatocytes.
Effects of hatching time on year-class strength in Norwegian spring-spawning herring (Clupea harengus)
Authors: Husebø Åse , Stenevik Erling Kåre , Slotte Aril , Fossum Petter , Salthaug Are , Vikebø Frode , Aanes Sondre , Folkvord Arild
Published: June 2009

Husebø, Å., Stenevik, E. K., Slotte, A., Fossum, P., Salthaug, A., Vikebø, F., Aanes, S., and Folkvord, A. 2009. Effects of hatching time on year-class strength in Norwegian spring-spawning herring (Clupea harengus). – ICES Journal of Marine Science, 66: 1710–1717. Effects of mean hatching date, post-hatching temperature, wintering temperature of adults, spawning stock size, and percentage of recruit spawners on larval survival in Norwegian spring-spawning herring (Clupea harengus) during the period 1987–2004 were analysed. In the final model, only hatching date proved to be significant. However, hatching date was itself negatively correlated with wintering temperature and positively correlated with the percentage of recruit spawners. This suggests indirect effects on larval survival, whereby low percentages of recruit spawners and high temperatures during gonad development lead to early spawning. Early hatching could be favourable for survival by allowing the larvae to drift away from areas where potential predators concentrate in spring, before predation pressure increases. Indirect support for this hypothesis was found in the activity of the purse-seine fishery for immature saithe (Pollachius virens) along the Norwegian coast. This fishery starts as soon as the saithe aggregate into large schools, which is presumed to reflect their feeding activity. The commercial catch data indicated that the saithe became active 2 months earlier in the area south of 67°N, than in areas to the north. Both field data and larval drift models confirmed that the majority of the early hatched larvae had passed across this border by that time of year.
Crystal Structure of the Complex between Pseudomonas Effector AvrPtoB and the Tomato Pto Kinase Reveals Both a Shared and a Unique Interface Compared with AvrPto-Pto
Authors: Dong Jing , Xiao Fangming , Fan Fenxia , Gu Lichuan , Cang Huaixing , Martin Gregory B. , Chai Jijie
Published: June 2009

Resistance to bacterial speck disease in tomato (Solanum lycopersicum) is activated upon recognition by the host Pto kinase of either one of two sequence-unrelated effector proteins, AvrPto or AvrPtoB, from Pseudomonas syringae pv tomato (Pst). Pto induces Pst immunity by acting in concert with the Prf protein. The recently reported structure of the AvrPto-Pto complex revealed that interaction of AvrPto with Pto appears to relieve an inhibitory effect of Pto, allowing Pto to activate Prf. Here, we present the crystal structure of the Pto binding domain of AvrPtoB (residues 121 to 205) at a resolution of 1.9Å and of the AvrPtoB121-205–Pto complex at a resolution of 3.3 Å. AvrPtoB121-205 exhibits a tertiary fold that is completely different from that of AvrPto, and its conformation remains largely unchanged upon binding to Pto. In common with AvrPto-Pto, the AvrPtoB-Pto complex relies on two interfaces. One of these interfaces is similar in both complexes, although the primary amino acid sequences from the two effector proteins are very different. Amino acid substitutions in Pto at the other interface disrupt the interaction of AvrPtoB-Pto but not that of AvrPto-Pto. Interestingly, substitutions in Pto affecting this unique interface also cause Pto to induce Prf-dependent host cell death independently of either effector protein.
Systematic review: non‐invasive methods of fibrosis analysis in chronic hepatitis C
Authors: SMITH J. O. , STERLING R. K.
Published: June 2009

Background  Accurate determination of the presence and degree of liver fibrosis is essential for prognosis and for planning treatment of patients with chronic hepatitis C virus (HCV). Non‐invasive methods of assessing fibrosis have been developed to reduce the need for biopsy.

Aim  To perform a review of these non‐invasive measures and their ability to replace biopsy for assessing hepatic fibrosis in patients with chronic HCV.

Methods  A systematic review of PUBMED and EMBASE was performed through 2008 using the following search terms: HCV, liver, elastography, hepatitis, Fibroscan, SPECT, noninvasive liver fibrosis, ultrasonography, Doppler, MRI, Fibrotest, Fibrosure, Actitest, APRI, Forns and breath tests, alone or in combination.

Results  We identified 151 studies: 87 using biochemical, 57 imaging and seven breath tests either alone or in combination.

Conclusions  Great strides are being made in the development of accurate non‐invasive methods for determination of fibrosis. Although no single non‐invasive test or model developed to date can match that information obtained from actual histology (i.e. inflammation, fibrosis, steatosis), combinations of two modalities of non‐invasive methods can reliably differentiate between minimal and significant fibrosis, and thereby avoid liver biopsy in a significant percentage of patients.
Reflux patterns in patients with short‐segment Barrett’s oesophagus: a study using impedance‐pH monitoring off and on proton pump inhibitor therapy
Authors: FRAZZONI M. , SAVARINO E. , MANNO M. , MELOTTI G. , MIRANTE V. G. , MUSSETTO A. , BERTANI H. , MANTA R. , CONIGLIARO R.
Published: June 2009

Background  In short‐segment Barrett’s oesophagus (SSBO) heartburn may be absent and oesophageal acid exposure time (OAET) assessed with pH‐only monitoring may be normal. By detecting reflux episodes independently of their acidity, multichannel intraluminal impedance‐pH (MII‐pH) monitoring allows a comprehensive characterization of reflux events, either off or on proton pump inhibitor (PPI) therapy.

Aim  To assess reflux parameters by MII‐pH monitoring in newly diagnosed SSBO, at baseline and as modified with PPI therapy.

Methods  Short‐segment Barrett’s oesophagus was defined by oesophageal intestinal metaplasia up to 3 cm in length. 24‐h MII‐pH monitoring was performed before and during PPI therapy.

Results  Fifty patients were studied prospectively. Normal OAET was found at baseline in 15 patients (30%), 8 and 2 of whom with a higher than normal number of acid and weakly acidic refluxes, respectively. Overall, abnormal reflux parameters were detected by MII‐pH monitoring in 90% of patients. Reflux events were prevalent in the upright period. On PPI therapy, acid refluxes decreased and a correspondent increase in weakly acidic refluxes was observed (median from 48.5 to 9 and from 16 to 57.5, respectively) (P < 0.001).

Conclusions  Acid refluxes, mainly in the upright period, characterize SSBO. PPI therapy transforms acid refluxes into weakly acidic refluxes.
Dyadic Developmental Psychotherapy is not ‘evidence‐based’: comments in response to Becker‐Weidman and Hughes
Authors: Mercer Jean , Pennington Randal S. , Pignotti Monica , Rosa Linda
Published: June 2009

A recent paper claimed that Dyadic Developmental Psychotherapy (DDP), a mental‐health intervention for children, was an evidence‐based treatment (EBT). We discuss the meaning of the EBT term and the accuracy of this claim, and conclude that DDP does not meet the criteria that would allow it to be called evidence‐based. We note other problems with this research report and suggest ways in which the authors could provide better support for their claim and make it easier for others to attempt independent replications.
Effect of an OT antagonist on the control of the midcycle LH surge in women
Authors: Vanakara P. , Dafopoulos K. , Papastergiopoulou L. , Kallitsaris A. , Papageorgiou I. , Messinis I. E.
Published: June 2009

Objective  Data in women regarding the role of OT in LH secretion during the LH surge are conflicting. As in previous studies blood samples for LH measurements were taken infrequently, we re‐examined this matter in women with a fully characterized midcycle LH surge.

Design  Normal women were studied over two cycles. When the dominant follicle reached a diameter of either 16–17 mm (Group 1) or 18–19 mm (Group 2), the women were infused intravenously for 3 h with normal saline (cycle‐1) or atosiban (cycle‐2).

Patients  Fifteen women (10 in group 1 and 5 in group 2) aged 23–35 years.

Measurements  Blood samples were obtained every 6 h to characterize the midcycle LH surge.

Results  The time interval (mean ± SEM) from the start of the infusion to the onset of the LH surge in the two cycles was 46·8 ± 4·8 and 45·6 ± 9·6 h in group 1 and 6·0 ± 2·4 and 7·5 ± 2·8 h, respectively, in group 2. LH values during the LH surge were similar in the two cycles except in group 1 at the point of 30 h at which LH value in cycle‐2 (41·2 ± 4·6 mIU/ml) was significantly lower than in cycle‐1 (52·8 ± 3·4 mIU/ml, P < 0·05). Nevertheless, in each group, the area under the curve for LH was similar in the two cycles.

Conclusions  Antagonism of endogenous OT action by atosiban does not alter the LH profile during a fully characterized midcycle LH surge, suggesting that OT is not a major regulator of LH secretion in women.
Monitoring disease activity using GH and IGF‐I in the follow‐up of 501 patients with acromegaly
Authors: Sherlock M. , Aragon Alonso A. , Reulen R. C. , Ayuk J. , Clayton R. N. , Holder G. , Sheppard M. C. , Bates A. , Stewart P. M.
Published: June 2009

Context  The aims of treatment in patients with acromegaly are to achieve serum GH/IGF‐I concentrations associated with cure or normalization of mortality and alleviation of symptoms.

Objective and methods  Using the West Midlands Acromegaly database (n = 501) we investigated the reliability of basal fasting GH in predicting nadir or mean GH during oral glucose tolerance test (OGTT) or GH day curve (GHDC), respectively, the degree of discordance between disease activity measured by GH and IGF‐I values and the effect of radiotherapy on the above relationships. In total 773 OGTT and 507 GHDC were performed.

Results  Basal fasting GH was strongly correlated with nadir/mean GH on OGTT/GHDC (r = +0·87, P < 0·0001, r = +0·93, P < 0·0001, respectively). A basal GH < 2·5 µg/l was associated with a nadir/mean GH during OGTT/GHDC < 2·5 µg/l in 98·6% and 88·2% of cases, respectively.

Elevated IGF‐I was seen in 32·4% and 46·4% of patients with GH nadir values during OGTT < 1 and < 2·5 µg/l, respectively, and in 21·2% and 45·9% of GHDC with mean GH < 1 and < 2·5 µg/l, respectively. Radiotherapy increased the discordance in GH and IGF‐I as markers of disease activity at GH < 2·5 µg/l (elevated IGF‐I‐values when OGTT nadir GH < 2·5 µg/l: radiotherapy 55·5%vs. no radiotherapy 36·9%, P = 0·002).

Conclusions  There is a close relationship between a basal fasting GH < 2·5 µg/l and nadir/mean GH < 2·5 µg/l during OGTT/GHDC. There is a large discordance between disease activity when assessed by GH and IGF‐I which is further increased by radiotherapy. These observations illustrate the challenge of defining appropriate biochemical end‐points to achieve control of disease and normalization of mortality in acromegaly.
Interpreting the smells of predation: how alarm cues and kairomones induce different prey defences
Authors: Schoeppner Nancy M. , Relyea Rick A.
Published: June 2009

1. For phenotypically plastic organisms to produce phenotypes that are well matched to their environment, they must acquire information about their environment. For inducible defences, cues from damaged prey and cues from predators both have the potential to provide important information, yet we know little about the relative importance of these separate sources of information for behavioural and morphological defences. We also do not know the point during a predation event at which kairomones are produced, i.e. whether they are produced constitutively, during prey attack or during prey digestion.

2. We exposed leopard frog tadpoles (Rana pipiens) to nine predator cue treatments involving several combinations of cues from damaged conspecifics or heterospecifics, starved predators, predators only chewing prey, predators only digesting prey or predators chewing and digesting prey.

3. We quantified two behavioural defences. Tadpole hiding behaviour was induced only by cues from crushed tadpoles. Reduced tadpole activity was induced only by cues from predators digesting tadpoles or predators chewing + digesting tadpoles.

4. We also quantified tadpole mass and two size‐adjusted morphological traits that are known to be phenotypically plastic. Mass was unaffected by the cue treatments. Relative body length was affected (i.e. there were differences among some treatments), but none of the treatments significantly differed from the no‐predator control. Relative tail depth was affected by the treatments and deeper tails were induced only when tadpoles were exposed to cues from predators digesting tadpoles or cues from predators chewing + digesting tadpoles.

5. These results demonstrate that some prey species can discriminate among a diverse set of potential cues from heterospecific prey, conspecific prey and predators. Moreover, the results illustrate that the cues responsible for the full suite of behavioural and morphological defences are not induced by tadpole crushing nor can they be induced by generalized digestive chemicals produced when predators digest their prey. Instead, both prey damage and predator digestion of conspecific tissues appear to be important for communicating predatory risk to phenotypically plastic anuran prey. Importantly, the production of chemical cues by predators may be unavoidable and prey have evolved the ability to eavesdrop on these signals.
A discussion of structural and thermal control of magnetic anomalies on the mid‐Norwegian margin
Authors: Ebbing Jörg , Gernigon Laurent , Pascal Christophe , Olesen Odleiv , Osmundsen Per Terje
Published: June 2009

We discuss the correlation between the depth extent of magnetic sources, the Curie temperature depth and crustal structures on the mid‐Norwegian margin. Spectral methods can be used to estimate the depth extent of magnetic sources, even if the bottom is located in the lower crust, however, only with limited resolution. The bottom of the magnetic surfaces is often regarded to represent the depth to the Curie isotherm. However, comparison with a 3D model based on the interpretation of potential field and seismic reflection data and thermal modelling shows that the depth extent of the magnetic sources is merely controlled by the overall geometry of the crystalline crust and not the temperature distribution. The observed changes in the magnetic field between the inner and outer part of the mid‐Norwegian margin appears not to reflect, as previously assumed, the depth to the Curie temperature but the geometry of the basement and lower crust. Our 3D model of the mid‐Norwegian margin reveals a basement configuration that involves a basement with different petrophysical properties, which can be connected with lithological basement units of onshore Norway.
Tumour‐derived prostaglandin E2and transforming growth factor‐β synergize to inhibit plasmacytoid dendritic cell‐derived interferon‐α
Authors: Bekeredjian‐Ding Isabelle , Schäfer Meike , Hartmann Evelyn , Pries Ralph , Parcina Marijo , Schneider Philip , Giese Thomas , Endres Stefan , Wollenberg Barbara , Hartmann Gunther
Published: June 2009

In previous studies we reported that plasmacytoid dendritic cells (PDC) infiltrating head and neck cancer tissue are functionally impaired, but the molecular basis for the functional deficiency remained unclear. Here we demonstrate that tumour‐derived prostaglandin E2 (PGE2) and transforming growth factor‐β (TGF‐β) increase interleukin‐8 (IL‐8) but synergistically inhibit interferon‐α (IFN‐α) and tumour necrosis factor (TNF) production of Toll‐like receptor 7 (TLR7)‐ and Toll‐like receptor 9 (TLR9)‐stimulated PDC. The inhibitory effect of PGE2could be mimicked by the induction of cyclic AMP (cAMP) and by inhibitors of cyclooxygenase. The contribution of tumour‐derived TGF‐β was confirmed by the TGF‐β antagonist SB‐431542. Suppression of tumour‐derived PGE2and TGF‐β restored TLR‐induced IFN‐α production of PDC. Additionally, PGE2‐ and TGF‐β‐treated PDC display a ‘tolerogenic’ phenotype because of a downregulation of CD40 accompanied by an upregulation of CD86. Finally, in TLR‐stimulated PDC, PGE2and TGF‐β reduce the CCR7 : CXCR4 ratio, suggesting that PDC are impaired in their ability to migrate to tumour‐draining lymph nodes but are retained in stromal cell‐derived factor 1 (SDF‐1)‐expressing tissues. Based on these data, cyclooxygenase inhibitors and TGF‐β antagonists may improve TLR7‐ and TLR9‐based tumour immunotherapy.
Potentially inappropriate urinary catheter indwelling among long‐term care facilities residents
Authors: Chen Yi‐Tsun , Lin Ming‐Hsien , Lai Hsiu‐Yun , Hwang Shinn‐Jang , Chen Liang‐Kung
Published: June 2009

Purpose  To evaluate the prevalence of long‐term urinary catheter (UC) indwelling and potentially inappropriate urinary catheterization among residents of long‐term care facilities (LTCFs) in Taiwan.

Method  From January to March of 2007, residents with long‐term urethral UC indwelling of LTCFs in northern Taipei were invited for study and were enrolled when the informed consent was obtained. For every subject, UC was removed by home care nurses, and self‐voiding (SV) status was determined after a 4‐hour observation period. Residual volume (RV) was measured when the UC was re‐indwelled. Potentially inappropriate UC indwelling was defined by the concomitant presence of SV and the RV less than 150 mL.

Results  In total, 252 residents from eight LTCFs were screened and 45 out of 62 residents with long‐term UC indwelling were enrolled (mean age = 80.4 ± 8.9 years, 40% were males, 95.6% were severely disabled). SV was noted in 86.7% (39/45) of study subjects, and 71.8% (28/39) self‐voided subjects had their RV less than 150 mL. By definition, the prevalence of potentially inappropriate UC indwelling in this study was 62.2%. The mean RV was significantly lower in subjects with SV (101.3 ± 66.1 vs. 221.7 ± 154.1 mL, P = 0.002) and subjects with SV were more prone to have the RV less than 150 mL (P = 0.018).

Conclusion  The prevalence of long‐term UC indwelling among Taiwanese LTCF residents was high and a high proportion of their UC may be removable. A national audit and introducing a practice guideline for continence care in LTCFs may help to promote quality of care for institutionalized older people in Taiwan.
Brief assessment of adult cancer patients' perceived needs: development and validation of the 34‐item Supportive Care Needs Survey (SCNS‐SF34)
Authors: Boyes Allison , Girgis Afaf , Lecathelinais Christophe
Published: June 2009

Objective  This study aimed to develop and validate a short version of the Supportive Care Needs Survey (SCNS) that would reduce respondent burden and could be used in routine cancer care, without compromising the psychometric properties of the original instrument.

Methods  Secondary analyses of the data from two studies (n = 888 and 250) were undertaken. All 59 items of the original SCNS were assessed using psychometric analyses and evaluated for clinical utility. The 34 items retained were examined for internal consistency, ceiling and floor effects, known groups validity, convergent validity, sensitivity and readability.

Results  The 34‐item instrument has five factors (psychological, health system and information, physical and daily living, patient care and support, and sexuality needs) identical to the original instrument, explaining 73% of the variance. Internal consistency was high with Cronbach's alpha coefficients for the five factors ranging from 0.86 to 0.96. Correlations of the 34‐item short‐form SCNS (SCNS‐SF34) with three other measures of psychosocial well‐being demonstrated convergent validity (r = 0.48–0.56). Kappa coefficients of at least 0.83 for each domain indicated almost perfect agreement between the 34‐item and 59‐item surveys to identify patients needing help. The 34‐item SCNS maintained the psychometric properties of the original instrument and could be readily comprehended by people with seventh to eighth grade education.

Conclusions  The SCNS‐SF34 is a valid instrument for measuring cancer patients' perceived needs across a range of domains, and could be utilized as part of routine cancer care.