bluuebunny/crossref_metadata_2025 huggingface dataset:
PHYLOGENETIC POSITION OF BOLBOCOLEON PILIFERUM (ULVOPHYCEAE, CHLOROPHYTA): EVIDENCE FROM REPRODUCTION, ZOOSPORE AND GAMETE ULTRASTRUCTURE, AND SMALL SUBUNIT RRNA GENE SEQUENCES1
Authors: O'kelly Charles J. , Bellows Wendy K. , Wysor Brian
Published: October 2010

Aspects of the reproduction of Bolbocoleon piliferum N. Pringsheim, a common, small, filamentous, endophytic marine green alga, were examined by LM and TEM. These observations were combined with phylogenetic analysis of nuclear‐encoded small subunit rRNA gene sequences to assess the phylogenetic position of B. piliferum. Quadriflagellate zoospores and planozygotes derived from fusion of isogametes yielded plants with identical morphology. Zoosporangia and gametangia divided by sequential cleavages. Plugs at the apices of zoosporangia and gametangia formed during development; tubes were found at zoosporangial and gametangial apices after swarmer release. Flagellar apparatuses of zoospores and gametes were similar to those of algae in the Ulvales (Ulvophyceae), except that terminal caps were entire rather than bilobed and rhizoplasts and “stacked” microtubular root configurations were absent. Structures associated with planozygotes were identical to those observed in other algae currently assigned to Ulotrichales and Ulvales. Molecular phylogenetic analyses placed B. piliferum within the Ulvophyceae, at the base of a clade that contains representatives of the families Ulvaceae, Ulvellaceae, and Kornmanniaceae. The results support an earlier hypothesis that B. piliferum constitutes a distinct lineage. Analyses including Kornmanniaceae recover monophyletic Ulotrichales and Ulvales, whereas analyses omitting the Kornmanniaceae indicate that Ulotrichales is paraphyletic. The structures associated with gamete fusion are conserved within Ulotrichales and Ulvales and perhaps more widely within Chlorophyta.
Fatty Acid and Sterol Composition of a Karenia Brevis Bloom in the Gulf of Mexico
Authors: Leblond J. D. , Chapman P. J.
Published: October 2010

In the Gulf of Mexico, recurring algal blooms caused by Karenia brevis (formerly known as Gymnodinium breve) have significant adverse health and economic impacts. K. brevis is one member of a small group of dinoflagellates, related morphologically and by DNA‐based phylogenetic analysis, that synthesize the carotenoid, gyroxanthin diester, in place of the more widely distributed peridinin. While this novel photopigment has been proposed as a biomarker, especially for remote‐sensing imaging technologies, to detect the emergence of K. brevis blooms, other chemicals such as sterols and triglycerides, respectively, with potential to report the distribution and physiological condition of K. brevis are required. Recent work from our laboratories characterizing the lipids of dinoflagellates has confirmed that K. brevis, together with those few close relatives lacking peridinin, possesses a relatively simple sterol profile comprised of two unusual primary 4‐methyl sterols, designated ED and NED, each with an ergosterol‐type side chain. A recent dinoflagellate bloom in the waters of the north‐west Gulf of Mexico near the Gulf Breeze EPA laboratory provided an opportunity to examine the usefulness of these sterols and other lipids as indicators of K. brevis in phytoplankton communities. Lipid extracts of filtered bloom samples, fractionated to separate free and esterified sterols, were examined by GC–MS of trimethylsilyl ether derivatives. ED and NED were the major sterols found in all bloom samples. Fatty acids found in lipid fractions containing membrane phospholipids, chloroplast‐associated glycolipids, and storage triglycerides, respectively, differed significantly. The glycolipid fraction was found to contain octadecapentaenoic acid [18 : 5(n‐3)], a fatty acid commonly associated with dinoflagellates. The phospholipid fraction was found to contain small amounts of the recently described highly unsaturated fatty acids, octacosaoctaenoic acid [28 : 8(n‐3)] and octacosaheptaenoic acid [28 : 7(n‐6)]. Fatty acids from the triglyceride fraction were more abundant than those associated with glycolipids or phospholipids.
A scalable multipass laser cavity based on injection by frequency conversion for noncollective Thomson scattering
Authors: Schaeffer D. B. , Kugland N. L. , Constantin C. G. , Everson E. T. , Van Compernolle B. , Ebbers C. A. , Glenzer S. H. , Niemann C.
Published: October 2010

A scalable setup using injection by frequency conversion to establish a multipassing cavity for noncollective Thomson scattering on low density plasmas is presented. The cavity is shown to support >10 passes through the target volume with a 400% increase in energy on target versus a single-pass setup. Rayleigh scattering experiments were performed and demonstrate the viability of the cell to study low density plasmas of the order of 1012–1013 cm−3. A high-repetition, low-energy, single-pass Thomson scattering setup was also performed on the University of California, Los Angeles Large Plasma Device and shows that the multipass cavity could have a significant advantage over the high-repetition approach due to the cavity setup’s inherently higher signal per shot.
Spatially distributed scintillator arrays for diagnosing runaway electron transport and energy behavior in tokamaks
Authors: James A. N. , Hollmann E. M. , Tynan G. R.
Published: October 2010

We present details of a new bismuth germanate [Bi4Ge3O12 (BGO)] scintillator array used to diagnose the transport and energy behavior of runaway electrons (REs) in DIII-D. BGO exhibits important properties for these compact detectors including high light yield which sufficiently excites photodiode detectors (8500 photons/MeV), high density and atomic numbers of constituent materials which maximizes sensitivity, and relative neutron blindness which minimizes complications in data interpretation. The detectors observe primarily hard x-ray radiation emitted in a forward beamed pattern by RE when they strike first wall materials or bulk ions and neutrals in the plasma, although we also address photoneutron signals. The arrangement of the array enables time resolved location of x-ray emission and associated asymmetries which help identify instabilities and confinement properties of RE. By shielding a subset of detectors with different thicknesses of lead, and with interpretative support of the code EGSNRC, we also measure RE energy, although due to the often distributed nature of RE strike points and the forward beamed character of emitted hard x-rays, we restrict interpretation as a lower bound for RE energy.
Dynamics of vapor emissions at wire explosion threshold
Authors: Belony Paul A. , Kim Yong W.
Published: October 2010

X-pinch plasmas have been actively studied in the recent years. Numerical simulation of the ramp-up of metallic vapor emissions from wire specimens shows that under impulsive Ohmic heating the wire core invariably reaches a supercritical state before explosion. The heating rate depends sensitively on the local wire resistance, leading to highly variable vapor emission flux along the wire. To examine the vapor emission process, we have visualized nickel wire explosions by means of shock formation in air. In a single explosion as captured by shadowgraphy, there usually appear several shocks with spherical or cylindrical wave front originating from different parts of the wire. Growth of various shock fronts in time is well characterized by a power-law scaling in one form or another. Continuum emission spectra are obtained and calibrated to measure temperature near the explosion threshold. Shock front structures and vapor plume temperature are examined.
Calculation of spatial response of 2D beam emission spectroscopy diagnostic on MAST
Authors: Ghim(Kim) Young-chul , Field A. R. , Zoletnik S. , Dunai D.
Published: October 2010

The beam emission spectroscopy (BES) turbulence diagnostic on MAST is to be upgraded in June 2010 from a one-dimensional trial system to a two-dimensional imaging system (8 radial×4 poloidal channels) based on a newly developed avalanche photodiode array camera. The spatial resolution of the new system is calculated in terms of the point spread function to account for the effects of field-line curvature, observation geometry, the finite lifetime of the excited state of the beam atoms, and beam attenuation and divergence. It is found that the radial spatial resolution is ∼2–3 cm and the poloidal spatial resolution ∼1–5 cm depending on the radial viewing location. The absolute number of detected photons is also calculated, hence the photon noise level can be determined.
Heavy ion beam probe operation in time varying equilibria of improved confinement reversed field pinch discharges
Authors: Demers D. R. , Chen X. , Schoch P. M. , Fimognari P. J.
Published: October 2010

Operation of a heavy ion beam probe (HIBP) on a reversed field pinch is unique from other toroidal applications because the magnetic field is more temporal and largely produced by plasma current. Improved confinement, produced through the transient application of a poloidal electric field which leads to a reduction of dynamo activity, exhibits gradual changes in equilibrium plasma quantities. A consequence of this is sweeping of the HIBP trajectories by the dynamic magnetic field, resulting in motion of the sample volume. In addition, the plasma potential evolves with the magnetic equilibrium. Measurement of the potential as a function of time is thus a combination of temporal changes of the equilibrium and motion of the sample volume. A frequent additional complication is a nonideal balance of ion current on the detectors resulting from changes in the beam trajectory (magnetic field) and energy (plasma potential). This necessitates use of data selection criteria. Nevertheless, the HIBP on the Madison Symmetric Torus has acquired measurements as a function of time throughout improved confinement. A technique developed to infer the potential in the improved confinement reversed field pinch from HIBP data in light of the time varying plasma equilibrium will be discussed.
Finite size effects on aluminum/Teflon reaction channels under combustive environment: A Rice–Ramsperger–Kassel–Marcus and transition state theory study of fluorination
Authors: Losada Martin , Chaudhuri Santanu
Published: October 2010

The effect of particle size on combustion efficiency is an important factor in combustion research. Gas-phase aluminum clusters in oxidizing environment constitute a relatively simple and extensively studied system. In an attempt to underscore the correlation between electronic structure, finite size effect, and reactivity in small aluminum clusters, reactions between aluminum, [Al13]− cluster, and Teflon decomposition fragments were studied using theoretical calculations at the density functional theoretical level. The unimolecular rate constants calculated using transition state and Rice–Ramsperger–Kassel–Marcus theory show that reactions with COF and CF2 species with aluminum are faster than those involving CF3 and COF2. The results show that the kinetic barriers along different exothermic reaction channels correlate with the trends in HOMO(R)−HOMO(TS) (HOMO denotes highest occupied molecular orbital) energy gap and related shifts of the HOMO levels of reactants. Overall reactions involving carbonyl fluoride species (COF and COF2) lead to CO elimination and fluorination of the Al cluster. The CF3/CF2 fragments lead to stable multicenter Al–C bond formation on the fluorinated Al cluster surface. Temperature-, energy-, and pressure-dependent rate constants are provided for extrapolating the expected reaction kinetics to conditions similar to known combustion reactions.
Two-dimensional infrared study of 3-azidopyridine as a potential spectroscopic reporter of protonation state
Authors: Nydegger Michael W. , Dutta Samrat , Cheatum Christopher M.
Published: October 2010

The lack of general spectroscopic probes that can be used in a range of systems to probe kinetics and dynamics is a major obstacle to the widespread application of two-dimensional infrared (2D IR) spectroscopy. We have studied 3-azidopyridine to characterize its potential as a probe of the protonation state of the pyridine ring. We find that the azido-stretching vibration is split by accidental Fermi resonance interactions with one or more overtones and combination states. Using 2D IR spectroscopy, we determine the state structure of the resulting eigenstates for complexes of 3-azidopyridine with formic acid and trifluoroacetic acid in which the pyridine ring is unprotonated and protonated, respectively. Based on the measurements, we develop a two-oscillator depurturbation model to determine the energies and couplings of the zeroth-order azido-stretching state and the perturbing dark state that couples to it. Based on these results, we conclude that the azido-stretching vibration is, in fact, sensitive to the protonation state of the pyridine shifting up in frequency by 8 cm−1 in the complex with trifluoroacetic acid relative to the formic acid complex. These results suggest that, although 3-azidopyridine is not suitable as a spectroscopic probe, the approach of employing an organic azide as a remote probe of protonation state holds significant promise.
Do surfaces with mixed hydrophilic and hydrophobic areas enhance pool boiling?
Authors: Betz Amy Rachel , Xu Jie , Qiu Huihe , Attinger Daniel
Published: October 2010

We demonstrate that smooth and flat surfaces combining hydrophilic and hydrophobic patterns improve pool boiling performance. Compared to a hydrophilic surface with 7° wetting angle, the measured critical heat flux and heat transfer coefficients of the enhanced surfaces are, up to respectively, 65% and 100% higher. Different networks combining hydrophilic and hydrophobic regions are characterized. While all tested networks enhance the heat transfer coefficient, large enhancements of critical heat flux are typically found for hydrophilic networks featuring hydrophobic islands. Hydrophilic networks indeed are shown to prevent the formation of an insulating vapor layer.
Perpendicular magnetic tunnel junctions with synthetic ferrimagnetic pinned layer
Authors: Choi Gyung-Min , Shin Il-Jae , Min Byoung-Chul , Shin Kyung-Ho
Published: October 2010

We have fabricated perpendicular magnetic tunnel junctions (p-MTJs) consisting of CoPt/Ru/CoFeB/MgO/CoFeB/Pt. The tunnel magnetoresistance (TMR) of the p-MTJs characterizes the magnetic configurations of the CoPt/Ru/CoFeB pinned layer. The magnetic moment of the CoFeB, which is naturally in-plane, can be aligned to the out-of-plane direction by an indirect exchange coupling with the hcp CoPt alloy having large perpendicular magnetic anisotropy. When the applied field is relatively smaller than the exchange coupling strength, the p-MTJs show a configurationally negative TMR as a consequence of an antiparallel alignment of the CoPt and CoFeB magnetic moments.
Monte Carlo based microscopic description of electron transport in GaAs/Al0.45Ga0.55As quantum-cascade laser structure
Authors: Borowik Piotr , Thobel Jean-Luc , Adamowicz Leszek
Published: October 2010

Results of multiparticle Monte Carlo simulations of midinfrared quantum cascade lasers structure initially fabricated by Page et al. are presented. The main aim of this paper is to discuss in details how electric current flows through the structure and which subbands are involved in this process. Monte Carlo method allows to predict the electron population inversion between the lasing levels and gives microscopic insight into processes leading to such behavior. Importance of a subband belonging to the laser injector region, with energy slightly below the upper lasing level, is demonstrated. The electron–electron Coulomb interactions influence the shapes of electron distribution functions; the values of average electron energies and effective subbands’ temperatures are calculated.
Including quantum decoherence in surface hopping
Authors: Granucci Giovanni , Persico Maurizio , Zoccante Alberto
Published: October 2010

In this paper we set up a method called overlap decoherence correction (ODC) to take into account the quantum decoherence effect in a surface hopping framework. While keeping the standard surface hopping approach based on independent trajectories, our method allows to account for quantum decoherence by evaluating the overlap between frozen Gaussian wavepackets, the time evolution of which is obtained in an approximate way. The ODC scheme mainly depends on the parameter σ, which is the Gaussian width of the wavepackets. The performance of the ODC method is tested versus full quantum calculations on three model systems, and by comparison with full multiple spawning (FMS) results for the S1→S0 decay in the azobenzene molecule.
Formation trends of ordered self-assembled nanoislands on stepped substrates
Authors: Liang S. , Zhu H. L. , Kong D. H. , Wang W.
Published: October 2010

The growth of ordered self-assembled nanoislands on stepped substrates is studied systematically by kinetic Monte Carlo simulations. As the terrace width is small, the formation of nanoislands is confined in the steps and nanoislands ordered in lines or nanowires can be obtained. The Schwoebel barrier at the step edges has a great influence on the evolution of both the size and space distributions of the islands. When the terrace width is relatively large, self-ordering of nanoislands in the center regions of the terraces happens. An unexpected trend of the nanoisland self-ordering is found as the deposition thickness is larger than 0.2 ML, which can be related to the attractive migrations between nearby islands.
Near band edge anisotropic optical transitions in wide band gap semiconductor Cu2ZnSiS4
Authors: Levcenco S. , Dumcenco D. , Huang Y. S. , Arushanov E. , Tezlevan V. , Tiong K. K. , Du C. H.
Published: October 2010

In this study, anisotropic near band edge transitions of Cu2ZnSiS4 single crystals grown by chemical vapor transport were characterized by using polarization-dependent absorption, piezoreflectance (PzR) and surface photovoltage (SPV) spectroscopy techniques at room temperature. The measurements were carried out on the as grown basal plane with the normal along [2 1 0] and the axis c parallel to the long edge of the crystal platelet. Analysis of absorption and SPV spectra reveal indirect allowed transitions for the absorption edge of Cu2ZnSiS4. The estimated values of indirect band gap are 2.97 eV and 3.07 eV, respectively, for E⊥c and E∥c polarization configurations. The polarization-dependent PzR and SPV spectra in the vicinity of the direct band gap of Cu2ZnSiS4 reveal features E⊥ex and E∥ex at around 3.32 eV and 3.41 eV for E⊥c and E∥c polarizations, respectively. Both features E⊥ex and E∥ex are associated with the interband excitonic transitions at point Γ and can be explained by crystal-field splitting of valence band. Based on the experimental observations, a plausible band structure near band edge of Cu2ZnSiS4 is proposed.
Atomic force microscopy of orb-spider-web-silks to measure surface nanostructuring and evaluate silk fibers per strand
Authors: Kane D. M. , Naidoo N. , Staib G. R.
Published: October 2010

Atomic force microscopy (AFM) study is used to measure the surface topology and roughness of radial and capture spider silks on the micro- and nanoscale. This is done for silks of the orb weaver spider Argiope keyserlingi. Capture silk has a surface roughness that is five times less than that for radial silk. The capture silk has an equivalent flatness of λ/100 (5–6 nm deep surface features) as an optical surface. This is equivalent to a very highly polished optical surface. AFM does show the number of silk fibers that make up a silk thread but geometric distortion occurs during sample preparation. This prevented AFM from accurately measuring the silk topology on the microscale in this study.
In-plane stray field induced spin-filtering in a two-dimensional electron gas under the modulation of surface ferromagnetic dual-gate
Authors: Wang Y. , Jiang Y. , Zhang X. W. , Yin Z. G.
Published: October 2010

Based upon a hybrid ferromagnet/semiconductor structure consisting of two-dimensional electron gas and a pair of surface ferromagnetic stripes on top, we have theoretically investigated the effect of in-plane stray field omitted frequently in previous studies on the spin-dependent ballistic transport properties in hybrid structure. It is demonstrated here that, in combination with an external-controllable electrostatic modulation, the concerned structure shows a similar function as a lateral spin-polarized resonant tunneling device, where the strong spin-filtering effect occurs and nearly single-mode polarization is anticipated for the proper modulation. More importantly, the spin polarity of transmission electron can be easily transferred from one extreme to the other by switching the magnetization of stripes, showing the promising application as an efficient spin aligner in the developing semiconductor spintronics.
Thermophysical properties of liquid carbon dioxide under shock compressions: Quantum molecular dynamic simulations
Authors: Wang Cong , Zhang Ping
Published: October 2010

Quantum molecular dynamics were used to calculate the equation of state, electrical, and optical properties of liquid carbon dioxide along the Hugoniot at shock pressures up to 74 GPa. The principal Hugoniot derived from the calculated equation of state is in good agreement with experimental results. Molecular dissociation and recombination are investigated through pair correlation functions and decomposition of carbon dioxide is found to be between 40 and 50 GPa along the Hugoniot, where nonmetal-metal transition is observed. In addition, the optical properties of shock compressed carbon dioxide are also theoretically predicted along the Hugoniot.
Characterization of memory and measurement history in photoconductivity of nanocrystal arrays
Authors: Fairfield Jessamyn A. , Dadosh Tali , Drndic Marija
Published: October 2010

Photoconductivity in nanocrystal films has been previously characterized, but memory effects have received little attention despite their importance for device applications. We show that the magnitude and temperature dependence of the photocurrent in CdSe/ZnS core-shell nanocrystal arrays depends on the illumination and electric field history. Changes in photoconductivity occur on a few-hour timescale, and subband gap illumination of nanocrystals prior to measurements modifies the photocurrent more than band gap illumination. The observed effects can be explained by charge traps within the band gap that are filled or emptied, which may alter nonradiative recombination processes and affect photocurrent.
The disordering effect of Ti observed in the microstructure and electrical properties of W0.95Ti0.05O3 thin films
Authors: Kalidindi N. R. , Bharathi K. Kamala , Ramana C. V.
Published: October 2010

We report on the inhibition of WO3 crystallization by the addition of Ti observed in sputter-deposited W0.95Ti0.05O3 films. The effect of growth-temperature on the crystallization indicates that the W0.95Ti0.05O3 films grown at temperatures <300 °C are amorphous compared to WO3 crystalline films at 100–200 °C. Phase transformation is induced in W0.95Ti0.05O3 resulting in tetragonal structure at ≥300 °C. The corresponding electrical properties exhibit a clear distinction as a function of these structural transformations. Temperature-dependent dc electrical conductivity (80–300 K) shows the semiconducting nature of W0.95Ti0.05O3 films and exhibits two distinct regions indicative of two different types of transport mechanisms.
Oxygen vacancies and donor impurities in β-Ga2O3
Authors: Varley J. B. , Weber J. R. , Janotti A. , Van de Walle C. G.
Published: October 2010

Using hybrid functionals we have investigated the role of oxygen vacancies and various impurities in the electrical and optical properties of the transparent conducting oxide β-Ga2O3. We find that oxygen vacancies are deep donors, and thus cannot explain the unintentional n-type conductivity. Instead, we attribute the conductivity to common background impurities such as silicon and hydrogen. Monatomic hydrogen has low formation energies and acts as a shallow donor in both interstitial and substitutional configurations. We also explore other dopants, where substitutional forms of Si, Ge, Sn, F, and Cl are shown to behave as shallow donors.
Communication: The application of the global isomorphism to the study of liquid-vapor equilibrium in two and three-dimensional Lennard-Jones fluids
Authors: Kulinskii V. L.
Published: October 2010

We analyze the interrelation between the coexistence curve of the Lennard-Jones fluid and the Ising model in two and three dimensions within the global isomorphism approach proposed earlier [V. L. Kulinskii, J. Phys. Chem. B 114, 2852 (2010)]. In case of two dimensions, we use the exact Onsager result to construct the binodal of the corresponding Lennard-Jones fluid and compare it with the results of the simulations. In the three-dimensional case, we use available numerical results for the Ising model for the corresponding mapping. The possibility to observe the singularity of the binodal diameter is discussed.
Epstein-Barr latent membrane protein 1 transformation site 2 activates NF-κB in the absence of NF-κB essential modifier residues 133–224 or 373–419
Authors: Boehm Daniela , Gewurz Benjamin E. , Kieff Elliott , Cahir-McFarland Ellen
Published: October 2010

Epstein Barr virus latent membrane protein 1 (LMP1) induces NF-κB activation through transformation effector sites (TES) 1 and 2, both of which are critical for B-lymphocyte transformation. TES2 principally activates canonical NF-κB, which we confirm is NF-κB essential modifier (NEMO)-dependent and requires an intact ubiquitin binding in A20 binding inhibitor of NF-κB and NEMO (UBAN) domain. LMP1 TES2 activated NF-κB in Jurkat cell lines harboring NEMO truncated at 372 (A45) or NEMO with an in-frame deletion of 133–224 (2C), whereas TNFα, 12-O-Tetradecanoylphorbol-13-acetate, human T-cell leukemia virus 1 Tax, and CD40 did not. In both A45 and 2C Jurkat cell lines, LMP1 TES2-mediated NF-κB activation was blocked by siRNAs to TNFα receptor-associated factor 6 and NEMO, by IκB kinase inhibitors, and by the IκBα superrepressor, indicating that the NEMO mutants function to support canonical NF-κB activation. Expression of A45 or 2C mutants in NEMO-deficient murine embryonic fibroblasts reproduced the Jurkat phenotypes: LMP1 TES2 activated NF-κB in fibroblasts lacking NEMO amino acids 133–224 or 373–419, but TNFα and Tax did not. Further analysis indicated that TES2 did not activate NF-κB in cells expressing the double deletion mutant Δ133–224/Δ372–419. These data provide further evidence of the essential role for NEMO in LMP1 TES2 NF-κB activation and highlight the importance of unique domains within NEMO for sensing distinct NF-κB stimuli.
Vibration and instability of a viscous-fluid-conveying single-walled carbon nanotube embedded in a visco-elastic medium
Authors: Soltani P , Taherian M M , Farshidianfar A
Published: October 2010

In this study, for the first time, the transverse vibrational model of a viscous-fluid-conveying single-walled carbon nanotube (SWCNT) embedded in biological soft tissue is developed. Nonlocal Euler–Bernoulli beam theory has been used to investigate fluid-induced vibration of the SWCNT while visco-elastic behaviour of the surrounding tissue is simulated by the Kelvin–Voigt model. The results indicate that the resonant frequencies and the critical flow velocity at which structural instability of nanotubes emerges are significantly dependent on the properties of the medium around the nanotube, the boundary conditions, the viscosity of the fluid and the nonlocal parameter. Detailed results are demonstrated for the dependence of damping and elastic properties of the medium on the resonant frequencies and the critical flow velocity. Three standard boundary conditions, namely clamped–clamped, clamped–pinned and pinned–pinned, are applied to study the effect of the supported end conditions. Furthermore, it is found that the visco-elastic foundation causes an obvious reduction in the critical velocity in comparison with the elastic foundation, in particular for a compliant medium, pinned–pinned boundary condition, high viscosity of the fluid and small values of the nonlocal coefficient.
First Report of Cucumber mosaic virus in Sweet Cherry in the People's Republic of China
Authors: Tan H. D. , Li S. Y. , Du X. F. , Seno M.
Published: October 2010

From the spring of 2003 to the summer of 2006, sweet cherry (Prunus avium) trees in orchards near Lvshun City, in the northeast People's Republic of China, had symptoms suggestive of those caused by Cucumber mosaic virus (CMV; genus Cucumovirus, family Bromoviridae). Symptoms included chlorotic patches or mottling on leaves that were also deformed (4). In April 2006, 20 symptomatic leaves sampled from 10 trees in each of four orchards were assayed for CMV with a CMV-specific antiserum (Agdia Inc., Elkhart, IN) in a double-antibody sandwich-ELISA. Of the 80 symptomatic leaf samples, 27 tested positive for the presence of CMV. CMV was detected in all four orchards, within which incidence varied between 0.5 and 4%. Viral nucleoproteins were purified by differential centrifugation and sucrose density gradient fractionation from symptomatic leaves. Transmission electron microscopy of nucleoproteins revealed isometric particles approximately 30 nm in diameter, which is also typical of CMV. Total RNA was also extracted from 100 mg of symptomatic tissue following a Trizol-based protocol (1). A reverse transcriptase-PCR assay with nucleocapsid gene-specific primers was then used (forward primer 5′-ATGGCGACGTCCTCGTTCA-3′; reverse primer 5′-CATCGTTCCCTTCAAAATAG-3′) (3). A PCR product of approximately 633 bp was obtained. The PCR product was cloned and sequenced. The sequence (GenBank Accession No. HM996559) had 95% identity with the RNA-1 sequence from CMV ‘Fny’ strain in GenBank (Accession No. D00356.1). The People's Republic of China is one of the major producers of sweet cherry in Asia and the spread of CMV in China may cause significant economic losses. Thus, virus-infected material should not be used for propagation and surveys should be undertaken to determine if the aphid vectors capable of transmitting CMV are present (2).To our knowledge, this is the first report of CMV occurring in sweet cherry orchards in the People's Republic of China.

References: (1) P. Chomczynski and K. Mackey. Biotechniques 19:942, 1995. (2) F. E. Gildow et al. Phytopathology 98:1233, 2008. (3) T. M. Rizzo and P. Palukaitis. J. Gen. Virol. 70:1, 1989. (4) J. Shang et al. Z. Naturforsch. C 65:73, 2010.
Characterization of Rhizoctonia spp. Isolates Associated with Damping-Off Disease in Cotton and Tobacco Seedlings in Greece
Authors: Bacharis C. , Gouziotis A. , Kalogeropoulou P. , Koutita O. , Tzavella-Klonari K. , Karaoglanidis G. S.
Published: October 2010

Isolates of Rhizoctonia spp. were obtained during the spring of 2007 from diseased cotton and tobacco seedlings showing damping-off symptoms. The sampled fields were located in the main cotton- and tobacco-cultivating regions of central and northern Greece. Among the 79 isolates obtained from cotton plants, 17 were binucleate and 62 were multinucleate whereas, among the 89 isolates obtained from tobacco plants, 87 were multinucleate and only 2 were binucleate. Characterization of anastomosis groups (AGs) was performed with hyphal anastomosis reactions using tester isolates of known AG groups. Anastomosis reactions in cotton mutlinucleate isolates showed that 54 of them belonged in Rhizoctonia solani AG-4, 6 in AG-7, 1 in AG-2, and 1 in AG-3. In the 87 tobacco multinucleate isolates, anastomosis reactions showed that 70 of them belonged in R. solani AG-2, 16 in AG-4, and 1 in AG-5. In addition, molecular characterization was carried out using the specific ribosomal DNA internal transcribed spacer region, in a randomly selected number of isolates. In cotton, the most prevalent AG was AG-4, with 18 isolates to the subgroup HG-I, 1 isolate to the subgroup HG-II, and 7 isolates to the subgroup HG-III, followed by AG-7 (7 isolates), AG-2-1 (1 isolate), and AG-3 (1 isolate). In tobacco, the most prevalent group was AG-2-1 (70 isolates), followed by AG-4 (6 isolates to the subgroup HG-I and 5 isolates to the subgroup HG-III) and a single isolate belonging to AG-5. Phylogenetic analysis showed that the isolates were distinctly separated based on their AG types. Pathogenicity and aggressiveness of the isolates to several hosts was determined. AG-4 isolates from either cotton or tobacco were the most aggressive on the hosts tested, while AG-2-1 isolates were of moderate aggressiveness and were not pathogenic on barley.
Radiation pharmacogenomics: A genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines
Authors: Niu Nifang , Qin Yuxin , Fridley Brooke L. , Hou Junmei , Kalari Krishna R. , Zhu Minjia , Wu Tse-Yu , Jenkins Gregory D. , Batzler Anthony , Wang Liewei
Published: October 2010

Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels and 1.3 million genome-wide single nucleotide polymorphism (SNP) markers from both Affymetrix and Illumina platforms were assayed for all 277 human LCLs. MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assays for radiation cytotoxicity were also performed to obtain area under the curve (AUC) as a radiation response phenotype for use in the association studies. Functional validation of candidate genes, selected from an integrated analysis that used SNP, expression, and AUC data, was performed with multiple cancer cell lines using specific siRNA knockdown, followed by MTS and colony-forming assays. A total of 27 loci, each containing at least two SNPs within 50 kb with P-values less than 10−4 were associated with radiation AUC. A total of 270 expression probe sets were associated with radiation AUC with P < 10−3. The integrated analysis identified 50 SNPs in 14 of the 27 loci that were associated with both AUC and the expression of 39 genes, which were also associated with radiation AUC (P < 10−3). Functional validation using siRNA knockdown in multiple tumor cell lines showed that C13orf34, MAD2L1, PLK4, TPD52, and DEPDC1B each significantly altered radiation sensitivity in at least two cancer cell lines. Studies performed with LCLs can help to identify novel biomarkers that might contribute to variation in response to radiation therapy and enhance our understanding of mechanisms underlying that variation.
The Arabidopsis Thylakoid Protein PAM68 Is Required for Efficient D1 Biogenesis and Photosystem II Assembly
Authors: Armbruster Ute , Zühlke Jessica , Rengstl Birgit , Kreller Renate , Makarenko Elina , Rühle Thilo , Schünemann Danja , Jahns Peter , Weisshaar Bernd , Nickelsen Jörg , Leister Dario
Published: October 2010

Photosystem II (PSII) is a multiprotein complex that functions as a light-driven water:plastoquinone oxidoreductase in photosynthesis. Assembly of PSII proceeds through a number of distinct intermediate states and requires auxiliary proteins. The photosynthesis affected mutant 68 (pam68) of Arabidopsis thaliana displays drastically altered chlorophyll fluorescence and abnormally low levels of the PSII core subunits D1, D2, CP43, and CP47. We show that these phenotypes result from a specific decrease in the stability and maturation of D1. This is associated with a marked increase in the synthesis of RC (the PSII reaction center-like assembly complex) at the expense of PSII dimers and supercomplexes. PAM68 is a conserved integral membrane protein found in cyanobacterial and eukaryotic thylakoids and interacts in split-ubiquitin assays with several PSII core proteins and known PSII assembly factors. Biochemical analyses of thylakoids from Arabidopsis and Synechocystis sp PCC 6803 suggest that, during PSII assembly, PAM68 proteins associate with an early intermediate complex that might contain D1 and the assembly factor LPA1. Inactivation of cyanobacterial PAM68 destabilizes RC but does not affect larger PSII assembly complexes. Our data imply that PAM68 proteins promote early steps in PSII biogenesis in cyanobacteria and plants, but their inactivation is differently compensated for in the two classes of organisms.
Low‐dose, short‐term ciclosporin (Neoral®) therapy is effective in improving patients’ quality of life as assessed by Skindex‐16 and GHQ‐28 in mild to severe psoriasis patients
Authors: OKUBO Yukari , NATSUME Shoko , USUI Kae , AMAYA Misato , TSUBOI Ryoji
Published: October 2010

Therapies for psoriasis have focused not only on ameliorating the severity of the skin lesions, but also on the quality of life (QOL). Here, the efficacy of low‐dose, short‐term administration of ciclosporin (Neoral®, as CyA) was investigated. Forty‐one psoriasis patients were given CyA orally (3 mg/kg per day) twice daily before breakfast and dinner until the psoriatic area and severity index (PASI) scores decreased by at least 75%. Surveys were conducted before and after the therapy to ascertain QOL, itch, nail condition, joint pain, stress associated with topical application and therapy satisfaction. QOL was assessed by using the Japanese version of Skindex‐16 specific to skin diseases, and the Japanese version of the GHQ‐28, which assesses mental health. Data collected from 35 patients were analyzed. Remission was achieved in 26 patients (74%), and the average length required to achieve remission was 101.5 days. The average PASI score significantly decreased from 17.8 to 3.3 after the therapy. Remission lasted 6 months or longer in 40% of the patients. The average length of time before restarting systemic therapy was 182.0 days. This duration for patients with PASI scores of <13 was 287.5 days while for patients with PASI scores of ≥13, it was significantly shorter at 120.1 days. Five adverse events were recorded in three patients, but were not serious. The total Skindex‐16 score significantly decreased especially in the “emotions’ and “functioning” categories. GHQ scores also significantly decreased in “somatic symptoms,”“anxiety and insomnia,” and “depression”. With regard to patients’ satisfaction with their therapy, 88.5% of the patients reported “satisfied” or “slightly satisfied”. These results demonstrate that low‐dose, short‐term administration of CyA (3 mg/kg per day) is one of the best therapies for psoriasis patients with PASI scores of <13, while QOL assessment is a very useful tool for evaluating the value of therapy.
How best to measure change in evaluations of treatment for substance use disorder
Authors: Marsden John , Eastwood Brian , Wright Craig , Bradbury Colin , Knight Jonathan , Hammond Paul
Published: October 2010

Aims  To compare the performance of the Jacobson & Truax (JT) reliable change index (RCI) with three alternative methods, using data from individuals receiving treatment for substance use disorders.

Design  English National Treatment Outcome Monitoring Database for publicly funded specialist community pharmacological and psychosocial interventions.

Participants  New adult admissions to treatment across England (1 January–31 December 2008), with in‐treatment clinic progress review conducted after an average of 122.8 days for 18 163 individuals.

Measurements  Self‐reported days using heroin, crack, cocaine powder and alcohol during the 4 weeks before admission and clinical review, recorded using the Treatment Outcomes Profile and analysed using a multi‐level, mixed‐linear model, with both observed and true scores to estimate the effect of regression to the mean (RTM). Differences in performance among the JT RCI and the alternative methods were assessed by the proportion assigned to a reliably ‘improved’, ‘unchanged’ or ‘reliably deteriorated’ category; level of agreement; difference in effect size for observed and true scores; and receiver operating characteristic parameters.

Findings  When compared to the alternative methods, the JT RCI was more conservative in assigning individuals to the improved category, and it showed no evidence of inferiority on any measure. For each method, all individuals categorized as reliably deteriorated and the majority of those categorized reliably improved had outcome scores which fell beyond that expected by RTM. Substituting true scores for observed scores moderated the size of the change effect associated with reduced use of the four substances, but this remained statistically significant.

Conclusions  The Jacobson & Truax Reliable Change Index appears to be the optimal measure of change for evaluations of treatment for substance use disorder, in that it is the most conservative for assessing improvement and at least as accurate on all other criteria. Any evaluation of change needs to take account of regression to the mean.
Opioid dependence latent structure: two classes with differing severity?
Authors: Shand Fiona L. , Slade Tim , Degenhardt Louisa , Baillie Andrew , Nelson Elliot C.
Published: October 2010

Aims  To examine the structure of illicit opioid abuse and dependence within an opioid dependent sample and its relationship to other clinical variables.

Design, setting and participants  A cross‐sectional study of 1511 opioid dependent individuals recruited through opioid pharmacotherapy clinics in the Sydney area, Australia.

Measurements  A face‐to‐face structured interview covering substance use and dependence, psychiatric history, child maltreatment, family background, adult violence and criminal history. Dimensional, latent class and factor mixture models were fit to the opioid abuse and dependence data. Classes were then compared on a range of demographic and clinical covariates.

Findings  A two‐class, one‐factor model provided the best fit of all the models tested. The two classes differed with respect to endorsement probabilities on a range of abuse and dependence criteria, and also with respect to the odds of other drug dependence diagnoses, antisocial personality disorder and non‐fatal opioid overdose. Within‐class severity was associated with similar variables: other drug dependence, borderline personality disorder and opioid overdose.

Conclusion  In an in‐treatment, opioid‐dependent sample, there appears to be two classes of individuals exhibiting distinct patterns of abuse and dependence criteria endorsement and to differ on externalizing but not internalizing disorders. This study provides preliminary evidence that the proposed DSM‐V opioid use disorder distinction between moderate and severely dependent people is valid. Class one participants were not only more severely dependent, but had greater odds for opioid overdoses, other drug dependence and antisocial personality disorder.
Can childhood asthma be predicted at birth?
Authors: Lødrup Carlsen K. C. , Mowinckel P. , Granum B. , Carlsen K.‐H.
Published: October 2010

Background
Early life appears optimal for prevention of asthma, but interventions require a relevant target population, to date not clearly identified at birth.

Objective
We therefore aimed to identify the predicting capacity of factors known around birth for asthma and rhinitis at 10 years.

Methods
The included 614 healthy term babies with lung function measured at birth in the 1992/1993 Environment and Childhood Asthma study in Oslo attended a 10‐year follow‐up visit including a structured interview and skin prick test (SPT) for allergies. The logistic regression analyses included 37 general variables from an extensive birth questionnaire; lung function; cord blood total immunoglobulin E and soluble CD14. A history of asthma, current asthma, history of rhinitis and ‘healthy’ (no history of asthma, rhinitis and negative SPT) was predicted on a group level and individual predicted probabilities were calculated.

Results
The predictability of the models [area under the curve (95% confidence intervals)] was 0.74 (0.69, 0.79), 0.72 (0.64, 0.78), 0.69 (0.54, 0.72) and 0.67 (0.62, 0.71) for a history of asthma, current asthma, rhinitis and ‘healthy’, respectively. The best model predicted a history of asthma correctly in 93/124 (75%), and incorrectly in 176/490 (36%) children without asthma. The positive predictive values for all outcomes were low (19–61), the highest predicting healthy.

Conclusion
Although at best 75% of children with a history of asthma could be predicted at birth, an intervention applied to our predicted high‐risk children would be started more often in children without than with future disease. Parental allergic disease alone appears insufficient to identify high‐risk populations in future studies of asthma and allergic disease.

Cite this as: K. C. Lødrup Carlsen, P. Mowinckel, B. Granum and K.‐H. Carlsen, Clinical & Experimental Allergy, 2010 (40) 1767–1775.
Semen quality in men with Y chromosome aberrations
Authors: Antonelli A. , Marcucci L. , Elli R. , Tanzi N. , Paoli D. , Radicioni A. , Lombardo F. , Lenzi A. , Gandini L.
Published: October 2010

Infertile males sometimes bear structurally balanced chromosome aberrations, such as translocations and inversions, which involve both autosomes and sex chromosomes. The aim of this study was to evaluate genotype–phenotype correlations in a sample of infertile men with various types of Y chromosome abnormalities. In particular, we examined the effect of (i) balanced structural aberrations such as translocations between sex chromosomes and autosomes; (ii) unbalanced structural aberrations such as deletions or isodicentrics, both [idic(Yp)] and [idic(Yq)]. We studied 13 subjects bearing Y chromosome aberrations. Each patient underwent seminal fluid examination, andrological inspection, hormone study, testicular ultrasound, conventional and molecular cytogenetic analysis and study of Y chromosome microdeletions. Comparison of genotype and sperm phenotype in infertile patients with various Y chromosome aberrations revealed the key role of meiotic pairing defects in arresting spermatogenesis, both in the presence and in the absence of azoospermic factor microdeletions and cell mosaicism. The failure of meiosis and, in consequence, spermatogenesis may be a result of the failure to inactivate the X chromosome in the meiotic prophase, which is necessary for normal male spermatogenesis to take place.
Smoking withdrawal shifts the spatiotemporal dynamics of neurocognition
Authors: Kozink Rachel V. , Lutz Avery M. , Rose Jed E. , Froeliger Brett , McClernon F. Joseph
Published: October 2010

Smoking withdrawal is associated with significant deficits in the ability to initiate and maintain attention for extended periods of time (i.e. sustained attention; SA). However, the effects of smoking abstinence on the temporal dynamics of neurocognition during SA have not been evaluated. Twenty adult smokers underwent functional magnetic resonance imaging scans following smoking as usual and after 24‐hours abstinence. During scanning they completed a SA task with two levels of task difficulty, designed to measure both sustained (i.e. over the duration of the task) and transient (i.e. event‐related) activation. Smoking abstinence significantly decreased task accuracy regardless of task difficulty. Compared to smoking as usual, abstinence resulted in decreased sustained activation in right inferior and middle frontal gyri but increased transient activation across dispersed cortical areas including precuneus and right superior frontal gyrus. Greater task difficulty was associated with even greater transient activation during abstinence in mostly right hemisphere regions including right inferior frontal gyrus. These findings suggest smoking withdrawal shifts the temporal and spatial dynamics of neurocognition from sustained, right prefrontal activation reflecting proactive cognitive control (Braver, Gray & Burgess 2009) to more dispersed and transient activation reflecting reactive control.