bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimizing stability, transport, and divertor operation through plasma shaping for steady-state scenario development in DIII-D
Authors: Holcomb C. T. , Ferron J. R. , Luce T. C. , Petrie T. W. , Politzer P. A. , Challis C. , DeBoo J. C. , Doyle E. J. , Greenfield C. M. , Groebner R. J. , Groth M. , Hyatt A. W. , Jackson G. L. , Kessel C. , La Haye R. J. , Makowski M. A. , McKee G. R. , Murakami M. , Osborne T. H. , Park J.-M. , Prater R. , Porter G. D. , Reimerdes H. , Rhodes T. L. , Shafer M. W. , Snyder P. B. , Turnbull A. D. , West W. P.
Published: May 2009

Recent studies on the DIII-D tokamak [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] have elucidated key aspects of the dependence of stability, confinement, and density control on the plasma magnetic configuration, leading to the demonstration of nearly noninductive operation for >1 s with pressure 30% above the ideal no-wall stability limit. Achieving fully noninductive tokamak operation requires high pressure, good confinement, and density control through divertor pumping. Plasma geometry affects all of these. Ideal magnetohydrodynamics modeling of external kink stability suggests that it may be optimized by adjusting the shape parameter known as squareness (ζ). Optimizing kink stability leads to an increase in the maximum stable pressure. Experiments confirm that stability varies strongly with ζ, in agreement with the modeling. Optimization of kink stability via ζ is concurrent with an increase in the H-mode edge pressure pedestal stability. Global energy confinement is optimized at the lowest ζ tested, with increased pedestal pressure and lower core transport. Adjusting the magnetic divertor balance about a double-null configuration optimizes density control for improved noninductive auxiliary current drive. The best density control is obtained with a slight imbalance toward the divertor opposite the ion grad(B) drift direction, consistent with modeling of these effects. These optimizations have been combined to achieve noninductive current fractions near unity for over 1 s with normalized pressure of 3.5<βN<3.9, bootstrap current fraction of >65%, and a normalized confinement factor of H98(y,2)≈1.5.
Strong enhancement of the Faraday rotation in Ce and Bi comodified epitaxial iron garnet thin films
Authors: Sekhar Manda Chandra , Hwang Jae-Yeol , Ferrera Marcello , Linzon Yoav , Razzari Luca , Harnagea Catalin , Zaezjev Michael , Pignolet Alain , Morandotti Roberto
Published: May 2009

Ce and Bi comodified iron garnet (Ce2.2Bi0.8Fe5O12) thin films for magneto-optic applications were epitaxially grown on a (111)-oriented Gd3Ga5O12 substrate by pulsed laser deposition. We found that epitaxial film quality could be achieved under a low-pressure Ar atmosphere. Surprisingly, our 1 μm thick epitaxial films showed a record Faraday rotation as high as 0.55 deg/μm, a value strongly dependent on the concentration of Bi3+ ions.
Exact solutions for axisymmetric nonlinear magnetohydrodynamic equilibria of aligned magnetic field and plasma flow with applications to astrophysics and plasma confinement devices
Authors: Khater A. H. , Moawad S. M.
Published: May 2009

The steady state equations of magnetohydrodynamic (MHD) flows for an inviscid fluid of high electrical conductivity are considered for an axisymmetric case, in which the physical quantities are independent of the coordinate ϕ of a cylindrical coordinate system (r,ϕ,z). The magnetic field is taken to be aligned to the plasma velocity, i.e., the magnetic lines of force and the streamlines of the velocity field coincide. Two classes of exact solutions are obtained. The obtained solutions are smooth everywhere and satisfy all necessary physical conditions, in which they have applications in astrophysics as well as plasma confinement devices, e.g., tokamak and reversed field pinch.
Magnetic ratchet for biotechnological applications
Authors: Auge A. , Weddemann A. , Wittbracht F. , Hütten A.
Published: May 2009

Transport and separation of magnetic beads are important in “lab on a chip” environments for biotechnological applications. One possible solution for this is the on-off ratchet concept. An asymmetric magnetic potential and Brownian motion of magnetic beads are required for such a ratchet. The asymmetric magnetic potential is achieved by combining an external magnetic field with a spatially periodic array of conducting lines. In this work finite element method simulations are carried out to design this asymmetric potential and to evaluate transport rates. Furthermore, experiments are carried out so as to compare to the simulation results.
Growth of silver nanoparticles of variable and controlled diameter in silica-based and soda-lime glasses by simultaneous continuous ultraviolet irradiation and heat treatment
Authors: Goutaland F. , Marin E. , Michalon J. Y. , Boukenter A.
Published: May 2009

We report on the space-selective precipitation of silver nanoparticles in silica-based and silver-exchanged soda-lime glasses by simultaneous continuous wave ultraviolet exposure and heat treatment. In silica-based glasses, we explain that simultaneous treatments lead to much higher silver nanoparticles concentration than similar treatments performed into two separated steps by minimizing the detrimental influence of oxidation on the nanoparticles’ growth. In the case of silver-exchanged soda-lime glasses, nanoparticles are observed with both small and larger diameters of about 1 and 7 nm, whose concentrations depend both on the laser power density and on the heating temperature.
Highly uniform and strain-free GaAs quantum dots fabricated by filling of self-assembled nanoholes
Authors: Heyn Ch. , Stemmann A. , Köppen T. , Strelow Ch. , Kipp T. , Grave M. , Mendach S. , Hansen W.
Published: May 2009

We demonstrate the self-assembled creation of a novel type of strain-free semiconductor quantum dot (QD) by local droplet etching (LDE) with Al to form nanoholes in AlGaAs or AlAs surfaces and subsequent filling with GaAs. Since the holes are filled with a precisely defined filling level, we achieve ultrauniform LDE QD ensembles with extremely narrow photoluminescence (PL) linewidth of less than 10 meV. The PL peaks agree with a slightly anisotropic parabolic potential. Small QDs reveal indications for transitions between electron and hole states with different quantization numbers. For large QDs, a very small fine-structure splitting is observed.
Bibliography of the History of Australian Science, No. 29, 2008
Authors: Cohn Helen M.
Published: May 2009

This bibliography, in geographic terms, covers principally Australia, but also New Zealand, New Guinea and other islands of the Pacific Ocean near Australia, and Antarctica. It includes material on the history of the natural sciences (mathematics, physical sciences, earth sciences and biological sciences), some of the applied sciences (including medical and health sciences, agriculture, manufacturing and engineering), and human sciences (psychology, anthropology and sociology). Biographical material on practitioners in these sciences is also of interest.
The sources used in compiling this bibliography include those that have proved useful in the past in finding relevant citations. The library catalogues of the Royal Botanic Gardens Melbourne, the National Library of Australia and the National Library of New Zealand Te Puna Matauranga O Aotearoa were particularly useful sources of information. Journals that have yielded articles for previous bibliographies were checked, as were some titles that have not previously been scanned. Hence a number of citations are included that were published earlier than 2008.
Assistance has been received from a number of people who sent items or information about items published in 2008 for inclusion in the bibliography. In particular, Professor Rod Home has been most helpful in forwarding relevant citations. Staff of the eScholarship Research Centre at the University of Melbourne, especially Helen Morgan, were of great assistance in the preparation of this bibliography. Readers may have access to information about relevant books, journal articles, conference papers, reports, Master's and PhD theses and reviews published in 2009. They are encouraged to send such information to the compiler at the above email address for inclusion in future bibliographies.
An inhibitory interaction between viral and cellular proteins underlies the resistance of tomato to nonadapted tobamoviruses
Authors: Ishibashi Kazuhiro , Naito Satoshi , Meshi Tetsuo , Ishikawa Masayuki
Published: May 2009

Any individual virus can infect only a limited range of hosts, and most plant species are “nonhosts” to a given virus; i.e., all members of the species are insusceptible to the virus. In nonhost plants, the factors that control virus resistance are not genetically tractable, and how the host range of a virus is determined remains poorly understood. Tomato (
Solanum lycopersicum
) is a nonhost species for
Tobacco mild green mosaic virus
(TMGMV) and
Pepper mild mottle virus
(PMMoV), members of the genus
Tobamovirus
. Previously, we identified
Tm-1
, a resistance gene of tomato to another tobamovirus,
Tomato mosaic virus
(ToMV), and found that Tm-1 binds to ToMV replication proteins to inhibit RNA replication.
Tm-1
is derived from a wild tomato species,
S. habrochaites
, and ToMV-susceptible tomato cultivars have the allelic gene
tm-1
. The tm-1 protein can neither bind to ToMV replication proteins nor inhibit ToMV multiplication. Here, we show that transgenic tobacco plants expressing
tm-1
exhibit resistance to TMGMV and PMMoV. The tm-1 protein bound to the replication proteins of TMGMV and PMMoV and inhibited their RNA replication in vitro. In one of the tm-1-expressing tobacco plants, a tm-1-insensitive TMGMV mutant emerged. In tomato protoplasts, this mutant TMGMV multiplied as efficiently as ToMV. However, in tomato plants, the mutant TMGMV multiplied with lower efficiency compared to ToMV and caused systemic necrosis. These results suggest that an inhibitory interaction between the replication proteins and tm-1 underlies a multilayered resistance mechanism to TMGMV in tomato.
Elucidation of a pH-folding switch in the
Pseudomonas syringae
effector protein AvrPto
Authors: Dawson Jennifer E. , Šečkutė Jolita , De Soumya , Schueler Samuel A. , Oswald Aaron B. , Nicholson Linda K.
Published: May 2009

Pathogenic bacteria have developed extraordinary strategies for invading host cells. The highly conserved type III secretion system (T3SS) provides a regulated conduit between the bacterial and host cytoplasm for delivery of a specific set of bacterial effector proteins that serve to disrupt host signaling and metabolism for the benefit of the bacterium. Remarkably, the inner diameter of the T3SS apparatus requires that effector proteins pass through in at least a partially unfolded form. AvrPto, an effector protein of the plant pathogen
Pseudomonas syringae
, adopts a helical bundle fold of low stability (Δ
G
F→U
= 2 kcal/mol at pH 7, 26.6 °C) and offers a model system for chaperone-independent secretion.
P. syringae
effector proteins encounter a pH gradient as they translocate from the bacterial cytoplasm (mildly acidic) into the host cell (neutral). Here, we demonstrate that AvrPto possesses a pH-sensitive folding switch controlled by conserved residue H87 that operates precisely in the pH range expected between the bacterial and host cytoplasm environments. These results provide a mechanism for how a bacterial effector protein employs an intrinsic pH sensor to unfold for translocation via the T3SS and refold once in the host cytoplasm and provide fundamental insights for developing strategies for delivery of engineered therapeutic proteins to target tissues.
Turning a plant tissue into a living cell froth through isotropic growth
Authors: Corson Francis , Hamant Olivier , Bohn Steffen , Traas Jan , Boudaoud Arezki , Couder Yves
Published: May 2009

The forms resulting from growth processes are highly sensitive to the nature of the driving impetus, and to the local properties of the medium, in particular, its isotropy or anisotropy. In turn, these local properties can be organized by growth. Here, we consider a growing plant tissue, the shoot apical meristem of
Arabidopsis thaliana
. In plants, the resistance of the cell wall to the growing internal turgor pressure is the main factor shaping the cells and the tissues. It is well established that the physical properties of the walls depend on the oriented deposition of the cellulose microfibrils in the extracellular matrix or cell wall; this order is correlated to the highly oriented cortical array of microtubules attached to the inner side of the plasma membrane. We used oryzalin to depolymerize microtubules and analyzed its influence on the growing meristem. This had no short-term effect, but it had a profound impact on the cell anisotropy and the resulting tissue growth. The geometry of the cells became similar to that of bubbles in a soap froth. At a multicellular scale, this switch to a local isotropy induced growth into spherical structures. A theoretical model is presented in which a cellular structure grows through the plastic yielding of its walls under turgor pressure. The simulations reproduce the geometrical properties of a normal tissue if cell division is included. If not, a “cell froth” very similar to that observed experimentally is obtained. Our results suggest strong physical constraints on the mechanisms of growth regulation.
The skeleton of tropical intraseasonal oscillations
Authors: Majda Andrew J. , Stechmann Samuel N.
Published: May 2009

The Madden–Julian oscillation (MJO) is the dominant mode of variability in the tropical atmosphere on intraseasonal timescales and planetary spatial scales. Despite the primary importance of the MJO and the decades of research progress since its original discovery, a generally accepted theory for its essential mechanisms has remained elusive. Here, we present a minimal dynamical model for the MJO that recovers robustly its fundamental features (i.e., its “skeleton”) on intraseasonal/planetary scales: (
i
) the peculiar dispersion relation of
d
ω/
dk
≈ 0, (
ii
) the slow phase speed of ≈5 m/s, and (
iii
) the horizontal quadrupole vortex structure. This is accomplished here in a model that is neutrally stable on planetary scales; i.e., it is tacitly assumed that the primary instabilities occur on synoptic scales. The key premise of the model is that modulations of synoptic scale wave activity are induced by low-level moisture preconditioning on planetary scales, and they drive the “skeleton” of the MJO through modulated heating. The “muscle” of the MJO—including tilts, vertical structure, etc.—is contributed by other potential upscale transport effects from the synoptic scales.
Tokamak plasma self-organization and the possibility to have the peaked density profile in ITER
Authors: Razumova K.A. , Andreev V.F. , Kislov A.Ya. , Kirneva N.A. , Lysenko S.E. , Pavlov Yu.D. , Shafranov T.V. , Donné A.J.H. , Hogeweij G.M.D. , Spakman G.W. , Jaspers R. , Kantor M. , Walsh M.
Published: May 2009

The self-organization of a tokamak plasma is a fundamental turbulent plasma phenomenon, which leads to the formation of a self-consistent pressure profile. This phenomenon has been investigated in several tokamaks with different methods of heating. It is shown that the normalized pressure profile has a universal shape for a wide class of tokamaks and regimes, if the normalized radius ρ = r/(I
p
R/κB)1/2 is used. The consequences of this phenomenon for low aspect ratio tokamaks, the optimal deposition of additional heating, fast velocity of heat/cold pulse propagation and the possibility of obtaining a peaked density profile in ITER are discussed.
Lateral-aspect, target-strength measurements of in situ herring (Clupea harengus)
Authors: Pedersen Geir , Handegard Nils Olav , Ona Egil
Published: May 2009

Pedersen, G., Handegard, N. O., and Ona, E. 2009. Lateral-aspect, target-strength measurements of in situ herring (Clupea harengus). – ICES Journal of Marine Science, 66: 1191–1196. Surveys of schooling herring with the new multibeam sonar (Simrad MS70) pose new challenges when converting the echo energy to estimates of biomass. Because the sonar projects horizontally, data and models of lateral-aspect, herring target strength (TS) are needed. In this study, the TS of herring is measured with a horizontally projecting, split-beam echosounder (Simrad EK60). Target-tracking methods are used to estimate swimming angles relative to the horizontal (θ) of individual herring within schools and layers and to evaluate how θ and TS change with depth (z). Measurements of θ and TS are used as inputs for a model describing TS as a function of θ and z. The results indicate that the mean lateral-aspect TS of in situ herring depends on z. Moreover, the mean lateral-aspect TS is more sensitive to z than the mean dorsal-aspect TS predicted by a published model. At z = 50 m, the mean lateral-aspect TS is nearly 2.5 dB higher than the mean dorsal-aspect TS. Conversely, at z = 350 m, the lateral-aspect TS is 5 dB lower. These results suggest that herring swimbladders do not compress uniformly with increasing pressure, but compress dorsoventrally more than laterally.
Calibration methods for two scientific multibeam systems
Authors: Ona Egil , Mazauric Valerie , Andersen Lars Nonboe
Published: May 2009

Ona, E., Mazauric, V., and Andersen, L. N. 2009. Calibration methods for two scientific multibeam systems. – ICES Journal of Marine Science, 66: 1326–1334. The new Simrad scientific multibeam systems, the MS70 sonar and the ME70 echosounder, each transmit over many electronically formed beams with centre frequencies spanning from 70 to 120 kHz. Calibrations of these systems are therefore more complex than for conventional split-beam echosounder systems. Two large tungsten-carbide spheres (75 and 84 mm diameter) were designed and manufactured to facilitate accurate field calibrations over the entire operational bandwidth. These are heavy and therefore stable when suspended beneath a ship, and have target strengths much larger than those of biological targets potentially within the measurement volume. This paper presents procedures for calibrating each system in the field and the results from two such experiments. Detailed inspections of the results for individual beams indicate that minor adjustments in the described procedures might further improve the reported calibration accuracy.
High-frequency acoustics and bio-optics in ecosystems research
Authors: Holliday D. V. , Donaghay P. L. , Greenlaw C. F. , Napp J. M. , Sullivan J. M.
Published: May 2009

Holliday, D. V., Donaghay, P. L., Greenlaw, C. F., Napp, J. M., and Sullivan, J. M. 2009. High-frequency acoustics and bio-optics in ecosystems research. – ICES Journal of Marine Science, 66: 974–980. The propagation of light and sound in the ocean’s interior is modified by the presence of phytoplankton, zooplankton, fish, gas bubbles, and dissolved and suspended material. Information is encoded in the levels and spectral characteristics of acoustic and optical scattering and absorption. Using acoustics and optics allows us to study the distribution of marine life and learn about ecosystem-relevant processes. Two studies are highlighted. In the first, multifrequency, upward-looking echosounders deployed near autonomous, bio-optical profilers were used to track vertical migration and the formation and size structure of <1 m thick, zooplankton layers in relation to the biomass and size structure of thin phytoplankton layers. In the second, a multifrequency sonar was used to track the temporal (seasonal) evolution of zooplankton biomass and size structure in the Bering Sea at intervals of 20 min. This paper focuses on how advanced technologies are being used to observe processes, distributions, and behaviour of marine life that have, until now, been hidden, as it were, from biological oceanographers.
Evaluating the uncertainty of abundance estimates from acoustic surveys using geostatistical simulations
Authors: Woillez Mathieu , Rivoirard Jacques , Fernandes Paul G.
Published: May 2009

Woillez, M., Rivoirard, J., and Fernandes, P. G. 2009. Evaluating the uncertainty of abundance estimates from acoustic surveys using geostatistical simulations. – ICES Journal of Marine Science, 66: 1377–1383. Geostatistical simulations, which can reproduce the spatial variability of a variable, are particularly helpful in estimating the uncertainty associated with the combination of different sources of variability. Acoustic surveys offer an example of such complex situations, where different data (e.g. acoustic backscatter, fish length, and fish age) must be combined to estimate abundance and its associated uncertainty. In this paper, the uncertainty of Scottish herring acoustic-survey estimates is investigated using these techniques. A specific multivariate, geostatistical model is used to describe the structural relationships, which includes highly skewed distributions of the acoustic-backscatter data and incorporates relationships between depth, mean length, and proportions-at-age. Conditional simulations, i.e. geostatistical simulations that honour the data values known at the data points, are used to generate multiple realizations of acoustic backscatter, mean length, and proportions-at-age. These are combined to produce multiple realizations of herring density over the sampled domain. Multiple realizations of total abundance and abundance-at-age are then provided. The uncertainty is assessed using basic statistics to track the significant variations of these values over the period 1989–2005. Higher coefficients of variation (CVs) are found on average for extreme ages (ages 1, 2i, 8, and 9+); otherwise, CVs are mostly around 12% for abundance-at-age and around 10% for total abundance.
David Mervyn Blow. 27 June 1931 — 8 June 2004
Authors: Henderson R. , Franks N. P.
Published: May 2009

David Blow helped build the foundations of protein crystallography and transform it into a highly effective methodology. In the early 1950s he was a member of the small group of scientists, led by Max Perutz, that developed the first methods and solved the first structures. With a background in physics and mathematics, together with a perceptive ability to foster productive collaborations, he made fundamental contributions to the two principal methods of structure determination in protein crystallography, known as isomorphous replacement and molecular replacement. His achievements, insight and organizational skill helped to establish two outstanding laboratories, the Medical Research Council Laboratory of Molecular Biology in Cambridge, where he worked from 1954 to 1977, and the Biophysics Section in the Physics Department at Imperial College in London, where he was a professor from 1977 onwards. His far-sighted and persuasive planning contributed to the harmonious and supportive culture that has characterized crystallography in the UK and influenced its development worldwide.
An evaluation of two commercially available ELISAs and one in-house reference laboratory ELISA for the determination of human anti-rabies virus antibodies
Authors: Welch Ryan J. , Anderson Brian L. , Litwin Christine M.
Published: May 2009

The envelope glycoprotein G of rabies virus in vaccines induces the production of neutralizing antibodies important in the protection against the disease. The measurement of anti-envelope glycoprotein antibodies is a good predictor of the degree of humoral immunity in people during anti-rabies treatment or after vaccination. Several assays exist for the serological determination of antibody protection against rabies virus infection. Antibody neutralization by the rapid fluorescent focus inhibition test (RFFIT) or the fluorescent antibody virus neutralization (FAVN) test is currently the gold standard. Performance of the highly complex RFFIT and FAVN tests, however, requires specialized reference laboratories with expertise with this assay. Although not widely used, ELISA test kits are available and may be an additional option for testing that is more accessible. The aim of the present study was to evaluate available ELISA assays for the determination of anti-rabies antibodies. We compared the Bio-Rad Platelia Rabies II ELISA, DRG Rabies Virus IgG Ab ELISA and Focus Diagnostics Rabies Antibody Detection by ELISA to RFFIT. Bland–Altman plots comparing the Bio-Rad Platelia assay and the Focus Diagnostics assay to RFFIT showed a low degree of variability between the ELISA assays and RFFIT results except in samples with high RFFIT values. The agreement, sensitivity and specificity of Bio-Rad Platelia Rabies II ELISA when compared to RFFIT were 95.1 %, 94.1 % and 95.8 %, respectively. The DRG Rabies assay compared to RFFIT had an agreement of 77.7 %, a sensitivity of 86.7 % and a specificity of 69.4 %. The agreement, sensitivity and specificity of Focus Diagnostics Rabies Detection by ELISA when compared to RFFIT were 82.2 %, 91.7 % and 73.0 %, respectively. Overall, the Bio-Rad Platelia assay showed higher accuracy and specificity than either the DRG or Focus assays. All of these ELISAs, however, measure all antibody types and do not discriminate the neutralizing antibodies as measured by functional assays (RFFIT and FAVN) and cannot be relied upon to predict the neutralizing activity of the sera. The results of this study offer insight into the availability of alternative, less-complex methods to monitor rabies antibody titres in at-risk individuals following vaccination.
Macrolide treatment failure in a case of secondary syphilis: a novel A2059G mutation in the 23S rRNA gene of Treponema pallidum subsp. pallidum
Authors: Matějková Petra , Flasarová Magdalena , Zákoucká Hana , Bořek Milan , Křemenová Soňa , Arenberger Petr , Woznicová Vladana , Weinstock George M. , Šmajs David
Published: May 2009

We report an occurrence of treatment failure after oral spiramycin therapy in a man with secondary syphilis and a reported penicillin and tetracycline allergy. Molecular detection revealed treponemal DNA in the blood of the patient and sequencing of the 23S rDNA identified an A to G transition at the gene position corresponding to position 2059 in the Escherichia coli 23S rRNA gene. The occurrence of this novel 23S rDNA mutation was examined among 7 rabbit-propagated syphilitic strains of Treponema pallidum and among 22 syphilis patient isolates from the Czech Republic. The prevalence of A2058G and A2059G mutations among clinical specimens was 18.2 and 18.2 %, respectively.
Immunological analysis and pathological examination of gnotobiotic mice monoassociated with Mycoplasma pneumoniae
Authors: Sekine Hideaki , Taguchi Haruhiko , Watanabe Hidehiro , Kawai Shin , Fujioka Yasunori , Goto Hajime , Kobayashi Hiroyuki , Kamiya Shigeru
Published: May 2009

Although mycoplasmal pneumonia has been generally considered to be a disease with good prognosis, a pathogenic host immune response has been associated with its occurrence. In the present study, the pathogenic significance of the immune response was examined using germ-free mice either infected intranasally withMycoplasma pneumoniaeor inoculated withM. pneumoniaeantigens (soluble antigen and partially purified antigen). In gnotobiotic mice monoassociated withM. pneumoniae, 104 c.f.u.M. pneumoniaeper lung were isolated 2–28 days after infection. Inflammatory changes with infiltration of lymphocytes were histopathologically detected in the perivascular area at 2 and 7 days after infection. In the mice intranasally inoculated with soluble antigen or partially purified antigens (F6 and F10 antigens), infiltration of neutrophils and lymphocytes was histopathologically detected at 2 days after inoculation. Severe pneumonia with tissue destruction was observed in the mice inoculated with F6 antigen. A gamma interferon (IFN-γ) dominant response in endogenous cytokine expression was observed in all the treated mice. These results indicate that inflammatory changes in the lung tissue were prolonged in gnotobiotic mice monoassociated withM. pneumoniaecompared with mice inoculated withM. pneumoniaeantigen. In addition, it was shown that IFN-γplays an important role in the pathogenesis of pneumonia in mice either infected withM. pneumoniaeor inoculated with its antigen. In particular, the F6 antigen has been considered to be an important virulence factor in terms of induction of tissue injury causing infiltration of lymphocytes and neutrophils in the lung, suggesting a close interaction between the immune response and the occurrence ofM. pneumoniaepneumonia.
In vitro activity of carvacrol against staphylococcal preformed biofilm by liquid and vapour contact
Authors: Nostro Antonia , Marino Andreana , Blanco Anna Rita , Cellini Luigina , Di Giulio Mara , Pizzimenti Francesco , Roccaro Andrea Sudano , Bisignano Giuseppe
Published: May 2009

Carvacrol is an important component of essential oils and recently has attracted much attention as a result of its biological properties, such as a wide spectrum of antimicrobial activity. The aim of this study was to evaluate the effect of carvacrol in liquid and vapour phase on preformed biofilms of Staphylococcus aureus and Staphylococcus epidermidis by determining biofilm biomass and cultivable cell numbers, and by using epifluorescence and scanning electron microscopy. Carvacrol was able to reduce biofilm biomass and cell viability more effectively when used with liquid contact rather than with vapour phase. The efficacy of treatment with carvacrol vapour was found to be dependent on exposure time. The predominance of red fluorescence using a LIVE/DEAD BacLight Viability kit (Molecular Probes) and the partially destroyed biofilm architecture as determined by microscopy in treated samples provided evidence for the efficacy of carvacrol. The findings of this investigation suggest a potential application for carvacrol in the inactivation of staphylococcal biofilms.
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing
Authors: Irvine Danielle V. , Goto Derek B. , Vaughn Matthew W. , Nakaseko Yukinobu , McCombie W. Richard , Yanagida Mitsuhiro , Martienssen Rob
Published: May 2009

Fission yeast is an important model for epigenetic studies due to the ease with which genetic mutants can be isolated. However, it can be difficult to complement epigenetic phenotypes with genomic libraries in order to identify the genes responsible. This is because epigenetic phenotypes are typically unstable, and can prohibit complementation if silencing cannot be reestablished. Here we have resequenced the fission yeast genome following mutagenesis to readily identify a novel mutant involved in heterochromatic silencing. Candidate genes were identified as functional single base changes linked to the mutation, which were then reconstituted in a wild-type strain to recapitulate the mutant phenotype. By this procedure we identified a weak allele of ubc4, which encodes an essential E2 ubiquitin ligase, as responsible for the swi*603 mutant phenotype. In combination with a large collection of mutants and suppressor plasmids, next-generation genomic resequencing promises to dramatically enhance the power of yeast genetics, permitting the isolation of subtle alleles of essential genes, alleles with quantitative effects, and enhancers and suppressors of heterochromatic silencing.
Parabolic flight primes cytotoxic capabilities of polymorphonuclear leucocytes in humans
Authors: Kaufmann I. , Schachtner T. , Feuerecker M. , Schelling G. , Thiel M. , Choukèr A.
Published: May 2009

Background  Previously performed in vitro studies suggested that gravitational stress may alter functions of immune cells. This study investigated the in vivo effects of parabolic flight manoeuvres as a short‐term model of micro‐ and hypergravity on the cytotoxic and microbicidal polymorphonuclear leucocyte (PMN) functions as the key element of innate immunity.

Material and methods  Twenty‐one healthy male volunteers underwent 30 subsequent parabolic flight manoeuvres. Each manoeuvre produced 22‐s periods of nearly weightlessness close to «0g», with each parabola starting with a pull‐up and ending with a pull‐out (hypergravity) at 1·8 g for about 20 s each. Blood samples were drawn 24 h prior to take off (T0), after 25–30 parabolas (T1), and 24 h (T2) and 48 h (T3) after flight for determination of (i) leucocyte number and subpopulations, (ii) PMNs’ capabilities to produce hydrogen peroxide (H2O2) and to adhere and phagocytose particles and (iii) plasma cytokines known to prime PMN functions [interleukin‐8 (IL‐8), tumour necrosis factor‐α (TNF‐α), granulocyte‐colony stimulating factor (G‐CSF) and granulocyte‐macrophage colony stimulating factor (GM‐CSF)].

Results  Parabolic flight induced an increase in leucocyte number with a significant elevation of the PMN fraction. The spontaneous H2O2 production by PMNs did not change; however, the capability of PMNs to produce H2O2 in response to soluble stimuli [N‐formyl‐methionyl‐leucyl‐phenylalanine (fMLP), fMLP and TNF‐α, calcium ionophore (A23187), phorbol myristate acetate (PMA)] was increased. Adhesive and phagocytic properties of PMNs were not altered. Regarding priming cytokines, IL‐8 and G‐CSF were significantly elevated.

Conclusions  Our data indicate that parabolic flight induces priming of the cytotoxic capabilities of PMNs without affecting microbicidal functions.
Brachial artery diameter is related to cardiovascular risk factors and intima‐media thickness
Authors: Holewijn S. , Den Heijer M. , Swinkels D. W. , Stalenhoef A. F. H. , De Graaf J.
Published: May 2009

Background  Previous reports showed inconsistent results about the potential role of flow‐mediated dilatation (FMD) in cardiovascular(CV) risk prediction. Few data are available about the role of nitroglycerin‐mediated dilatation (NMD), but recently, brachial artery diameter(BAD) appeared to have predictive value in CV risk prediction.We determined the relation of FMD, BAD and NMD with known CV risk factors and intima‐media thickness (IMT), a well‐established surrogate marker of atherosclerosis, in a community‐based population, the Nijmegen Biomedical Study (NBS).

Materials and methods  FMD, BAD and NMD were measured in the brachial, and IMT in the common carotid artery ultrasononically in 337 participants, aged 50–70 years. Traditional clinical and biochemical parameters were determined.

Results  Both FMD and NMD were not correlated with most CV risk factors or prevalent CVD. However, both IMT and BAD did show significant correlations with CV risk factors. In accordance, both IMT and BAD were significantly correlated with prevalent CVD (r = 0·62 and r = −0·37, respectively) . Furthermore, FMD was not correlated with IMT and did hardly (R2 = 1·1%) improve the prediction of IMT by CV risk factors in regression analysis. However, both BAD and NMD did correlate with IMT (r = −0·29 and r = 0·25, respectively).

Conclusion  In our study, FMD and NMD were not related to known CV risk factors and prevalent CVD, and FMD was not correlated with IMT, a surrogate marker of atherosclerosis. Most intriguingly, BAD was significantly correlated with some CV risk factors, prevalent CVD and IMT. So, BAD is a potential valuable tool in CV risk prediction in middle‐aged low‐risk populations, whereas FMD is not.
Towards an understanding of resilience in isolated coral reefs
Authors: HALFORD ANDREW R. , CALEY M. JULIAN
Published: May 2009

In 1998, seawater temperature anomalies led to unprecedented levels of coral bleaching on reefs worldwide. We studied the direct effects of this thermal event on benthic communities and its indirect effects on their associated coral reef fish communities at a group of remote reefs off NW Australia. Long‐term monitoring of benthic and fish assemblages on these reefs allowed us to compare the responses of these communities to coral bleaching using a data series that included 4 years before, and 6 years following, this bleaching event. While bleaching mortality was evident to >30 m depth, it was patchy among the shallower survey sites with decreases in live coral cover ranging from 30% to 90% across seven surveyed locations Within 2 years of the bleaching, hard coral recovery had begun at all sites and by 2003 reef‐wide coral cover had increased to ∼39% of its preimpact levels. We exploited this pattern of differential survival of corals among sites, the associated changes in these benthic communities, and their patterns of recovery, to better understand links between benthic community dynamics and their associated fish communities. Temporal changes in the resident fish communities strongly reflected the differential shifts in the benthic communities, but were lagged by 12–18 months. Five years after the bleaching event, the fish communities on five of the seven surveyed locations showed evidence of recovery, however, none had regained their preimpact structures. Analyses of these communities by taxonomic family revealed a range of responses to the disturbance reflective of their life‐histories and trophic and habitat affiliations. The slow but recognizable recovery of this isolated reef system has parallels with other relatively isolated systems that displayed resilience to the 1998 bleaching event, e.g. the Chagos archipelago, but it also contrasts sharply with low levels of resilience documented in other isolated reef systems subject to the same disturbance, e.g. the Seychelles. In this context, our results highlight the significant knowledge gaps remaining in understanding the resilience of these ecosystems to disturbance.
Assessment of bioactive and bio‐adhesive therapies to enhance stem cell attachment to root surface dentine
Authors: Elseed M. A. , Murray P. E. , Garcia‐Godoy F. , Namerow K. N.
Published: May 2009

Aim  To compare bioactive and bio‐adhesive therapies to enhance stem cell attachment to the root dentine of human teeth.

Methodology  Dentine slabs (n = 72) were cut from the lower 3 mm of the roots of extracted human permanent teeth. The root dentine slabs were untreated, or coated with bio‐adhesive, or human recombinant transforming growth factor‐beta1 (hrTGF‐B1), or human recombinant bone morphogenic protein‐2 (hrBMP‐2). The dentine slabs were placed with the root surface in contact with confluent periodontal stem cell (PSC) cultures using aseptic techniques. The cells and dentine slabs were submerged in culture media for 4, 24 and 72 h. The specimens were fixed in formalin, dehydrated and processed for scanning electron microscopy (SEM).

Results  SEM micrographs at ×2000 magnification revealed PSC extensive adherence to root dentine for all of the bio‐adhesive and bioactive treatments. The addition of bioactive molecules did not improve PSC attachment. Few cells attached to the negative control treatments.

Conclusions  Bio‐adhesive and bioactive growth factors were not needed to promote PSC attachment to the root dentine of human teeth, because it already appears to have good natural properties to promote PSC attachment. This suggests PSC can be used for the clinical replantation of avulsed teeth without the need for bio‐adhesive and bioactive treatments.
The upregulation of oncostatin M in inflamed human dental pulps
Authors: Huang F‐M , Tsai C‐H , Yang S‐F , Chang Y‐C
Published: May 2009

Aim  To compare oncostatin M (OSM) expression in clinically healthy and inflamed specimened human pulp tissue.

Methodology  Thirty pulpal tissue specimens (15 clinically healthy and 15 inflamed) were obtained from extracted third molars with informed consent from patients. The levels of OSM were compared between clinically healthy pulp and inflamed pulp tissues using the semi‐quantitative reverse‐transcriptase polymerase chain reaction. In addition, immunohistochemistry was used to identify the in situ localization of OSM expression in pulp specimens. For testing of differences in the OSM between the clinically healthy and inflamed human dental pulps, the Wilcoxon–Mann–Whitney rank sum test was applied. Differences in OSM expression between tissue with low and high levels of inflammation were subsequently analysed by Fisher’s exact test.

Results  Inflamed pulps exhibited significantly higher OSM mRNA gene expression than clinically healthy pulps (P < 0.05). Immunohistochemistry demonstrated that OSM expression was significantly higher in inflamed than clinically healthy pulps (P < 0.05). OSM staining was detected in odontoblasts, fibroblasts, inflammatory infiltrates and endothelial cells.

Conclusions  Oncostatin M expression was elevated in inflamed pulp tissue. OSM is potentially involved in the disease process of pulpal inflammation.
Predictive value of on‐treatment response during full‐dose antiviral therapy of patients with hepatitis C virus cirrhosis and portal hypertension
Authors: Giannini E. G. , Basso M. , Savarino V. , Picciotto A.
Published: May 2009

Objective.  Therapy with full‐dose pegylated interferon (PEG‐IFN) and weight‐based ribavirin has been evaluated in limited series of patients with hepatitis C virus (HCV) and advanced disease. In this study, we evaluated the efficacy and tolerability of full‐dose antiviral therapy in patients with compensated, fully developed cirrhosis, and assessed the predictive value of on‐treatment virological response.

Design and subjects.  We studied 85 HCV‐positive cirrhotic patients (82 Child‐Pugh class A; 41 treatment‐naïve) who were treated with PEG‐IFN α‐2a (1.5 μg kg−1week−1) or α‐2b (180 μg week−1) and weight‐based ribavirin for 24 (genotype 2–3) or 48 (genotype 1–4) weeks. Forty‐three patients were genotype 1 (51%), and HCV‐RNA was >600 000 IU mL−1 in 53 patients (62%). Prevalence of portal hypertension and diabetes was 81% and 18% respectively.

Results.  Sustained virological response (SVR) was obtained in 22 patients (26%). Positive serum HCV‐RNA at week 4 and week 12 of therapy predicted nonresponse (NR) in 85% (52/61) and 100% (38/38) of patients, respectively. Treatment was discontinued due to adverse events in 14 patients (16%). Genotype 1–4 (P = 0.02) and HCV‐RNA >600 000 IU mL−1 (P = 0.02) were the baseline parameters significantly associated with lack of SVR, whilst positive serum HCV‐RNA at week 12 was the only parameter independently associated with NR (100% negative predictive value).

Conclusion.  Full‐dose antiviral therapy with PEG‐IFN and ribavirin can be safely carried out even in patients with compensated, fully established cirrhosis and portal hypertension. Selecting patients on the basis of HCV genotype and viral load, and application of on‐treatment stopping rule may help rationalize treatment in patients who are unlikely to obtain SVR.
Analysing laser‐scanned digital terrain models of gravel bed surfaces: linking morphology to sediment transport processes and hydraulics
Authors: HODGE REBECCA , BRASINGTON JAMES , RICHARDS KEITH
Published: May 2009

The grain‐scale topography of a sediment surface is a key component of a fluvial system, affecting aspects including sediment transport, flow resistance and ecology. However, its effect is hard to quantify because of the need for grain‐scale elevation data from in situ fluvial gravel surfaces which are difficult to collect. The sediment surface properties are, therefore, commonly estimated as a function of the sediment grain‐size distribution; however, because of additional factors, such as grain packing and shape, there is not necessarily a unique relationship between the two. A new methodology has been developed that uses terrestrial laser scanning to collect grain‐scale topographic data from in situ fluvial gravel surfaces, from which digital terrain models are created. This paper investigates methods of analysing such digital terrain models, and possible sedimentological interpretations that can be drawn from the analysis. Eleven digital terrain models from exposed gravel surfaces in two contrasting rivers (the River Feshie and Bury Green Brook) were analysed by calculating: the distribution of surface elevations, semivariograms, surface inclinations, surface slopes and aspects and grain orientation. The distribution of surface elevations and surface slope and aspect analysis were found to be most informative. In the River Feshie, grain‐size was interpreted as being a dominant control on sediment surface structure and gravel imbrication was identified. In Bury Green Brook, the location of the digital terrain models within the riffle–pool sequence was the dominant control on surface structure and grain orientation. Such digital terrain models therefore provide a new approach to measuring and quantifying the topography of fluvial sediment surfaces.
Aeolian dune‐field development in a water table‐controlled system: Skeiđarársandur, Southern Iceland
Authors: MOUNTNEY NIGEL P. , RUSSELL ANDREW J.
Published: May 2009

Aeolian dune fields characterized by partly vegetated bedforms undergoing active construction and with interdune depressions that lie at or close to the water table are widespread on Skeiđarársandur, Southern Iceland. The largest aeolian dune complex on the sandur covers an area of 80 km2 and is characterized by four distinct landform types: (i) spatially isolated aeolian dunes; (ii) extensive areas of damp and wet (flooded) interdune flat with small fluvial channels; (iii) small aeolian dune fields composed of assemblages of bedforms with simple morphologies and small, predominantly damp, interdune corridors; and (iv) larger aeolian dune fields composed of assemblages of complex bedforms floored by older aeolian dune deposits that are themselves raised above the level of the surrounding wet sandur plain. The morphology of each of these landform areas reflects a range of styles of interaction between aeolian dune, interdune and fluvial processes that operate coevally on the sandur surface. The geometry, scale, orientation and facies composition of sets of strata in the cores of the aeolian dunes, and their relationship to adjoining interdune strata, have been analysed to explain the temporal behaviour of the dunes in terms of their mode of initiation, construction, pattern of migration, style of accumulation and nature of preservation. Seasonal and longer‐term flooding‐induced changes in water table level have caused episodic expansion and contraction of the wet interdune ponds. Most of the dunes are currently undergoing active construction and migration and, although sediment availability is limited because of the high water table, substantial aeolian transport must occur, especially during winter months when the surface of the wet interdune ponds is frozen and sand can be blown across the sandur without being trapped by surface moisture. Bedforms within the larger dune fields have grown to a size whereby formerly damp interdune flats have been reduced to dry enclosed depressions and dry aeolian system accumulation via bedform climb is ongoing. Despite regional uplift of the proximal sandur surface in response to glacial retreat and unloading over the past century, sediment compaction‐induced subsidence of the distal sandur is progressively placing aeolian deposits below the water table and is enabling the accumulation of wet aeolian systems and increasing the likelihood of their long‐term preservation. Wet, dry and stabilizing aeolian system types all co‐exist on Skeiđarársandur and the dunes are variously undergoing coeval construction, accumulation, bypass, stabilization and destruction as a result of interactions between localized factors.