bluuebunny/crossref_metadata_2025 huggingface dataset:
Time-dependent density functional theory/discrete reaction field spectra of open shell systems: The visual spectrum of [FeIII(PyPepS)2]− in aqueous solution
Authors: van Duijnen Piet Th. , Greene Shannon N. , Richards Nigel G. J.
Published: July 2007

We report the calculated visible spectrum of [FeIII(PyPepS)2]− in aqueous solution. From all-classical molecular dynamics simulations on the solute and 200 water molecules with a polarizable force field, 25 solute/solvent configurations were chosen at random from a 50ps production run and subjected the systems to calculations using time-dependent density functional theory (TD-DFT) for the solute, combined with a solvation model in which the water molecules carry charges and polarizabilities. In each calculation the first 60 excited states were collected in order to span the experimental spectrum. Since the solute has a doublet ground state several excitations to states are of type “three electrons in three orbitals,” each of which gives rise to a manifold of a quartet and two doublet states which cannot properly be represented by single Slater determinants. We applied a tentative scheme to analyze this type of spin contamination in terms of Δ and Δ transitions between the same orbital pairs. Assuming the associated states as pure single determinants obtained from restricted calculations, we construct conformation state functions (CFSs), i.e., eigenfunctions of the Hamiltonian Ŝz and Ŝ2, for the two doublets and the quartet for each Δ,Δ pair, the necessary parameters coming from regular and spin-flip calculations. It appears that the lower final states remain where they were originally calculated, while the higher states move up by some tenths of an eV. In this case filtering out these higher states gives a spectrum that compares very well with experiment, but nevertheless we suggest investigating a possible (re)formulation of TD-DFT in terms of CFSs rather than determinants.
Spectral decomposition of Bell operators for multiqubit systems
Authors: Urías Jesús
Published: July 2007

The spectral decomposition of multipartite Bell operators for two dichotomic observables per site, as introduced by Werner and Wolf [Phys. Rev. A 64, 032112 (2001)], is done. Implications on the characterization of Bell inequalities as criteria of entanglement are discussed.
Emission of drops from the tip of an electrified jet of an inviscid liquid of infinite electrical conductivity
Authors: Higuera F. J.
Published: July 2007

A numerical description is presented of the emission of drops from the tip of a long axisymmetric jet, which may develop when an inviscid liquid of infinite electrical conductivity is injected into a dielectric medium under the action of a strong electric field. The applied field is intensified by the presence of the equipotential surface of the jet, leading to a strong electric stress normal to the surface that accelerates a stretch of liquid and cuts it from the jet. The jet consists of a long region of stationary flow followed by a long oscillatory region where the drops develop and detach. The process of drop generation comprises different stages and is dominated by the electric stress and the inertia of the liquid, with little effect of its surface tension. Order-of-magnitude estimates are used to determine conditions under which these results can be applied to jets of liquids of finite electrical conductivity.
Type I intermittency related to the spatiotemporal dynamics of double layers and ion-acoustic instabilities in plasma
Authors: Chiriac S. , Dimitriu D. G. , Sanduloviciu M.
Published: July 2007

Anodic double layer instabilities occur in low-temperature diffusion filament-type discharge plasma by applying a certain positive bias with respect to the plasma potential to an additional electrode. Periodic nonlinear regimes, characterized by proper dynamics of double layers, are sustained if excitation and ionization rates in front of the electrode reach the value for which current limitation effects appear in the static current-voltage characteristic. It was experimentally shown that under specific experimental conditions these ordered spatiotemporal phenomena can evolve into chaotic states by type I intermittency. This transition was verified by the evolution of time series, fast Fourier transform amplitude plots, three–dimensional reconstructed state spaces, power laws, and flickering phenomena spectrum, as well as by the return map and tangent bifurcation.
Effects of adiabatic hot dust on arbitrary amplitude electrostatic solitary structures in magnetoplasmas
Authors: Mahmood S. , Akhtar N. , Saleem H.
Published: July 2007

The effects of dust temperature on arbitrary amplitude dust acoustic solitary waves in a homogeneous magnetized plasma are studied. It is found that the dust temperature is destructive for the formation of solitons in magnetized plasmas. This behavior is similar to the case of unmagnetized hot dusty plasmas. However, the soliton amplitude increases with the increase in the obliqueness of the wave propagation. The numerical results are also shown for illustrative purposes.
Quantum ion acoustic shock waves in planar and nonplanar geometry
Authors: Sahu Biswajit , Roychoudhury Rajkumar
Published: July 2007

The effects of unbounded planar geometry and bounded nonplanar geometry on quantum ion acoustic shock waves (QIASWs) in unmagnetized plasmas, where plasma kinematic viscosities are taken into account, are investigated. By the reductive perturbation method, deformed Korteweg–de Vries Burger (dKdVB), cylindrical, and spherical dKdVB equations are obtained for quantum ion acoustic shock waves in an unmagnetized two-species quantum plasma system, comprising electrons and ions. The properties of quantum ion acoustic shock waves are studied taking into account the quantum-mechanical effects in planar and nonplanar geometry. It is shown that quantum ion acoustic shock waves in nonplanar geometry differ from planar geometry. We have studied the change of QIASW structure due to the effect of the geometry, quantum parameter H, and ion kinematic viscosities by numerical calculations of the planar dKdVB, cylindrical, and spherical dKdVB equations.
On the existence of two-dimensional nonlinear steady states in plane Couette flow
Authors: Rincon F.
Published: July 2007

The problem of two-dimensional steady nonlinear dynamics in plane Couette flow is revisited using homotopy from either plane Poiseuille flow or from plane Couette flow perturbed by a small symmetry-preserving identity operator. Our results show that it is not possible to obtain the nonlinear plane Couette flow solutions reported by Cherhabili and Ehrenstein [Eur. J. Mech. B/Fluids 14, 667 (1995)] using their Poiseuille-Couette homotopy. We also demonstrate that the steady solutions obtained by Mehta and Healey [Phys. Fluids 17, 094108 (2005)] for small symmetry-preserving perturbations are influenced by an artefact of the modified system of equations used in their paper. However, using a modified version of their model does not help to find plane Couette flow solution in the limit of vanishing symmetry-preserving perturbations either. The issue of the existence of two-dimensional nonlinear steady states in plane Couette flow remains unsettled.
Rapid structural mapping of ternary metallic alloy systems using the combinatorial approach and cluster analysis
Authors: Long C. J. , Hattrick-Simpers J. , Murakami M. , Srivastava R. C. , Takeuchi I. , Karen V. L. , Li X.
Published: July 2007

We are developing a procedure for the quick identification of structural phases in thin film composition spread experiments which map large fractions of compositional phase diagrams of ternary metallic alloy systems. An in-house scanning x-ray microdiffractometer is used to obtain x-ray spectra from 273 different compositions on a single composition spread library. A cluster analysis software is then used to sort the spectra into groups in order to rapidly discover the distribution of phases on the ternary diagram. The most representative pattern of each group is then compared to a database of known structures to identify known phases. Using this method, the arduous analysis and classification of hundreds of spectra is reduced to a much shorter analysis of only a few spectra.
Cooperative transport in a potassium ion channel
Authors: Gwan Jean-Fang , Baumgaertner Artur
Published: July 2007

Our current understanding of ion permeation through the selectivity filter of the KcsA potassium channel is based on the concept of a multi-ion transport mechanism. The details of this concerted movement, however, are not well understood. In the present paper we report on molecular dynamics simulations which provides new insights. It is shown that ion translocation is based on the collective hopping of ions and water molecules which is mediated by the flexible charged carbonyl groups lining the backbone of the pore. In particular, there is strong evidence for pairwise translocations where one ion and one water molecule form a bound state. We suggest a physical explanation of the observed phenomena employing a simple lattice model. It is argued that the water molecules can act as rectifiers during the hopping of ion-water pairs.
Infrared spectra of helium clusters seeded with nitrous oxide, HeN4–N2O, with N=1–80
Authors: McKellar A. R. W.
Published: July 2007

High resolution infrared spectra of HeN–N2O clusters are studied in the 2200cm−1 region of the N2O ν1 fundamental band. The clusters are produced in a pulsed supersonic jet expansion from a cooled nozzle source and probed using a tunable diode laser operating in a rapid-scan mode. Three isotopic forms are used (N14N14O16, N15N14O16, and N15N15O16) in order to support the spectral analyses. For clusters up to N≈24, the individual spectra are resolved, assigned, and analyzed together with complementary microwave data. Assignments for larger clusters are uncertain due to overlapping transitions, but an approximate analysis is still possible for N≈25–80. Compared to helium clusters containing the related CO2 or OCS molecules, the rotational dynamics of HeN–N2O clusters show similarities but also important differences. In particular, HeN–N2O has more irregular behavior in the range of N=6–17, indicating that conventional molecular structure plays a greater role. In general terms, these differences can be attributed to a greater degree of angular anisotropy in the He–N2O intermolecular potential.
Application of a charge-coupled device photon-counting technique to three-dimensional element analysis of a plant seed (alfalfa) using a full-field x-ray fluorescence imaging microscope
Authors: Hoshino Masato , Ishino Toyoaki , Namiki Takashi , Yamada Norimitsu , Watanabe Norio , Aoki Sadao
Published: July 2007

A full-field x-ray fluorescence imaging microscope using a Wolter mirror was constructed at Photon Factory BL3C2. White x rays from a bending magnet were used to excite x-ray fluorescence and to enhance the x-ray fluorescence intensity. A photon-counting method using a charge-coupled device was applied to obtain an x-ray fluorescence spectrum at the image plane. The spatial distributions of some specific atoms such as Fe and Zn were obtained from photon-counting calculations. An energy resolution of 220eV at the FeKα line was obtained from the x-ray fluorescence spectrum by the photon-counting method. The newly developed three-dimensional element mappings of the specific atoms were accomplished by the photon-counting method and a reconstruction technique using computed tomography.
Cooperative downconversion in GdAl3(BO3)4:RE3+,Yb3+ (RE=Pr, Tb, and Tm)
Authors: Zhang Q. Y. , Yang G. F. , Jiang Z. H.
Published: July 2007

An efficient near-infrared (NIR) quantum cutting (QC) in GdAl3(BO3)4:RE3+,Yb3+ (RE=Pr, Tb, and Tm) phosphors has been demonstrated, which involves the conversion of the visible photon into the NIR emission with an optimal quantum efficiency approaching 200%, by exploring the cooperative downconversion mechanism from RE3+ (RE=Pr, Tb, and Tm) excitons to the two activator ions, Yb3+. The development of NIR QC phosphors could open up a new approach in achieving high efficiency silicon-based solar cells by means of downconversion in the visible part of the solar spectrum to ∼1000nm photons with a twofold increase in the photon number.
Photocurrent analysis of a fast Ge p-i-n detector on Si
Authors: Oehme M. , Werner J. , Kasper E. , Klinger S. , Berroth M.
Published: July 2007

Germanium vertical p-i-n photodetectors grown on silicon with molecular beam epitaxy are investigated. The photocurrent of a high speed detector structure is analyzed at infrared wavelengths of around 1.3μm. The dark current and photocurrent were measured for reverse and forward biased detectors. It is clearly shown that the photocurrent is proportional to the width of the depletion layer. This means that the fast carriers from the depletion layer generate mainly the photocurrent and by this the high speed operation of the germanium detector is explained. Nearly abrupt junctions and low background doping allow zero bias operation of these detectors.
Nanoimprinted circular grating distributed feedback dye laser
Authors: Chen Yan , Li Zhenyu , Zhang Zhaoyu , Psaltis Demetri , Scherer Axel
Published: July 2007

The authors demonstrate an optically pumped surface emitting polymer dye laser fabricated by nanoimprint lithography. The laser is based on an organic dye hosted within a poly(methylmethacrylate) matrix coated on a transparent substrate, and the laser cavity consists of a second order circular grating distributed feedback structure. The authors achieved lasing at 618nm with 0.18nm linewidth and 1.31μJ∕mm2 pump threshold. The nanoimprinted solid-state dye laser offers a low-cost coherent light source for laboratory-on-chip spectroscopy systems. The laser also has a low pump threshold and a geometry well matched to light-emitting diode pump sources, which provide an interesting alternative for constructing portable polymer laser devices.
Object localization with 10nm accuracy by x-ray phase contrast projection imaging
Authors: Ollinger C. , Fuhse C. , Kalbfleisch S. , Tucoulou R. , Salditt T.
Published: July 2007

The present work focuses on the question of localizing single object by hard x-ray phase contrast projection imaging. The authors present a setup where an x-ray channel waveguide defines a “quasi-point source” used to illuminate and image an object in a highly coherent cone beam. Knife edge fluorescence scans revealed a beam diameter of 75nm at a distance of 30μm behind the guide. The recorded image corresponds to an in-line hologram of the object which can be reconstructed numerically. Object translations and associated shifts in the hologram allow for the 10nm localization accuracy.
Single-step fabrication of Fresnel microlens array on sapphire substrate of flip-chip gallium nitride light emitting diode by focused ion beam
Authors: Lee Ming-Kwei , Kuo Kwei-Kuan
Published: July 2007

A simple one-step focused ion beam milling technique was used to fabricate a Fresnel microlens array on the backside of sapphire substrate of a gallium nitride blue light emitting diode. The optical output power from the flip-chip gallium nitride blue light emitting diode is enhanced to about 1.68 times at the injection current of 20mA. The spatial light distribution from the backside of flip-chip gallium nitride blue light emitting diode with a Fresnel microlens array shows a uniform and stronger light emission.
Spin Hall effect of excitons with spin-orbit coupling
Authors: Wang Jian-Wei , Li Shu-Shen
Published: July 2007

The center-of-mass motion of a quasi-two-dimensional exciton with spin-orbit coupling (SOC) in the presence of a perpendicular electric field is calculated by perturbation theory. The results indicate that a quasi-two-dimensional exciton with SOC can exhibit the spin Hall effect (SHE), which is similar to two-dimensional electrons and holes. A likely way to establish exciton SHE in experiments and a possible phase transition from dark to bright state driven by SOC are suggested.
Silicon optical amplifier based on surface-plasmon-polariton enhancement
Authors: Wang Yi , Zhou Zhiping
Published: July 2007

A silicon optical amplifier based on surface-plasmon-polariton enhancement is proposed, designed, and simulated. The gain coefficient of the Si:SiEr-metal-silicon structure is increased 24% at 1.54μm and the loss is greatly reduced, comparing with a conventional stack structure. The net gain achieved by the Si:SiEr-metal-silicon structure is in the range of 1–36cm−1 when thickness of the thin gold film is less than 20nm.
Deep subsurface waveguides with circular cross section produced by femtosecond laser writing
Authors: Diez-Blanco V. , Siegel J. , Ferrer A. , Ruiz de la Cruz A. , Solis J.
Published: July 2007

A combination of low numerical aperture focusing optics, in order to minimize spherical aberration, and beam shaping with a slit has been used to produce waveguides in fused silica by femtosecond laser writing. Waveguides with circular cross section and low losses are produced over a large depth window (>7mm) without changing any experimental parameter. Diffraction induces beam divergence along the axis perpendicular to the slit, leading to a shift of the focal plane. The focal intensity distribution can be predicted by a hybrid model combining Gaussian beam propagation with imaging of the slit into the material.
Local surface potential distribution in oriented ferroelectric thin films
Authors: Kim Yunseok , Bühlmann Simon , Kim Jiyoon , Park Moonkyu , No Kwangsoo , Kim Yong Kwan , Hong Seungbum
Published: July 2007

Using Kelvin force microscopy, the authors have investigated the potential distribution on ferroelectric films. The local distribution of potential was observed on downward, prepoled areas. The polarity of the potential corresponds to the screen charge. It was found that the electrical properties of the grain boundary affect the potential distribution. Most of the grain boundaries show a lower potential than the area inside the grain. The authors identified certain regions at the grain boundary with a very low potential. Such potential pits may act as efficient screen charge draining paths and may lead to important perturbations on the device level.
Reduction of speckles in retinal reflection
Authors: Albanis Vassilios , Ribak Erez N. , Carmon Yuval
Published: July 2007

Speckle noise can deteriorate the quality of wave-front sensors measuring ocular aberrations. To counter that, a narrow laser beam was acoustically modulated before entering the eye and creating a spot on the retina. Light was scattered back through the aberrations into the sensor. The increased spot size, wider angular spread, and temporal modulation of the incoming beam averaged out the speckles, producing a more uniform response of the wave-front sensor. The method applies also to retinal imagers and to nonbiological speckle.
Aluminum buffer layer for high durability of all-solid-state switchable mirror based on magnesium-nickel thin film
Authors: Tajima Kazuki , Yamada Yasusei , Bao Shanhu , Okada Masahisa , Yoshimura Kazuki
Published: July 2007

Aluminum buffer layer was inserted in all-solid-state switchable mirror based on Mg–Ni thin film to improve its durability. Optical switching speed of the device has been improved because the buffer layer might work to transport electrons and protons promptly as an electrode. Durability of the device was evaluated by cyclic switching test. The device with buffer layer showed three times higher stable durability than that of the device without buffer layer. The authors found that the aluminum buffer layer effectively works to suppress the diffusion of nickel and palladium atoms into the Ta2O5 thin film during cyclic switching test, resulted in high durability.
Confinement of fractional quantum Hall states in narrow conducting channels
Authors: Willett R. L. , Manfra M. J. , Pfeiffer L. N. , West K. W.
Published: July 2007

Confinement of small gapped fractional quantum Hall states facilitates quasiparticle manipulation and is an important step toward quasiparticle interference measurements. Demonstrated here is conduction through top gate defined, narrow channels in high density, ultrahigh mobility heterostructures. Transport evidence for the persistence of a correlated state at a filling fraction of 5∕3 is shown in channels of 2μm length but is gated to near 0.3μm in width. The methods employed to achieve this confinement hold promise for interference devices proposed for studying potential non-Abelian statistics at a filling fraction of 5∕2.
Electrical characterization of protein molecules by a solid-state nanopore
Authors: Fologea Daniel , Ledden Bradley , McNabb David S. , Li Jiali
Published: July 2007

The authors measured ionic current blockages caused by protein translocation through voltage-biased silicon nitride nanopores in ionic solution. By calculating the mean amplitude, time duration, and the integral of current blockages, they estimated the relative charge and size of protein molecules at a single molecule level. The authors measured the change in protein charge of bovine serum albumin (BSA) protein induced by pH variation. They also confirmed that BSA molecules indeed traverse nanopores using an improved chemiluminescent analysis. They demonstrated that a larger protein fibrinogen could be distinguished from BSA by a solid-state nanopore measurement.
Valence band anticrossing in GaBixAs1−x
Authors: Alberi K. , Dubon O. D. , Walukiewicz W. , Yu K. M. , Bertulis K. , Krotkus A.
Published: July 2007

The optical properties of GaBixAs1−x(0.04<x<0.08) grown by molecular beam epitaxy have been studied by photomodulated reflectance spectroscopy. The alloys exhibit a strong reduction in the band gap as well as an increase in the spin-orbit splitting energy with increasing Bi concentration. These observations are explained by a valence band anticrossing model, which shows that a restructuring of the valence band occurs as the result of an anticrossing interaction between the extended states of the GaAs valence band and the resonant T2 states of the Bi atoms.
Biophysical correlates of relative abundances of marine megafauna at Ningaloo Reef, Western Australia
Authors: Sleeman Jai C. , Meekan Mark G. , Wilson Steven G. , Jenner Curt K. S. , Jenner Micheline N. , Boggs Guy S. , Steinberg Craig C. , Bradshaw Corey J. A.
Published: July 2007

Changes in the relative abundance of marine megafauna (whales, dolphins, sharks, turtles, manta rays, dugongs) from aerial survey sightings in the waters adjacent to Ningaloo Reef between June 2000 and April 2002 are described. Generalised linear models were used to explore relationships between different trophic guilds of animals (based on animal sighting biomass estimates) and biophysical features of the oceanscape that were likely to indicate foraging habitats (regions of primary/secondary production) including sea surface temperature (SST), SST gradient, chlorophyll-a (Chl-a), bathymetry (BTH) and bathymetry gradient (BTHg). Relative biomass of krill feeders (i.e. minke whales, whale sharks, manta rays) were related to SST, Chl-a and bathymetry (model [AICc] weight = 0.45) and the model combining these variables explained a relatively large amount (32.3%) of the variation in relative biomass. Relative biomass of fish/cephalopod feeders (dolphins, sharks) were weakly correlated with changes in SST, whereas that of other invertebrate/macroalgal feeders (turtles, dugong) was weakly correlated with changes in steepness of the shelf (bathymetry gradient). Our results indicate that biophysical variables describe only a small proportion of the variance in the relative abundance and biomass of marine megafauna at Ningaloo reef.
Diversity and depth-related patterns of mobile invertebrates associated with kelp forests
Authors: Coleman Melinda A. , Vytopil Elaine , Goodsell Paris J. , Gillanders Bronwyn M. , Connell Sean D.
Published: July 2007

It is remarkable that although the importance of depth is firmly rooted in the discipline of marine ecology, so little is understood about depth-related patterns of invertebrates in kelp forests, particularly in temperate Australia. We tested for the existence of broad scale patterns in depth-related diversity and abundance of mobile invertebrates in kelp holdfasts (Ecklonia radiata) across several spatial scales along 500 km of coastline. There was a greater abundance and richness of common taxa in holdfasts from shallow relative to deep waters. Strikingly, a disproportionately large percentage (60%) of species was unique to holdfasts from shallow reefs, suggesting that shallow environments create conditions that facilitate a rich biodiversity of invertebrate fauna. We conclude that depth-related variation in kelp forests may not be completely idiosyncratic, and coherent research programs of a broader scale and scope may unify subsets of fragmented knowledge that previously provided little insight into general depth-related patterns of invertebrate assemblages.
Single-molecule fluorescence spectroscopy in (bio)catalysis
Authors: Roeffaers Maarten B. J. , De Cremer Gert , Uji-i Hiroshi , Muls Benîot , Sels Bert F. , Jacobs Pierre A. , De Schryver Frans C. , De Vos Dirk E. , Hofkens Johan
Published: July 2007

The ever-improving time and space resolution and molecular detection sensitivity of fluorescence microscopy offer unique opportunities to deepen our insights into the function of chemical and biological catalysts. Because single-molecule microscopy allows for counting the turnover events one by one, one can map the distribution of the catalytic activities of different sites in solid heterogeneous catalysts, or one can study time-dependent activity fluctuations of individual sites in enzymes or chemical catalysts. By experimentally monitoring individuals rather than populations, the origin of complex behavior, e.g., in kinetics or in deactivation processes, can be successfully elucidated. Recent progress of temporal and spatial resolution in single-molecule fluorescence microscopy is discussed in light of its impact on catalytic assays. Key concepts are illustrated regarding the use of fluorescent reporters in catalytic reactions. Future challenges comprising the integration of other techniques, such as diffraction, scanning probe, or vibrational methods in single-molecule fluorescence spectroscopy are suggested.
Reversible atomic processes as basic mechanisms of the glass transition
Authors: Ye Feng , Sprengel Wolfgang , Wunderlich Rainer K. , Fecht Hans-Jörg , Schaefer Hans-Eckhardt
Published: July 2007

Reversible formation and disappearance of vacant spaces (vacancy-type defects) in bulk Zr
57
Cu
15.4
Ni
12.6
Nb
5
Al
10
glass are directly evidenced by high-resolution, time-differential dilatometry studies. The vacancy kinetics are strongly temperature-dependent, with an effective migration enthalpy of
H
V
M
= 3.34 eV. This may explain the strong temperature dependence of glass properties such as viscosity. The results presented here are of general importance for understanding amorphous condensed matter and biomaterials and for the technical development of amorphous steels.
Prolonged Permian–Triassic ecological crisis recorded by molluscan dominance in Late Permian offshore assemblages
Authors: Clapham Matthew E. , Bottjer David J.
Published: July 2007

The end-Permian mass extinction was the largest biotic crisis in the history of animal life, eliminating as many as 95% of all species and dramatically altering the ecological structure of marine communities. Although the causes of this pronounced ecosystem shift have been widely debated, the broad consensus based on inferences from global taxonomic diversity patterns suggests that the shift from abundant brachiopods to dominant molluscs was abrupt and largely driven by the catastrophic effects of the end-Permian mass extinction. Here we analyze relative abundance counts of >33,000 fossil individuals from 24 silicified Middle and Late Permian paleocommunities, documenting a substantial ecological shift to numerical dominance by molluscs in the Late Permian, before the major taxonomic shift at the end-Permian mass extinction. This ecological change was coincident with the development of fluctuating anoxic conditions in deep marine basins, suggesting that numerical dominance by more tolerant molluscs may have been driven by variably stressful environmental conditions. Recognition of substantial ecological deterioration in the Late Permian also implies that the end-Permian extinction was the climax of a protracted environmental crisis. Although the Late Permian shift to molluscan dominance was a pronounced ecological change, quantitative counts of 847 Carboniferous–Cretaceous collections from the Paleobiology Database indicate that it was only the first stage in a stepwise transition that culminated with the final shift to molluscan dominance in the Late Jurassic. Therefore, the ecological transition from brachiopods to bivalves was more protracted and complex than their simple Permian–Triassic switch in diversity.
DNA damage-site recognition by lysine conjugates
Authors: Breiner Boris , Schlatterer Jörg C. , Alabugin Igor V. , Kovalenko Serguei V. , Greenbaum Nancy L.
Published: July 2007

Simple lysine conjugates are capable of selective DNA damage at sites approximating a variety of naturally occurring DNA-damage patterns. This process transforms single-strand DNA cleavage into double-strand cleavage with a potential impact on gene and cancer therapy or on the design of DNA constructs that require disassembly at a specific location. This study constitutes an example of DNA damage site recognition by molecules that are two orders of magnitude smaller than DNA-processing enzymes and presents a strategy for site-selective cleavage of single-strand nucleotides, which is based on their annealing with two shorter counterstrands designed to recreate the above duplex damage site.
Signaling through FcγRIII is required for optimal T helper type (Th)2 responses and Th2-mediated airway inflammation
Authors: Bandukwala Hozefa S. , Clay Bryan S. , Tong Jiankun , Mody Purvi D. , Cannon Judy L. , Shilling Rebecca A. , Verbeek J. Sjef , Weinstock Joel V. , Solway Julian , Sperling Anne I.
Published: July 2007

Although inhibitory Fcγ receptors have been demonstrated to promote mucosal tolerance, the role of activating Fcγ receptors in modulating T helper type (Th)2-dependent inflammatory responses characteristic of asthma and allergies remains unclear. Here, we demonstrate that signaling via activating Fcγ receptors in conjunction with Toll-like receptor 4 stimulation modulated cytokine production from bone marrow–derived dendritic cells (DCs) and augmented their ability to promote Th2 responses. Ligation of the low affinity receptor FcγRIII was specifically required for the enhanced Th2 responses, as FcγRIII−/− DCs failed to augment Th2-mediated airway inflammation in vivo or induce Th2 differentiation in vitro. Further, FcγRIII−/− mice had impaired Th2 cytokine production and exhibited reduced airway inflammation, whereas no defect was found in FcγRI−/− mice. The augmentation of Th2 immunity was regulated by interleukin 10 production from the DCs but was distinct and independent of the well-established role of FcγRIII in augmenting antigen presentation. Thus, our studies reveal a novel and specific role for FcγRIII signaling in the regulation of Th cell responses and suggest that in addition to immunoglobulin (Ig)E, antigen-specific IgG also contributes to the pathogenesis of Th2-mediated diseases such as asthma and allergies.
Signal transducer of inflammation gp130 modulates atherosclerosis in mice and man
Authors: Luchtefeld Maren , Schunkert Heribert , Stoll Monika , Selle Tina , Lorier Rachel , Grote Karsten , Sagebiel Christian , Jagavelu Kumaravelu , Tietge Uwe J.F. , Assmus Ulrike , Streetz Konrad , Hengstenberg Christian , Fischer Marcus , Mayer Björn , Maresso Karen , El Mokhtari Nour Eddine , Schreiber Stefan , Müller Werner , Bavendiek Udo , Grothusen Christina , Drexler Helmut , Trautwein Christian , Broeckel Ulrich , Schieffer Bernhard
Published: July 2007

Liver-derived acute phase proteins (APPs) emerged as powerful predictors of cardiovascular disease and cardiovascular events, but their functional role in atherosclerosis remains enigmatic. We report that the gp130 receptor, which is a key component of the inflammatory signaling pathway within hepatocytes, influences the risk of atherosclerosis in a hepatocyte-specific gp130 knockout. Mice on an atherosclerosis-prone genetic background exhibit less aortic atherosclerosis (P < 0.05) with decreased plaque macrophages (P < 0.01). Translating these findings into humans, we show that genetic variation within the human gp130 homologue, interleukin 6 signal transducer (IL6ST), is significantly associated with coronary artery disease (CAD; P < 0.05). We further show a significant association of atherosclerotic disease at the ostium of the coronary arteries (P < 0.005) as a clinically important and heritable subphenotype in a large sample of families with myocardial infarction (MI) and a second independent population–based cohort. Our results reveal a central role of a hepatocyte-specific, gp130-dependent acute phase reaction for plaque development in a murine model of atherosclerosis, and further implicate IL6ST as a genetic susceptibility factor for CAD and MI in humans. Thus, the acute phase reaction should be considered an important target for future drug development in the management of CAD.
Fibrin deposition accelerates neurovascular damage and neuroinflammation in mouse models of Alzheimer's disease
Authors: Paul Justin , Strickland Sidney , Melchor Jerry P.
Published: July 2007

Cerebrovascular dysfunction contributes to the pathology and progression of Alzheimer's disease (AD), but the mechanisms are not completely understood. Using transgenic mouse models of AD (TgCRND8, PDAPP, and Tg2576), we evaluated blood–brain barrier damage and the role of fibrin and fibrinolysis in the progression of amyloid-β pathology. These mouse models showed age-dependent fibrin deposition coincident with areas of blood–brain barrier permeability as demonstrated by Evans blue extravasation. Three lines of evidence suggest that fibrin contributes to the pathology. First, AD mice with only one functional plasminogen gene, and therefore with reduced fibrinolysis, have increased neurovascular damage relative to AD mice. Conversely, AD mice with only one functional fibrinogen gene have decreased blood–brain barrier damage. Second, treatment of AD mice with the plasmin inhibitor tranexamic acid aggravated pathology, whereas removal of fibrinogen from the circulation of AD mice with ancrod treatment attenuated measures of neuroinflammation and vascular pathology. Third, pretreatment with ancrod reduced the increased pathology from plasmin inhibition. These results suggest that fibrin is a mediator of inflammation and may impede the reparative process for neurovascular damage in AD. Fibrin and the mechanisms involved in its accumulation and clearance may present novel therapeutic targets in slowing the progression of AD.
The neutrophil serine protease inhibitor serpinb1 preserves lung defense functions in Pseudomonas aeruginosa infection
Authors: Benarafa Charaf , Priebe Gregory P. , Remold-O'Donnell Eileen
Published: July 2007

Neutrophil serine proteases (NSPs; elastase, cathepsin G, and proteinase-3) directly kill invading microbes. However, excess NSPs in the lungs play a central role in the pathology of inflammatory pulmonary disease. We show that serpinb1, an efficient inhibitor of the three NSPs, preserves cell and molecular components responsible for host defense against Pseudomonas aeruginosa. On infection, wild-type (WT) and serpinb1-deficient mice mount similar early responses, including robust production of cytokines and chemokines, recruitment of neutrophils, and initial containment of bacteria. However, serpinb1−/− mice have considerably increased mortality relative to WT mice in association with late-onset failed bacterial clearance. We found that serpinb1-deficient neutrophils recruited to the lungs have an intrinsic defect in survival accompanied by release of neutrophil protease activity, sustained inflammatory cytokine production, and proteolysis of the collectin surfactant protein–D (SP-D). Coadministration of recombinant SERPINB1 with the P. aeruginosa inoculum normalized bacterial clearance in serpinb1−/− mice. Thus, regulation of pulmonary innate immunity by serpinb1 is nonredundant and is required to protect two key components, the neutrophil and SP-D, from NSP damage during the host response to infection.
Naive CD8+ T cells differentiate into protective memory-like cells after IL-2–anti–IL-2 complex treatment in vivo
Authors: Kamimura Daisuke , Bevan Michael J.
Published: July 2007

An optimal CD8+ T cell response requires signals from the T cell receptor (TCR), co-stimulatory molecules, and cytokines. In most cases, the relative contribution of these signals to CD8+ T cell proliferation, accumulation, effector function, and differentiation to memory is unknown. Recent work (Boyman, O., M. Kovar, M.P. Rubinstein, C.D. Surh, and J. Sprent. 2006. Science. 311:1924–1927; Kamimura, D., Y. Sawa, M. Sato, E. Agung, T. Hirano, and M. Murakami. 2006. J. Immunol. 177:306–314) has shown that anti–interleukin (IL) 2 monoclonal antibodies that are neutralizing in vitro enhance the potency of IL-2 in vivo. We investigated the role of IL-2 signals in driving CD8+ T cell proliferation in the absence of TCR stimulation by foreign antigen. IL-2 signals induced rapid activation of signal transducer and activator of transcription 5 in all CD8+ T cells, both naive and memory phenotype, and promoted the differentiation of naive CD8+ T cells into effector cells. IL-2–anti–IL-2 complexes induced proliferation of naive CD8+ T cells in an environment with limited access to self–major histocompatibility complex (MHC) and when competition for self-MHC ligands was severe. After transfer into wild-type animals, IL-2–activated CD8+ T cells attained and maintained a central memory phenotype and protected against lethal bacterial infection. IL-2–anti–IL-2 complex–driven memory-like CD8+ T cells had incomplete cellular fitness compared with antigen-driven memory cells regarding homeostatic turnover and cytokine production. These results suggest that intense IL-2 signals, with limited contribution from the TCR, program the differentiation of protective memory-like CD8+ cells but are insufficient to guarantee overall cellular fitness.
An intense form of homeostatic proliferation of naive CD8+ cells driven by IL-2
Authors: Cho Jae-Ho , Boyman Onur , Kim Hee-Ok , Hahm Bumsuk , Rubinstein Mark P. , Ramsey Chris , Kim David M. , Surh Charles D. , Sprent Jonathan
Published: July 2007

In conditions of T lymphopenia, interleukin (IL) 7 levels rise and, via T cell receptor for antigen–self–major histocompatibility complex (MHC) interaction, induce residual naive T cells to proliferate. This pattern of lymphopenia-induced “homeostatic” proliferation is typically quite slow and causes a gradual increase in total T cell numbers and differentiation into cells with features of memory cells. In contrast, we describe a novel form of homeostatic proliferation that occurs when naive T cells encounter raised levels of IL-2 and IL-15 in vivo. In this situation, CD8+ T cells undergo massive expansion and rapid differentiation into effector cells, thus closely resembling the T cell response to foreign antigens. However, the responses induced by IL-2/IL-15 are not seen in MHC-deficient hosts, implying that the responses are driven by self-ligands. Hence, homeostatic proliferation of naive T cells can be either slow or fast, with the quality of the response to self being dictated by the particular cytokine (IL-7 vs. IL-2/IL-15) concerned. The relevance of the data to the gradual transition of naive T cells into memory-phenotype (MP) cells with age is discussed.
The role of gear technologists in supporting an ecosystem approach to fisheries
Authors: Jennings Simon , Revill Andrew S.
Published: July 2007

Jennings, S., and Revill, A. S. 2007. The role of gear technologists in supporting an ecosystem approach to fisheries. – ICES Journal of Marine Science, 64: 1525–1534. Central to an ecosystem approach to fisheries (EAF) is reconciling the short-term need for catches with the long-term need for sustainability of target species and other ecosystem components. We assess the role of gear technology in supporting the objectives and implementation of EAF and identify the circumstances in which investment in the environmental performance of fishing gear provides the greatest benefits. The greatest benefits are usually achieved when gear technologists embed the new technology in the management system and when there are clear incentives to use it. We propose a framework for comparing combinations of management measures that might support EAF, based on knowledge of the environmental impacts of different gears in different areas and management systems. This framework helps us assess when fishing effects “matter” and when gear technologists should contribute to mitigating unwanted effects. Incentives and effective enforcement will be key to introducing gears with lower environmental impact. We expect that future emphasis on marine spatial planning, the use of environmental impact assessment and strategic environmental assessment for fisheries, more equitable treatment of fisheries and other marine sectors, and rising oil prices will lead to greater pressure on gear technologists to support EAF.
Growth hormone (GH) treatment reduces peripheral thyroid hormone action in girls with Turner syndrome
Authors: Susperreguy S. , Miras M. B. , Montesinos M. M. , Mascanfroni I. D. , Muñoz L. , Sobrero G. , Silvano L. , Masini‐Repiso A. M. , Coleoni A. H. , Targovnik H. M. , Pellizas C. G.
Published: July 2007

Objective  Turner syndrome (TS) is an indication for GH therapy in spite of the modest growth response. Somatic growth depends not only on GH insulin‐like growth factor I (IGF‐I) axis but also on thyroid hormone (TH) status. We have previously reported that supraphysiological IGF‐I levels diminished TH actions in rat tissues by reducing the nuclear TH receptor (TR). GH treatment to TS patients induces high IGF‐I levels and therefore a reduction of TH action in tissues may be expected. We aimed at evaluating the effect of GH therapy in TS girls on peripheral TH action.

Design and patients  We set up a reverse transcription‐polymerase chain reaction (RT‐PCR) for TR mRNA estimation in peripheral blood mononuclear cells (PBMC) and compared TR mRNA levels from 10 normal, 10 TS and 10 TS girls under GH therapy (0·33 mg/kg/week for 0·5–2 years).

Measurements  After RNA extraction from PBMC, TR and β‐actin mRNAs were coamplified by RT‐PCR. In addition serum biochemical markers of TH action were measured: thyrotropin (TSH), sex hormone binding globulin (SHBG), osteocalcin (OC), β‐crosslaps (β‐CL), iodothyronines by electrochemiluminescency and IGF‐I by immunoradiometric assay (IRMA) with extraction.

Results  TR mRNAs from PBMC were reduced in TS patients under GH treatment. In turn, serum TSH, OC, β‐CL and IGF‐I were increased while SHBG was reduced by GH treatment in TS patients.

Conclusions  GH treatment reduced TR expression in PBMC and biochemical serum markers of TH action. These results suggest that GH treatment in TS patients impair peripheral TH action at tissue level and prompt a role in the reduced growth response to the therapy.
Reduced thyroid volume and nodularity in dyslipidaemic patients on statin treatment
Authors: Cappelli Carlo , Castellano Maurizio , Pirola Ilenia , De Martino Elvira , Gandossi Elena , Delbarba Andrea , Salvi Andrea , Rosei Enrico Agabiti
Published: July 2007

Background  Little information is available concerning the possible antiproliferative effects of 3‐hydroxy‐3‐methylglutaryl coenzyme A (HMG‐CoA) reductase inhibitors (statins) on the thyroid gland. We have hypothesized that the antiproliferative effects of statins observed in thyroid cell lines in vitro may have a clinical counterpart that could be detected by investigating the prevalence and size of thyroid nodules in patients on long‐term treatment with statins.

Methods  We retrospectively evaluated 135 dyslipidaemic patients receiving statin therapy continuously for at least 5 years, and 137 controls. All the subjects were submitted to ultrasound investigation of the thyroid gland, to establish prevalence, number and volume of thyroid nodules.

Results  Subjects treated with statins showed markedly lower prevalence of thyroid nodules (36·3%vs. 67·9%, P < 0·001), as well as reduced number and smaller total volume of lesions, as compared to the control group. A logistic regression analysis, taking into account age, sex, risk factors for the development of thyroid nodules and concomitant drug treatment, revealed that treatment with statins remained the only important predictor of the presence of thyroid nodules [odds ratio (OR) 0·312, 95% confidence interval (CI) 0·156–0·625, P < 0·001] besides risk factors.

Conclusions  Our data provide the first circumstantial evidence of an association between HMG‐CoA reductase inhibitor treatment and reduced prevalence, number and volume of thyroid nodules. This finding may be explained by an antiproliferative and/or pro‐apoptotic effect of long‐term statin treatment on thyroid cells, in vivo.
Altered distribution of adiponectin isoforms in children with Prader–Willi syndrome (PWS): association with insulin sensitivity and circulating satiety peptide hormones
Authors: Haqq Andrea M. , Muehlbauer Michael , Svetkey Laura P. , Newgard Christopher B. , Purnell Jonathan Q. , Grambow Steven C. , Freemark Michael S.
Published: July 2007

Objective  Prader–Willi syndrome (PWS) is a genetic syndrome characterized by relative hypoinsulinaemia and normal or increased insulin sensitivity despite profound obesity. We hypothesized that this increased insulin sensitivity is mediated by increased levels of total and high molecular weight adiponectin and associated with changes in levels of satiety hormones.

Design, patients and measurements  We measured total adiponectin and its isoforms [high molecular weight (HMW), middle molecular weight (MMW) and low molecular weight (LMW) adiponectin] and satiety hormones in 14 children with PWS [median age 11·35 years, body mass index (BMI) Z‐score 2·15] and 14 BMI‐matched controls (median age 11·97 years, BMI Z‐score 2·34).

Results  Despite comparable BMI Z‐scores and leptin levels, the PWS children exhibited lower fasting insulin and HOMA‐IR (homeostasis model assessment of insulin resistance) scores compared to obese controls. For any given BMI Z‐score, the PWS children showed higher concentrations of fasting total and HMW adiponectin and higher HMW/total adiponectin ratios. The HMW/total adioponectin ratio was preserved in children with PWS at high degrees of obesity. In PWS children, fasting plasma total adiponectin, HMW adiponectin and HMW/total adiponectin ratio correlated negatively with age (P < 0·05), HOMA‐IR (P < 0·01), BMI Z‐score (P < 0·05), insulin (P < 0·01) and leptin (P < 0·05). In addition to higher fasting ghrelin concentrations, the PWS children showed significantly higher fasting levels of total peptide YY (PYY) and gastric inhibitory polypeptide (GIP) compared to obese controls.

Conclusions  Relative to controls of similar age and BMI Z‐score, the PWS children had significantly higher levels of total and HMW adiponectin, and increased ratios of HMW/total adiponectin. These findings may explain in part the heightened insulin sensitivity of PWS children relative to BMI‐matched controls.