bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase-sensitive swept source optical coherence tomography for imaging and quantifying of microbubbles in clear and scattering media
Authors: Manapuram Ravi Kiran , Manne Venu Gopal Reddy , Larin Kirill V.
Published: May 2009

A phase resolved system based on swept source optical coherence tomography (SSOCT) called as phase-sensitive SSOCT to detect and quantify gas microbubbles in aqueous and tissue simulated media is developed. The structural images of gas microbubbles are obtained using conventional SSOCT, while common path SSOCT was used to perform the phase-sensitive measurements. The system shows an axial resolution of 10μm, a phase sensitivity of 0.03rad, an imaging depth of up to 6mm in air, and a scanning speed of 20kHz for a single A-line. The structural images of the bubbles show an accuracy of 10μm, whereas the temporal phase response show an accuracy of 0.01μm. Images of rapidly moving bubbles are also presented which indicate that the SSOCT could be ultimately applied for the rapid assessment of microbubbles in biofluids and tissues.
A review of some recent developments in polarization-sensitive optical imaging techniques for the study of articular cartilage
Authors: Matcher Stephen J.
Published: May 2009

This article reviews recent developments in the optical imaging of articular cartilage using polarized-light methods, with an emphasis on tools that could be of use in tissue engineering approaches to treatment. Both second-harmonic generation microscopy and polarization-sensitive optical coherence tomography are described and their potential role in the treatment of cartilage disorders such as osteoarthritis is suggested. Key results are reviewed and future developments are discussed.
Application of biophysical technologies in dental research
Authors: Higham Susan M. , Pender Neil , de Josselin de Jong Elbert , Smith Philip W.
Published: May 2009

There is a wealth of evidence to indicate that if dental caries can be recognized at an early stage, it is possible to halt its progression or even reverse it. This has led to an increased interest in the development of diagnostic techniques capable of visualizing caries at an early stage in addition to providing clinicians with an aid to diagnosis. Several techniques are available for research and clinical applications for detecting early demineralization. This manuscript has reviewed some of the techniques currently available to determine their advantages, whether they have any limitations and their applicability to dental research and clinical dentistry. Not one method is the perfect choice in all situations, but what is clear is that the development and application of biophysical technologies have allowed major advances to be made in dental research as well as in clinical dentistry. With continued developments these technologies will play an important role in the future management of dental disease.
Thrombin generation test in microfluidic systems
Authors: Koch Kaspar , van Berkel Sander S. , van de Wal Marloes M. E. B. , Nieuwland Pieter J. , van Hest Jan C. M. , Rutjes Floris P. J. T.
Published: May 2009

The thrombin generation test is one of the diagnostic tests currently in use as a universal method for measuring hemostatic disorders. We envisioned that conventional monitoring of thrombin generation could be miniaturized resulting in a time-saving, accurate, easy-to-operate, and cost-efficient test. For the translation of the conventional thrombin generation test to microfluidic devices, our focus was directed to parameters such as the detection limit, temperature, protein-surface interactions (i.e., hydrophilicity of microchannels), and mixing behavior. Scaling down to microchannels (e.g., capillaries) resulted in volume reduction and allowed us to study the effect of a microchannel surface (either hydrophilic or hydrophobic) on the thrombin activity. Finally, the use of a micromixer enabled us to perform efficient on-chip mixing, resulting in the successful measurement of a thrombin generation in a microfluidic device.
Mechanism of voltage production and frequency dependence of the ultrasonic vibration potential
Authors: Nguyen Cuong K. , Wang Shougang , Diebold Gerald
Published: May 2009

Imaging with the ultrasonic vibration potential is based on voltage generation by a colloidal or ionic suspension in response to the passage of ultrasound. The polarization within a body arising from the oscillatory displacement in the ultrasonic field produces a current in a pair of external electrodes that is measured as a function of time or frequency. Existing theory gives the current in the electrodes as arising from both a time varying polarization and ionic conduction. Here, experiments are reported that show the production of the polarization current is the dominant mechanism for current generation in soft tissue. Experiments are also reported giving the frequency dependence of the ultrasonic vibration current in canine blood and in several dilutions of aqueous silica suspensions.
Achieving consistency of Young’s modulus determination from nanoscale deformation of low-k films
Authors: Nagao S. , Fujikane M. , Tymiak N. , Nowak R.
Published: May 2009

The present study proposes a method for determining indenter shape-independent Young’s moduli of thin low-k films from a composite film/substrate nanoindentation response. In contrast to the previous models utilizing empirical fitting parameters, the present authors introduce substrate effect factor determined by the elastic film/substrate mismatch, film thickness, and indenter angle. The new method overcomes several deficiencies of the previous models. Such deficiencies include inability to explain/account for the observed difference in the scale of substrate effect sampled by Berkovich and cube corner indenters. The present model provides consistent Young’s moduli of 5.8–6.1 GPa for both types of indenters.
Theoretical studies of the optical properties of plasmon resonance on silver nanoparticles in the near-field optics
Authors: Ma Ye-Wan , Zhang Yu , Wu Zhao-Wang , Zhang Li-Hua , Zhang Jie , Jian Guo-Shu , Wu Shi-Fa
Published: May 2009

Near-field spectral characteristics, images, and optical parameters of silver nanoparticles are studied using Green’s tensor. The Lippmann–Schwinger integral equation is discretized, and numerically solved with complex-conjugate gradient method-fast Fourier transform algorithm. Simulation models include placing nanoparticles in either an infinitely homogeneous medium or on a substrate, and illuminated either directly with plane waves or through a glass substrate under total internal reflection. Simulation results suggest that local plasmon resonance redshifts to longer wavelengths when dielectric constant of the surrounding medium increases or when a substrate is presented, but blueshifts to shorter wavelengths when the height of a nanoparticle increases. Due to the exponential attenuation behavior of evanescent waves, total intensity of electrical field attenuates quickly as the detection distance increases. Optical efficiencies, scattering efficiencies, absorption, and extinction efficiencies of Ag nanoparticles are also reported.
Coherent homogenization of periodic structures: Transformation from structurally periodic (photonic band gap) structures to optically uniform materials
Authors: Sadeghi S. M. , Li W.
Published: May 2009

A relevant feature of periodic structures that serves as the cornerstone of many optical devices and photonic systems is alternative variations of refractive index and/or gain (loss). In this paper we will show how in Bragg multiquantum well active photonic gap structures, wherein refractive index periodicity comes with super-radiant excitons, one can use an infrared laser to design optical materials with fundamentally unique features. This includes coherent formation of a state of optical materials wherein within a frequency range around the Bragg wavelength the periodic structure becomes optically homogeneous, i.e., its material and structural periodicity are concealed from a probe field. For active photonic band structures containing structural defects, we show that this process can lead to full removal of the optical mode associated with the defect, making a uniform defectless optical material, or to generation of another defect mode at a different frequency. Applications of the results for ultrafast switching and time delay control are discussed.
Singularities of two-dimensional invertible piecewise isometric dynamics
Authors: Kahng Byungik
Published: May 2009

We investigate the singularity structure of two-dimensional invertible piecewise isometric dynamics. The main purpose of this research is to establish the connection between the geometrical properties of the singularity and the dynamics of the system. We classify the singularity of two-dimensional bounded invertible piecewise isometric dynamics into three types with respect to their geometrical properties. Among the three, we show that one type of the singularity can be removed by lifting up the dynamics to a suitably defined (branched) manifold. Among the remaining two, we prove that only one of them contributes to the intricate orbit structure of the system and generates the sensitive dependence on the initial condition, while the other does nothing.
Development and validation of a predictive model for the pedestal height
Authors: Snyder P. B. , Groebner R. J. , Leonard A. W. , Osborne T. H. , Wilson H. R.
Published: May 2009

The pressure at the top of the edge transport barrier (or “pedestal height”) strongly impacts tokamak fusion performance. Predicting the pedestal height in future devices such as ITER [ITER Physics Basis Editors, Nucl. Fusion 39, 2137 (1999)] remains an important challenge. While uncertainties remain, magnetohydrodynamic stability calculations at intermediate wavelength (the “peeling-ballooning” model), accounting for diamagnetic stabilization, have been largely successful in determining the observed maximum pedestal height, when the edge barrier width is taken as an input. Here, we develop a second relation between the pedestal width in normalized poloidal flux (Δ) and pedestal height (Δ=0.076βθ,ped1/2), using an argument based upon kinetic ballooning mode turbulence and observation. Combining this relation with direct calculations of peeling-ballooning stability yields two constraints, which together determine both the height and width of the pedestal. The resulting model, EPED1, allows quantitative prediction of the pedestal height and width in both existing and future experiments. EPED1 is successfully tested both against a dedicated experiment on the DIII-D [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] tokamak, in which predictions were made before the experiment, and against a broader DIII-D data set, including ITER demonstration discharges. EPED1 is found to quantitatively capture the observed complex dependencies of the pedestal height and width. An initial set of pedestal predictions for the ITER device is presented.
Plasma rotation driven by static nonresonant magnetic fields
Authors: Garofalo A. M. , Solomon W. M. , Lanctot M. , Burrell K. H. , DeBoo J. C. , deGrassie J. S. , Jackson G. L. , Park J.-K. , Reimerdes H. , Schaffer M. J. , Strait E. J.
Published: May 2009

Recent experiments in high temperature DIII-D tokamak [J. L. Luxon, Nucl. Fusion 42, 64 (2002)] plasmas reported the first observation of plasma acceleration driven by the application of static nonresonant magnetic fields (NRMFs), with resulting improvement in the global energy confinement time. Although the braking effect of static magnetic field asymmetries is well known, recent theory [A. J. Cole et al., Phys. Rev. Lett. 99, 065001 (2007)] predicts that in some circumstances they lead instead to an increase in rotation frequency toward a “neoclassical offset” rate in a direction opposed to the plasma current. We report the first experimental confirmation of this surprising result. The measured NRMF torque shows a strong dependence on both plasma density and temperature, above expectations from neoclassical theory. The consistency between theory and experiment improves with modifications to the expression of the NRMF torque accounting for a significant role of the plasma response to the external field and for the beta dependence of the plasma response, although some discrepancy remains. The magnitude and direction of the observed offset rotation associated with the NRMF torque are consistent with neoclassical theory predictions. The offset rotation rate is about 1% of the Alfven frequency or more than double the rotation needed for stable operation at high βN above the n=1 no-wall kink limit in DIII-D.
t
-topology on the n-dimensional Minkowski space
Authors: Agrawal Gunjan , Shrivastava Sampada
Published: May 2009

In this paper, a topological study of the n-dimensional Minkowski space, n>1, with t-topology, denoted by Mt, has been carried out. This topology, unlike the usual Euclidean one, is more physically appealing being defined by means of the Lorentzian metric. It shares many topological properties with similar candidate topologies and it has the advantage of being first countable. Compact sets of Mt and continuous maps into Mt are studied using the notion of Zeno sequences besides characterizing those sets that have the same subspace topologies induced from the Euclidean and t-topologies on n-dimensional Minkowski space. A necessary and sufficient condition for a compact set in the Euclidean n-space to be compact in Mt is obtained, thereby proving that the n-cube, n>1, as a subspace of Mt, is not compact, while a segment on a timelike line is compact in Mt. This study leads to the nonsimply connectedness of Mt, for n=2. Further, Minkowski space with s-topology has also been dealt with.
Out-of-equilibrium dynamics of a fractal model gel
Authors: Suarez M.-A. , Kern N. , Pitard E. , Kob W.
Published: May 2009

Using molecular dynamics computer simulations we investigate the dynamics of a gel. We start from a fractal structure generated by the diffusion limited cluster aggregation-deflection algorithm, onto which we then impose an interaction potential consisting of a short-range attraction as well as a long-range repulsion. After relaxing the system at zero temperature, we let it evolve at a fixed finite temperature. Depending on the temperature T we find different scenarios for the dynamics. For T≳0.2 the fractal structure is unstable and breaks up into small clusters which relax to equilibrium. For T≲0.2 the structure is stable and the dynamics slows down with increasing waiting time. At intermediate and low T the mean squared displacement scales as t2/3 and we discuss several mechanisms for this anomalous time dependence. For intermediate T, the self-intermediate scattering function is given by a compressed exponential at small wave vectors and by a stretched exponential at large wave vectors. In contrast, for low T it is a stretched exponential for all wave vectors. This behavior can be traced back to a subtle interplay between elastic rearrangements, fluctuations of chainlike filaments, and heterogeneity.
Unfolding polyelectrolytes in trivalent salt solutions using dc electric fields: A study by Langevin dynamics simulations
Authors: Wei Yu-Fu , Hsiao Pai-Yi
Published: May 2009

We study the behavior of single linear polyelectrolytes condensed by trivalent salt under the action of electric fields through computer simulations. The chain is unfolded when the strength of the electric field is stronger than a critical value. This critical electric field follows a scaling law against chain length, and the exponent of the scaling law is −0.77(1), smaller than the theoretical prediction, −3ν/2 [R. R. Netz, Phys. Rev. Lett. 90, 128104 (2003)], and the one obtained by simulations in tetravalent salt solutions, −0.453(3) [P.-Y. Hsiao and K.-M. Wu, J. Phys. Chem. B 112, 13177 (2008)]. It demonstrates that the scaling exponent depends sensitively on the salt valence. Hence, it is easier to unfold chains condensed by multivalent salt of a smaller valence. Moreover, the absolute value of chain electrophoretic mobility increases drastically when the chain is unfolded in an electric field. The fact that the mobility depends on electric field and on chain length provides a plausible way to impart chain-length dependence in free-solution electrophoresis via chain unfolding transition induced by electric fields. Finally, we show that, in addition to an elongated structure, a condensed chain can be unfolded into a U-shaped structure. The formation of this structure in our study is purely a result of the electric polarization, not of the elastohydrodynamics dominated in sedimentation of polymers.
Exact ionization potentials from wavefunction asymptotics: The extended Koopmans’ theorem, revisited
Authors: Vanfleteren Diederik , Van Neck Dimitri , Ayers Paul W. , Morrison Robert C. , Bultinck Patrick
Published: May 2009

A simple explanation is given for the exactness of the extended Koopmans’ theorem, (EKT) for computing the removal energy of any many-electron system to the lowest-energy ground state ion of a given symmetry. In particular, by removing the electron from a “removal orbital” of appropriate symmetry that is concentrated in the asymptotic region, one obtains the exact ionization potential and the exact Dyson orbital for the corresponding state of the ion. It is argued that the EKT is not restricted to many-electron systems but holds for any finite many-body system, provided that the interaction vanishes for increasing interparticle distance. A necessary and sufficient condition for the validity of the EKT for any state (not just the lowest-energy states of a given symmetry) in terms of the third-order reduced density matrix is stated and derived.
A new low drift integrator system for the Experiment Advanced Superconductor Tokamak
Authors: Liu D. M. , Wan B. N. , Wang Y. , Wu Y. C. , Shen B. , Ji Z. S. , Luo J. R.
Published: May 2009

A new type of the integrator system with the low drift characteristic has been developed to accommodate the long pulse plasma discharges on Experiment Advanced Superconductor Tokamak (EAST). The integrator system is composed of the Ethernet control module and the integral module which includes one integrator circuit, followed by two isolation circuits and two program-controlled amplifier circuits. It compensates automatically integration drift and is applied in real-time control. The performance test and the experimental results in plasma discharges show that the developed integrator system can meet the requirements of plasma control on the accuracy and noise level of the integrator in long pulse discharges.
Aspect-ratio effects in the driven, flux-core spheromak
Authors: Hooper E. B. , Romero-Talamás C. A. , LoDestro L. L. , Wood R. D. , McLean H. S.
Published: May 2009

Resistive magnetohydrodynamic simulations are used to evaluate the effects of the aspect ratio A (length to radius ratio) in a spheromak driven by coaxial helicity injection. The simulations are benchmarked against the Sustained Spheromak Physics Experiment (SSPX) [R. D. Wood et al., Nucl. Fusion 45, 1582 (2005)]. Amplification of the bias (“gun”) poloidal flux is fitted well by a linear dependence (insensitive to A) on the ratio of gun current and bias flux above a threshold dependent on A. For low flux amplifications in the simulations, the n=1 mode is coherent and the mean-field geometry looks like a tilted spheromak. Because the mode has relatively large amplitude the field lines are open everywhere, allowing helicity penetration. Strongly driven helicity injection at A≤1.4 in simulations generates reconnection events which generate cathode-voltage spikes, relaxation of the symmetry-breaking modes, and open, stochastic magnetic field lines; this state is characteristic of SSPX. The time sequences of these events suggest that they are representative of a chaotic process. Near the spheromak tilt-mode limit, A≈1.67 for a cylindrical flux conserver, the tilt approaches 90°; reconnection events are not generated up to the strongest drives simulated. Implications for spheromak experiments are discussed.
Magnetic anisotropy from density functional calculations. Comparison of different approaches: Mn12O12 acetate as a test case
Authors: van Wüllen Christoph
Published: May 2009

Magnetic anisotropy is the capability of a system in a triplet or higher spin state to store magnetic information. Although the source of the magnetic anisotropy is the zero-field splitting of the ground state of the system, there is a difference between these two quantities that has to be fully rationalized before one makes comparisons. This is especially important for small spins such as triplets, where the magnetic anisotropy energy is only half of the zero-field splitting. Density functional calculations of magnetic anisotropy energies correspond to a high-field limit where the spins are aligned by the external magnetic field. Data are presented for the well-studied molecular magnet Mn12O12 acetate. Both perturbative and self-consistent treatments, different quasirelativistic Hamiltonians (zeroth order regular approximation, Douglas–Kroll, effective core potentials) and exchange-correlation functionals are compared. It is shown that some effects usually considered minor, such as the inclusion of the exchange-correlation potential in the effective one-particle spin-orbit operator, lead to sizable differences when computing magnetic anisotropy energies. Higher-order contributions, that is, the difference between self-consistent and perturbative results, increase the magnetic anisotropy energy somewhat but do not introduce sizeable quartic terms or an in-plane anisotropy. In numerical experiments, on can switch off and on spin-orbit coupling at individual atomic sites. This procedure yields single-site contributions to the overall magnetic anisotropy energy that could be used as parameters in phenomenological spin Hamiltonians. If ferrimagnetic systems are treated with broken symmetry density functional methods where the Kohn–Sham reference function is not a spin eigenfunction, corrections are needed which depend on the size of the exchange couplings in the system and must therefore be evaluated case by case.
Many-body effects on terahertz quantum well detectors
Authors: Guo X. G. , Tan Z. Y. , Cao J. C. , Liu H. C.
Published: May 2009

Many-body effects have been investigated in the design of terahertz quantum well photon detectors. A large discrepancy between the theoretical and experimental photoresponse peak positions exist without considering the many-body interactions. The calculated results agree with the experimental data quantitatively with including the exchange-correlation and depolarization effects within the local density approximation. Our numerical results show that it is a must to consider the many-body interactions for designing the quantum well detectors for the terahertz region.
Long time evolution of phase oscillator systems
Authors: Ott Edward , Antonsen Thomas M.
Published: May 2009

It is shown, under weak conditions, that the dynamical evolution of large systems of globally coupled phase oscillators with Lorentzian distributed oscillation frequencies is, in an appropriate physical sense, time-asymptotically attracted toward a reduced manifold of the system states. This manifold was previously known and used to facilitate the discovery of attractors and bifurcations of such systems. The result of this paper establishes that attractors for the order parameter dynamics obtained by restriction to this reduced manifold are, in fact, the only such attractors of the full system. Thus all long time dynamical behaviors of the order parameters of these systems can be obtained by restriction to the reduced manifold.
Pairwise energies for polypeptide coarse-grained models derived from atomic force fields
Authors: Betancourt Marcos R. , Omovie Sheyore J.
Published: May 2009

The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.
Dynamics of single vortices in grain boundaries: I-V characteristics on the femtovolt scale
Authors: Kalisky B. , Kirtley J. R. , Nowadnick E. A. , Dinner R. B. , Zeldov E. , Ariando  , Wenderich S. , Hilgenkamp H. , Feldmann D. M. , Moler K. A.
Published: May 2009

We employed a scanning Hall probe microscope to detect the hopping of individual vortices between pinning sites along grain boundaries in YBa2Cu3O6+δ thin films in the presence of an applied current. Detecting the motion of individual vortices allowed us to probe the current-voltage (I-V) characteristics of the grain boundary with voltage sensitivity below a femtovolt. We find a very sharp onset of dissipation with V∝In with an unprecedented high exponent of n≈290 that shows essentially no dependence on temperature or grain boundary angle. Our data have no straightforward explanation within the existing grain boundary transport models.
Molecular dynamics in supercooled glycerol: Results from C13 NMR spectroscopy
Authors: Jain P. , Levchenko A. , Yu P. , Sen S.
Published: May 2009

C 13 NMR spectra of glycerol are collected over the entire temperature range of supercooling: Tg(185 K)≤T≤Tm(293 K). The temperature dependent evolution of the C13 NMR line shape indicates dynamical averaging of the chemical shift anisotropy at the carbon sites with increasing temperature, resulting from isotropic tumbling of the constituent molecules. This isotropic reorientation dynamics involves random molecular jumps over all possible angles, and its time scale is in excellent agreement with the α-relaxation time scale of the supercooled liquid. The increasing activation energy of such molecular jumps with decreasing temperature and hence the fragility of supercooled glycerol are likely to be related to the corresponding temperature dependence of the average number of hydrogen bonds per molecule. The absence of any β peak in the dielectric relaxation spectra of supercooled glycerol is possibly related to a strong coupling between intramolecular dynamics and the tumbling of the entire molecule as a whole.
The influence of adsorbate-surface interaction energy on adsorption and recognition of diblock copolymers on patterned surfaces
Authors: Sumithra K.
Published: May 2009

The adsorption and pinning of a single diblock chain on patterned surfaces with varying block-surface interactions are investigated using Monte Carlo simulations. Previous investigations [K. Sumithra and E. Straube, J. Chem. Phys. 125, 154701 (2006)] on diblock copolymers on stripe-patterned surfaces have shown that the adsorption takes place in two stages for certain specific adsorbate-surface interactions. We have found that interesting changes from the usual adsorption behavior occurs for a series of interaction parameters for the copolymer on the surface patterns. It is also seen that the junction point of the different blocks gets pinned to the interface between the different surface sites. It is possible to get the polymer blocks completely localized on respective sites by suitably adjusting the polymer-surface interactions. We find that unlike in the random heteropolymer adsorption on random surface where the second transition is the result of the rearrangement of the already adsorbed polymers, in this case, it is seen that the process not only involves rearrangement but also optimizes the energetics of the chain by optimizing the extent of adsorption. The static and conformational properties of the copolymer are also discussed.
Highly temperature insensitive, deep-well 4.8 μm emitting quantum cascade semiconductor lasers
Authors: Shin J. C. , D’Souza M. , Liu Z. , Kirch J. , Mawst L. J. , Botez D. , Vurgaftman I. , Meyer J. R.
Published: May 2009

4.8   μ m emitting, quantum cascade (QC) lasers that suppress carrier leakage out of their active regions to the continuum have been realized by using deep (in energy) quantum wells in the active regions, tall barriers in and around the active regions, and tapered conduction-band-edge relaxation regions. The characteristic temperature coefficients T0 and T1 for the threshold current density Jth and slope efficiency, respectively, reach values of 238 K over the 20–60 °C temperature range, which means that Jth and the slope efficiency vary with temperature half as fast as those of conventional QC lasers. In turn, significantly improved continuous wave performance is expected.
Growth-rate induced epitaxial orientation of CeO2 on Al2O3(0001)
Authors: Kuchibhatla Satyanarayana V. N. T. , Nachimuthu P. , Gao F. , Jiang W. , Shutthanandan V. , Engelhard M. H. , Seal S. , Thevuthasan S.
Published: May 2009

High-quality CeO2 films were grown on Al2O3(0001) substrates using oxygen plasma-assisted molecular beam epitaxy. The epitaxial orientation of the films is found to be CeO2(100) and CeO2(111) at low (<8 Å/min) and higher growth rates (>12 Å/min), respectively. CeO2(100) film grows as three-dimensional islands, while CeO2(111) film grows as two-dimensional layers. The CeO2(100) film exhibits better epitaxial quality compared to CeO2(111) film. However, the CeO2(100) film on Al2O3(0001) shows three in-plane domains at 30° to each other. While the epitaxial quality is attributed to the close match between oxygen sublattices of CeO2(100) and Al2O3(0001), the three in-plane domains in CeO2(100) are attributed to the threefold symmetry of the substrate. The relative stability of different epitaxial orientations of CeO2 films on Al2O3(0001) obtained from molecular dynamics simulations strongly supports the experimental observations.
Water structures near charged (100) and (111) silicon surfaces
Authors: Xu Dongyan , Leng Yongsheng , Chen Yunfei , Li Deyu
Published: May 2009

Molecular dynamics simulations show that the layering structure of water molecules near solid surfaces can be significantly altered by surface charges. The first layer of water near the (100) silicon surface can be split into two layers as the surface charge density increases to −0.1 C/m2 because of the much more aligned distribution of water molecules. However, this splitting is not observed for the (111) silicon surface due to the higher surface atom density, which prevents water molecules from getting very close to the surface.
Differential recruitment of limb patterning genes during development and diversification of beetle horns
Authors: Moczek Armin P. , Rose Debra J.
Published: May 2009

The origins of novel complex phenotypes represent one of the most fundamental, yet largely unresolved, issues in evolutionary biology. Here we explore the developmental genetic regulation of beetle horns, a class of traits that lacks obvious homology to traits in other insects. Furthermore, beetle horns are remarkably diverse in their expression, including sexual dimorphisms, male dimorphisms, and interspecific differences in location of horn expression. At the same time, beetle horns share aspects of their development with that of more traditional appendages. We used larval RNA interference-mediated gene function analysis of 3 cardinal insect appendage patterning genes,
dachshund
,
homothorax
, and
Distal-less
, to investigate their role in development and diversification of beetle horns within and between species. Transcript depletion of all 3 patterning genes generated phenotypic effects very similar to those documented in previous studies that focused on general insect development. In addition, we found that
Distal-less
and
homothorax
, but not
dachshund
, regulate horn expression in a species-, sex-, body region-, and body size-dependent manner. Our results demonstrate differential co-option of appendage patterning genes during the evolution and radiation of beetle horns. Furthermore, our results illustrate that regulatory genes whose functions are otherwise highly conserved nevertheless retain the capacity to acquire additional functions, and that little phylogenetic distance appears necessary for the evolution of sex- and species-specific differences in these functions.
The NADPH-dependent thioredoxin system constitutes a functional backup for cytosolic glutathione reductase in
Arabidopsis
Authors: Marty Laurent , Siala Wafi , Schwarzländer Markus , Fricker Mark D. , Wirtz Markus , Sweetlove Lee J. , Meyer Yves , Meyer Andreas J. , Reichheld Jean-Philippe , Hell Rüdiger
Published: May 2009

Tight control of cellular redox homeostasis is essential for protection against oxidative damage and for maintenance of normal metabolism as well as redox signaling events. Under oxidative stress conditions, the tripeptide glutathione can switch from its reduced form (GSH) to oxidized glutathione disulfide (GSSG), and thus, forms an important cellular redox buffer. GSSG is normally reduced to GSH by 2 glutathione reductase (GR) isoforms encoded in the
Arabidopsis
genome, cytosolic GR1 and GR2 dual-targeted to chloroplasts and mitochondria. Measurements of total GR activity in leaf extracts of wild-type and 2
gr1
deletion mutants revealed that ≈65% of the total GR activity is attributed to GR1, whereas ≈35% is contributed by GR2. Despite the lack of a large share in total GR activity,
gr1
mutants do not show any informative phenotype, even under stress conditions, and thus, the physiological impact of GR1 remains obscure. To elucidate its role in plants, glutathione-specific redox-sensitive GFP was used to dynamically measure the glutathione redox potential (
E
GSH
) in the cytosol. Using this tool, it is shown that
E
GSH
in
gr1
mutants is significantly shifted toward more oxidizing conditions. Surprisingly, dynamic reduction of GSSG formed during induced oxidative stress in
gr1
mutants is still possible, although significantly delayed compared with wild-type plants. We infer that there is functional redundancy in this critical pathway. Integrated biochemical and genetic assays identify the NADPH-dependent thioredoxin system as a backup system for GR1. Deletion of both, NADPH-dependent thioredoxin reductase A and GR1, prevents survival due to a pollen lethal phenotype.
Developmental sources of conservation and variation in the evolution of the primate eye
Authors: Dyer Michael A. , Martins Rodrigo , da Silva Filho Manoel , Muniz José Augusto P. C. , Silveira Luiz Carlos L. , Cepko Constance L. , Finlay Barbara L.
Published: May 2009

Conserved developmental programs, such as the order of neurogenesis in the mammalian eye, suggest the presence of useful features for evolutionary stability and variability. The owl monkey,Aotus azarae, has developed a fully nocturnal retina in recent evolution. Description and quantification of cell cycle kinetics show that embryonic cytogenesis is extended inAotuscompared with the diurnal New World monkeyCebus apella.Combined with the conserved mammalian pattern of retinal cell specification, this single change in retinal progenitor cell proliferation can produce the multiple alterations of the nocturnal retina, including coordinated reduction in cone and ganglion cell numbers, increase in rod and rod bipolar numbers, and potentially loss of the fovea.
Animal evolution, bioturbation, and the sulfate concentration of the oceans
Authors: Canfield Donald E. , Farquhar James
Published: May 2009

As recognized already by Charles Darwin, animals are geobiological agents. Darwin observed that worms aerate and mix soils on a massive scale, aiding in the decomposition of soil organic matter. A similar statement can be made about marine benthic animals. This mixing, also known as bioturbation, not only aides in the decomposition of sedimentary organic material, but as contended here, it has also significantly influenced the chemistry of seawater. In particular, it is proposed that sediment mixing by bioturbating organisms resulted in a severalfold increase in seawater sulfate concentration. For this reason, the evolution of bioturbation is linked to the significant deposition of sulfate evaporate minerals, which is largely a phenomena of the Phanerozoic, the last 542 million years and the time over which animals rose to prominence.
Molecular basis of substrate selection by the N-end rule adaptor protein ClpS
Authors: Román-Hernández Giselle , Grant Robert A. , Sauer Robert T. , Baker Tania A.
Published: May 2009

The N-end rule is a conserved degradation pathway that relates the stability of a protein to its N-terminal amino acid. Here, we present crystal structures of ClpS, the bacterial N-end rule adaptor, alone and engaged with peptides containing N-terminal phenylalanine, leucine, and tryptophan. These structures, together with a previous structure of ClpS bound to an N-terminal tyrosine, illustrate the molecular basis of recognition of the complete set of primary N-end rule amino acids. In each case, the α-amino group and side chain of the N-terminal residue are the major determinants of recognition. The binding pocket for the N-end residue is preformed in the free adaptor, and only small adjustments are needed to accommodate N-end rule residues having substantially different sizes and shapes. M53A ClpS is known to mediate degradation of an expanded repertoire of substrates, including those with N-terminal valine or isoleucine. A structure of Met53A ClpS engaged with an N-end rule tryptophan reveals an essentially wild-type mechanism of recognition, indicating that the Met
53
side chain directly enforces specificity by clashing with and excluding β-branched side chains. Finally, experimental and structural data suggest mechanisms that make proteins with N-terminal methionine bind very poorly to ClpS, explaining why these high-abundance proteins are not degraded via the N-end rule pathway in the cell.
Central and autonomic nervous system interaction is altered by short-term meditation
Authors: Tang Yi-Yuan , Ma Yinghua , Fan Yaxin , Feng Hongbo , Wang Junhong , Feng Shigang , Lu Qilin , Hu Bing , Lin Yao , Li Jian , Zhang Ye , Wang Yan , Zhou Li , Fan Ming
Published: May 2009

Five days of integrative body–mind training (IBMT) improves attention and self-regulation in comparison with the same amount of relaxation training. This paper explores the underlying mechanisms of this finding. We measured the physiological and brain changes at rest before, during, and after 5 days of IBMT and relaxation training. During and after training, the IBMT group showed significantly better physiological reactions in heart rate, respiratory amplitude and rate, and skin conductance response (SCR) than the relaxation control. Differences in heart rate variability (HRV) and EEG power suggested greater involvement of the autonomic nervous system (ANS) in the IBMT group during and after training. Imaging data demonstrated stronger subgenual and adjacent ventral anterior cingulate cortex (ACC) activity in the IBMT group. Frontal midline ACC theta was correlated with high-frequency HRV, suggesting control by the ACC over parasympathetic activity. These results indicate that after 5 days of training, the IBMT group shows better regulation of the ANS by a ventral midfrontal brain system than does the relaxation group. This changed state probably reflects training in the coordination of body and mind given in the IBMT but not in the control group. These results could be useful in the design of further specific interventions.
Cumulative delivery rate in an in vitro fertilization program with a single embryo transfer policy
Authors: SUNDSTRÖM PER , SALDEEN PIA
Published: May 2009

Objective. To investigate the cumulative delivery rate for women completing three fresh embryo transfer cycles or giving birth after the first or second transfer cycle in an in vitro fertilization program with a single embryo transfer (SET) policy. Setting. Privately run infertility clinic in southern Sweden (Skåne region). Population. Four hundred fifty‐three consecutive, unselected public patients beginning an ovum pick‐up cycle between July 2002 and June 2004. Method. Retrospective, observational study. Main outcome measure: Cumulative delivery rates. Results. Of 370 women who completed the study with up to three fresh ET cycles (90% SETs), 244 women (66%) progressed to delivery. Among the deliveries were three sets of twins (1%), one dizygotic. Cumulative delivery rates showed significant differences relative to age <36 (71%) and ≥36 years (47%), and delivery rates relative to rank of ET cycle (first and second vs. third ET cycle – 35, 34, and 21% delivery rates, respectively). Conclusions. The 66% cumulative delivery rate is in accordance with rates in similar observational studies and in estimation studies, in which predominantly two embryos were used for transfer. The multiple delivery rate was low. We suggest that repeated SET cycles can be implemented on a large scale even in a primarily unselected patient population without compromising the outcome.
Diagnostic delay experienced among gynecological cancer patients: a nationwide survey in Denmark
Authors: ROBINSON KIRSTINE M. , OTTESEN BENT , CHRISTENSEN KARL BANG , KRASNIK ALLAN
Published: May 2009

Objective. To examine diagnostic delay among gynecological cancer patients. Design. Nationwide study. Setting. The cohort comprised all women receiving their first treatment for cervical, endometrial, or ovarian cancer between 1 October 2006 and 1 December 2007 in four of the five centers for gynecological cancer surgery in Denmark. Sample. Of the 911 women alive, 648 participated, resulting in a response rate of 71.1%; of these, 30.1% were diagnosed with cervical cancer, 31.0% with endometrial cancer, and 38.9% with ovarian cancer. Methods. Questionnaire survey. Main outcome measures. Diagnostic delay calculated as total delay, patient delay, general practitioner referral delay, gynecologist appointment delay, and secondary care delay. Results. Diagnostic delays were found in all parts of the diagnostic pathway. Total diagnostic delay has remained long with a median delay of 12 weeks from the time patients experience symptoms until the time they receive treatment; the 10% experiencing the longest delay wait for >41 weeks. For all types of delay, distributions were non‐normal. This indicates that the greatest potential for optimizing clinical outcomes may be among the minority of patients experiencing very long delays. Ovarian cancer patients experienced significantly shorter delays compared with other gynecological cancer patients in all parts of the health care system. Conclusions. Delays occur in all parts of the diagnostic process, suggesting that a multifaceted approach should be adopted with special focus on reducing the very long delays experienced by some patients. By reducing the total diagnostic delays, outcomes such as three‐year survival rates can potentially be improved.
Intravascular ultrasound with a vector phased-array probe (acunav) is feasible in endovascular abdominal aortic aneurysm repair
Authors: Eriksson M.-O. , Wanhainen A. , Nyman R.
Published: May 2009

Background: The ideal imaging method for endovascular aneurysm repair (EVAR) should provide all data regarding diagnosis, measurements, and guiding of stent-graft deployment. Contrast-enhanced computed tomography (CT) is used for preoperative EVAR planning, together with intraoperative angiography. However, the administered contrast volume might result in contrast-induced nephropathy (CIN).

Purpose: To develop a technique for aortic measurements, vessel wall evaluation, and stent-graft positioning by using a vector phased-array intravascular ultrasound probe with color Doppler function (AcuNav) in elective EVAR.

Material and Methods: Thirteen elective EVAR patients were included. AcuNav was compared to pre- and postoperative CT examinations, perioperative angiography, and postoperative duplex.

Results: Measurements for stent-graft sizing were easily obtained and facilitated by the color Doppler function and corresponded well with CT and angiography. The combined information from AcuNav and fluoroscopy provided exact positioning of the stent graft. An aortic placement of the probe provided superior imaging results compared to an inferior vena cava approach. Detection of endoleak was found to be difficult. No complications were registered.

Conclusion: The use of AcuNav combined with fluoroscopy in EVAR was found to be safe, effective, and feasible in planning and guiding EVAR procedures. Best results were seen with the probe placed in the artery. AcuNav might be used to replace contrast-enhanced CT and angiography, hence reducing the risk of CIN, especially in high-risk patients.
An experimental investigation of the determinants and consequences of self‐handicapping strategies across motivational climates
Authors: Coudevylle Guillaume R. , Martin Ginis Kathleen A. , Famose Jean‐Pierre , Gernigon Christophe
Published: May 2009

The aim of the present study was to determine whether the use of claimed and behavioural self‐handicaps and their correlates differed across experimentally manipulated motivational climates. Fifty‐six competitive basketball players participated in the study. A crossover design was used, such that all participants completed the experimental task (i.e. a test of basketball skill) in both mastery and performance climates. Analyses of variance showed that claimed self‐handicaps were used more in the performance than the mastery condition but only for the men. In addition, greater behavioural self‐handicapping occurred in the performance than the mastery climate. Contrary to expectation, neither type of self‐handicap was related to performance on the basketball task in either climate. These findings reinforce the conceptual distinction between claimed and behavioural self‐handicaps and suggest that individual and environmental factors may differentially influence each type of handicap.
Zinc transporter Znt5/Slc30a5 is required for the mast cell–mediated delayed-type allergic reaction but not the immediate-type reaction
Authors: Nishida Keigo , Hasegawa Aiko , Nakae Susumu , Oboki Keisuke , Saito Hirohisa , Yamasaki Satoru , Hirano Toshio
Published: May 2009

Zinc (Zn) is an essential nutrient and its deficiency causes immunodeficiency. However, it remains unknown how Zn homeostasis is regulated in mast cells and if Zn transporters are involved in allergic reactions. We show that Znt5/Slc30a5 is required for contact hypersensitivity and mast cell–mediated delayed-type allergic response but not for immediate passive cutaneous anaphylaxis. In mast cells from Znt5−/− mice, Fcε receptor I (FcεRI)–induced cytokine production was diminished, but degranulation was intact. Znt5 was involved in FcεRI-induced translocation of protein kinase C (PKC) to the plasma membrane and the nuclear translocation of nuclear factor κB. In addition, the Zn finger–like motif of PKC was required for its plasma membrane translocation and binding to diacylglycerol. Thus, Znt5 is selectively required for the mast cell–mediated delayed-type allergic response, and it is a novel player in mast cell activation.